0s autopkgtest [23:26:53]: starting date and time: 2026-02-09 23:26:53+0000 0s autopkgtest [23:26:53]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:26:53]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fas15y6g/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-cran-lmertest --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-ppc64el-14.secgroup --name adt-resolute-ppc64el-r-cran-lmertest-20260209-232653-juju-7f2275-prod-proposed-migration-environment-20-b22c053d-8cce-4bc5-9e34-e9aadc2be1a4 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-r-cran-lmertest-20260209-232653-juju-7f2275-prod-proposed-migration-environment-20-b22c053d-8cce-4bc5-9e34-e9aadc2be1a4 from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)... 118s autopkgtest [23:28:51]: testbed dpkg architecture: ppc64el 118s autopkgtest [23:28:51]: testbed apt version: 3.1.15 119s autopkgtest [23:28:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 119s autopkgtest [23:28:52]: testbed release detected to be: None 119s autopkgtest [23:28:52]: updating testbed package index (apt update) 120s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 120s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 120s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 120s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 120s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 123s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 123s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 123s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB] 123s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB] 126s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB] 126s Fetched 3774 kB in 6s (617 kB/s) 127s Reading package lists... 127s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 128s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Calculating upgrade... 129s The following packages will be upgraded: 129s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 129s libip6tc2 libxtables12 wget 129s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 3125 kB of archives. 129s After this operation, 78.8 kB of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB] 129s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB] 129s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB] 129s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB] 129s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB] 131s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB] 131s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB] 131s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB] 131s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB] 132s dpkg-preconfigure: unable to re-open stdin: No such file or directory 132s Fetched 3125 kB in 3s (1103 kB/s) 132s (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 ... 122003 files and directories currently installed.) 132s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ... 132s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 133s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ... 133s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 134s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ... 134s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 134s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 134s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 134s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ... 134s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 134s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 134s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 135s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ... 135s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 135s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ... 135s Setting up wget (1.25.0-2ubuntu4) ... 135s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ... 135s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ... 135s Setting up dracut-install (109-11ubuntu1) ... 135s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ... 135s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 135s Setting up iptables (1.8.11-2ubuntu3) ... 135s Setting up iproute2 (6.18.0-1ubuntu1) ... 136s Processing triggers for man-db (2.13.1-1build1) ... 138s Processing triggers for install-info (7.2-5) ... 138s Processing triggers for libc-bin (2.42-2ubuntu4) ... 139s autopkgtest [23:29:12]: upgrading testbed (apt dist-upgrade and autopurge) 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Solving dependencies... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s autopkgtest [23:29:15]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:13:51 UTC 2026 143s autopkgtest [23:29:16]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-lmertest 144s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (dsc) [2247 B] 144s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (tar) [198 kB] 144s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-lmertest 3.2-0-1 (diff) [3788 B] 144s gpgv: Signature made Thu Jan 22 00:11:29 2026 UTC 144s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 144s gpgv: issuer "plessy@debian.org" 144s gpgv: Can't check signature: No public key 144s dpkg-source: warning: cannot verify inline signature for ./r-cran-lmertest_3.2-0-1.dsc: no acceptable signature found 144s autopkgtest [23:29:17]: testing package r-cran-lmertest version 3.2-0-1 145s autopkgtest [23:29:18]: build not needed 146s autopkgtest [23:29:19]: test run-unit-test: preparing testbed 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s The following NEW packages will be installed: 147s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 147s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 147s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 147s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 147s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 147s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 147s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 147s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 147s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 147s r-base-core r-cran-backports r-cran-boot r-cran-broom r-cran-cli 147s r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl r-cran-deriv 147s r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver 147s r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 r-cran-glue 147s r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr 147s r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 147s r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass r-cran-matrix 147s r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme r-cran-nloptr 147s r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 147s r-cran-pkgkitten r-cran-purrr r-cran-quadprog r-cran-quantmod r-cran-r6 147s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 147s r-cran-rcppeigen r-cran-rdpack r-cran-reformulas r-cran-rlang r-cran-s7 147s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble 147s r-cran-tidyr r-cran-tidyselect r-cran-timedate r-cran-tseries r-cran-ttr 147s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 147s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo unzip x11-common xdg-utils zip 147s 0 upgraded, 130 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 116 MB of archives. 147s After this operation, 269 MB of additional disk space will be used. 147s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 148s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 151s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 151s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 151s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 151s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 151s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 155s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 155s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 155s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 155s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 155s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 155s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 156s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 156s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB] 156s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 158s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 158s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 158s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 159s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 159s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 159s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB] 159s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 159s Get:24 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 159s Get:25 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 159s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 159s Get:27 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 159s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 165s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 165s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 165s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 165s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 165s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 165s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 165s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 165s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 166s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 166s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB] 166s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 168s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 168s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 168s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 168s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 168s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 168s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 170s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 170s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-normalize.css all 8.0.1-5.1 [10.4 kB] 170s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB] 170s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 170s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 170s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 224s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-backports ppc64el 1.5.0-2 [122 kB] 224s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-boot all 1.3-32-1 [636 kB] 225s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB] 229s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-generics all 0.1.4-1 [84.0 kB] 229s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB] 229s Get:57 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB] 232s Get:58 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 232s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 232s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB] 232s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 235s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 235s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB] 235s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB] 236s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 236s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB] 236s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB] 236s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyselect ppc64el 1.2.1+dfsg-1 [222 kB] 236s Get:69 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dplyr ppc64el 1.1.4-4 [1542 kB] 239s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-purrr ppc64el 1.0.4-1 [555 kB] 240s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringi ppc64el 1.8.4-1build2 [947 kB] 242s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB] 242s Get:73 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB] 242s Get:74 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB] 244s Get:75 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 247s Get:76 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-colorspace ppc64el 2.1-1+dfsg-1 [1570 kB] 249s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 249s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 252s Get:79 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-s7 ppc64el 0.2.0-1 [330 kB] 252s Get:80 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB] 255s Get:81 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 255s Get:82 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 255s Get:83 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB] 257s Get:84 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB] 258s Get:85 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 268s Get:86 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 269s Get:87 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-curl ppc64el 7.0.0+dfsg-1 [205 kB] 269s Get:88 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-deriv all 4.2.0-1 [154 kB] 269s Get:89 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fracdiff ppc64el 1.5-3-1 [118 kB] 269s Get:90 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lattice ppc64el 0.22-7-1 [1366 kB] 272s Get:91 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-zoo ppc64el 1.8-15-1 [1028 kB] 274s Get:92 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lmtest ppc64el 0.9.40-1build1 [401 kB] 274s Get:93 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nnet ppc64el 7.3-20-1 [119 kB] 274s Get:94 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB] 274s Get:95 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 274s Get:96 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB] 278s Get:97 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-timedate ppc64el 4052.112-1 [1299 kB] 283s Get:98 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quadprog ppc64el 1.5-8-1build2 [38.8 kB] 283s Get:99 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xts ppc64el 0.14.1-1 [1209 kB] 285s Get:100 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ttr ppc64el 0.24.4-1 [516 kB] 285s Get:101 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-jsonlite ppc64el 1.9.1+dfsg-1 [452 kB] 285s Get:102 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quantmod all 0.4.28-1 [1037 kB] 287s Get:103 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tseries ppc64el 0.10-59-3 [390 kB] 287s Get:104 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB] 292s Get:105 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-urca ppc64el 1.3-4-1build1 [1056 kB] 293s Get:106 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpparmadillo ppc64el 15.2.3-1-1 [935 kB] 295s Get:107 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-forecast ppc64el 8.23.0-1 [1598 kB] 298s Get:108 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 300s Get:109 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 309s Get:110 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-modelr all 0.1.11-1 [195 kB] 309s Get:111 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-microbenchmark ppc64el 1.5.0-1 [67.9 kB] 309s Get:112 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-doby all 4.7.1-3 [4741 kB] 318s Get:113 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-evaluate all 1.0.5-1 [117 kB] 318s Get:114 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xfun ppc64el 0.55+dfsg-1 [589 kB] 319s Get:115 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB] 319s Get:116 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB] 319s Get:117 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 330s Get:118 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-knitr all 1.51+dfsg-1 [847 kB] 332s Get:119 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-minqa ppc64el 1.2.8-1 [141 kB] 332s Get:120 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libnlopt0 ppc64el 2.7.1-7ubuntu1 [292 kB] 332s Get:121 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nloptr ppc64el 2.2.1-2 [251 kB] 332s Get:122 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rbibutils ppc64el 2.3-1 [1047 kB] 334s Get:123 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rdpack all 2.6.3-1 [636 kB] 335s Get:124 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-reformulas all 0.4.4-1 [151 kB] 335s Get:125 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcppeigen ppc64el 0.3.4.0.2-1 [1477 kB] 338s Get:126 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-statmod ppc64el 1.5.0-1 [298 kB] 338s Get:127 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lme4 ppc64el 1.1-38-1 [4220 kB] 346s Get:128 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 346s Get:129 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lmertest all 3.2-0-1 [535 kB] 347s Get:130 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pbkrtest all 0.5.5-1 [217 kB] 348s Preconfiguring packages ... 348s Fetched 116 MB in 3min 20s (580 kB/s) 348s Selecting previously unselected package fonts-dejavu-mono. 348s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 122006 files and directories currently installed.) 348s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ... 348s Unpacking fonts-dejavu-mono (2.37-8build1) ... 348s Selecting previously unselected package fonts-dejavu-core. 348s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ... 348s Unpacking fonts-dejavu-core (2.37-8build1) ... 348s Selecting previously unselected package fontconfig-config. 348s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 348s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 348s Selecting previously unselected package libfontconfig1:ppc64el. 348s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 348s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 348s Selecting previously unselected package fontconfig. 348s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 348s Unpacking fontconfig (2.17.1-3ubuntu1) ... 348s Selecting previously unselected package fonts-glyphicons-halflings. 348s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 348s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 348s Selecting previously unselected package fonts-mathjax. 348s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 348s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 348s Selecting previously unselected package libblas3:ppc64el. 348s Preparing to unpack .../007-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 348s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 348s Selecting previously unselected package libpixman-1-0:ppc64el. 348s Preparing to unpack .../008-libpixman-1-0_0.46.4-1_ppc64el.deb ... 348s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 348s Selecting previously unselected package libxcb-render0:ppc64el. 348s Preparing to unpack .../009-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 348s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 348s Selecting previously unselected package libxcb-shm0:ppc64el. 348s Preparing to unpack .../010-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 348s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 348s Selecting previously unselected package libxrender1:ppc64el. 348s Preparing to unpack .../011-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 348s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 348s Selecting previously unselected package libcairo2:ppc64el. 348s Preparing to unpack .../012-libcairo2_1.18.4-3_ppc64el.deb ... 348s Unpacking libcairo2:ppc64el (1.18.4-3) ... 348s Selecting previously unselected package libdatrie1:ppc64el. 348s Preparing to unpack .../013-libdatrie1_0.2.14-1_ppc64el.deb ... 348s Unpacking libdatrie1:ppc64el (0.2.14-1) ... 348s Selecting previously unselected package libdeflate0:ppc64el. 348s Preparing to unpack .../014-libdeflate0_1.23-2build1_ppc64el.deb ... 348s Unpacking libdeflate0:ppc64el (1.23-2build1) ... 348s Selecting previously unselected package libgfortran5:ppc64el. 348s Preparing to unpack .../015-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 348s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 348s Selecting previously unselected package libgomp1:ppc64el. 348s Preparing to unpack .../016-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 348s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 348s Selecting previously unselected package libgraphite2-3:ppc64el. 348s Preparing to unpack .../017-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ... 348s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 348s Selecting previously unselected package libharfbuzz0b:ppc64el. 348s Preparing to unpack .../018-libharfbuzz0b_12.3.2-1_ppc64el.deb ... 348s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ... 348s Selecting previously unselected package x11-common. 348s Preparing to unpack .../019-x11-common_1%3a7.7+24ubuntu1_all.deb ... 348s Unpacking x11-common (1:7.7+24ubuntu1) ... 348s Selecting previously unselected package libice6:ppc64el. 348s Preparing to unpack .../020-libice6_2%3a1.1.1-1build1_ppc64el.deb ... 348s Unpacking libice6:ppc64el (2:1.1.1-1build1) ... 348s Selecting previously unselected package libjpeg-turbo8:ppc64el. 348s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-4ubuntu3_ppc64el.deb ... 348s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 348s Selecting previously unselected package libjpeg8:ppc64el. 348s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 348s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 348s Selecting previously unselected package libjs-bootstrap. 348s Preparing to unpack .../023-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 348s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 348s Selecting previously unselected package libjs-highlight.js. 348s Preparing to unpack .../024-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 348s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 348s Selecting previously unselected package libjs-jquery. 349s Preparing to unpack .../025-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 349s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 349s Selecting previously unselected package libjs-jquery-datatables. 349s Preparing to unpack .../026-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 349s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 349s Selecting previously unselected package liblapack3:ppc64el. 349s Preparing to unpack .../027-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 349s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 349s Selecting previously unselected package liblerc4:ppc64el. 349s Preparing to unpack .../028-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ... 349s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 349s Selecting previously unselected package libthai-data. 349s Preparing to unpack .../029-libthai-data_0.1.30-1_all.deb ... 349s Unpacking libthai-data (0.1.30-1) ... 349s Selecting previously unselected package libthai0:ppc64el. 349s Preparing to unpack .../030-libthai0_0.1.30-1_ppc64el.deb ... 349s Unpacking libthai0:ppc64el (0.1.30-1) ... 349s Selecting previously unselected package libpango-1.0-0:ppc64el. 349s Preparing to unpack .../031-libpango-1.0-0_1.57.0-1_ppc64el.deb ... 349s Unpacking libpango-1.0-0:ppc64el (1.57.0-1) ... 349s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 349s Preparing to unpack .../032-libpangoft2-1.0-0_1.57.0-1_ppc64el.deb ... 349s Unpacking libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 349s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 349s Preparing to unpack .../033-libpangocairo-1.0-0_1.57.0-1_ppc64el.deb ... 349s Unpacking libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 349s Selecting previously unselected package libpaper2:ppc64el. 349s Preparing to unpack .../034-libpaper2_2.2.5-0.3build1_ppc64el.deb ... 349s Unpacking libpaper2:ppc64el (2.2.5-0.3build1) ... 349s Selecting previously unselected package libpaper-utils. 349s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3build1_ppc64el.deb ... 349s Unpacking libpaper-utils (2.2.5-0.3build1) ... 349s Selecting previously unselected package libsharpyuv0:ppc64el. 349s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1build1_ppc64el.deb ... 349s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 349s Selecting previously unselected package libsm6:ppc64el. 349s Preparing to unpack .../037-libsm6_2%3a1.2.6-1build1_ppc64el.deb ... 349s Unpacking libsm6:ppc64el (2:1.2.6-1build1) ... 349s Selecting previously unselected package libtcl8.6:ppc64el. 349s Preparing to unpack .../038-libtcl8.6_8.6.17+dfsg-1build1_ppc64el.deb ... 349s Unpacking libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 349s Selecting previously unselected package libjbig0:ppc64el. 349s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu3_ppc64el.deb ... 349s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu3) ... 349s Selecting previously unselected package libwebp7:ppc64el. 349s Preparing to unpack .../040-libwebp7_1.5.0-0.1build1_ppc64el.deb ... 349s Unpacking libwebp7:ppc64el (1.5.0-0.1build1) ... 349s Selecting previously unselected package libtiff6:ppc64el. 349s Preparing to unpack .../041-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ... 349s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ... 349s Selecting previously unselected package libxft2:ppc64el. 349s Preparing to unpack .../042-libxft2_2.3.6-1build2_ppc64el.deb ... 349s Unpacking libxft2:ppc64el (2.3.6-1build2) ... 349s Selecting previously unselected package libxss1:ppc64el. 349s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build4_ppc64el.deb ... 349s Unpacking libxss1:ppc64el (1:1.2.3-1build4) ... 349s Selecting previously unselected package libtk8.6:ppc64el. 349s Preparing to unpack .../044-libtk8.6_8.6.17-1_ppc64el.deb ... 349s Unpacking libtk8.6:ppc64el (8.6.17-1) ... 349s Selecting previously unselected package libxt6t64:ppc64el. 349s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.3_ppc64el.deb ... 349s Unpacking libxt6t64:ppc64el (1:1.2.1-1.3) ... 349s Selecting previously unselected package node-normalize.css. 349s Preparing to unpack .../046-node-normalize.css_8.0.1-5.1_all.deb ... 349s Unpacking node-normalize.css (8.0.1-5.1) ... 349s Selecting previously unselected package zip. 349s Preparing to unpack .../047-zip_3.0-15ubuntu3_ppc64el.deb ... 349s Unpacking zip (3.0-15ubuntu3) ... 349s Selecting previously unselected package unzip. 349s Preparing to unpack .../048-unzip_6.0-29ubuntu1_ppc64el.deb ... 349s Unpacking unzip (6.0-29ubuntu1) ... 349s Selecting previously unselected package xdg-utils. 349s Preparing to unpack .../049-xdg-utils_1.2.1-2ubuntu2_all.deb ... 349s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 349s Selecting previously unselected package r-base-core. 349s Preparing to unpack .../050-r-base-core_4.5.2-1ubuntu2_ppc64el.deb ... 349s Unpacking r-base-core (4.5.2-1ubuntu2) ... 349s Selecting previously unselected package r-cran-backports. 349s Preparing to unpack .../051-r-cran-backports_1.5.0-2_ppc64el.deb ... 349s Unpacking r-cran-backports (1.5.0-2) ... 349s Selecting previously unselected package r-cran-boot. 349s Preparing to unpack .../052-r-cran-boot_1.3-32-1_all.deb ... 349s Unpacking r-cran-boot (1.3-32-1) ... 349s Selecting previously unselected package r-cran-cli. 349s Preparing to unpack .../053-r-cran-cli_3.6.4-1_ppc64el.deb ... 349s Unpacking r-cran-cli (3.6.4-1) ... 349s Selecting previously unselected package r-cran-generics. 349s Preparing to unpack .../054-r-cran-generics_0.1.4-1_all.deb ... 349s Unpacking r-cran-generics (0.1.4-1) ... 349s Selecting previously unselected package r-cran-glue. 349s Preparing to unpack .../055-r-cran-glue_1.8.0-1_ppc64el.deb ... 349s Unpacking r-cran-glue (1.8.0-1) ... 349s Selecting previously unselected package r-cran-rlang. 349s Preparing to unpack .../056-r-cran-rlang_1.1.5-3_ppc64el.deb ... 349s Unpacking r-cran-rlang (1.1.5-3) ... 350s Selecting previously unselected package r-cran-lifecycle. 350s Preparing to unpack .../057-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 350s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 350s Selecting previously unselected package r-cran-magrittr. 350s Preparing to unpack .../058-r-cran-magrittr_2.0.3-1_ppc64el.deb ... 350s Unpacking r-cran-magrittr (2.0.3-1) ... 350s Selecting previously unselected package r-cran-utf8. 350s Preparing to unpack .../059-r-cran-utf8_1.2.4-1_ppc64el.deb ... 350s Unpacking r-cran-utf8 (1.2.4-1) ... 350s Selecting previously unselected package r-cran-vctrs. 350s Preparing to unpack .../060-r-cran-vctrs_0.6.5-1_ppc64el.deb ... 350s Unpacking r-cran-vctrs (0.6.5-1) ... 350s Selecting previously unselected package r-cran-pillar. 350s Preparing to unpack .../061-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 350s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 350s Selecting previously unselected package r-cran-r6. 350s Preparing to unpack .../062-r-cran-r6_2.6.1-1_all.deb ... 350s Unpacking r-cran-r6 (2.6.1-1) ... 350s Selecting previously unselected package r-cran-fansi. 350s Preparing to unpack .../063-r-cran-fansi_1.0.6-2_ppc64el.deb ... 350s Unpacking r-cran-fansi (1.0.6-2) ... 350s Selecting previously unselected package r-cran-pkgconfig. 350s Preparing to unpack .../064-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 350s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 350s Selecting previously unselected package r-cran-tibble. 350s Preparing to unpack .../065-r-cran-tibble_3.2.1+dfsg-3_ppc64el.deb ... 350s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 350s Selecting previously unselected package r-cran-withr. 350s Preparing to unpack .../066-r-cran-withr_3.0.2+dfsg-1_all.deb ... 350s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 350s Selecting previously unselected package r-cran-tidyselect. 350s Preparing to unpack .../067-r-cran-tidyselect_1.2.1+dfsg-1_ppc64el.deb ... 350s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 350s Selecting previously unselected package r-cran-dplyr. 350s Preparing to unpack .../068-r-cran-dplyr_1.1.4-4_ppc64el.deb ... 350s Unpacking r-cran-dplyr (1.1.4-4) ... 350s Selecting previously unselected package r-cran-purrr. 350s Preparing to unpack .../069-r-cran-purrr_1.0.4-1_ppc64el.deb ... 350s Unpacking r-cran-purrr (1.0.4-1) ... 350s Selecting previously unselected package r-cran-stringi. 350s Preparing to unpack .../070-r-cran-stringi_1.8.4-1build2_ppc64el.deb ... 350s Unpacking r-cran-stringi (1.8.4-1build2) ... 350s Selecting previously unselected package r-cran-stringr. 350s Preparing to unpack .../071-r-cran-stringr_1.5.1-1_all.deb ... 350s Unpacking r-cran-stringr (1.5.1-1) ... 350s Selecting previously unselected package r-cran-cpp11. 350s Preparing to unpack .../072-r-cran-cpp11_0.5.3-1_all.deb ... 350s Unpacking r-cran-cpp11 (0.5.3-1) ... 350s Selecting previously unselected package r-cran-tidyr. 350s Preparing to unpack .../073-r-cran-tidyr_1.3.1-1_ppc64el.deb ... 350s Unpacking r-cran-tidyr (1.3.1-1) ... 350s Selecting previously unselected package r-cran-broom. 350s Preparing to unpack .../074-r-cran-broom_1.0.12+dfsg-1_all.deb ... 350s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 350s Selecting previously unselected package r-cran-colorspace. 350s Preparing to unpack .../075-r-cran-colorspace_2.1-1+dfsg-1_ppc64el.deb ... 350s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 350s Selecting previously unselected package r-cran-gtable. 350s Preparing to unpack .../076-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 350s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 350s Selecting previously unselected package r-cran-isoband. 350s Preparing to unpack .../077-r-cran-isoband_0.2.7-1_ppc64el.deb ... 350s Unpacking r-cran-isoband (0.2.7-1) ... 350s Selecting previously unselected package r-cran-s7. 350s Preparing to unpack .../078-r-cran-s7_0.2.0-1_ppc64el.deb ... 350s Unpacking r-cran-s7 (0.2.0-1) ... 350s Selecting previously unselected package r-cran-farver. 350s Preparing to unpack .../079-r-cran-farver_2.1.2-1_ppc64el.deb ... 350s Unpacking r-cran-farver (2.1.2-1) ... 350s Selecting previously unselected package r-cran-labeling. 350s Preparing to unpack .../080-r-cran-labeling_0.4.3-1_all.deb ... 350s Unpacking r-cran-labeling (0.4.3-1) ... 350s Selecting previously unselected package r-cran-rcolorbrewer. 350s Preparing to unpack .../081-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 350s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 350s Selecting previously unselected package r-cran-viridislite. 350s Preparing to unpack .../082-r-cran-viridislite_0.4.3-1_all.deb ... 350s Unpacking r-cran-viridislite (0.4.3-1) ... 350s Selecting previously unselected package r-cran-scales. 350s Preparing to unpack .../083-r-cran-scales_1.4.0-1_all.deb ... 350s Unpacking r-cran-scales (1.4.0-1) ... 350s Selecting previously unselected package r-cran-ggplot2. 350s Preparing to unpack .../084-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 350s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 350s Selecting previously unselected package r-cran-cowplot. 350s Preparing to unpack .../085-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 350s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 350s Selecting previously unselected package r-cran-curl. 350s Preparing to unpack .../086-r-cran-curl_7.0.0+dfsg-1_ppc64el.deb ... 350s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 350s Selecting previously unselected package r-cran-deriv. 350s Preparing to unpack .../087-r-cran-deriv_4.2.0-1_all.deb ... 350s Unpacking r-cran-deriv (4.2.0-1) ... 350s Selecting previously unselected package r-cran-fracdiff. 350s Preparing to unpack .../088-r-cran-fracdiff_1.5-3-1_ppc64el.deb ... 350s Unpacking r-cran-fracdiff (1.5-3-1) ... 350s Selecting previously unselected package r-cran-lattice. 350s Preparing to unpack .../089-r-cran-lattice_0.22-7-1_ppc64el.deb ... 350s Unpacking r-cran-lattice (0.22-7-1) ... 350s Selecting previously unselected package r-cran-zoo. 350s Preparing to unpack .../090-r-cran-zoo_1.8-15-1_ppc64el.deb ... 350s Unpacking r-cran-zoo (1.8-15-1) ... 350s Selecting previously unselected package r-cran-lmtest. 350s Preparing to unpack .../091-r-cran-lmtest_0.9.40-1build1_ppc64el.deb ... 350s Unpacking r-cran-lmtest (0.9.40-1build1) ... 350s Selecting previously unselected package r-cran-nnet. 350s Preparing to unpack .../092-r-cran-nnet_7.3-20-1_ppc64el.deb ... 350s Unpacking r-cran-nnet (7.3-20-1) ... 351s Selecting previously unselected package r-cran-littler. 351s Preparing to unpack .../093-r-cran-littler_0.3.22-1_ppc64el.deb ... 351s Unpacking r-cran-littler (0.3.22-1) ... 351s Selecting previously unselected package r-cran-pkgkitten. 351s Preparing to unpack .../094-r-cran-pkgkitten_0.2.4-1_all.deb ... 351s Unpacking r-cran-pkgkitten (0.2.4-1) ... 351s Selecting previously unselected package r-cran-rcpp. 351s Preparing to unpack .../095-r-cran-rcpp_1.1.0-1_ppc64el.deb ... 351s Unpacking r-cran-rcpp (1.1.0-1) ... 351s Selecting previously unselected package r-cran-timedate. 351s Preparing to unpack .../096-r-cran-timedate_4052.112-1_ppc64el.deb ... 351s Unpacking r-cran-timedate (4052.112-1) ... 351s Selecting previously unselected package r-cran-quadprog. 351s Preparing to unpack .../097-r-cran-quadprog_1.5-8-1build2_ppc64el.deb ... 351s Unpacking r-cran-quadprog (1.5-8-1build2) ... 351s Selecting previously unselected package r-cran-xts. 351s Preparing to unpack .../098-r-cran-xts_0.14.1-1_ppc64el.deb ... 351s Unpacking r-cran-xts (0.14.1-1) ... 351s Selecting previously unselected package r-cran-ttr. 351s Preparing to unpack .../099-r-cran-ttr_0.24.4-1_ppc64el.deb ... 351s Unpacking r-cran-ttr (0.24.4-1) ... 351s Selecting previously unselected package r-cran-jsonlite. 351s Preparing to unpack .../100-r-cran-jsonlite_1.9.1+dfsg-1_ppc64el.deb ... 351s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 351s Selecting previously unselected package r-cran-quantmod. 351s Preparing to unpack .../101-r-cran-quantmod_0.4.28-1_all.deb ... 351s Unpacking r-cran-quantmod (0.4.28-1) ... 351s Selecting previously unselected package r-cran-tseries. 351s Preparing to unpack .../102-r-cran-tseries_0.10-59-3_ppc64el.deb ... 351s Unpacking r-cran-tseries (0.10-59-3) ... 351s Selecting previously unselected package r-cran-nlme. 351s Preparing to unpack .../103-r-cran-nlme_3.1.168-1_ppc64el.deb ... 351s Unpacking r-cran-nlme (3.1.168-1) ... 351s Selecting previously unselected package r-cran-urca. 351s Preparing to unpack .../104-r-cran-urca_1.3-4-1build1_ppc64el.deb ... 351s Unpacking r-cran-urca (1.3-4-1build1) ... 351s Selecting previously unselected package r-cran-rcpparmadillo. 351s Preparing to unpack .../105-r-cran-rcpparmadillo_15.2.3-1-1_ppc64el.deb ... 351s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 351s Selecting previously unselected package r-cran-forecast. 351s Preparing to unpack .../106-r-cran-forecast_8.23.0-1_ppc64el.deb ... 351s Unpacking r-cran-forecast (8.23.0-1) ... 351s Selecting previously unselected package r-cran-mass. 351s Preparing to unpack .../107-r-cran-mass_7.3-65-1_ppc64el.deb ... 351s Unpacking r-cran-mass (7.3-65-1) ... 351s Selecting previously unselected package r-cran-matrix. 351s Preparing to unpack .../108-r-cran-matrix_1.7-4-1_ppc64el.deb ... 351s Unpacking r-cran-matrix (1.7-4-1) ... 351s Selecting previously unselected package r-cran-modelr. 351s Preparing to unpack .../109-r-cran-modelr_0.1.11-1_all.deb ... 351s Unpacking r-cran-modelr (0.1.11-1) ... 351s Selecting previously unselected package r-cran-microbenchmark. 351s Preparing to unpack .../110-r-cran-microbenchmark_1.5.0-1_ppc64el.deb ... 351s Unpacking r-cran-microbenchmark (1.5.0-1) ... 351s Selecting previously unselected package r-cran-doby. 351s Preparing to unpack .../111-r-cran-doby_4.7.1-3_all.deb ... 351s Unpacking r-cran-doby (4.7.1-3) ... 351s Selecting previously unselected package r-cran-evaluate. 351s Preparing to unpack .../112-r-cran-evaluate_1.0.5-1_all.deb ... 351s Unpacking r-cran-evaluate (1.0.5-1) ... 351s Selecting previously unselected package r-cran-xfun. 351s Preparing to unpack .../113-r-cran-xfun_0.55+dfsg-1_ppc64el.deb ... 351s Unpacking r-cran-xfun (0.55+dfsg-1) ... 351s Selecting previously unselected package r-cran-highr. 351s Preparing to unpack .../114-r-cran-highr_0.11+dfsg-1_all.deb ... 351s Unpacking r-cran-highr (0.11+dfsg-1) ... 351s Selecting previously unselected package r-cran-yaml. 351s Preparing to unpack .../115-r-cran-yaml_2.3.10-1_ppc64el.deb ... 351s Unpacking r-cran-yaml (2.3.10-1) ... 351s Selecting previously unselected package libjs-mathjax. 351s Preparing to unpack .../116-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 351s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 352s Selecting previously unselected package r-cran-knitr. 352s Preparing to unpack .../117-r-cran-knitr_1.51+dfsg-1_all.deb ... 352s Unpacking r-cran-knitr (1.51+dfsg-1) ... 352s Selecting previously unselected package r-cran-minqa. 352s Preparing to unpack .../118-r-cran-minqa_1.2.8-1_ppc64el.deb ... 352s Unpacking r-cran-minqa (1.2.8-1) ... 352s Selecting previously unselected package libnlopt0:ppc64el. 352s Preparing to unpack .../119-libnlopt0_2.7.1-7ubuntu1_ppc64el.deb ... 352s Unpacking libnlopt0:ppc64el (2.7.1-7ubuntu1) ... 352s Selecting previously unselected package r-cran-nloptr. 352s Preparing to unpack .../120-r-cran-nloptr_2.2.1-2_ppc64el.deb ... 352s Unpacking r-cran-nloptr (2.2.1-2) ... 352s Selecting previously unselected package r-cran-rbibutils. 352s Preparing to unpack .../121-r-cran-rbibutils_2.3-1_ppc64el.deb ... 352s Unpacking r-cran-rbibutils (2.3-1) ... 352s Selecting previously unselected package r-cran-rdpack. 352s Preparing to unpack .../122-r-cran-rdpack_2.6.3-1_all.deb ... 352s Unpacking r-cran-rdpack (2.6.3-1) ... 352s Selecting previously unselected package r-cran-reformulas. 352s Preparing to unpack .../123-r-cran-reformulas_0.4.4-1_all.deb ... 352s Unpacking r-cran-reformulas (0.4.4-1) ... 352s Selecting previously unselected package r-cran-rcppeigen. 352s Preparing to unpack .../124-r-cran-rcppeigen_0.3.4.0.2-1_ppc64el.deb ... 352s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 352s Selecting previously unselected package r-cran-statmod. 352s Preparing to unpack .../125-r-cran-statmod_1.5.0-1_ppc64el.deb ... 352s Unpacking r-cran-statmod (1.5.0-1) ... 352s Selecting previously unselected package r-cran-lme4. 352s Preparing to unpack .../126-r-cran-lme4_1.1-38-1_ppc64el.deb ... 352s Unpacking r-cran-lme4 (1.1-38-1) ... 352s Selecting previously unselected package r-cran-numderiv. 352s Preparing to unpack .../127-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 352s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 352s Selecting previously unselected package r-cran-lmertest. 352s Preparing to unpack .../128-r-cran-lmertest_3.2-0-1_all.deb ... 352s Unpacking r-cran-lmertest (3.2-0-1) ... 352s Selecting previously unselected package r-cran-pbkrtest. 352s Preparing to unpack .../129-r-cran-pbkrtest_0.5.5-1_all.deb ... 352s Unpacking r-cran-pbkrtest (0.5.5-1) ... 352s Setting up libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 352s Setting up libpixman-1-0:ppc64el (0.46.4-1) ... 352s Setting up libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 352s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 352s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 352s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 352s Setting up libxrender1:ppc64el (1:0.9.12-1) ... 352s Setting up libdatrie1:ppc64el (0.2.14-1) ... 352s Setting up libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 352s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 352s Setting up unzip (6.0-29ubuntu1) ... 352s Setting up x11-common (1:7.7+24ubuntu1) ... 353s Setting up libdeflate0:ppc64el (1.23-2build1) ... 353s Setting up libnlopt0:ppc64el (2.7.1-7ubuntu1) ... 353s Setting up libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 353s Setting up libgomp1:ppc64el (15.2.0-12ubuntu1) ... 353s Setting up libjbig0:ppc64el (2.1-6.1ubuntu3) ... 353s Setting up zip (3.0-15ubuntu3) ... 353s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ... 353s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 353s Setting up fonts-dejavu-mono (2.37-8build1) ... 353s Setting up libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 353s Setting up fonts-dejavu-core (2.37-8build1) ... 353s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 353s Setting up libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 353s Setting up libwebp7:ppc64el (1.5.0-0.1build1) ... 353s Setting up libjs-highlight.js (10.7.3+dfsg-2) ... 353s Setting up libharfbuzz0b:ppc64el (12.3.2-1) ... 353s Setting up libthai-data (0.1.30-1) ... 353s Setting up libxss1:ppc64el (1:1.2.3-1build4) ... 353s Setting up libpaper2:ppc64el (2.2.5-0.3build1) ... 353s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 353s Setting up node-normalize.css (8.0.1-5.1) ... 353s Setting up xdg-utils (1.2.1-2ubuntu2) ... 353s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 353s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 353s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 353s Setting up libice6:ppc64el (2:1.1.1-1build1) ... 353s Setting up liblapack3:ppc64el (3.12.1-7ubuntu1) ... 353s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 353s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 353s Setting up libpaper-utils (2.2.5-0.3build1) ... 353s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 353s Setting up libthai0:ppc64el (0.1.30-1) ... 353s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 353s Setting up libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 353s Setting up libsm6:ppc64el (2:1.2.6-1build1) ... 353s Setting up fontconfig (2.17.1-3ubuntu1) ... 355s Regenerating fonts cache... done. 355s Setting up libxft2:ppc64el (2.3.6-1build2) ... 355s Setting up libtk8.6:ppc64el (8.6.17-1) ... 355s Setting up libpango-1.0-0:ppc64el (1.57.0-1) ... 355s Setting up libcairo2:ppc64el (1.18.4-3) ... 355s Setting up libxt6t64:ppc64el (1:1.2.1-1.3) ... 355s Setting up libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 355s Setting up libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 355s Setting up r-base-core (4.5.2-1ubuntu2) ... 355s Creating config file /etc/R/Renviron with new version 356s Setting up r-cran-labeling (0.4.3-1) ... 356s Setting up r-cran-lattice (0.22-7-1) ... 356s Setting up r-cran-nlme (3.1.168-1) ... 356s Setting up r-cran-farver (2.1.2-1) ... 356s Setting up r-cran-viridislite (0.4.3-1) ... 356s Setting up r-cran-statmod (1.5.0-1) ... 356s Setting up r-cran-nnet (7.3-20-1) ... 356s Setting up r-cran-r6 (2.6.1-1) ... 356s Setting up r-cran-pkgkitten (0.2.4-1) ... 356s Setting up r-cran-numderiv (2016.8-1.1-3build1) ... 356s Setting up r-cran-magrittr (2.0.3-1) ... 356s Setting up r-cran-microbenchmark (1.5.0-1) ... 356s Setting up r-cran-quadprog (1.5-8-1build2) ... 356s Setting up r-cran-littler (0.3.22-1) ... 356s Setting up r-cran-rcpp (1.1.0-1) ... 356s Setting up r-cran-curl (7.0.0+dfsg-1) ... 356s Setting up r-cran-nloptr (2.2.1-2) ... 356s Setting up r-cran-boot (1.3-32-1) ... 356s Setting up r-cran-rlang (1.1.5-3) ... 356s Setting up r-cran-xfun (0.55+dfsg-1) ... 356s Setting up r-cran-urca (1.3-4-1build1) ... 356s Setting up r-cran-withr (3.0.2+dfsg-1) ... 356s Setting up r-cran-backports (1.5.0-2) ... 356s Setting up r-cran-deriv (4.2.0-1) ... 356s Setting up r-cran-generics (0.1.4-1) ... 356s Setting up r-cran-yaml (2.3.10-1) ... 356s Setting up r-cran-evaluate (1.0.5-1) ... 356s Setting up r-cran-timedate (4052.112-1) ... 356s Setting up r-cran-highr (0.11+dfsg-1) ... 356s Setting up r-cran-fansi (1.0.6-2) ... 356s Setting up r-cran-mass (7.3-65-1) ... 356s Setting up r-cran-glue (1.8.0-1) ... 356s Setting up r-cran-fracdiff (1.5-3-1) ... 356s Setting up r-cran-cli (3.6.4-1) ... 356s Setting up r-cran-rbibutils (2.3-1) ... 356s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 356s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 356s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 356s Setting up r-cran-utf8 (1.2.4-1) ... 356s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 356s Setting up r-cran-stringi (1.8.4-1build2) ... 356s Setting up r-cran-s7 (0.2.0-1) ... 356s Setting up r-cran-cpp11 (0.5.3-1) ... 356s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 356s Setting up r-cran-isoband (0.2.7-1) ... 356s Setting up r-cran-scales (1.4.0-1) ... 356s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 356s Setting up r-cran-zoo (1.8-15-1) ... 356s Setting up r-cran-matrix (1.7-4-1) ... 356s Setting up r-cran-knitr (1.51+dfsg-1) ... 356s Setting up r-cran-lmtest (0.9.40-1build1) ... 356s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 356s Setting up r-cran-vctrs (0.6.5-1) ... 356s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 356s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 356s Setting up r-cran-minqa (1.2.8-1) ... 356s Setting up r-cran-stringr (1.5.1-1) ... 356s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 356s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 356s Setting up r-cran-xts (0.14.1-1) ... 356s Setting up r-cran-rdpack (2.6.3-1) ... 356s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 356s Setting up r-cran-purrr (1.0.4-1) ... 356s Setting up r-cran-dplyr (1.1.4-4) ... 356s Setting up r-cran-reformulas (0.4.4-1) ... 356s Setting up r-cran-ttr (0.24.4-1) ... 356s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 356s Setting up r-cran-lme4 (1.1-38-1) ... 356s Setting up r-cran-lmertest (3.2-0-1) ... 356s Setting up r-cran-tidyr (1.3.1-1) ... 356s Setting up r-cran-quantmod (0.4.28-1) ... 356s Setting up r-cran-tseries (0.10-59-3) ... 356s Setting up r-cran-broom (1.0.12+dfsg-1) ... 356s Setting up r-cran-forecast (8.23.0-1) ... 356s Setting up r-cran-modelr (0.1.11-1) ... 356s Setting up r-cran-doby (4.7.1-3) ... 356s Setting up r-cran-pbkrtest (0.5.5-1) ... 356s Processing triggers for libc-bin (2.42-2ubuntu4) ... 356s Processing triggers for man-db (2.13.1-1build1) ... 356s Processing triggers for install-info (7.2-5) ... 357s autopkgtest [23:32:50]: test run-unit-test: [----------------------- 358s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 358s BEGIN TEST test_a_utils.R 358s 358s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 358s Copyright (C) 2025 The R Foundation for Statistical Computing 358s Platform: powerpc64le-unknown-linux-gnu 358s 358s R is free software and comes with ABSOLUTELY NO WARRANTY. 358s You are welcome to redistribute it under certain conditions. 358s Type 'license()' or 'licence()' for distribution details. 358s 358s R is a collaborative project with many contributors. 358s Type 'contributors()' for more information and 358s 'citation()' on how to cite R or R packages in publications. 358s 358s Type 'demo()' for some demos, 'help()' for on-line help, or 358s 'help.start()' for an HTML browser interface to help. 358s Type 'q()' to quit R. 358s 358s > # test_a_utils.R 358s > 358s > library(lmerTest) 358s Loading required package: lme4 358s Loading required package: Matrix 360s 360s Attaching package: 'lmerTest' 360s 360s The following object is masked from 'package:lme4': 360s 360s lmer 360s 360s The following object is masked from 'package:stats': 360s 360s step 360s 360s > 360s > # test safeDeparse() - equivalence and differences to deparse(): 360s > deparse_args <- formals(deparse) 360s > safeDeparse_args <- formals(lmerTest:::safeDeparse) 360s > stopifnot( 360s + all.equal(names(deparse_args), names(safeDeparse_args)), 360s + all.equal(deparse_args[!names(deparse_args) %in% c("control", "width.cutoff")], 360s + safeDeparse_args[!names(safeDeparse_args) %in% c("control", "width.cutoff")]), 360s + all.equal(deparse_args[["width.cutoff"]], 60L), 360s + all(eval(safeDeparse_args[["control"]]) %in% eval(deparse_args[["control"]])), 360s + all.equal(safeDeparse_args[["width.cutoff"]], 500L) 360s + ) 360s > 360s > 360s BEGIN TEST test_anova.R 360s 360s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 360s Copyright (C) 2025 The R Foundation for Statistical Computing 360s Platform: powerpc64le-unknown-linux-gnu 360s 360s R is free software and comes with ABSOLUTELY NO WARRANTY. 360s You are welcome to redistribute it under certain conditions. 360s Type 'license()' or 'licence()' for distribution details. 360s 360s R is a collaborative project with many contributors. 360s Type 'contributors()' for more information and 360s 'citation()' on how to cite R or R packages in publications. 360s 360s Type 'demo()' for some demos, 'help()' for on-line help, or 360s 'help.start()' for an HTML browser interface to help. 360s Type 'q()' to quit R. 360s 360s > # test_anova.R 360s > library(lmerTest) 360s Loading required package: lme4 360s Loading required package: Matrix 362s 362s Attaching package: 'lmerTest' 362s 362s > 362s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 362s > # even in tests: 362s > assertError <- function(expr, ...) 362s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 362s > assertWarning <- function(expr, ...) 362s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 362s > 362s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 362s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 362s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 362s The following object is masked from 'package:lme4': 362s 362s lmer 362s 362s The following object is masked from 'package:stats': 362s 362s step 362s 362s > 362s > data("sleepstudy", package="lme4") 362s > TOL <- 1e-4 362s > 362s > #################################### 362s > ## Basic anova tests 362s > #################################### 362s > 362s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 362s > 362s > ####### ddf argument: 362s > (an1 <- anova(m)) # Also testing print method. 362s Type III Analysis of Variance Table with Satterthwaite's method 362s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 362s Days 30031 30031 1 17 45.853 3.264e-06 *** 362s --- 362s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 362s > (an2 <- anova(m, ddf="Satterthwaite")) 362s Type III Analysis of Variance Table with Satterthwaite's method 362s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 362s Days 30031 30031 1 17 45.853 3.264e-06 *** 362s --- 362s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 362s > (an2b <- anova(m, ddf="Satterthwaite", type=3)) 362s Type III Analysis of Variance Table with Satterthwaite's method 362s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 362s Days 30031 30031 1 17 45.853 3.264e-06 *** 362s --- 362s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 362s > (an2c <- anova(m, ddf="Satterthwaite", type=2)) 362s Type II Analysis of Variance Table with Satterthwaite's method 362s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 362s Days 30031 30031 1 17 45.853 3.264e-06 *** 362s --- 362s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 362s > stopifnot(isTRUE( 362s + all.equal(an1, an2, tolerance=TOL) 362s + )) 362s > (an3 <- anova(m, ddf="Sat")) ## Abbreviated argument 362s Type III Analysis of Variance Table with Satterthwaite's method 362s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 362s Days 30031 30031 1 17 45.853 3.264e-06 *** 362s --- 362s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 362s > stopifnot(isTRUE( 362s + all.equal(an1, an3, tolerance=TOL) 362s + )) 362s > if(has_pbkrtest) { 362s + (anova(m, ddf="Kenward-Roger")) 362s + (anova(m, ddf="Kenward-Roger", type=3)) 362s + } 363s Type III Analysis of Variance Table with Kenward-Roger's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an1 <- anova(m, ddf="lme4")) 363s Analysis of Variance Table 363s npar Sum Sq Mean Sq F value 363s Days 1 30031 30031 45.853 363s > (an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4" 363s Analysis of Variance Table 363s npar Sum Sq Mean Sq F value 363s Days 1 30031 30031 45.853 363s > stopifnot(isTRUE( 363s + all.equal(an1, an2, tolerance=TOL) 363s + )) 363s > res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg. 363s > stopifnot( 363s + grepl("'arg' should be one of ", unlist(res[[1]])$message) 363s + ) 363s > 363s > ## lme4 method: 363s > an1 <- anova(m, ddf="lme4") 363s > an2 <- anova(as(m, "lmerMod")) 363s > stopifnot(isTRUE( 363s + all.equal(an1, an2, tolerance=TOL) 363s + )) 363s > 363s > ###### type argument: 363s > (an1 <- anova(m, type="1")) # valid type arg. 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type="I")) # same 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot(isTRUE( 363s + all.equal(an1, an2, tolerance=TOL) 363s + )) 363s > (an3 <- anova(m, type=1)) # Not strictly valid, but accepted 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot(isTRUE( 363s + all.equal(an1, an3, tolerance=TOL) 363s + )) 363s > 363s > (an1 <- anova(m, type="2")) # valid type arg. 363s Type II Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type="II")) # same 363s Type II Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot(isTRUE( 363s + all.equal(an1, an2, tolerance=TOL) 363s + )) 363s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot(isTRUE( 363s + all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL) 363s + )) 363s > 363s > (an1 <- anova(m, type="3")) # valid type arg. 363s Type III Analysis of Variance Table with Satterthwaite's method 363s refitting model(s) with ML (instead of REML) 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type="III")) # same 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot(isTRUE( 363s + all.equal(an1, an2, tolerance=TOL) 363s + )) 363s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s Days 30031 30031 1 17 45.853 3.264e-06 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot(isTRUE( 363s + all.equal(an1, an3, tolerance=TOL) 363s + )) 363s > assertError(anova(m, type=0)) # Not valid arg. 363s > assertError(anova(m, type="i")) # Not valid arg. 363s > 363s > ####### Model comparison: 363s > fm <- lm(Reaction ~ Days, sleepstudy) 363s > (an <- anova(m, fm)) 363s Data: sleepstudy 363s Models: 363s fm: Reaction ~ Days 363s m: Reaction ~ Days + (Days | Subject) 363s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 363s fm 3 1906.3 1915.9 -950.15 1900.3 363s m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 *** 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot( 363s + nrow(an) == 2L, 363s + rownames(an)[2] == "m" 363s + ) 363s > 363s > m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 363s > (an <- anova(m, m2, refit=FALSE)) 363s Data: sleepstudy 363s Models: 363s m: Reaction ~ Days + (Days | Subject) 363s m2: Reaction ~ Days + I(Days^2) + (Days | Subject) 363s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 363s m 6 1755.6 1774.8 -871.81 1743.6 363s m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673 363s > stopifnot( 363s + nrow(an) == 2L, 363s + rownames(an)[1] == "m" 363s + ) 363s > 363s > 363s > #################################### 363s > ## Example with factor fixef: 363s > #################################### 363s > 363s > ## 'temp' is continuous, 'temperature' an ordered factor with 6 levels 363s > data("cake", package="lme4") 363s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 363s > (an <- anova(m)) 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 4.00 2.00 2 254.02 0.0957 0.9088 363s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an_lme4 <- anova(m, ddf="lme4")) 363s Analysis of Variance Table 363s npar Sum Sq Mean Sq F value 363s recipe 2 10.39 5.20 0.2488 363s temp 1 1966.71 1966.71 94.1632 363s recipe:temp 2 1.74 0.87 0.0417 363s > 363s > if(has_pbkrtest) { 363s + (an_KR <- anova(m, ddf="Kenward-Roger")) 363s + # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 363s + # an_lme4[, c("Sum Sq", "Mean Sq", "F value")]) 363s + # stopifnot(isTRUE(res)) 363s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 363s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 363s + stopifnot(isTRUE(res)) 363s + } 363s > stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6), 363s + all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL)) 363s > 363s > an3 <- anova(m, type=3) 363s > an2 <- anova(m, type=2) 363s > an1 <- anova(m, type=1) 363s > 363s > ## Data is balanced, so Type II and III should be identical: 363s > ## One variable is continuous, so Type I and II/III are different: 363s > stopifnot( 363s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)), 363s + !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8)) 363s + ) 363s > 363s > # Using an ordered factor: 363s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 363s > (an1 <- anova(m, type=1)) 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type=2)) 363s Type II Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > # Type 3 is also available with ordered factors: 363s > (an3 <- anova(m, type=3)) 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > ## Balanced data and only factors: Type I, II and III should be the same: 363s > stopifnot( 363s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 363s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)) 363s + ) 363s > 363s > (an <- anova(m, type=1)) 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an_lme4 <- anova(m, type=1, ddf="lme4")) 363s Analysis of Variance Table 363s npar Sum Sq Mean Sq F value 363s recipe 2 10.19 5.09 0.2488 363s temperature 5 2100.30 420.06 20.5199 363s recipe:temperature 10 205.98 20.60 1.0062 363s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 363s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 363s > stopifnot(isTRUE(res)) 363s > if(has_pbkrtest) { 363s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 363s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 363s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 363s + stopifnot(isTRUE(res)) 363s + } 363s > stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL), 363s + all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL)) 363s > 363s > ######## 363s > ## Make case with balanced unordered factors: 363s > cake2 <- cake 363s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 363s > # str(cake2) 363s > stopifnot( 363s + !is.ordered(cake2$temperature) 363s + ) 363s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 363s > (an1 <- anova(m, type=1)) 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type=2)) 363s Type II Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an3 <- anova(m, type=3)) 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.19 5.09 2 42 0.2488 0.7809 363s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 363s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > ## Balanced data and only factors: Type I, II, and III should be the same: 363s > stopifnot( 363s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 363s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)) 363s + ) 363s > ######## 363s > 363s > # No intercept: 363s > m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake) 363s > (an <- anova(m, type=1)) 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 21442.9 7147.6 3 42 342.2200 <2e-16 *** 363s temp 1966.7 1966.7 1 222 94.1632 <2e-16 *** 363s recipe:temp 1.7 0.9 2 222 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type=2)) 363s Type II Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 4.48 1.49 3 254.02 0.0714 0.9752 363s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type=3)) 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 4.48 1.49 3 254.02 0.0714 0.9752 363s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > if(has_pbkrtest) 363s + (an_KR <- anova(m, ddf="Kenward-Roger")) 363s Type III Analysis of Variance Table with Kenward-Roger's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 4.48 1.49 3 254.02 0.0714 0.9752 363s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an_lme4 <- anova(m, ddf="lme4")) 363s Analysis of Variance Table 363s npar Sum Sq Mean Sq F value 363s recipe 3 21442.9 7147.6 342.2200 363s temp 1 1966.7 1966.7 94.1632 363s recipe:temp 2 1.7 0.9 0.0417 363s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 363s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 363s > stopifnot(isTRUE(res)) 363s > 363s > # ML-fit: 363s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE) 363s > (an <- anova(m, type=1)) 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.99 5.49 2 45 0.2666 0.7672 363s temp 1966.71 1966.71 1 225 95.4357 <2e-16 *** 363s recipe:temp 1.74 0.87 2 225 0.0423 0.9586 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > if(has_pbkrtest) 363s + assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be REML 363s > (an_lme4 <- anova(m, ddf="lme4")) 363s Analysis of Variance Table 363s npar Sum Sq Mean Sq F value 363s recipe 2 10.99 5.49 0.2666 363s temp 1 1966.71 1966.71 95.4357 363s recipe:temp 2 1.74 0.87 0.0423 363s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 363s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 363s > stopifnot(isTRUE(res)) 363s > 363s > #################################### 363s > ## Using contr.sum: 363s > #################################### 363s > 363s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, 363s + contrasts = list('recipe' = "contr.sum")) 363s > (an <- anova(m, type=1)) 363s Type I Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 10.39 5.20 2 42 0.2488 0.7809 363s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an2 <- anova(m, type=2)) 363s Type II Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 4.00 2.00 2 254.02 0.0957 0.9088 363s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > (an3 <- anova(m, type=3)) 363s Type III Analysis of Variance Table with Satterthwaite's method 363s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 363s recipe 4.00 2.00 2 254.02 0.0957 0.9088 363s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 363s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 363s --- 363s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 363s > stopifnot( 363s + isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL)) 363s + ) 363s > if(has_pbkrtest) 363s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 364s Type I Analysis of Variance Table with Kenward-Roger's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s recipe 10.39 5.20 2 42 0.2488 0.7809 364s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 364s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_lme4 <- anova(m, ddf="lme4")) 364s Analysis of Variance Table 364s npar Sum Sq Mean Sq F value 364s recipe 2 10.39 5.20 0.2488 364s temp 1 1966.71 1966.71 94.1632 364s recipe:temp 2 1.74 0.87 0.0417 364s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 364s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 364s > stopifnot(isTRUE(res)) 364s > 364s > 364s > #################################### 364s > ## Example with continuous fixef: 364s > #################################### 364s > 364s > # Example with no fixef: 364s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 364s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 364s > stopifnot(length(fixef(m)) == 0L) 364s > (an <- anova(m, type=1)) 364s Type I Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s > (an_2 <- anova(m, type=2)) 364s Type II Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s > (an_3 <- anova(m, type=3)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s > stopifnot(nrow(an) == 0L, 364s + nrow(an_2) == 0L, 364s + nrow(an_3) == 0L) 364s > # anova(m, ddf="lme4") # Bug in lme4 it seems 364s > if(has_pbkrtest) { 364s + (an_KR <- anova(m, ddf="Kenward-Roger")) 364s + stopifnot( 364s + nrow(an_KR) == 0L 364s + ) 364s + } 364s > 364s > # Example with intercept only: 364s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 364s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 364s > stopifnot(length(fixef(m)) == 1L, 364s + names(fixef(m)) == "(Intercept)") 364s > (an <- anova(m)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s > (an_2 <- anova(m, type=2)) 364s Type II Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s > (an_3 <- anova(m, type=3)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s > (an_lme4 <- anova(m, ddf="lme4")) 364s Analysis of Variance Table 364s npar Sum Sq Mean Sq F value 364s > stopifnot(nrow(an) == 0L, 364s + nrow(an_2) == 0L, 364s + nrow(an_3) == 0L, 364s + nrow(an_lme4) == 0L) 364s > if(has_pbkrtest) { 364s + (an_KR <- anova(m, ddf="Kenward-Roger")) 364s + stopifnot( 364s + nrow(an_KR) == 0L 364s + ) 364s + } 364s > 364s > # Example with 1 fixef without intercept: 364s > # for packageVersion("lme4") < 1.1.20 364s > # mOld <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy) 364s > # for packageVersion("lme4") >= 1.1.20 we need to specify the old default 364s > # optimizer to get the model to converge well enough. 364s > m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy, 364s + control=lmerControl(optimizer="bobyqa")) 364s > # m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) # alternative 364s > stopifnot(length(fixef(m)) == 1L, 364s + names(fixef(m)) == "Days") 364s > (an <- anova(m)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 93564 93564 1 17 142.86 1.069e-09 *** 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_2 <- anova(m, type=2)) 364s Type II Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 93564 93564 1 17 142.86 1.069e-09 *** 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_3 <- anova(m, type=3)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 93564 93564 1 17 142.86 1.069e-09 *** 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_lme4 <- anova(m, ddf="lme4")) 364s Analysis of Variance Table 364s npar Sum Sq Mean Sq F value 364s Days 1 93564 93564 142.86 364s > stopifnot(nrow(an) == 1L, 364s + nrow(an_2) == 1L, 364s + nrow(an_3) == 1L, 364s + nrow(an_lme4) == 1L) 364s > if(has_pbkrtest) { 364s + (an_KR <- anova(m, ddf="Kenward-Roger")) 364s + stopifnot( 364s + nrow(an_KR) == 1L 364s + ) 364s + } 364s > 364s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 364s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 364s > stopifnot(isTRUE(res)) 364s > stopifnot(isTRUE(all.equal( 364s + c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL 364s + ))) 364s > 364s > # Example with >1 fixef without intercept: 364s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 364s Warning message: 364s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 364s Model failed to converge with max|grad| = 0.00492394 (tol = 0.002, component 1) 364s See ?lme4::convergence and ?lme4::troubleshooting. 364s > stopifnot(length(fixef(m)) == 2L, 364s + names(fixef(m)) == c("Days", "I(Days^2)")) 364s > (an <- anova(m)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 22142.5 22142.5 1 69.049 33.946 1.639e-07 *** 364s I(Days^2) 744.3 744.3 1 143.667 1.141 0.2872 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_2 <- anova(m, type=2)) 364s Type II Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 22142.5 22142.5 1 69.049 33.946 1.639e-07 *** 364s I(Days^2) 744.3 744.3 1 143.667 1.141 0.2872 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_3 <- anova(m, type=3)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 22142.5 22142.5 1 69.049 33.946 1.639e-07 *** 364s I(Days^2) 744.3 744.3 1 143.667 1.141 0.2872 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_lme4 <- anova(m, ddf="lme4")) 364s Analysis of Variance Table 364s npar Sum Sq Mean Sq F value 364s Days 1 93183 93183 142.854 364s I(Days^2) 1 744 744 1.141 364s > stopifnot(nrow(an) == 2L, 364s + nrow(an_3) == 2L, 364s + nrow(an_lme4) == 2L) 364s > if(has_pbkrtest) { 364s + (an_KR <- anova(m, ddf="Kenward-Roger")) 364s + stopifnot( 364s + nrow(an_KR) == 2L 364s + ) 364s + } 364s > # Here is a diff in SSQ which doesn't seem well-defined anyway... 364s > # SSQ for I(Days^2) agree though. 364s > # t-statistics also agree: 364s > coef(summary(m)) 364s Estimate Std. Error df t value Pr(>|t|) 364s Days 15.8893172 2.7271762 69.04928 5.826289 1.639457e-07 364s I(Days^2) 0.2794617 0.2616254 143.66747 1.068175 2.872332e-01 364s > Lmat <- diag(length(fixef(m))) 364s > lmerTest:::rbindall(lapply(1:nrow(Lmat), function(i) contest1D(m, Lmat[i, ]))) 364s Estimate Std. Error df t value Pr(>|t|) 364s 1 15.8893172 2.7271762 69.04928 5.826289 1.639457e-07 364s 2 0.2794617 0.2616254 143.66747 1.068175 2.872332e-01 364s > 364s > # Example with >1 fixef and intercept: 364s > m <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 364s > stopifnot(length(fixef(m)) == 3L) 364s > (an <- anova(m, type=1)) 364s Type I Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 29894.8 29894.8 1 17 45.8530 3.264e-06 *** 364s I(Days^2) 1079.5 1079.5 1 143 1.6558 0.2003 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_2 <- anova(m, type=2)) 364s Type II Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 364s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_3 <- anova(m, type=3)) 364s Type III Analysis of Variance Table with Satterthwaite's method 364s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 364s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 364s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 364s --- 364s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 364s > (an_lme4 <- anova(m, ddf="lme4")) 364s Analysis of Variance Table 364s npar Sum Sq Mean Sq F value 364s Days 1 29894.8 29894.8 45.8530 364s I(Days^2) 1 1079.5 1079.5 1.6558 364s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 364s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 364s > stopifnot(isTRUE(res)) 364s > 364s > if(has_pbkrtest) { 364s + (an_KR <- anova(m, ddf="Kenward-Roger")) 364s + res <- all.equal(an_3[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], 364s + an_KR[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], tolerance=TOL) 364s + stopifnot(isTRUE(res)) 364s + } 364s > 364s > ## FIXME: Test the use of refit arg to lme4:::anova.merMod 364s > 364s > ############################## 364s > # Test that type III anova is the same regardless of contrast coding: 364s > # 3 x 3 factorial with missing diagonal 364s > data("cake", package="lme4") 364s > cake4 <- cake 364s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 364s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 364s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 364s + (recipe == "B" & temperature == "185") | 364s + (recipe == "C" & temperature == "195") ))) 364s > str(cake4) 364s 'data.frame': 90 obs. of 5 variables: 364s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 2 2 2 2 ... 364s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 2 2 3 3 1 1 2 2 ... 364s $ temperature: Factor w/ 3 levels "175","185","195": 2 3 1 3 1 2 2 3 1 3 ... 364s $ angle : int 46 47 39 51 46 44 29 35 35 47 ... 364s $ temp : num 185 195 175 195 175 185 185 195 175 195 ... 364s > with(cake4, table(recipe, temperature)) 364s temperature 364s recipe 175 185 195 364s A 0 15 15 364s B 15 0 15 364s C 15 15 0 364s > # load_all(r2path) 364s > 364s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 364s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 364s > fm2 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 364s + contrasts=list(recipe="contr.sum", temperature="contr.SAS")) 364s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 365s > fm3 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 365s + contrasts=list(recipe="contr.sum", temperature="contr.poly")) 365s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 365s > fm4 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 365s + contrasts=list(recipe=contr.helmert, temperature="contr.poly")) 365s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 365s > (an1 <- anova(fm1)) 365s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 365s Interpret type III hypotheses with care. 365s Type III Analysis of Variance Table with Satterthwaite's method 365s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 365s recipe 2.282 1.141 2 45.888 0.0871 0.916766 365s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 365s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 365s --- 365s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 365s > (an2 <- anova(fm2)) 365s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 365s Interpret type III hypotheses with care. 365s Type III Analysis of Variance Table with Satterthwaite's method 365s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 365s recipe Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 365s Interpret type III hypotheses with care. 365s 2.282 1.141 2 45.888 0.0871 0.916766 365s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 365s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 365s --- 365s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 365s > (an3 <- anova(fm3)) 365s Type III Analysis of Variance Table with Satterthwaite's method 365s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 365s recipe 2.282 1.141 2 45.888 0.0871 0.916766 365s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 365s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 365s --- 365s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 365s > (an4 <- anova(fm4)) 365s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 365s Interpret type III hypotheses with care. 365s Type III Analysis of Variance Table with Satterthwaite's method 365s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 365s recipe 2.282 1.141 2 45.888 0.0871 0.916766 365s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 365s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 365s --- 365s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 365s > options("contrasts") 365s $contrasts 365s unordered ordered 365s "contr.treatment" "contr.poly" 365s 365s > options(contrasts = c("contr.sum", "contr.poly")) 365s > fm5 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 365s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 365s > (an5 <- anova(fm5)) 365s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 365s Interpret type III hypotheses with care. 365s Type III Analysis of Variance Table with Satterthwaite's method 365s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 365s recipe 2.282 1.141 2 45.888 0.0871 0.916766 365s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 365s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 365s --- 365s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 365s > options(contrasts = c("contr.treatment", "contr.poly")) 365s > options("contrasts") 365s $contrasts 365s [1] "contr.treatment" "contr.poly" 365s 365s > stopifnot( 365s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 365s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)), 365s + isTRUE(all.equal(an1, an4, check.attributes=FALSE, tolerance=TOL)), 365s + isTRUE(all.equal(an1, an5, check.attributes=FALSE, tolerance=TOL)) 365s + ) 365s > 365s > 365s BEGIN TEST test_compare_sas.R 365s 365s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 365s Copyright (C) 2025 The R Foundation for Statistical Computing 365s Platform: powerpc64le-unknown-linux-gnu 365s 365s R is free software and comes with ABSOLUTELY NO WARRANTY. 365s You are welcome to redistribute it under certain conditions. 365s Type 'license()' or 'licence()' for distribution details. 365s 365s R is a collaborative project with many contributors. 365s Type 'contributors()' for more information and 365s 'citation()' on how to cite R or R packages in publications. 365s 365s Type 'demo()' for some demos, 'help()' for on-line help, or 365s 'help.start()' for an HTML browser interface to help. 365s Type 'q()' to quit R. 365s 365s > # test_compare_sas.R 365s > library(lmerTest) 365s Loading required package: lme4 365s Loading required package: Matrix 367s > 367s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 367s > # even in tests: 367s > assertError <- function(expr, ...) 367s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 367s > assertWarning <- function(expr, ...) 367s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 367s > 367s > ##################################################################### 367s > 367s > 367s > 367s Attaching package: 'lmerTest' 367s 367s The following object is masked from 'package:lme4': 367s 367s lmer 367s 367s The following object is masked from 'package:stats': 367s 367s step 367s 367s # Use contrasts to get particular estimates for the summary table: 367s > l <- list(Frequency="contr.SAS", Income="contr.SAS") 367s > m.carrots <- lmer(Preference ~ sens2*Frequency*Income 367s + +(1+sens2|Consumer), data=carrots, contrasts=l) 367s fixed-effect model matrix is rank deficient so dropping 12 columns / coefficients 367s > an.m <- anova(m.carrots) 367s 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. 367s Interpret type III hypotheses with care. 367s > 367s > TOL <- 1e-4 367s > TOL2 <- 1e-5 367s > # with 4 decimals should agree with SAS output 367s > # numbers before decimals should agree with SAS output 367s > stopifnot( 367s + all.equal(an.m[,"Pr(>F)"], 367s + c(2e-5, 0.15512, 0.06939, 0.08223, 0.52459, 0.03119, 0.48344), 367s + tolerance = TOL), 367s + all.equal(round(an.m$DenDF), c(83, 83, 83, 83, 83, 83, 83)) 367s + ) 367s > 367s > sm <- summary(m.carrots) 367s > stopifnot( 367s + isTRUE(all.equal(sm$coefficients[,"Pr(>|t|)"], 367s + c(1e-10, 0.005061, 0.6865554, 0.342613, 0.129157, 367s + 0.088231, 0.846000, 0.354472, 0.526318, 0.020646, 0.010188, 367s + 0.031242, 0.055356, 0.694689, 0.099382, 0.28547, 367s + 0.977774, 0.855653, 0.427737, 0.321086, 0.417465 , 0.204385, 0.784437, 367s + 0.681434, 0.106180, 0.149122, 0.390870, 0.273686), tolerance=TOL, 367s + check.attributes = FALSE)) 367s + ) 367s > 367s > # Takes too long to run: 367s > # if(requireNamespace("pbkrtest", quietly = TRUE)) { 367s > # sm.kr <- summary(m.carrots, ddf = "Kenward-Roger") 367s > # 367s > # ## coefficients for Sat and KR agree in this example 367s > # # cbind(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"]) 367s > # all.equal(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"], 367s > # tol=TOL) 367s > # } 367s > 367s > ################################################################################ 367s > ## checking lsmeans and difflsmeans 367s > ## compare with SAS output 367s > m <- lmer(Informed.liking ~ Product*Information*Gender 367s + + (1|Product:Consumer) + (1|Consumer) , data=ham) 367s > 367s > 367s > lsm <- lsmeansLT(m, which = "Product") 367s > # head(lsm) 367s > 367s > stopifnot( 367s + isTRUE(all.equal(lsm[, "Estimate"], c(5.8084, 5.1012, 6.0909, 5.9256), 367s + tol=TOL, check.attributes = FALSE)), 367s + isTRUE(all.equal(round(lsm[, "t value"], 2), c(24.93, 21.89, 26.14, 25.43), tolerance=TOL, 367s + check.attributes = FALSE)), 367s + isTRUE(all.equal(lsm[, "lower"], c(5.3499, 4.6428, 5.6324, 5.4672), tolerance=TOL, 367s + check.attributes = FALSE)), 367s + isTRUE(all.equal(lsm[, "upper"], c(6.2668, 5.5597, 6.5493, 6.3840), tolerance=TOL, 367s + check.attributes = FALSE)) 367s + ) 367s > 367s > ################################################################################ 367s > # Not actually 'hard-coded' tests versus SAS results... 367s > 367s > m.carrots <- lmer(Preference ~ 0 + sens2 + Homesize + 367s + (1+sens2 | Consumer), data=carrots, 367s + control=lmerControl(optimizer="bobyqa")) 367s > summary(m.carrots) 367s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 367s lmerModLmerTest] 367s Formula: Preference ~ 0 + sens2 + Homesize + (1 + sens2 | Consumer) 367s Data: carrots 367s Control: lmerControl(optimizer = "bobyqa") 367s 367s REML criterion at convergence: 3748.9 367s 367s Scaled residuals: 367s Min 1Q Median 3Q Max 367s -3.5322 -0.5571 0.0308 0.6297 2.8552 367s 367s Random effects: 367s Groups Name Variance Std.Dev. Corr 367s Consumer (Intercept) 0.195168 0.44178 367s sens2 0.002779 0.05271 0.18 367s Residual 1.070441 1.03462 367s Number of obs: 1233, groups: Consumer, 103 367s 367s Fixed effects: 367s Estimate Std. Error df t value Pr(>|t|) 367s sens2 7.068e-02 9.545e-03 1.020e+02 7.404 3.89e-11 *** 367s Homesize1 4.910e+00 7.056e-02 1.013e+02 69.586 < 2e-16 *** 367s Homesize3 4.661e+00 7.850e-02 1.013e+02 59.374 < 2e-16 *** 367s --- 367s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 367s 367s Correlation of Fixed Effects: 367s sens2 Homsz1 367s Homesize1 0.061 367s Homesize3 0.055 0.003 367s > 367s > (an.1 <- anova(m.carrots, type=1)) 367s Type I Analysis of Variance Table with Satterthwaite's method 367s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 367s sens2 60.5 60.5 1 102.01 56.539 2.211e-11 *** 367s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 367s --- 367s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 367s > (an.3 <- anova(m.carrots)) 367s Type III Analysis of Variance Table with Satterthwaite's method 367s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 367s sens2 58.7 58.7 1 102.01 54.821 3.892e-11 *** 367s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 367s --- 367s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 367s > (an.lme4 <- anova(m.carrots, ddf = "lme4")) # difference in SSQ MS and F-values 367s Analysis of Variance Table 367s npar Sum Sq Mean Sq F value 367s sens2 1 0.0 0.0 0.0122 367s Homesize 2 8927.2 4463.6 4169.8634 367s > # Is this a problem with lme4? 367s > # fm <- lm(Preference ~ 0 + sens2 + Homesize, data=carrots) 367s > # anova(fm) 367s > # coef(summary(fm)) 367s > # Here the F value is a little greater than the squared t-value (as expected) 367s > 367s > stopifnot(all.equal(an.1[, "F value"], c(56.5394, 4169.87), tolerance = TOL2), 367s + all.equal(an.3[, "F value"], c(54.8206, 4169.87), tolerance = TOL2)) 367s > 367s > 367s > ################################################################################ 367s > # Check exmaple from GLM SAS report 367s > 367s > ### example from the paper GLM SAS 101 report 367s > a <- factor(c(1,1,1,2,2,2,2,2,1,2)) 367s > b <- factor(c(1,1,2,1,2,2,2,2,2,1)) 367s > f=factor(c(1,2,1,2,1,2,1,2,1,2)) 367s > y <- c(12,14,11,20,17,23,35,46,15,16) 367s > dd <- data.frame(a=a, b=b, y=y, f=f) 367s > 367s > ## check type 2 is order independent 367s > model <- lmer(y ~ a*b + (1|f), data=dd) 367s boundary (singular) fit: see help('isSingular') 367s > model2 <- lmer(y ~ b*a + (1|f), data=dd) 368s boundary (singular) fit: see help('isSingular') 368s > (an <- anova(model, type=2)) 368s Type II Analysis of Variance Table with Satterthwaite's method 368s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 368s a 336.00 336.00 1 6 3.9013 0.09566 . 368s b 114.33 114.33 1 6 1.3275 0.29308 368s a:b 85.75 85.75 1 6 0.9956 0.35689 368s --- 368s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 368s > (an2 <- anova(model2, type=2)) 368s Type II Analysis of Variance Table with Satterthwaite's method 368s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 368s b 114.33 114.33 1 6 1.3275 0.29308 368s a 336.00 336.00 1 6 3.9013 0.09566 . 368s b:a 85.75 85.75 1 6 0.9956 0.35689 368s --- 368s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 368s > stopifnot( 368s + isTRUE(all.equal(an,an2[c(2,1,3),], check.attributes = FALSE, tolerance=TOL2)) 368s + ) 368s > 368s > ## check the results are the same as from SAS proc mixed 368s > stopifnot( 368s + isTRUE(all.equal(an[,"F value"], c(3.90131, 1.32753, 0.99565), tolerance=TOL2)) 368s + ) 368s > ################################################################################ 368s > ## Check type II and III anova tables versus SAS 368s > 368s > m.carrots <- lmer(Preference ~ sens2*Homesize 368s + +(1+sens2|Consumer), data=carrots) 368s > (ancar <- anova(m.carrots, type=2)) 368s Type II Analysis of Variance Table with Satterthwaite's method 368s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 368s sens2 58.697 58.697 1 101.02 54.8339 4.042e-11 *** 368s Homesize 5.526 5.526 1 100.99 5.1621 0.02521 * 368s sens2:Homesize 1.103 1.103 1 101.02 1.0303 0.31251 368s --- 368s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 368s > 368s > stopifnot( 368s + isTRUE(all.equal(ancar[,"F value"], c(54.8361, 5.16138, 1.03035), tolerance = TOL)) 368s + ) 368s > 368s > m <- lmer(Informed.liking ~ Product*Age 368s + + (1|Consumer) , data=ham) 368s > (an <- anova(m, type=2)) 368s Type II Analysis of Variance Table with Satterthwaite's method 368s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 368s Product 32.498 10.8327 3 561 2.4814 0.06014 . 368s Age 0.024 0.0235 1 79 0.0054 0.94168 368s Product:Age 19.442 6.4808 3 561 1.4845 0.21772 368s --- 368s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 368s > 368s > stopifnot( 368s + isTRUE(all.equal(an[,"F value"], c(2.48135, .005387, 1.48451), tolerance = TOL2)) 368s + ) 368s > 368s > 368s > fm <- lmer(Preference ~ sens2*Homesize*sens1 + (1|Product), 368s + data=carrots) 368s > (ant2 <- anova(fm, type=2)) 368s Type II Analysis of Variance Table with Satterthwaite's method 368s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 368s sens2 21.0228 21.0228 1 7.97 16.4832 0.0036583 ** 368s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 368s sens1 0.6709 0.6709 1 7.98 0.5260 0.4889911 368s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 368s sens2:sens1 0.1372 0.1372 1 7.98 0.1076 0.7513796 368s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 368s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 368s --- 368s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 368s > (ant3 <- anova(fm, type=3)) 368s Type III Analysis of Variance Table with Satterthwaite's method 368s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 368s sens2 21.5710 21.5710 1 8.02 16.9130 0.0033602 ** 368s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 368s sens1 0.6136 0.6136 1 8.03 0.4811 0.5074890 368s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 368s sens2:sens1 0.0946 0.0946 1 8.02 0.0742 0.7922017 368s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 368s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 368s --- 368s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 368s > 368s > stopifnot( 368s + isTRUE(all.equal(ant2[,"F value"], 368s + c(16.4842, 14.0010, .526076, 1.18144, 368s + .107570, .335177, 1.05946), tolerance = TOL)), 368s + isTRUE(all.equal(ant3[,"F value"], 368s + c(16.9140, 14.0010,.481148, 1.18144, 368s + .074201, .335177, 1.05946), tolerance = TOL)) 368s + ) 368s > 368s > ################################################################################ 368s > 368s > 368s > 368s BEGIN TEST test_contest1D.R 368s 368s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 368s Copyright (C) 2025 The R Foundation for Statistical Computing 368s Platform: powerpc64le-unknown-linux-gnu 368s 368s R is free software and comes with ABSOLUTELY NO WARRANTY. 368s You are welcome to redistribute it under certain conditions. 368s Type 'license()' or 'licence()' for distribution details. 368s 368s R is a collaborative project with many contributors. 368s Type 'contributors()' for more information and 368s 'citation()' on how to cite R or R packages in publications. 368s 368s Type 'demo()' for some demos, 'help()' for on-line help, or 368s 'help.start()' for an HTML browser interface to help. 368s Type 'q()' to quit R. 368s 368s > # test_contest1D.R 368s > library(lmerTest) 368s Loading required package: lme4 368s Loading required package: Matrix 370s 370s Attaching package: 'lmerTest' 370s 370s The following object is masked from 'package:lme4': 370s 370s lmer 370s 370s The following object is masked from 'package:stats': 370s 370s step 370s 370s > 370s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 370s > # even in tests: 370s > assertError <- function(expr, ...) 370s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 370s > assertWarning <- function(expr, ...) 370s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 370s > 370s > TOL <- 1e-4 370s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 370s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 370s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 370s > 370s > data("sleepstudy", package="lme4") 370s > 370s > #################################### 370s > ## Tests of contest1D 370s > #################################### 370s > 370s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 370s + sleepstudy) 370s > # Basic tests: 370s > L <- c(0, 1, 0) 370s > contest1D(fm, L) 370s Estimate Std. Error df t value Pr(>|t|) 370s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 370s > contest1D(fm, L, confint = TRUE) 370s Estimate Std. Error df t value lower upper Pr(>|t|) 370s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 370s > contest1D(fm, L, confint = TRUE, level=0.99) 370s Estimate Std. Error df t value lower upper Pr(>|t|) 370s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 370s > if(has_pbkrtest) 370s + contest1D(fm, L, ddf="Kenward-Roger") 370s Estimate Std. Error df t value Pr(>|t|) 370s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 370s > 370s > # Test too long L 370s > assertError(contest1D(fm, c(0, 1, 1, 1))) 370s > 370s > # Test too short L 370s > assertError(contest1D(fm, c(0, 1))) 370s > 370s > # Test matrix L 370s > contest1D(fm, matrix(L, nrow=1)) 370s Estimate Std. Error df t value Pr(>|t|) 370s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 370s > contest1D(fm, matrix(L, ncol=1)) 370s Estimate Std. Error df t value Pr(>|t|) 370s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 370s > assertError(contest1D(fm, matrix(c(0, 1), ncol=1))) 370s > assertError(contest1D(fm, matrix(c(0, 1, 0, 0), nrow=1))) 370s > L <- matrix(numeric(0L), ncol=3) 370s > assertError(contest1D(fm, L)) # "empty" matrix 370s > assertError(contest1D(fm, matrix(1, ncol=3, nrow=2))) 370s > 370s > # Test list L 370s > assertError(contest1D(fm, list(c(0, 1, 0)))) 370s > 370s > # Test equivalence to coef(summary(fm)): 370s > Lmat <- diag(length(fixef(fm))) 370s > (coef_mat <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 370s + contest1D(fm, Lmat[i, ])))) 370s Estimate Std. Error df t value Pr(>|t|) 370s 1 255.4493728 7.5663677 26.22939 33.761163 3.810057e-23 370s 2 7.4340850 2.8242827 114.99433 2.632203 9.648080e-03 370s 3 0.3370223 0.2616475 144.63110 1.288078 1.997759e-01 370s > (coef_mat_lme4 <- coef(summary(fm, ddf="lme4"))) 370s Estimate Std. Error t value 370s (Intercept) 255.4493728 7.5663677 33.761163 370s Days 7.4340850 2.8242827 2.632203 370s I(Days^2) 0.3370223 0.2616475 1.288078 370s > rownames(coef_mat) <- rownames(coef_mat_lme4) 370s > stopifnot(isTRUE( 370s + all.equal(as.data.frame(coef_mat_lme4), 370s + coef_mat[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 370s + )) 370s > 370s > if(has_pbkrtest) { 370s + (coef_mat_KR <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 370s + contest1D(fm, Lmat[i, ], ddf="Kenward-Roger")))) 370s + rownames(coef_mat_KR) <- rownames(coef_mat_lme4) 370s + stopifnot(isTRUE( 370s + all.equal(as.data.frame(coef_mat_lme4), 370s + coef_mat_KR[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 370s + )) 370s + } 371s > # Test of 0-length beta 371s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 371s + sleepstudy) 371s > stopifnot(length(fixef(fm1)) == 0L) 371s > if(has_pbkrtest) { 371s + (ans <- contest1D(fm1, numeric(0L), ddf="Kenward-Roger")) 371s + stopifnot(nrow(ans) == 0L) 371s + } 371s > 371s > ## Test rhs argument: 371s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 371s > contest1D(fm, L=cbind(0, 1)) 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 10.46729 1.54579 16.99998 6.771481 3.263824e-06 371s > contest1D(fm, L=cbind(0, 1), rhs=10) 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 371s > if(has_pbkrtest) { 371s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger") 371s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 371s + } 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 10.46729 1.54579 17 0.302296 0.7660937 371s > 371s > contest1D(fm, L=c(0, 1), rhs = 10.467) 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 10.46729 1.54579 16.99998 0.0001849926 0.9998546 371s > 371s > (ct1 <- contest1D(fm, L=cbind(c(0, 1)), rhs = 10)) 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 371s > (ct2 <- contestMD(fm, L=rbind(c(0, 1)), rhs = 10)) 371s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 371s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 371s > stopifnot( 371s + isTRUE(all.equal(ct1[, "t value"]^2, ct2[, "F value"], tolerance=1e-6)) 371s + ) 371s > 371s > ## Test 'lmerMod' method: 371s > fm <- lme4::lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 371s + sleepstudy) 371s > # Basic tests: 371s > L <- c(0, 1, 0) 371s > contest1D(fm, L) 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 371s > contest1D(fm, L, confint = TRUE) 371s Estimate Std. Error df t value lower upper Pr(>|t|) 371s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 371s > contest1D(fm, L, confint = TRUE, level=0.99) 371s Estimate Std. Error df t value lower upper Pr(>|t|) 371s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 371s > if(has_pbkrtest) 371s + contest1D(fm, L, ddf="Kenward-Roger") 371s Estimate Std. Error df t value Pr(>|t|) 371s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 371s > 371s > 371s BEGIN TEST test_contestMD.R 371s 371s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 371s Copyright (C) 2025 The R Foundation for Statistical Computing 371s Platform: powerpc64le-unknown-linux-gnu 371s 371s R is free software and comes with ABSOLUTELY NO WARRANTY. 371s You are welcome to redistribute it under certain conditions. 371s Type 'license()' or 'licence()' for distribution details. 371s 371s R is a collaborative project with many contributors. 371s Type 'contributors()' for more information and 371s 'citation()' on how to cite R or R packages in publications. 371s 371s Type 'demo()' for some demos, 'help()' for on-line help, or 371s 'help.start()' for an HTML browser interface to help. 371s Type 'q()' to quit R. 371s 371s > # test_contestMD.R 371s > library(lmerTest) 371s Loading required package: lme4 371s Loading required package: Matrix 373s 373s Attaching package: 'lmerTest' 373s 373s The following object is masked from 'package:lme4': 373s 373s lmer 373s 373s The following object is masked from 'package:stats': 373s 373s step 373s 373s > 373s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 373s > # even in tests: 373s > assertError <- function(expr, ...) 373s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 373s > assertWarning <- function(expr, ...) 373s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 373s > 373s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 373s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 373s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 373s > 373s > data("sleepstudy", package="lme4") 373s > 373s > #################################### 373s > ## Tests of contestMD 373s > #################################### 373s > 373s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 373s + sleepstudy) 374s > # Basic tests: 374s > L <- diag(3L) 374s > contestMD(fm, L) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 374s > 374s > # Tests of ddf arg: 374s > contestMD(fm, L, ddf="Sat") 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 374s > if(has_pbkrtest) 374s + contestMD(fm, L, ddf="Kenward-Roger") 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 990089.3 330029.8 3 38.84733 490.1937 6.706733e-31 374s > assertError(contestMD(fm, L, ddf="sat")) # Invalid ddf arg. 374s > 374s > # Tests of simple 2-df test: 374s > (ans <- contestMD(fm, L[2:3, ], ddf="Sat")) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 30399.15 15199.57 2 54.40752 23.36102 4.744897e-08 374s > stopifnot(nrow(ans) == 1L, 374s + ans$NumDF == 2L) 374s > if(has_pbkrtest) { 374s + (ans <- contestMD(fm, L[2:3, ], ddf="Kenward-Roger")) 374s + stopifnot(nrow(ans) == 1L, 374s + ans$NumDF == 2L) 374s + } 374s > 374s > # Tests of simple 1-df test: 374s > (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Sat")) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 374s > stopifnot(nrow(ans) == 1L, 374s + ans$NumDF == 1L) 374s > if(has_pbkrtest) { 374s + (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Kenward-Roger")) 374s + stopifnot(nrow(ans) == 1L, 374s + ans$NumDF == 1L) 374s + } 374s > 374s > # Test of vector input: 374s > (ans <- contestMD(fm, L[3, ], ddf="Sat")) # OK since length(L[3, ]) == length(fixef(fm)) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 374s > stopifnot(nrow(ans) == 1L, 374s + ans$NumDF == 1L) 374s > assertError(contestMD(fm, c(1, 0))) # L is too short 374s > assertError(contestMD(fm, c(1, 0, 1, 1))) # L is too long 374s > 374s > # Test of list input: 374s > assertError(contestMD(fm, list(L[3, , drop=FALSE]), ddf="Sat")) # Need L to be a matrix 374s > 374s > # zero-row L's are allowed (if ncol(L) is correct): 374s > ans1 <- contestMD(fm, L[0, , drop=FALSE], ddf="Sat") 374s > stopifnot(nrow(ans1) == 0L) 374s > if(has_pbkrtest) { 374s + ans2 <- contestMD(fm, L[0, , drop=FALSE], ddf="Kenward-Roger") 374s + stopifnot(nrow(ans2) == 0L) 374s + } 374s > 374s > # Test wrong ncol(L): 374s > assertError(contestMD(fm, L[2:3, 2:3])) # need ncol(L) == length(fixef(fm)) 374s > 374s > # row-rank deficient L are allowed: 374s > L <- rbind(c(1, 0, 1), 374s + c(0, 1, 0), 374s + c(1, -1, 1)) 374s > ans <- contestMD(fm, L) 374s > stopifnot(nrow(L) == 3L, 374s + qr(L)$rank == 2, 374s + ans$NumDF == 2) 374s > if(has_pbkrtest) { 374s + ans_KR <- contestMD(fm, L, ddf="Kenward-Roger") 374s + stopifnot(ans_KR$NumDF == 2) 374s + } 374s > 374s > # Test of 0-length beta 374s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 374s + sleepstudy) 374s > stopifnot(length(fixef(fm1)) == 0L) 374s > L <- numeric(0L) 374s > (ans <- contestMD(fm1, L)) 374s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s <0 rows> (or 0-length row.names) 374s > stopifnot(nrow(ans) == 0L) 374s > L <- matrix(numeric(0L), ncol=0L) 374s > (ans <- contestMD(fm1, L)) 374s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s <0 rows> (or 0-length row.names) 374s > stopifnot(nrow(ans) == 0L) 374s > 374s > 374s > ## rhs argument: 374s > data("cake", package="lme4") 374s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 374s > (L <- diag(length(fixef(model)))[2:3, ]) 374s [,1] [,2] [,3] [,4] [,5] [,6] 374s [1,] 0 1 0 0 0 0 374s [2,] 0 0 1 0 0 0 374s > (an <- anova(model, type="marginal")) 374s Marginal Analysis of Variance Table with Satterthwaite's method 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s recipe 4.00 2.00 2 254.02 0.0957 0.9088 374s temp 620.24 620.24 1 222.00 29.6961 1.339e-07 *** 374s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 374s --- 374s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 374s > 374s > ct <- contestMD(model, L, rhs = 0) 374s > ct2 <- contestMD(model, L, rhs = c(2, 2)) 374s > stopifnot( 374s + isTRUE(all.equal(ct[1, ], an[1, ], check.attributes=FALSE, tolerance=1e-6)), 374s + ct[, "F value"] < ct2[, "F value"] 374s + ) 374s > 374s > L2 <- rbind(L, L[1, ] + L[2, ]) # rank deficient! 374s > contestMD(model, L2, rhs = c(0, 0, 0)) # no warning 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 3.996684 1.998342 2 254.0158 0.09567796 0.9087894 374s > assertWarning(contestMD(model, L2, rhs = c(2, 2, 2))) # warning since L2 is rank def. 374s > if(has_pbkrtest) 374s + assertWarning(contestMD(model, L2, rhs = c(2, 2, 2), ddf="Kenward-Roger")) 374s > 374s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 374s > contestMD(fm, L=cbind(0, 1)) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 374s > contestMD(fm, L=cbind(0, 1), rhs=10) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 374s > if(has_pbkrtest) { 374s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 374s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 374s + } 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 374s > 374s > 374s > ## Test 'lmerMod' method: 374s > fm <- lme4::lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 374s > contestMD(fm, L=cbind(0, 1)) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 374s > contestMD(fm, L=cbind(0, 1), rhs=10) 374s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 374s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 374s > if(has_pbkrtest) { 374s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 374s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 374s + } 375s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 375s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 375s > 375s BEGIN TEST test_contrast_utils.R 375s 375s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 375s Copyright (C) 2025 The R Foundation for Statistical Computing 375s Platform: powerpc64le-unknown-linux-gnu 375s 375s R is free software and comes with ABSOLUTELY NO WARRANTY. 375s You are welcome to redistribute it under certain conditions. 375s Type 'license()' or 'licence()' for distribution details. 375s 375s R is a collaborative project with many contributors. 375s Type 'contributors()' for more information and 375s 'citation()' on how to cite R or R packages in publications. 375s 375s Type 'demo()' for some demos, 'help()' for on-line help, or 375s 'help.start()' for an HTML browser interface to help. 375s Type 'q()' to quit R. 375s 375s > # test_contrast_utils.R 375s > 375s > library(lmerTest) 375s Loading required package: lme4 375s Loading required package: Matrix 377s 377s Attaching package: 'lmerTest' 377s 377s The following object is masked from 'package:lme4': 377s 377s lmer 377s 377s The following object is masked from 'package:stats': 377s 377s step 377s 377s > 377s > ########## 377s > # Test that a message is printed if some cells have zero data: 377s > # Missing a single cell: 377s > data("cake", package="lme4") 377s > cake4 <- cake 377s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 377s > cake4 <- droplevels(subset(cake4, !(recipe == "A" & temperature == "175") )) 377s > with(cake4, table(recipe, temperature)) 377s temperature 377s recipe 175 185 195 205 215 225 377s A 0 15 15 15 15 15 377s B 15 15 15 15 15 15 377s C 15 15 15 15 15 15 377s > 377s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 377s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 377s > an <- anova(fm1) 377s Missing cells for: recipeA:temperature175. 377s Interpret type III hypotheses with care. 377s > txt <- capture.output(an <- anova(fm1), type = "message") 377s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 377s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 377s > 377s > ########## 377s > # Test that a message is printed if some cells have zero data: 377s > # Missing diagonal: 377s > cake4 <- cake 377s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 377s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 377s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 377s + (recipe == "B" & temperature == "185") | 377s + (recipe == "C" & temperature == "195") ))) 377s > cake4$temp0 <- cake4$temp - mean(cake4$temp) 377s > with(cake4, table(recipe, temperature)) 377s temperature 377s recipe 175 185 195 377s A 0 15 15 377s B 15 0 15 377s C 15 15 0 377s > 377s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 377s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 377s > an <- anova(fm1) 377s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 377s Interpret type III hypotheses with care. 377s > txt <- capture.output(an <- anova(fm1), type = "message") 377s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 377s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 377s > 377s > ########## 377s > # Test that a message is NOT printed with centered covariates: 377s > fm1 <- lmer(angle ~ recipe * temp0 + (1|recipe:replicate), cake4) 377s > an <- anova(fm1) 377s > txt <- capture.output(an <- anova(fm1), type = "message") 377s > stopifnot(length(grep("Missing cells for:", txt)) == 0, 377s + length(grep("Interpret type III hypotheses with care.", txt)) == 0) 377s > # Note: in many cases a message would not be printed anyway because the 377s > # columns sums in the rdX design matrix would not be exactly zero but just a 377s > # small number very close to zero. 377s > 377s > 377s > 377s > 377s BEGIN TEST test_devfun_vp.R 377s 377s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 377s Copyright (C) 2025 The R Foundation for Statistical Computing 377s Platform: powerpc64le-unknown-linux-gnu 377s 377s R is free software and comes with ABSOLUTELY NO WARRANTY. 377s You are welcome to redistribute it under certain conditions. 377s Type 'license()' or 'licence()' for distribution details. 377s 377s R is a collaborative project with many contributors. 377s Type 'contributors()' for more information and 377s 'citation()' on how to cite R or R packages in publications. 377s 377s Type 'demo()' for some demos, 'help()' for on-line help, or 377s 'help.start()' for an HTML browser interface to help. 377s Type 'q()' to quit R. 377s 377s > # test_devfun_vp.R 377s > 377s > # library(devtools) 377s > # # has_devel() 377s > # r2path <- "~/GitHub/lmerTestR/lmerTest" 377s > # # document(pkg=r2path) 377s > # load_all(r2path) 377s > # 377s > # # ?`Covariance-class` 377s > 377s > library(lmerTest) 377s Loading required package: lme4 377s Loading required package: Matrix 379s 379s Attaching package: 'lmerTest' 379s 379s The following object is masked from 'package:lme4': 379s 379s lmer 379s 379s > 379s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 379s The following object is masked from 'package:stats': 379s 379s step 379s 379s + requireNamespace("numDeriv", quietly = TRUE) && 379s + requireNamespace("lme4", quietly = TRUE) 379s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 379s > 379s > if(has_pkgs && is_lme4_2_0_0) { 379s + ## Functions: 379s + devfun_vp <- lmerTest:::devfun_vp 379s + getOptPar <- lmerTest:::getOptPar 379s + getVarPar <- lmerTest:::getVarPar 379s + 379s + ## Unstructured 379s + fm1.us <- lme4::lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 379s + ## Diagional 379s + fm1.diag <- lme4::lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 379s + fm1.diag.hom <- lme4::lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 379s + sleepstudy) 379s + ## Compound symmetry 379s + fm1.cs <- lme4::lmer(Reaction ~ Days + cs(Days | Subject), sleepstudy) 379s + fm1.cs.hom <- lme4::lmer(Reaction ~ Days + cs(Days | Subject, hom = TRUE), 379s + sleepstudy) 379s + ## Auto-regressive order 1 379s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 379s + fm1.ar1 <- lme4::lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 379s + sleepstudy, REML = TRUE) 379s + 379s + lme4models <- namedList(fm1.us, 379s + fm1.diag, 379s + fm1.diag.hom, 379s + fm1.cs, 379s + fm1.cs.hom, 379s + fm1.ar1) 379s + 379s + for(model in lme4models) { # model <- lme4models[[1]] 379s + ## Native devfun: 379s + devfun <- update(model, devFunOnly=TRUE) 379s + ## Evaluate native devfun at optimum: 379s + devfun(getOptPar(model)) 379s + ## Check that devfun returns the same value as that saved in the model object: 379s + stopifnot( 379s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 379s + devfun(getOptPar(model)), tolerance=1e-6) # TRUE 379s + ) 379s + ## Get varpar (including residual SD): 379s + (varpar <- getVarPar(model)) 379s + ## Evaluate devfun_vp at the optimum: 379s + devfun_vp(varpar, devfun, reml=TRUE) 379s + ## Check that devfun_vp returns the same value as native devfun: 379s + stopifnot( 379s + all.equal(unname(getME(model, "devcomp")$cmp["REML"]), 379s + devfun(getOptPar(model))) # TRUE 379s + ) 379s + } 379s + 379s + ## Here we also want to check that devfun and and devfun_vp returns the same 379s + ## value at non-optimum values of varpar. 379s + ## Because sigma is profiled out of devfun this cannot be done right away. 379s + ## We need to optimize over all parameters to get equivalence. 379s + ## We should be able to set one of the parameters in common to a 379s + ## particular value and optimize the rest. This will build confidence that 379s + ## the likelihood in devfun_vp is the same as that returned by 379s + ## lme4::lmer(., devFunOnly=TRUE). 379s + 379s + do_trace <- 0 379s + for(i in seq_along(lme4models)) { # i <- 4 379s + if(do_trace) print(i) 379s + model <- lme4models[[i]] 379s + devfun <- update(model, devFunOnly=TRUE) 379s + (optpar <- getOptPar(model)) 379s + (varpar <- getVarPar(model)) 379s + (optpar2 <- optpar * 1.1) 379s + (varpar2 <- c(optpar2, varpar[length(varpar)])) 379s + 379s + ## Evaluate gradients to ensure that devfun and devfun_vp are both 379s + ## functions with optima at optpar and varpar respectively: 379s + (g_devfun <- numDeriv::grad(devfun, optpar)) 379s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar, devfun=devfun, reml=TRUE)) 379s + stopifnot( 379s + if(i != 4) all(abs(g_devfun) < 1e-3) else all(abs(g_devfun) < 1e-2), 379s + if(i != 4) all(abs(g_devfun_vp) < 1e-3) else all(abs(g_devfun_vp) < 1e-2) 379s + ) 379s + ## These are not zero as expected: 379s + (g_devfun <- numDeriv::grad(devfun, optpar2)) 379s + (g_devfun_vp <- numDeriv::grad(devfun_vp, varpar2, devfun=devfun, reml=TRUE)) 379s + ## Try optimizing devfun_vp: 379s + x <- nlminb(start=varpar2, objective = devfun_vp, devfun=devfun, reml=TRUE, 379s + control=list(trace=do_trace)) 379s + ## Check that the optimum is re-achieved: 379s + stopifnot( 379s + all(abs(varpar - x$par) < 1e-4), 379s + abs(devfun_vp(varpar, devfun=devfun, reml=TRUE) - 379s + devfun_vp(x$par, devfun=devfun, reml=TRUE)) < 1e-6 379s + ) 379s + 379s + ## Optimize devfun and devfun_vp over all but one of the parameters in turn to 379s + ## check that devfun and devfun_vp gives the same deviance and parameter values 379s + ## for settings away from the REML optimum. This is to build confidence that 379s + ## devfun_vp is a valid implementation of the deviance function from LLMs. 379s + if(length(optpar) > 1) for(j in seq_along(optpar)) { # j <- 1 379s + ## Check that all parameters are within bounds: 379s + stopifnot( 379s + model@lower < optpar, 379s + optpar < attr(model, "upper"), 379s + model@lower < optpar2, 379s + optpar2 < attr(model, "upper") 379s + ) 379s + ## Evaluate deviance function at optimum (for safety): 379s + devfun(optpar) 379s + ## Optimize devfun over all but the j'th parameter: 379s + (startpar <- optpar[-j]) 379s + res <- nlminb(start=startpar, objective = function(p) { 379s + (Par <- optpar2) 379s + (Par[-j] <- p) 379s + devfun(Par) 379s + }, control = list(trace=do_trace), 379s + lower = model@lower[-j], 379s + upper = attr(model, "upper")[-j]) 379s + ## Evaluate devfun_vp: 379s + devfun_vp(varpar, devfun=devfun, reml=TRUE) 379s + ## Optimize devfun_vp over all but the j'th parameter: 379s + (startpar_vp <- varpar[-j]) 379s + (np <- length(startpar_vp)) 379s + res_vp <- nlminb(start=startpar_vp, objective = function(p) { 379s + (Par <- optpar2) 379s + (Par[-j] <- p[-np]) 379s + Par <- c(Par, p[np]) 379s + devfun_vp(Par, devfun=devfun, reml=TRUE) 379s + }, control = list(trace=do_trace), 379s + lower = c(model@lower[-j], 0), 379s + upper = c(attr(model, "upper")[-j], Inf)) 379s + ## Compare parameter estimates (except for sigma): 379s + res$objective - res_vp$objective 379s + res$par - res_vp$par[seq_along(res$par)] 379s + ## Check that parameter estimates and deviance values agree: 379s + stopifnot( 379s + abs(res$objective - res_vp$objective) < 1e-8, 379s + all(abs(res$par - res_vp$par[seq_along(res$par)]) < 1e-4) 379s + ) 379s + } 379s + } 379s + 379s + } 379s > 379s > 379s > 379s BEGIN TEST test_drop1.R 379s 379s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 379s Copyright (C) 2025 The R Foundation for Statistical Computing 379s Platform: powerpc64le-unknown-linux-gnu 379s 379s R is free software and comes with ABSOLUTELY NO WARRANTY. 379s You are welcome to redistribute it under certain conditions. 379s Type 'license()' or 'licence()' for distribution details. 379s 379s R is a collaborative project with many contributors. 379s Type 'contributors()' for more information and 379s 'citation()' on how to cite R or R packages in publications. 379s 379s Type 'demo()' for some demos, 'help()' for on-line help, or 379s 'help.start()' for an HTML browser interface to help. 379s Type 'q()' to quit R. 379s 379s > # test_drop1.R 379s > 379s > library(lmerTest) 379s Loading required package: lme4 379s Loading required package: Matrix 382s > 382s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 382s > # even in tests: 382s > assertError <- function(expr, ...) 382s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 382s > assertWarning <- function(expr, ...) 382s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 382s > 382s > TOL <- 1e-4 382s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 382s 382s Attaching package: 'lmerTest' 382s 382s The following object is masked from 'package:lme4': 382s 382s lmer 382s 382s The following object is masked from 'package:stats': 382s 382s step 382s 382s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 382s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 382s > 382s > data("sleepstudy", package="lme4") 382s > 382s > ######### Basic usage 382s > 382s > data("cake", package="lme4") 382s > cake2 <- cake 382s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 382s > fm <- lmer(angle ~ recipe + temperature + (1|recipe:replicate), cake2) 382s > (an1 <- drop1(fm)) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s angle ~ recipe + temperature + (1 | recipe:replicate) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s recipe 10.19 5.09 2 42 0.2488 0.7809 382s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > (an2 <- drop1(fm, force_get_contrasts = TRUE)) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s angle ~ recipe + temperature + (1 | recipe:replicate) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s recipe 10.19 5.09 2 42 0.2488 0.7809 382s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > drop1(fm, ddf="lme4", test="Chi") 382s Single term deletions 382s 382s Model: 382s angle ~ recipe + temperature + (1 | recipe:replicate) 382s npar AIC LRT Pr(Chi) 382s 1709.6 382s recipe 2 1706.1 0.530 0.7672 382s temperature 5 1785.7 86.106 <2e-16 *** 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > if(has_pbkrtest) 382s + drop1(fm, ddf="Kenward-Roger") 382s Single term deletions using Kenward-Roger's method: 382s 382s Model: 382s angle ~ recipe + temperature + (1 | recipe:replicate) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s recipe 10.19 5.09 2 42 0.2488 0.7809 382s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > 382s > tests1 <- show_tests(an1) 382s > tests2 <- show_tests(an2) 382s > 382s > stopifnot( 382s + # Tests are the same: 382s + isTRUE(all.equal(an1, an2, check.attributes = FALSE, tolerance=TOL)), 382s + # But contrast matrices are not: 382s + all(!mapply(function(x, y) isTRUE(all.equal(x, y)), tests1, tests2)) 382s + ) 382s > 382s > fm <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 382s > drop1(fm) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s angle ~ recipe * temperature + (1 | recipe:replicate) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 382s > drop1(fm, ddf="lme4") 382s Single term deletions 382s 382s Model: 382s angle ~ recipe * temperature + (1 | recipe:replicate) 382s npar AIC 382s 1719.0 382s recipe:temperature 10 1709.6 382s > if(has_pbkrtest) 382s + drop1(fm, ddf="Kenward-Roger") 382s Single term deletions using Kenward-Roger's method: 382s 382s Model: 382s angle ~ recipe * temperature + (1 | recipe:replicate) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 382s > 382s > # Incorrect arguments: 382s > assertError(drop1(fm, scope="recipe")) # Correct Error 382s > assertError(drop1(fm, scope=3)) # Correct Error 382s > assertError(drop1(fm, scope=list("recipe"))) # Correct Error 382s > 382s > # Polynomial terms: 382s > 382s > fm <- lmer(Reaction ~ 0 + (Days|Subject), sleepstudy) 382s > (an0 <- drop1(fm)) # No fixef! 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s Reaction ~ 0 + (Days | Subject) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 382s > (an1 <- drop1(fm)) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s Reaction ~ Days + (Days | Subject) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s Days 30031 30031 1 17 45.853 3.264e-06 *** 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > fm <- lmer(Reaction ~ Days + I(Days^2) + (Days|Subject), sleepstudy) 382s > (an2 <- (drop1(fm))) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s Reaction ~ Days + I(Days^2) + (Days | Subject) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 382s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > fm <- lmer(Reaction ~ poly(Days, 2) + (Days|Subject), sleepstudy) 382s > (an3 <- drop1(fm)) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s Reaction ~ poly(Days, 2) + (Days | Subject) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s poly(Days, 2) 30974 15487 2 29.115 23.754 7.625e-07 *** 382s --- 382s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 382s > stopifnot( 382s + nrow(an0) == 0L, 382s + nrow(an1) == 1L, 382s + nrow(an2) == 2L, 382s + nrow(an3) == 1L 382s + ) 382s > 382s > # Consider a rank-deficient design matrix: 382s > fm <- lmer(angle ~ recipe + temp + temperature + (1|recipe:replicate), cake) 382s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 382s > # Here temp accounts for the linear effect of temperature, and 382s > # temperature is an (ordered) factor that accounts for the remaining 382s > # variation between temperatures (4 df). 382s > (an4 <- drop1(fm)) 382s Single term deletions using Satterthwaite's method: 382s 382s Model: 382s angle ~ recipe + temp + temperature + (1 | recipe:replicate) 382s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 382s recipe 10.189 5.094 2 42 0.2488 0.7809 382s temp 382s temperature 133.595 33.399 4 220 1.6311 0.1674 382s > # While temperature is in the model, we cannot test the effect of dropping 382s > # temp. After removing temperature we can test the effect of dropping temp: 382s > (an5 <- drop1(update(fm, ~.-temperature))) 383s Single term deletions using Satterthwaite's method: 383s 383s Model: 383s angle ~ recipe + temp + (1 | recipe:replicate) 383s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 383s recipe 10.3 5.15 2 42 0.2488 0.7809 383s temp 1966.7 1966.71 1 224 94.9759 <2e-16 *** 383s --- 383s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 383s > 383s > stopifnot( 383s + nrow(an4) == 3, 383s + rownames(an4)[2] == "temp", 383s + all(is.na(an4[2, ])), 383s + all(!is.na(an4[-2, ])), 383s + all(rownames(an5) == c("recipe", "temp")) 383s + ) 383s > 383s > 383s > 383s > 383s BEGIN TEST test_legacy.R 383s 383s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 383s Copyright (C) 2025 The R Foundation for Statistical Computing 383s Platform: powerpc64le-unknown-linux-gnu 383s 383s R is free software and comes with ABSOLUTELY NO WARRANTY. 383s You are welcome to redistribute it under certain conditions. 383s Type 'license()' or 'licence()' for distribution details. 383s 383s R is a collaborative project with many contributors. 383s Type 'contributors()' for more information and 383s 'citation()' on how to cite R or R packages in publications. 383s 383s Type 'demo()' for some demos, 'help()' for on-line help, or 383s 'help.start()' for an HTML browser interface to help. 383s Type 'q()' to quit R. 383s 383s > # test_legacy.R 383s > library(lmerTest) 383s Loading required package: lme4 383s Loading required package: Matrix 385s 385s Attaching package: 'lmerTest' 385s 385s The following object is masked from 'package:lme4': 385s 385s lmer 385s 385s The following object is masked from 'package:stats': 385s 385s step 385s 385s > TOL <- 1e-4 385s > ##################################################################### 385s > 385s > # Read in data set 385s > load(system.file("testdata", "legacy_fits.RData", package="lmerTest")) 385s > # Generated with the following code using lmerTest version 2.0-37.9002 385s > # 385s > # library("lmerTest") 385s > # packageVersion("lmerTest") 385s > # fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 385s > # (an1 <- anova(fm1)) 385s > # (sfm1 <- summary(fm1)) 385s > # 385s > # fm2 <- lmer(Informed.liking ~ Product + Information + Gender + 385s > # (1|Product:Consumer) , data=ham) 385s > # (an2 <- anova(fm2)) 385s > # (sfm2 <- summary(fm2)) 385s > # 385s > # save(fm1, an1, sfm1, fm2, an2, sfm2, 385s > # file="~/GitHub/lmerTestR/package/inst/testdata/legacy_fits.RData") 385s > 385s > 385s > ####################################### 385s > ### Check that arguments for merModLmerTest and lmerModLmerTest methods match up: 385s > 385s > stopifnot( 385s + isTRUE(all.equal(formals(lmerTest:::anova.merModLmerTest), 385s + formals(lmerTest:::anova.lmerModLmerTest))), 385s + isTRUE(all.equal(formals(lmerTest:::summary.merModLmerTest), 385s + formals(lmerTest:::summary.lmerModLmerTest))), 385s + isTRUE(all.equal(formals(lmerTest:::drop1.merModLmerTest), 385s + formals(lmerTest:::drop1.lmerModLmerTest))), 385s + isTRUE(all.equal(formals(lmerTest:::step.merModLmerTest), 385s + formals(lmerTest:::step.lmerModLmerTest))), 385s + isTRUE(all.equal(formals(lmerTest:::ls_means.merModLmerTest), 385s + formals(lmerTest:::ls_means.lmerModLmerTest))), 385s + isTRUE(all.equal(formals(lmerTest:::difflsmeans.merModLmerTest), 385s + formals(lmerTest:::difflsmeans.lmerModLmerTest)))) 385s > 385s > 385s > ####################################### 385s > ## Tests for fm1: 385s > 385s > (an1new <- anova(fm1)) 385s Type III Analysis of Variance Table with Satterthwaite's method 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s Days 30031 30031 1 17 45.853 3.264e-06 *** 385s --- 385s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 385s > (sfm1new <- summary(fm1)) 385s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 385s lmerModLmerTest] 385s Formula: Reaction ~ Days + (Days | Subject) 385s Data: sleepstudy 385s 385s REML criterion at convergence: 1743.6 385s 385s Scaled residuals: 385s Min 1Q Median 3Q Max 385s -3.9536 -0.4634 0.0231 0.4634 5.1793 385s 385s Random effects: 385s Groups Name Variance Std.Dev. Corr 385s Subject (Intercept) 612.09 24.740 385s Days 35.07 5.922 0.07 385s Residual 654.94 25.592 385s Number of obs: 180, groups: Subject, 18 385s 385s Fixed effects: 385s Estimate Std. Error df t value Pr(>|t|) 385s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 385s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 385s --- 385s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 385s 385s Correlation of Fixed Effects: 385s (Intr) 385s Days -0.138 385s > 385s > stopifnot( 385s + isTRUE(all.equal(an1new, an1, check.attributes=FALSE, tol=TOL)), 385s + isTRUE(all.equal(coef(sfm1new), coef(sfm1), tol=TOL)) 385s + ) 385s > 385s > contest(fm1, c(0, 1)) 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s 1 30031.01 30031.01 1 17 45.853 3.26379e-06 385s > contest(fm1, c(0, 1), joint=FALSE) 385s Estimate Std. Error df t value lower upper Pr(>|t|) 385s 1 10.46729 1.545789 17 6.771485 7.205956 13.72862 3.26379e-06 385s > drop1(fm1) 385s Single term deletions using Satterthwaite's method: 385s 385s Model: 385s Reaction ~ Days + (Days | Subject) 385s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s Days 30031 30031 1 17 45.853 3.264e-06 *** 385s --- 385s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 385s > ranova(fm1) 385s ANOVA-like table for random-effects: Single term deletions 385s 385s Model: 385s Reaction ~ Days + (Days | Subject) 385s npar logLik AIC LRT Df Pr(>Chisq) 385s 6 -871.81 1755.6 385s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 385s --- 385s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 385s > step(fm1) 385s Backward reduced random-effect table: 385s 385s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 385s 6 -871.81 1755.6 385s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 385s 385s 385s Days in (Days | Subject) *** 385s --- 385s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 385s 385s Backward reduced fixed-effect table: 385s Degrees of freedom method: Satterthwaite 385s 385s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 385s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 385s --- 385s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 385s 385s Model found: 385s Reaction ~ Days + (Days | Subject) 385s > 385s > fm1new <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, 385s + control=lmerControl(optimizer="bobyqa")) 385s > stopifnot( 385s + isTRUE(all.equal(drop1(fm1), drop1(fm1new), tol=TOL)), 385s + isTRUE(all.equal(ranova(fm1), ranova(fm1new), tol=TOL)), 385s + isTRUE(all.equal(contest(fm1, c(0, 1)), contest(fm1new, c(0, 1)), tol=TOL)), 385s + isTRUE(all.equal(contest(fm1, c(0, 1), joint=FALSE), 385s + contest(fm1new, c(0, 1), joint=FALSE), tol=TOL)) 385s + ) 385s > 385s > # Test that lme4 methods work: 385s > coef(fm1) 385s $Subject 385s (Intercept) Days 385s 308 253.6637 19.6662579 385s 309 211.0065 1.8475828 385s 310 212.4449 5.0184061 385s 330 275.0956 5.6529547 385s 331 273.6653 7.3973914 385s 332 260.4446 10.1951153 385s 333 268.2455 10.2436615 385s 334 244.1725 11.5418620 385s 335 251.0714 -0.2848731 385s 337 286.2955 19.0955699 385s 349 226.1950 11.6407002 385s 350 238.3351 17.0814910 385s 351 255.9829 7.4520288 385s 352 272.2687 14.0032993 385s 369 254.6806 11.3395026 385s 370 225.7922 15.2897506 385s 371 252.2121 9.4791309 385s 372 263.7196 11.7513157 385s 385s attr(,"class") 385s [1] "coef.mer" 385s > fixef(fm1) 385s (Intercept) Days 385s 251.40510 10.46729 385s > resid(fm1) 385s 1 2 3 4 5 6 385s -4.1036703 -14.6252282 -42.1955860 8.7773561 24.5231982 62.6951403 385s 7 8 9 10 11 12 385s 10.5425825 -101.1788754 19.5915667 35.6935088 11.7273721 -7.5883107 385s 13 14 15 16 17 18 385s -11.7238935 -11.8422762 -10.6807590 -4.2826418 -8.4617246 -6.2124074 385s 19 20 21 22 23 24 385s -1.4914902 9.6794271 -13.3909590 -23.1310650 11.8383289 5.3415228 385s 25 26 27 28 29 30 385s -3.2110832 -17.0789893 -7.1344953 8.1773986 8.4203926 -10.0952135 385s 31 32 33 34 35 36 385s 46.4469967 19.6516420 -2.5450126 -6.9214673 -11.9101220 -5.7748766 386s 37 38 39 40 41 42 386s -28.7737313 3.5950141 -14.9697406 28.0765048 13.9425924 3.9373010 386s 43 44 45 46 47 48 386s 13.3605097 24.2578183 13.0224270 -17.3335644 -27.9746558 9.3706529 386s 49 50 51 52 53 54 386s -39.0975385 31.3392701 -25.5840308 -27.8279461 -7.8735614 18.7388233 386s 55 56 57 58 59 60 386s 16.2378080 -1.4226073 132.5465774 15.0206621 -11.7052532 -98.3362685 386s 61 62 63 64 65 66 386s 15.5968640 11.0658025 -11.9635591 0.8331794 -12.0491821 18.7026564 386s 67 68 69 70 71 72 386s 2.3189949 8.8887334 -16.8348282 1.6043103 21.3005744 20.4868123 386s 73 74 75 76 77 78 386s -23.8915497 -24.1258118 -11.3155738 -17.6906358 -7.8988979 6.5573401 386s 79 80 81 82 83 84 386s -0.7605219 29.2497160 -9.4631090 23.1606642 3.9890373 20.5853104 386s 85 86 87 88 89 90 386s 1.5199836 4.9891567 -3.9098701 -13.7662970 -13.0383239 -11.2609507 386s 91 92 93 94 95 96 386s 26.0711443 8.4147744 -32.8753955 2.5400346 3.0546647 10.0651947 386s 97 98 99 100 101 102 386s 3.3912248 -3.2721451 16.8042850 0.7611151 9.9082056 -7.5189947 386s 103 104 105 106 107 108 386s -10.5507949 -6.1950951 -22.0474953 -14.6240955 -14.4743957 0.4221041 386s 109 110 111 112 113 114 386s 16.9600039 20.6838037 17.9616518 -11.9623391 -16.2935301 -34.0525210 386s 115 116 117 118 119 120 386s -37.7446120 5.9820971 38.6204061 5.0128151 19.5001242 -3.0158668 386s 121 122 123 124 125 126 386s -5.4564400 36.6226312 -0.9930976 2.2500737 -13.9636551 11.3905161 386s 127 128 129 130 131 132 386s -12.9485127 -41.5516414 5.9426298 24.5143010 -50.5915973 11.9219034 386s 133 134 135 136 137 138 386s 26.6032041 32.5769048 20.4583056 10.5435063 -1.8618930 -9.8591922 386s 139 140 141 142 143 144 386s -8.6544915 -9.7566908 17.2429421 2.4168396 -20.1171630 -11.0424656 386s 145 146 147 148 149 150 386s 14.7836319 5.8354293 -24.5822732 14.0658242 -5.1165783 9.7770191 386s 151 152 153 154 155 156 386s -0.5282354 -6.5584860 -17.4709366 -31.1884871 -19.4139377 41.9527117 386s 157 158 159 160 161 162 386s -36.3826389 14.7650105 17.0527600 8.8288094 17.6682554 10.7515245 386s 163 164 165 166 167 168 386s 6.7284937 1.1399628 -10.9581681 -15.0957989 -49.8211298 -13.9354607 386s 169 170 171 172 173 174 386s 22.7355085 31.9448776 5.6920558 -1.9969599 10.3745244 11.6580087 386s 175 176 177 178 179 180 386s -23.5523070 7.1313773 0.2542616 -2.7589541 11.4115302 -5.3578855 386s > 386s > ####################################### 386s > ## Tests for fm2: 386s > (an2new <- anova(fm2)) 386s Type III Analysis of Variance Table with Satterthwaite's method 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 386s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 386s Gender 1.8634 1.8634 1 319 1.1064 0.29366 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s > (sfm2new <- summary(fm2)) 386s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 386s lmerModLmerTest] 386s Formula: 386s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 386s Data: ham 386s 386s REML criterion at convergence: 2712.2 386s 386s Scaled residuals: 386s Min 1Q Median 3Q Max 386s -3.1568 -0.5087 0.0338 0.4913 3.1623 386s 386s Random effects: 386s Groups Name Variance Std.Dev. 386s Product:Consumer (Intercept) 3.526 1.878 386s Residual 1.684 1.298 386s Number of obs: 648, groups: Product:Consumer, 324 386s 386s Fixed effects: 386s Estimate Std. Error df t value Pr(>|t|) 386s (Intercept) 5.8290 0.2640 343.6885 22.082 <2e-16 *** 386s Product2 -0.7037 0.3284 319.0000 -2.143 0.0329 * 386s Product3 0.2840 0.3284 319.0000 0.865 0.3879 386s Product4 0.1173 0.3284 319.0000 0.357 0.7212 386s Information2 0.2006 0.1020 323.0000 1.968 0.0500 * 386s Gender2 -0.2443 0.2322 319.0000 -1.052 0.2937 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s 386s Correlation of Fixed Effects: 386s (Intr) Prdct2 Prdct3 Prdct4 Infrm2 386s Product2 -0.622 386s Product3 -0.622 0.500 386s Product4 -0.622 0.500 0.500 386s Informatin2 -0.193 0.000 0.000 0.000 386s Gender2 -0.434 0.000 0.000 0.000 0.000 386s > 386s > stopifnot( 386s + isTRUE(all.equal(an2new, an2, check.attributes=FALSE, tol=TOL)), 386s + isTRUE(all.equal(coef(sfm2new), coef(sfm2), tol=TOL)) 386s + ) 386s > 386s > drop1(fm2) 386s Single term deletions using Satterthwaite's method: 386s 386s Model: 386s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 386s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 386s Gender 1.8634 1.8634 1 319 1.1064 0.29366 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s > ranova(fm2) 386s ANOVA-like table for random-effects: Single term deletions 386s 386s Model: 386s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 386s npar logLik AIC LRT Df Pr(>Chisq) 386s 8 -1356.1 2728.2 386s (1 | Product:Consumer) 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s > ls_means(fm2) 386s Least Squares Means table: 386s 386s Estimate Std. Error df t value lower upper Pr(>|t|) 386s Product1 5.80713 0.23223 319.0 25.006 5.35025 6.26402 < 2.2e-16 *** 386s Product2 5.10343 0.23223 319.0 21.976 4.64654 5.56032 < 2.2e-16 *** 386s Product3 6.09108 0.23223 319.0 26.229 5.63420 6.54797 < 2.2e-16 *** 386s Product4 5.92442 0.23223 319.0 25.511 5.46753 6.38131 < 2.2e-16 *** 386s Information1 5.63121 0.12682 437.8 44.404 5.38196 5.88046 < 2.2e-16 *** 386s Information2 5.83183 0.12682 437.8 45.986 5.58258 6.08107 < 2.2e-16 *** 386s Gender1 5.85366 0.16320 319.0 35.868 5.53257 6.17475 < 2.2e-16 *** 386s Gender2 5.60937 0.16523 319.0 33.949 5.28430 5.93445 < 2.2e-16 *** 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s 386s Confidence level: 95% 386s Degrees of freedom method: Satterthwaite 386s > difflsmeans(fm2) 386s Least Squares Means table: 386s 386s Estimate Std. Error df t value lower 386s Product1 - Product2 7.0370e-01 3.2841e-01 319 2.1428 5.7578e-02 386s Product1 - Product3 -2.8395e-01 3.2841e-01 319 -0.8646 -9.3008e-01 386s Product1 - Product4 -1.1728e-01 3.2841e-01 319 -0.3571 -7.6341e-01 386s Product2 - Product3 -9.8765e-01 3.2841e-01 319 -3.0074 -1.6338e+00 386s Product2 - Product4 -8.2099e-01 3.2841e-01 319 -2.4999 -1.4671e+00 386s Product3 - Product4 1.6667e-01 3.2841e-01 319 0.5075 -4.7946e-01 386s Information1 - Information2 -2.0062e-01 1.0196e-01 323 -1.9676 -4.0121e-01 386s Gender1 - Gender2 2.4428e-01 2.3224e-01 319 1.0519 -2.1263e-01 386s upper Pr(>|t|) 386s Product1 - Product2 1.3498e+00 0.032890 * 386s Product1 - Product3 3.6218e-01 0.387898 386s Product1 - Product4 5.2884e-01 0.721234 386s Product2 - Product3 -3.4153e-01 0.002845 ** 386s Product2 - Product4 -1.7486e-01 0.012926 * 386s Product3 - Product4 8.1279e-01 0.612159 386s Information1 - Information2 -2.6433e-05 0.049970 * 386s Gender1 - Gender2 7.0120e-01 0.293660 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s 386s Confidence level: 95% 386s Degrees of freedom method: Satterthwaite 386s > nbeta <- length(fixef(fm2)) 386s > L <- diag(nbeta) 386s > L[1:4, ] <- 0 386s > contest(fm2, L) 386s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s 1 8.383419 4.19171 2 320.9875 2.488919 0.08460028 386s > contest(fm2, diag(nbeta), joint=FALSE) 386s Estimate Std. Error df t value lower upper 386s 1 5.8289672 0.2639677 343.6885 22.0821233 5.309772e+00 6.34816269 386s 2 -0.7037037 0.3284114 319.0000 -2.1427506 -1.349830e+00 -0.05757783 386s 3 0.2839506 0.3284114 319.0000 0.8646187 -3.621753e-01 0.93007650 386s 4 0.1172840 0.3284114 319.0000 0.3571251 -5.288419e-01 0.76340983 386s 5 0.2006173 0.1019607 323.0000 1.9675949 2.643318e-05 0.40120813 386s 6 -0.2442835 0.2322396 319.0000 -1.0518599 -7.011983e-01 0.21263128 386s Pr(>|t|) 386s 1 6.753241e-68 386s 2 3.288952e-02 386s 3 3.878978e-01 386s 4 7.212343e-01 386s 5 4.997000e-02 386s 6 2.936600e-01 386s > step(fm2) 386s Backward reduced random-effect table: 386s 386s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 386s 8 -1356.1 2728.2 386s (1 | Product:Consumer) 0 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s 386s Backward reduced fixed-effect table: 386s Degrees of freedom method: Satterthwaite 386s 386s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 386s Gender 1 1.8634 1.8634 1 319 1.1064 0.29366 386s Product 0 17.6926 5.8975 3 320 3.5018 0.01579 * 386s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 386s --- 386s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 386s 386s Model found: 386s Informed.liking ~ Product + Information + (1 | Product:Consumer) 386s > 386s > fm2new <- lmer(Informed.liking ~ Product + Information + Gender + 386s + (1|Product:Consumer), data=ham) 386s > stopifnot( 386s + isTRUE(all.equal(drop1(fm2), drop1(fm2new), tol=TOL)), 386s + isTRUE(all.equal(ranova(fm2), ranova(fm2new), tol=TOL)), 386s + isTRUE(all.equal(ls_means(fm2), ls_means(fm2new), tol=TOL)), 386s + isTRUE(all.equal(difflsmeans(fm2), difflsmeans(fm2new), tol=TOL)) 386s + ) 386s > 386s > # Test that lme4 methods work: 386s > coef(fm2) 386s $`Product:Consumer` 386s (Intercept) Product2 Product3 Product4 Information2 Gender2 386s 1:1 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:2 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:3 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:4 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:5 4.468805 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:6 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:7 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:8 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:9 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:10 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:11 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:12 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:13 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:14 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:15 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:16 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:17 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:18 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:19 8.307721 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:20 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:21 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:22 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:23 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:24 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:25 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:26 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:29 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:30 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:31 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:32 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:33 4.271615 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:34 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:35 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:36 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:37 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:38 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:39 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:40 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:41 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:42 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:43 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:44 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:45 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:46 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:47 2.047141 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:48 6.890469 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:49 3.464393 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:50 3.257973 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:51 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:52 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:53 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:54 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:55 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:56 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:57 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:58 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:59 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:60 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:61 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:62 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:63 5.679637 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:64 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:65 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:66 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:67 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:68 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:69 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:70 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:71 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:73 2.854363 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:74 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:75 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:76 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:77 3.257973 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:78 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:79 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:80 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:81 5.886057 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:82 6.890469 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:83 3.868004 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 1:84 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:1 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:2 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:3 5.646881 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:4 3.628827 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:5 4.229629 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:6 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:7 3.018797 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:8 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:9 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:10 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:11 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:12 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:13 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:14 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:15 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:16 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:17 5.646881 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:18 3.628827 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:19 2.417995 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:20 3.225216 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:21 2.821606 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:22 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:23 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:24 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:25 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:26 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:29 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:30 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:31 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:32 5.440461 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:33 2.417995 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:34 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:35 5.036850 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:36 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:37 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:38 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:39 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:40 3.826018 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:41 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:42 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:43 4.436049 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:44 5.036850 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:45 5.440461 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:46 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:47 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:48 2.615186 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:49 7.261323 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:50 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:51 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:52 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:53 8.068545 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:54 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:55 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:56 7.054903 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:57 6.857713 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:58 8.472155 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:59 8.068545 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:60 5.243270 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:61 4.839659 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:62 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:63 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:64 7.862125 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:65 4.436049 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:66 5.844071 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:67 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:68 3.826018 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:69 7.458514 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:70 4.229629 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:71 7.664934 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:73 9.072957 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:74 6.651293 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:75 8.875766 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:76 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:77 8.265735 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:78 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:79 7.458514 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:80 7.054903 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:81 4.032438 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:82 8.669346 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:83 6.050491 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 2:84 6.454102 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:1 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:2 7.468480 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:3 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:4 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:5 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:6 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:7 7.064869 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:8 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:9 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:10 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:11 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:12 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:13 5.450426 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:14 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:15 6.464068 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:16 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:17 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:18 5.656846 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:19 1.620739 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:20 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:21 3.638793 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:22 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:23 2.625152 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:24 7.674900 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:25 6.060457 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:26 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:29 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:30 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:31 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:32 7.468480 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:33 2.427961 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:34 6.060457 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:35 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:36 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:37 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:38 4.042404 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:39 5.656846 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:40 7.468480 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:41 5.253236 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:42 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:43 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:44 4.239594 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:45 2.625152 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:46 5.253236 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:47 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:48 5.450426 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:49 6.464068 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:50 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:51 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:52 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:53 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:54 7.064869 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:55 6.464068 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:56 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:57 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:58 7.271289 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:59 7.674900 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:60 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:61 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:62 7.872091 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:63 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:64 6.257648 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:65 3.638793 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:66 3.835984 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:67 6.867678 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:68 1.817930 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:69 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:70 3.028762 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:71 8.078510 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:73 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:74 8.275701 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:75 3.235182 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:76 5.854037 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:77 6.661258 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:78 8.078510 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:79 4.239594 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:80 3.028762 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:81 3.638793 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:82 7.468480 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:83 4.849625 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 3:84 5.656846 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:1 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:2 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:3 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:4 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:5 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:6 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:7 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:8 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:9 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:10 6.598604 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:11 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:12 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:13 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:14 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:15 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:16 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:17 3.773330 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:18 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:19 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:20 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:21 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:22 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:23 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:24 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:25 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:26 4.777742 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:29 2.356078 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:30 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:31 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:32 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:33 4.176940 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:34 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:35 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:36 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:37 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:38 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:39 4.176940 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:40 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:41 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:42 7.809437 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:43 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:44 2.759689 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:45 5.181353 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:46 1.755276 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:47 1.952467 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:48 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:49 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:50 6.392185 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:51 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:52 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:53 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:54 7.603017 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:55 5.387772 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:56 2.759689 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:57 7.002215 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:58 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:59 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:60 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:61 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:62 8.006627 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:63 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:64 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:65 3.369719 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:66 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:67 6.194994 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:68 5.584963 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:69 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:70 6.795795 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:71 4.984162 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:73 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:74 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:75 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:76 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:77 8.410238 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:78 7.405826 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:79 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:80 3.970521 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:81 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:82 5.988574 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:83 5.791383 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 4:84 4.580551 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 386s 386s attr(,"class") 386s [1] "coef.mer" 386s > fixef(fm2) 386s (Intercept) Product2 Product3 Product4 Information2 Gender2 386s 5.8289672 -0.7037037 0.2839506 0.1172840 0.2006173 -0.2442835 386s > resid(fm2) 386s 1 2 3 4 5 6 386s -0.07883589 -0.27945318 -0.13595549 -0.33657278 -1.13357551 0.66580721 386s 7 8 9 10 11 12 386s 0.09133291 -0.10928437 -0.03174324 -0.23236053 0.27864107 1.07802378 386s 13 14 15 16 17 18 386s 0.49185308 0.29123580 0.33120421 0.13058692 0.30672140 0.10610412 386s 19 20 21 22 23 24 386s -1.94317685 1.85620587 -0.15162889 0.64775382 2.09133291 -2.10928437 386s 25 26 27 28 29 30 386s 0.30672140 0.10610412 0.07487654 -1.12574075 -0.13357551 -0.33419279 386s 31 32 33 34 35 36 386s -0.50505641 0.29432631 -1.22452189 0.57486083 -0.28164149 -0.48225877 386s 37 38 39 40 41 42 386s -0.89370421 0.90567850 0.73481489 -0.46580240 -0.07883589 -0.27945318 386s 43 44 45 46 47 48 386s 0.46043383 -0.74018345 0.44476043 0.24414315 -2.10144573 1.69793698 386s 49 50 51 52 53 54 386s 1.14298202 -0.05763526 -1.07080946 -0.27142674 -0.10453624 0.69484647 386s 55 56 57 58 59 60 386s 0.15647895 -1.04413834 -0.28966792 0.50971479 -0.34678752 0.45259519 386s 61 62 63 64 65 66 386s -1.15162889 1.64775382 0.47689021 0.27627292 -0.28966792 0.50971479 386s 67 68 69 70 71 72 386s -0.34678752 0.45259519 0.44476043 0.24414315 -1.31227776 1.48710495 386s 73 74 75 76 77 78 386s 0.51755343 -0.68306385 0.23154842 1.03093113 -0.55523957 1.24414315 386s 79 80 81 82 83 84 386s 0.28411156 0.08349428 0.73937134 0.53875406 -0.66719878 -0.86781607 386s 85 86 87 88 89 90 386s 3.10629579 -3.09432150 0.73481489 -0.46580240 -0.41730054 -0.61791782 386s 91 92 93 94 95 96 386s -0.66719878 -0.86781607 -0.29731489 0.50206783 0.52398286 0.32336557 386s 97 98 99 100 101 102 386s 0.54659270 0.34597541 -0.66719878 -0.86781607 0.50990646 -0.69071082 386s 103 104 105 106 107 108 386s 0.52398286 0.32336557 1.14298202 -0.05763526 -0.66719878 -0.86781607 386s 109 110 111 112 113 114 386s -0.87565083 -0.07626811 1.13842556 -1.06219172 -0.67522522 0.12415750 386s 115 116 117 118 119 120 386s -0.15400888 0.64537384 0.25198178 0.05136450 -0.11949912 0.67988360 386s 121 122 123 124 125 126 386s 2.37186743 -2.82874985 -0.66719878 -0.86781607 -0.89370421 0.90567850 386s 127 128 129 130 131 132 386s -1.26518511 1.53419760 -0.09688928 0.70249344 0.05682315 -0.14379413 386s 133 134 135 136 137 138 386s -0.15162889 0.64775382 0.10938630 -1.09123099 1.49950005 -0.70111724 386s 139 140 141 142 143 144 386s 0.07487654 -1.12574075 0.05920314 -0.14141415 -0.11949912 0.67988360 386s 145 146 147 148 149 150 386s 0.69227869 0.49166141 -0.71429143 -0.91490872 -0.90469010 -1.10530738 386s 151 152 153 154 155 156 386s -0.10144573 -0.30206302 0.30672140 0.10610412 -0.52151279 -0.72213007 386s 157 158 159 160 161 162 386s -0.15162889 0.64775382 0.89855427 -1.30206302 0.30672140 0.10610412 386s 163 164 165 166 167 168 386s -1.11790211 -0.31851939 0.07725652 -1.12336076 -0.69783506 0.10154766 386s 169 170 171 172 173 174 386s 2.16103540 -2.03958188 -0.66719878 -0.86781607 1.12434917 -2.07626811 386s 175 176 177 178 179 180 386s 0.15647895 -1.04413834 0.75742473 -0.44319256 -0.66719878 -0.86781607 386s 181 182 183 184 185 186 386s -0.66481880 -0.86543608 1.15647895 -2.04413834 0.49950005 0.29888276 386s 187 188 189 190 191 192 386s 0.44238045 0.24176316 1.04114975 -0.15946753 -0.11949912 0.67988360 386s 193 194 195 196 197 198 386s -0.07883589 -0.27945318 -0.15400888 0.64537384 -0.34440754 0.45497518 386s 199 200 201 202 203 204 386s -0.11949912 0.67988360 0.95020337 -0.25041391 -0.66719878 -0.86781607 386s 205 206 207 208 209 210 386s -0.70092557 1.09845715 1.34925759 -1.85135969 -3.62813257 3.17125015 386s 211 212 213 214 215 216 386s -0.66719878 -0.86781607 0.29907443 0.09845715 -1.22907835 -0.42969563 386s 217 218 219 220 221 222 386s 0.16103540 -0.03958188 1.08586242 -0.11475486 -0.29731489 0.50206783 386s 223 224 225 226 227 228 386s 0.73481489 -0.46580240 -0.28966792 0.50971479 1.03876977 -0.16184751 386s 229 230 231 232 233 234 386s 0.84837111 -0.35224618 0.47689021 0.27627292 0.54659270 0.34597541 386s 235 236 237 238 239 240 386s -0.49247352 0.30690920 0.49185308 0.29123580 -0.86157444 0.93780828 386s 241 242 243 244 245 246 386s -1.27161454 0.52776818 -0.71429143 -0.91490872 -1.71191145 0.08747127 386s 247 248 249 250 251 252 386s 1.70577562 -2.49484166 -0.67522522 0.12415750 -0.15400888 0.64537384 386s 253 254 255 256 257 258 386s 0.65559246 -0.54502482 -0.11949912 0.67988360 -1.24257527 1.55680744 386s 259 260 261 262 263 264 386s -1.08886284 0.71051987 -1.29731489 1.50206783 0.33120421 0.13058692 386s 265 266 267 268 269 270 386s 0.16103540 -0.03958188 0.27864107 1.07802378 0.29907443 0.09845715 386s 271 272 273 274 275 276 386s 1.33120421 -0.86941308 -1.46439319 0.33498953 -0.15400888 0.64537384 386s 277 278 279 280 281 282 386s 0.84837111 -0.35224618 -0.50505641 0.29432631 0.71033208 -0.49028521 386s 283 284 285 286 287 288 386s -0.13595549 -0.33657278 0.67364584 -1.52697144 0.30216494 -0.89845234 386s 289 290 291 292 293 294 386s -0.69327860 1.10610412 -0.55761955 1.24176316 -0.94079686 0.85858585 386s 295 296 297 298 299 300 386s -0.29422438 -0.49484166 -2.41730054 1.38208218 -0.87803081 -0.07864810 386s 301 302 303 304 305 306 386s 0.49185308 0.29123580 1.52398286 -0.67663443 0.11394275 -0.08667453 386s 307 308 309 310 311 312 386s -0.53956617 0.25981655 0.46281381 -0.73780347 0.30216494 -0.89845234 386s 313 314 315 316 317 318 386s -0.48244657 0.31693615 -0.15400888 0.64537384 -0.15162889 0.64775382 386s 319 320 321 322 323 324 386s 0.07327953 0.87266225 0.90311072 -0.29750656 1.26765518 -1.93296210 386s 325 326 327 328 329 330 386s -0.15162889 0.64775382 0.49494359 -0.70567369 -1.83896460 1.96041812 386s 331 332 333 334 335 336 386s -1.08886284 0.71051987 -0.27926151 -0.47987879 -0.63268902 -0.83330631 386s 337 338 339 340 341 342 386s 0.73937134 0.53875406 -1.49247352 1.30690920 -0.66481880 -0.86543608 386s 343 344 345 346 347 348 386s 0.94564692 -1.25497037 1.92116411 -2.27945318 1.23154842 0.03093113 386s 349 350 351 352 353 354 386s -2.53718619 2.26219653 -0.87256032 -1.07317760 -0.80285783 -1.00347511 386s 355 356 357 358 359 360 386s 4.10391580 -4.09670148 1.10629579 -1.09432150 -0.82546767 -1.02608496 386s 361 362 363 364 365 366 386s 0.35381405 0.15319677 -0.66719878 -0.86781607 -0.49009354 0.30928918 386s 367 368 369 370 371 372 386s 0.13842556 -0.06219172 -0.46439319 -0.66501047 -0.55761955 1.24176316 386s 373 374 375 376 377 378 386s -0.74801822 1.05136450 -0.11949912 0.67988360 -0.01368986 -1.21430714 386s 379 380 381 382 383 384 386s 0.08586242 0.88524514 0.68463173 0.48401444 -0.26518511 0.53419760 386s 385 386 387 388 389 390 386s -0.83896460 0.96041812 -0.31774826 1.48163446 0.68463173 0.48401444 386s 391 392 393 394 395 396 386s 0.71676150 0.51614422 0.73937134 0.53875406 0.10391580 -0.09670148 386s 397 398 399 400 401 402 386s -0.29731489 0.50206783 -0.84352105 -0.04413834 -0.07883589 -0.27945318 386s 403 404 405 406 407 408 386s 1.63515909 -0.56545819 -0.13357551 -0.33419279 0.88050088 -0.32011640 386s 409 410 411 412 413 414 386s -0.41730054 -0.61791782 0.08586242 0.88524514 -0.10453624 0.69484647 386s 415 416 417 418 419 420 386s 0.52398286 0.32336557 1.32477478 -1.87584250 -2.53956617 2.25981655 386s 421 422 423 424 425 426 386s 1.25198178 -0.94863550 -2.50505641 2.29432631 -0.24257527 0.55680744 386s 427 428 429 430 431 432 386s -0.10691623 0.69246649 -0.87565083 -0.07626811 -0.63268902 -0.83330631 386s 433 434 435 436 437 438 386s -0.07883589 -0.27945318 -0.15400888 0.64537384 -1.15162889 1.64775382 386s 439 440 441 442 443 444 386s -0.11949912 0.67988360 0.51755343 -0.68306385 0.23154842 1.03093113 386s 445 446 447 448 449 450 386s -0.55523957 1.24414315 0.47689021 0.27627292 -0.48244657 0.31693615 386s 451 452 453 454 455 456 386s -0.36484091 1.43454181 1.04114975 -0.15946753 0.68772224 -0.51289505 386s 457 458 459 460 461 462 386s 0.51755343 -0.68306385 0.46043383 -0.74018345 0.86642449 -1.33419279 386s 463 464 465 466 467 468 386s 1.30216494 -1.89845234 0.90311072 -0.29750656 -0.13595549 -0.33657278 386s 469 470 471 472 473 474 386s -0.13357551 -0.33419279 0.68772224 -0.51289505 -0.03174324 -0.23236053 386s 475 476 477 478 479 480 386s 0.27864107 1.07802378 1.08824240 -0.11237488 1.12037218 -0.08024511 386s 481 482 483 484 485 486 386s 0.56464608 -0.63597120 1.08586242 -0.11475486 -0.89370421 0.90567850 386s 487 488 489 490 491 492 386s 0.54203624 -0.65858105 1.37186743 -1.82874985 1.08586242 -0.11475486 386s 493 494 495 496 497 498 386s -0.29731489 0.50206783 0.54203624 -0.65858105 0.49950005 0.29888276 386s 499 500 501 502 503 504 386s -0.73234482 0.06703790 0.07725652 -1.12336076 -0.48700303 -0.68762031 386s 505 506 507 508 509 510 386s -0.83896460 0.96041812 2.10391580 -2.09670148 -2.87565083 1.92373189 386s 511 512 513 514 515 516 386s 2.13842556 -2.06219172 0.11394275 -0.08667453 1.03876977 -0.16184751 386s 517 518 519 520 521 522 386s 0.84837111 -0.35224618 -0.31227776 0.48710495 1.95020337 -1.25041391 386s 523 524 525 526 527 528 386s -0.87803081 -0.07864810 -0.85759745 -1.05821473 2.54203624 -2.65858105 386s 529 530 531 532 533 534 386s -0.62813257 0.17125015 0.48947310 0.28885581 -0.70092557 1.09845715 386s 535 536 537 538 539 540 386s 0.33120421 0.13058692 -0.24257527 0.55680744 -1.28164149 0.51774123 386s 541 542 543 544 545 546 386s -0.06842948 -1.26904676 -0.66879579 1.13058692 1.92116411 -2.27945318 386s 547 548 549 550 551 552 386s 0.03876977 0.83815249 0.63753908 0.43692179 -0.10144573 -0.30206302 386s 553 554 555 556 557 558 386s -1.61007918 0.18930353 0.87503039 0.67441311 0.68463173 0.48401444 386s 559 560 561 562 563 564 386s 0.13842556 -0.06219172 -0.24257527 0.55680744 -0.70330555 1.09607717 386s 565 566 567 568 569 570 386s 0.68463173 0.48401444 0.71676150 0.51614422 -0.67522522 0.12415750 386s 571 572 573 574 575 576 386s 0.82793774 0.62732046 -0.51913280 -0.71975009 0.47689021 0.27627292 386s 577 578 579 580 581 582 386s -2.62813257 2.17125015 -0.31774826 1.48163446 -2.89370421 2.90567850 386s 583 584 585 586 587 588 386s 0.71676150 0.51614422 -2.01368986 0.78569286 -0.31774826 1.48163446 386s 589 590 591 592 593 594 386s 0.29907443 0.09845715 0.71676150 0.51614422 0.92116411 -1.27945318 386s 595 596 597 598 599 600 386s -1.34678752 1.45259519 0.63753908 0.43692179 0.47689021 0.27627292 386s 601 602 603 604 605 606 386s -0.04979663 0.74958609 0.48947310 0.28885581 -0.27926151 -0.47987879 386s 607 608 609 610 611 612 386s 0.13842556 -0.06219172 -0.04979663 0.74958609 1.89308377 -1.30753351 386s 613 614 615 616 617 618 386s 0.93157052 -2.26904676 -0.84352105 -0.04413834 0.11394275 -0.08667453 386s 619 620 621 622 623 624 386s -0.32873414 -0.52935142 -0.92274348 -0.12336076 -1.69783506 1.10154766 386s 625 626 627 628 629 630 386s 2.35381405 -1.84680323 1.27864107 0.07802378 1.49185308 -0.70876420 386s 631 632 633 634 635 636 386s 0.13842556 -0.06219172 -2.86800386 1.93137885 -2.34678752 2.45259519 386s 637 638 639 640 641 642 386s -1.13357551 0.66580721 1.09133291 -1.10928437 0.51755343 -0.68306385 386s 643 644 645 646 647 648 386s 0.24960180 0.04898452 -1.94079686 1.85858585 0.30216494 -0.89845234 386s > 386s > 386s BEGIN TEST test_lmer.R 386s 386s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 386s Copyright (C) 2025 The R Foundation for Statistical Computing 386s Platform: powerpc64le-unknown-linux-gnu 386s 386s R is free software and comes with ABSOLUTELY NO WARRANTY. 386s You are welcome to redistribute it under certain conditions. 386s Type 'license()' or 'licence()' for distribution details. 386s 386s R is a collaborative project with many contributors. 386s Type 'contributors()' for more information and 386s 'citation()' on how to cite R or R packages in publications. 386s 386s Type 'demo()' for some demos, 'help()' for on-line help, or 386s 'help.start()' for an HTML browser interface to help. 386s Type 'q()' to quit R. 386s 386s > # test_lmer.R 386s > 386s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 386s > data("sleepstudy", package="lme4") 386s > f <- function(form, data) lmerTest::lmer(form, data=data) 386s > form <- "Reaction ~ Days + (Days|Subject)" 386s > fm <- f(form, data=sleepstudy) 388s > anova(fm) 388s Type III Analysis of Variance Table with Satterthwaite's method 388s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 388s Days 30031 30031 1 17 45.853 3.264e-06 *** 388s --- 388s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 388s > summary(fm) 388s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 388s lmerModLmerTest] 388s Formula: form 388s Data: data 388s 388s REML criterion at convergence: 1743.6 388s 388s Scaled residuals: 388s Min 1Q Median 3Q Max 388s -3.9536 -0.4634 0.0231 0.4634 5.1793 388s 388s Random effects: 388s Groups Name Variance Std.Dev. Corr 388s Subject (Intercept) 612.10 24.741 388s Days 35.07 5.922 0.07 388s Residual 654.94 25.592 388s Number of obs: 180, groups: Subject, 18 388s 388s Fixed effects: 388s Estimate Std. Error df t value Pr(>|t|) 388s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 388s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 388s --- 388s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 388s 388s Correlation of Fixed Effects: 388s (Intr) 388s Days -0.138 388s > 388s > # cf. GitHub issue #2: 388s > test <- function() { 388s + tmp <- sleepstudy 388s + m <- lmerTest::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 388s + summary(m) 388s + } 388s > test() 389s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 389s lmerModLmerTest] 389s Formula: Reaction ~ Days + (Days | Subject) 389s Data: tmp 389s 389s REML criterion at convergence: 1743.6 389s 389s Scaled residuals: 389s Min 1Q Median 3Q Max 389s -3.9536 -0.4634 0.0231 0.4634 5.1793 389s 389s Random effects: 389s Groups Name Variance Std.Dev. Corr 389s Subject (Intercept) 612.10 24.741 389s Days 35.07 5.922 0.07 389s Residual 654.94 25.592 389s Number of obs: 180, groups: Subject, 18 389s 389s Fixed effects: 389s Estimate Std. Error df t value Pr(>|t|) 389s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 389s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 389s --- 389s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 389s 389s Correlation of Fixed Effects: 389s (Intr) 389s Days -0.138 389s > test <- function() { 389s + tmp <- sleepstudy 389s + m <- lme4::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 389s + if(requireNamespace("lmerTest", quietly = TRUE)) { 389s + summary(lmerTest::as_lmerModLmerTest(m)) 389s + } 389s + } 389s > test() 389s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 389s lmerModLmerTest] 389s Formula: Reaction ~ Days + (Days | Subject) 389s Data: tmp 389s 389s REML criterion at convergence: 1743.6 389s 389s Scaled residuals: 389s Min 1Q Median 3Q Max 389s -3.9536 -0.4634 0.0231 0.4634 5.1793 389s 389s Random effects: 389s Groups Name Variance Std.Dev. Corr 389s Subject (Intercept) 612.10 24.741 389s Days 35.07 5.922 0.07 389s Residual 654.94 25.592 389s Number of obs: 180, groups: Subject, 18 389s 389s Fixed effects: 389s Estimate Std. Error df t value Pr(>|t|) 389s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 389s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 389s --- 389s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 389s 389s Correlation of Fixed Effects: 389s (Intr) 389s Days -0.138 389s > 389s > library(lmerTest) 389s Loading required package: lme4 389s Loading required package: Matrix 389s > 389s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 389s > # even in tests: 389s > assertError <- function(expr, ...) 389s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 389s > assertWarning <- function(expr, ...) 389s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 389s > 389s > TOL <- 1e-4 389s > 389s > ##################################################################### 389s > # Check that lme4::lmer and lmerTest::lmer have the same arguments 389s > 389s > lmer_args <- formals(lme4::lmer) 389s > names(lmer_args) 389s [1] "formula" "data" "REML" "control" "start" 389s [6] "verbose" "subset" 389s Attaching package: 'lmerTest' 389s 389s The following object is masked from 'package:lme4': 389s 389s lmer 389s 389s The following object is masked from 'package:stats': 389s 389s step 389s 389s "weights" "na.action" "offset" 389s [11] "contrasts" "devFunOnly" 389s > lmerTest_args <- formals(lmerTest::lmer) 389s > seq_args <- seq_along(lmerTest_args) 389s > if(packageVersion("lme4") > '1.1.21') { 389s + stopifnot( 389s + all.equal(names(lmer_args), names(lmerTest_args)), 389s + all.equal(lmer_args, lmerTest_args) 389s + ) 389s + } else { # Older versions of 'lme4' has a "..." argument: 389s + stopifnot( 389s + all.equal(names(lmer_args)[seq_args], names(lmerTest_args[seq_args])), 389s + all.equal(lmer_args[seq_args], lmerTest_args[seq_args]) 389s + ) 389s + } 389s > 389s > ##################################################################### 389s > # Test evaluation of update inside a function: 389s > myupdate <- function(m, ...) { 389s + update(m, ...) 389s + } 389s > 389s > data("sleepstudy", package="lme4") 389s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 389s > tmp <- sleepstudy 389s > rm(sleepstudy) 389s > fmA <- update(fm1, data = tmp) # works 389s > fmB <- myupdate(fm1, data = tmp) # also works 389s > # Same except for 'call': 389s > fmB@call <- fmA@call 389s > stopifnot(isTRUE(all.equal(fmA, fmB, tolerance=TOL))) 389s > # Based on bug-report by Henrik Singmann, github issue #3 389s > 389s > ##################################################################### 389s > # Test update when formula is a character vector: 389s > 389s > form <- "Informed.liking ~ Product+Information+ 389s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 389s > m <- lmer(form, data=ham) 389s > class(m) 389s [1] "lmerModLmerTest" 389s attr(,"package") 389s [1] "lmerTest" 389s > class(update(m, ~.- Product)) 389s [1] "lmerModLmerTest" 389s attr(,"package") 389s [1] "lmerTest" 389s > stopifnot(inherits(update(m, ~.- Product), "lmerModLmerTest")) 389s > 389s > # In version < 3.0-1.9002 class(update(m, ~.- Product)) was "lmerMod" 389s > ##################################################################### 389s > # Test error message from as_lmerModLmerTest: 389s > data("sleepstudy", package="lme4") 389s > myfit <- function(formula, data) { 389s + lme4::lmer(formula = formula, data = data) 389s + } 389s > fm2 <- myfit(Reaction ~ Days + (Days|Subject), sleepstudy) 389s > m <- assertError(as_lmerModLmerTest(fm2)) 389s > stopifnot( 389s + grepl("Unable to extract deviance function from model fit", m[[1]], fixed=TRUE) 389s + ) 389s > 389s > ##################################################################### 389s > # Check that devFunOnly argument works: 389s > data("sleepstudy", package="lme4") 389s > fun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = TRUE) 389s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 389s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 389s > fun <- update(fm1, devFunOnly=TRUE) 389s > stopifnot(is.function(fun)) # && names(formals(fun)[1]) == "theta") 389s > # devFunOnly = FALSE: 389s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = FALSE) 389s > stopifnot(inherits(notfun, "lmerModLmerTest")) 389s > # Partial matching: 389s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFun = FALSE) 389s > stopifnot(inherits(notfun, "lmerModLmerTest")) 389s > 389s > ##################################################################### 389s > # Use of as_lmerModLmerTest 389s > data("sleepstudy", package="lme4") 389s > m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 390s > bm <- lmerTest:::as_lmerModLmerTest(m) 390s > stopifnot( 390s + inherits(bm, "lmerModLmerTest"), 390s + !inherits(m, "lmerModLmerTest"), 390s + inherits(bm, "lmerMod"), 390s + all(c("vcov_varpar", "Jac_list", "vcov_beta", "sigma") %in% slotNames(bm)) 390s + ) 390s > 390s > ##################################################################### 390s > # Update method 390s > 390s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 390s > m1 <- update(m, ~.-Days) 390s > m2 <- lmer(Reaction ~ (Days | Subject), sleepstudy) 390s > 390s > stopifnot( 390s + inherits(m, "lmerModLmerTest"), 390s + inherits(m1, "lmerModLmerTest"), 390s + inherits(m2, "lmerModLmerTest"), 390s + all.equal(m1, m2, tolerance=1e-6) 390s + ) 390s > 390s > 390s BEGIN TEST test_lmerTest_paper.R 390s 390s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 390s Copyright (C) 2025 The R Foundation for Statistical Computing 390s Platform: powerpc64le-unknown-linux-gnu 390s 390s R is free software and comes with ABSOLUTELY NO WARRANTY. 390s You are welcome to redistribute it under certain conditions. 390s Type 'license()' or 'licence()' for distribution details. 390s 390s R is a collaborative project with many contributors. 390s Type 'contributors()' for more information and 390s 'citation()' on how to cite R or R packages in publications. 390s 390s Type 'demo()' for some demos, 'help()' for on-line help, or 390s 'help.start()' for an HTML browser interface to help. 390s Type 'q()' to quit R. 390s 390s > # test_lmerTest_paper.R 390s > 390s > library(lmerTest) 390s Loading required package: lme4 390s Loading required package: Matrix 392s 392s Attaching package: 'lmerTest' 392s 392s > 392s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 392s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 392s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 392s The following object is masked from 'package:lme4': 392s 392s lmer 392s 392s The following object is masked from 'package:stats': 392s 392s step 392s 392s > 392s > # Read in data set 392s > load(system.file("testdata","test_paper_objects.RData", package="lmerTest")) 392s > 392s > # Evaluate code from paper: 392s > ## Section 8.2: 392s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + (1 | Assessor) + 392s + (1 | Assessor:TVset) + (1 | Assessor:Picture), data = TVbo, 392s + control=lmerControl(optimizer="bobyqa")) 392s > 392s > (an8.2 <- anova(tv)) 392s Type III Analysis of Variance Table with Satterthwaite's method 392s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 392s TVset 1.765 0.8825 2 14 0.2437 0.7869818 392s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 392s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 392s --- 392s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 392s > 392s > if(has_pbkrtest) 392s + (ankr8.2 <- anova(tv, type=2, ddf="Kenward-Roger")) 393s Type II Analysis of Variance Table with Kenward-Roger's method 393s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 393s TVset 1.765 0.8825 2 14 0.2437 0.7869818 393s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 393s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 393s --- 393s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 393s > 393s > ## Section 8.3: 393s > m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 393s + (1 | Product), data=carrots, 393s + control=lmerControl(optimizer="bobyqa")) 393s boundary (singular) fit: see help('isSingular') 393s > (sum8.3 <- coef(summary(m.carrots))) 393s Estimate Std. Error df t value Pr(>|t|) 393s (Intercept) 4.79911155 0.07529231 20.721707 63.7397325 2.920366e-25 393s sens1 0.01082919 0.01502844 9.167954 0.7205797 4.891328e-01 393s sens2 0.07064553 0.01727803 10.944381 4.0887481 1.812086e-03 393s > 393s > ## Section 8.4: 393s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + 393s + (1 | Assessor:TVset) + (1 | Assessor:Picture) + 393s + (1 | Assessor:Picture:TVset) + (1 | Repeat) + (1 | Repeat:Picture) + 393s + (1 | Repeat:TVset) + (1 | Repeat:TVset:Picture) + (1 | Assessor), 393s + data = TVbo, 393s + control=lmerControl(optimizer="bobyqa")) 394s boundary (singular) fit: see help('isSingular') 394s > st <- step(tv) 394s boundary (singular) fit: see help('isSingular') 394s boundary (singular) fit: see help('isSingular') 395s boundary (singular) fit: see help('isSingular') 395s boundary (singular) fit: see help('isSingular') 395s boundary (singular) fit: see help('isSingular') 396s boundary (singular) fit: see help('isSingular') 396s boundary (singular) fit: see help('isSingular') 396s boundary (singular) fit: see help('isSingular') 397s boundary (singular) fit: see help('isSingular') 397s boundary (singular) fit: see help('isSingular') 397s boundary (singular) fit: see help('isSingular') 397s boundary (singular) fit: see help('isSingular') 398s boundary (singular) fit: see help('isSingular') 398s boundary (singular) fit: see help('isSingular') 398s boundary (singular) fit: see help('isSingular') 398s boundary (singular) fit: see help('isSingular') 399s boundary (singular) fit: see help('isSingular') 399s boundary (singular) fit: see help('isSingular') 399s boundary (singular) fit: see help('isSingular') 399s boundary (singular) fit: see help('isSingular') 399s boundary (singular) fit: see help('isSingular') 399s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 400s boundary (singular) fit: see help('isSingular') 401s boundary (singular) fit: see help('isSingular') 401s boundary (singular) fit: see help('isSingular') 401s boundary (singular) fit: see help('isSingular') 401s boundary (singular) fit: see help('isSingular') 401s > (elim_tab_random8.4 <- st$random) 401s Backward reduced random-effect table: 401s 401s Eliminated npar logLik AIC LRT Df 401s 21 -412.70 867.41 401s (1 | Assessor:Picture:TVset) 1 20 -412.70 865.41 0.0000 1 401s (1 | Repeat) 2 19 -412.70 863.41 0.0000 1 401s (1 | Repeat:Picture) 3 18 -412.70 861.41 0.0000 1 401s (1 | Repeat:TVset:Picture) 4 17 -412.70 859.41 0.0000 1 401s (1 | Repeat:TVset) 5 16 -412.70 857.41 0.0000 1 401s (1 | Assessor:TVset) 0 15 -414.10 858.20 2.7891 1 401s (1 | Assessor:Picture) 0 15 -418.88 867.76 12.3473 1 401s (1 | Assessor) 0 15 -416.44 862.88 7.4698 1 401s Pr(>Chisq) 401s 401s (1 | Assessor:Picture:TVset) 1.0000000 401s (1 | Repeat) 1.0000000 401s (1 | Repeat:Picture) 1.0000000 401s (1 | Repeat:TVset:Picture) 1.0000000 401s (1 | Repeat:TVset) 1.0000000 401s (1 | Assessor:TVset) 0.0949061 . 401s (1 | Assessor:Picture) 0.0004416 *** 401s (1 | Assessor) 0.0062742 ** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s > (elim_tab_fixed8.4 <- st$fixed) 401s Backward reduced fixed-effect table: 401s Degrees of freedom method: Satterthwaite 401s 401s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 401s TVset:Picture 0 90.767 15.128 6 138 4.1777 0.0006845 *** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s > (an8.4 <- anova(get_model(st))) 401s Type III Analysis of Variance Table with Satterthwaite's method 401s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 401s TVset 1.765 0.8825 2 14 0.2437 0.7869818 401s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 401s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 401s --- 401s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 401s > 401s > ## Section 8.5: 401s > # L <- matrix(0, ncol = 12, nrow = 6) 401s > # L[1, 7] <- L[2, 8] <- L[3, 9] <- L[4, 10] <- L[5, 11] <- L[6, 12] <- 1 401s > L <- cbind(array(0, dim=c(6, 6)), diag(6)) 401s > (con1_8.5 <- calcSatterth(tv, L)) 401s $denom 401s [1] 138 401s 401s $Fstat 401s [,1] 401s [1,] 4.177655 401s 401s $pvalue 401s [,1] 401s [1,] 0.0006844792 401s 401s $ndf 401s [1] 6 401s 401s > (con2_8.5 <- contest(tv, L)) 401s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 401s 1 90.76719 15.12786 6 138 4.177655 0.0006844792 401s > 401s > ## Section C: 401s > # m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 401s > # (1 | product), data = carrots) 401s > # step(m.carrots, reduce.fixed = FALSE) 401s > (ran_C <- ranova(m.carrots)) 402s boundary (singular) fit: see help('isSingular') 402s boundary (singular) fit: see help('isSingular') 402s ANOVA-like table for random-effects: Single term deletions 402s 402s Model: 402s Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + (1 | Product) 402s npar logLik AIC LRT Df 402s 11 -1869.7 3761.5 402s sens1 in (1 + sens1 + sens2 | Consumer) 8 -1870.7 3757.3 1.8274 3 402s sens2 in (1 + sens1 + sens2 | Consumer) 8 -1874.5 3765.0 9.5464 3 402s (1 | Product) 10 -1878.7 3777.4 17.9080 1 402s Pr(>Chisq) 402s 402s sens1 in (1 + sens1 + sens2 | Consumer) 0.60899 402s sens2 in (1 + sens1 + sens2 | Consumer) 0.02284 * 402s (1 | Product) 2.318e-05 *** 402s --- 402s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 402s > 402s > # Compare to validated outputs: 402s > TOL <- 1e-4 402s > stopifnot( 402s + isTRUE(all.equal(an8.2_save, an8.2, check.attributes = FALSE, tolerance=TOL)), 402s + isTRUE(all.equal(sum8.3_save, sum8.3, check.attributes = FALSE, tolerance=TOL)), 402s + isTRUE(all.equal(elim_tab_random8.4_save, elim_tab_random8.4, 402s + check.attributes = FALSE, tolerance=TOL)), 402s + isTRUE(all.equal(elim_tab_fixed8.4_save, elim_tab_fixed8.4, 402s + check.attributes = FALSE, tolerance=TOL)), 402s + isTRUE(all.equal(an8.4_save, an8.4, check.attributes = FALSE, tolerance=TOL)), 402s + isTRUE(all.equal(con1_8.5_save, con1_8.5, check.attributes = FALSE, tolerance=TOL)), 402s + isTRUE(all.equal(con2_8.5_save, con2_8.5, check.attributes = FALSE, tolerance=TOL)) 402s + ) 402s Warning message: 402s Model failed to converge with 1 negative eigenvalue: -1.6e+03 402s > if(has_pbkrtest) { 402s + stopifnot( 402s + isTRUE(all.equal(ankr8.2_save, ankr8.2, check.attributes = FALSE, tolerance=TOL)) 402s + ) 402s + } 402s > 402s > 402s BEGIN TEST test_ls_means.R 402s 402s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 402s Copyright (C) 2025 The R Foundation for Statistical Computing 402s Platform: powerpc64le-unknown-linux-gnu 402s 402s R is free software and comes with ABSOLUTELY NO WARRANTY. 402s You are welcome to redistribute it under certain conditions. 402s Type 'license()' or 'licence()' for distribution details. 402s 402s R is a collaborative project with many contributors. 402s Type 'contributors()' for more information and 402s 'citation()' on how to cite R or R packages in publications. 402s 402s Type 'demo()' for some demos, 'help()' for on-line help, or 402s 'help.start()' for an HTML browser interface to help. 402s Type 'q()' to quit R. 402s 402s > # test_lsmeans.R 402s > 402s > library(lmerTest) 402s Loading required package: lme4 402s Loading required package: Matrix 404s > 404s > TOL <- 1e-4 404s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 404s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 404s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 404s 404s Attaching package: 'lmerTest' 404s 404s The following object is masked from 'package:lme4': 404s 404s lmer 404s 404s The following object is masked from 'package:stats': 404s 404s step 404s 404s > 404s > ########### Basic model structures: 404s > 404s > # Factor * covariate: 404s > data("cake", package="lme4") 404s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 404s > (lsm <- ls_means(model)) 404s Least Squares Means table: 404s 404s Estimate Std. Error df t value lower upper Pr(>|t|) 404s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 404s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 404s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 404s --- 404s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 404s 404s Confidence level: 95% 404s Degrees of freedom method: Satterthwaite 404s > stopifnot( 404s + nrow(lsm) == 3L, 404s + ncol(lsm) == 7L, 404s + # Balanced, so LS-means equal raw means: 404s + isTRUE(all.equal(c(with(cake, tapply(angle, recipe, mean))), lsm[, "Estimate"], 404s + check.attributes=FALSE, tolerance=TOL)) 404s + ) 404s > 404s > # Pairwise differences of LS-means: 404s > plsm <- ls_means(model, pairwise = TRUE) 404s > plsm2 <- difflsmeans(model) 404s > C <- as.matrix(lmerTest:::get_pairs(rownames(lsm))) 404s > stopifnot( 405s + isTRUE(all.equal(plsm, plsm2, tolerance=TOL)), 405s + isTRUE(all.equal(plsm[, "Estimate"], c(lsm[, "Estimate"] %*% C), 405s + check.attributes=FALSE, tolerance=TOL)) 405s + ) 405s > 405s > # Contrasts vectors: 405s > show_tests(lsm) 405s $recipe 405s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 405s recipeA 1 0 0 200 0 0 405s recipeB 1 1 0 200 200 0 405s recipeC 1 0 1 200 0 200 405s 405s > show_tests(plsm) 405s $recipe 405s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 405s recipeA - recipeB 0 -1 0 0 -200 0 405s recipeA - recipeC 0 0 -1 0 0 -200 405s recipeB - recipeC 0 1 -1 0 200 -200 405s 405s > 405s > # Factor * Ordered: 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 405s > (lsm2 <- ls_means(model)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper 405s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 405s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 405s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 405s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 405s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 405s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 405s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 405s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 405s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 405s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 405s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 405s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 405s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 405s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 405s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 405s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 405s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 405s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 405s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 405s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 405s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 405s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 405s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 405s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 405s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 405s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 405s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 405s Pr(>|t|) 405s recipeA < 2.2e-16 *** 405s recipeB < 2.2e-16 *** 405s recipeC < 2.2e-16 *** 405s temperature175 < 2.2e-16 *** 405s temperature185 < 2.2e-16 *** 405s temperature195 < 2.2e-16 *** 405s temperature205 < 2.2e-16 *** 405s temperature215 < 2.2e-16 *** 405s temperature225 < 2.2e-16 *** 405s recipeA:temperature175 < 2.2e-16 *** 405s recipeB:temperature175 < 2.2e-16 *** 405s recipeC:temperature175 < 2.2e-16 *** 405s recipeA:temperature185 < 2.2e-16 *** 405s recipeB:temperature185 < 2.2e-16 *** 405s recipeC:temperature185 < 2.2e-16 *** 405s recipeA:temperature195 < 2.2e-16 *** 405s recipeB:temperature195 < 2.2e-16 *** 405s recipeC:temperature195 < 2.2e-16 *** 405s recipeA:temperature205 < 2.2e-16 *** 405s recipeB:temperature205 < 2.2e-16 *** 405s recipeC:temperature205 < 2.2e-16 *** 405s recipeA:temperature215 < 2.2e-16 *** 405s recipeB:temperature215 < 2.2e-16 *** 405s recipeC:temperature215 < 2.2e-16 *** 405s recipeA:temperature225 < 2.2e-16 *** 405s recipeB:temperature225 < 2.2e-16 *** 405s recipeC:temperature225 < 2.2e-16 *** 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > stopifnot( 405s + nrow(lsm2) == 3 + 6 + 3*6, 405s + ncol(lsm) == 7L, 405s + # Balanced, so LS-means equal raw means: 405s + isTRUE(all.equal(lsm[1:3, ], lsm2[1:3, ], 405s + check.attributes=FALSE, tolerance=TOL)) 405s + ) 405s > 405s > 405s > # Factor * Factor: 405s > cake2 <- cake 405s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 405s > (lsm3 <- ls_means(model)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper 405s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 405s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 405s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 405s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 405s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 405s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 405s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 405s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 405s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 405s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 405s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 405s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 405s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 405s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 405s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 405s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 405s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 405s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 405s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 405s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 405s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 405s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 405s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 405s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 405s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 405s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 405s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 405s Pr(>|t|) 405s recipeA < 2.2e-16 *** 405s recipeB < 2.2e-16 *** 405s recipeC < 2.2e-16 *** 405s temperature175 < 2.2e-16 *** 405s temperature185 < 2.2e-16 *** 405s temperature195 < 2.2e-16 *** 405s temperature205 < 2.2e-16 *** 405s temperature215 < 2.2e-16 *** 405s temperature225 < 2.2e-16 *** 405s recipeA:temperature175 < 2.2e-16 *** 405s recipeB:temperature175 < 2.2e-16 *** 405s recipeC:temperature175 < 2.2e-16 *** 405s recipeA:temperature185 < 2.2e-16 *** 405s recipeB:temperature185 < 2.2e-16 *** 405s recipeC:temperature185 < 2.2e-16 *** 405s recipeA:temperature195 < 2.2e-16 *** 405s recipeB:temperature195 < 2.2e-16 *** 405s recipeC:temperature195 < 2.2e-16 *** 405s recipeA:temperature205 < 2.2e-16 *** 405s recipeB:temperature205 < 2.2e-16 *** 405s recipeC:temperature205 < 2.2e-16 *** 405s recipeA:temperature215 < 2.2e-16 *** 405s recipeB:temperature215 < 2.2e-16 *** 405s recipeC:temperature215 < 2.2e-16 *** 405s recipeA:temperature225 < 2.2e-16 *** 405s recipeB:temperature225 < 2.2e-16 *** 405s recipeC:temperature225 < 2.2e-16 *** 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > stopifnot( 405s + isTRUE(all.equal(lsm2, lsm3, check.attributes=FALSE, tolerance=TOL)) 405s + ) 405s > 405s > # Covariate (only): 405s > data("sleepstudy", package="lme4") 405s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 405s > (lsm <- ls_means(m)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper Pr(>|t|) 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > stopifnot( 405s + nrow(lsm) == 0L, 405s + ncol(lsm) == 7L 405s + ) 405s > 405s > # No fixef: 405s > m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) 405s > (lsm <- ls_means(m)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper Pr(>|t|) 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > stopifnot( 405s + nrow(lsm) == 0L, 405s + ncol(lsm) == 7L 405s + ) 405s > 405s > ########### Arguments and options: 405s > 405s > # which 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 405s > (lsm4 <- ls_means(model, which = "recipe")) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper Pr(>|t|) 405s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 405s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 405s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > stopifnot( 405s + nrow(lsm4) == 3L, 405s + ncol(lsm4) == 7L, 405s + isTRUE(all.equal(lsm3[1:3, ], lsm4, check.attributes=FALSE, tolerance=TOL)) 405s + ) 405s > 405s > # KR: 405s > if(has_pbkrtest) 405s + (lsm5 <- ls_means(model, which = "recipe", ddf = "Kenward-Roger")) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper Pr(>|t|) 405s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 405s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 405s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Kenward-Roger 405s > 405s > # level: 405s > (lsm6 <- ls_means(model, which = "recipe", level=0.99)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper Pr(>|t|) 405s recipeA 33.1222 1.7368 42 19.070 28.4361 37.8083 < 2.2e-16 *** 405s recipeB 31.6444 1.7368 42 18.220 26.9584 36.3305 < 2.2e-16 *** 405s recipeC 31.6000 1.7368 42 18.194 26.9139 36.2861 < 2.2e-16 *** 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 99% 405s Degrees of freedom method: Satterthwaite 405s > 405s > stopifnot( 405s + all(lsm6[, "lower"] < lsm4[, "lower"]), 405s + all(lsm6[, "upper"] > lsm4[, "upper"]) 405s + ) 405s > 405s > 405s > 405s > ########### Missing cels -> unestimable contrasts: 405s > 405s > # Missing cell: 405s > cake3 <- cake 405s > cake3$temperature <- factor(cake3$temperature, ordered=FALSE) 405s > cake3 <- droplevels(subset(cake3, temperature %in% levels(cake3$temperature)[1:3])) 405s > cake3 <- droplevels(subset(cake3, !(recipe == "C" & temperature == "195") )) 405s > str(cake3) 405s 'data.frame': 120 obs. of 5 variables: 405s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 2 2 ... 405s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 1 2 2 2 3 3 1 1 ... 405s $ temperature: Factor w/ 3 levels "175","185","195": 1 2 3 1 2 3 1 2 1 2 ... 405s $ angle : int 42 46 47 39 46 51 46 44 47 29 ... 405s $ temp : num 175 185 195 175 185 195 175 185 175 185 ... 405s > with(cake3, table(recipe, temperature)) 405s temperature 405s recipe 175 185 195 405s A 15 15 15 405s B 15 15 15 405s C 15 15 0 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 405s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 405s > (lsm7 <- ls_means(model)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper 405s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 405s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 405s recipeC NA NA NA NA NA NA 405s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 405s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 405s temperature195 NA NA NA NA NA NA 405s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 405s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 405s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 405s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 405s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 405s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 405s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 405s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 405s recipeC:temperature195 NA NA NA NA NA NA 405s Pr(>|t|) 405s recipeA < 2.2e-16 *** 405s recipeB < 2.2e-16 *** 405s recipeC NA 405s temperature175 < 2.2e-16 *** 405s temperature185 < 2.2e-16 *** 405s temperature195 NA 405s recipeA:temperature175 < 2.2e-16 *** 405s recipeB:temperature175 < 2.2e-16 *** 405s recipeC:temperature175 < 2.2e-16 *** 405s recipeA:temperature185 < 2.2e-16 *** 405s recipeB:temperature185 < 2.2e-16 *** 405s recipeC:temperature185 < 2.2e-16 *** 405s recipeA:temperature195 < 2.2e-16 *** 405s recipeB:temperature195 < 2.2e-16 *** 405s recipeC:temperature195 NA 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > 405s > # Using show_tests with options: 405s > show_tests(lsm7, fractions = TRUE) 405s $recipe 405s (Intercept) recipeB recipeC temperature185 temperature195 405s recipeA 1 0 0 1/3 1/3 405s recipeB 1 1 0 1/3 1/3 405s recipeC 1 0 1 1/3 1/3 405s recipeB:temperature185 recipeC:temperature185 recipeB:temperature195 405s recipeA 0 0 0 405s recipeB 1/3 0 1/3 405s recipeC 0 1/3 0 405s recipeC:temperature195 405s recipeA 0 405s recipeB 0 405s recipeC 1/3 405s 405s $temperature 405s (Intercept) recipeB recipeC temperature185 temperature195 405s temperature175 1 1/3 1/3 0 0 405s temperature185 1 1/3 1/3 1 0 405s temperature195 1 1/3 1/3 0 1 405s recipeB:temperature185 recipeC:temperature185 405s temperature175 0 0 405s temperature185 1/3 1/3 405s temperature195 0 0 405s recipeB:temperature195 recipeC:temperature195 405s temperature175 0 0 405s temperature185 0 0 405s temperature195 1/3 1/3 405s 405s $`recipe:temperature` 405s (Intercept) recipeB recipeC temperature185 405s recipeA:temperature175 1 0 0 0 405s recipeB:temperature175 1 1 0 0 405s recipeC:temperature175 1 0 1 0 405s recipeA:temperature185 1 0 0 1 405s recipeB:temperature185 1 1 0 1 405s recipeC:temperature185 1 0 1 1 405s recipeA:temperature195 1 0 0 0 405s recipeB:temperature195 1 1 0 0 405s recipeC:temperature195 1 0 1 0 405s temperature195 recipeB:temperature185 405s recipeA:temperature175 0 0 405s recipeB:temperature175 0 0 405s recipeC:temperature175 0 0 405s recipeA:temperature185 0 0 405s recipeB:temperature185 0 1 405s recipeC:temperature185 0 0 405s recipeA:temperature195 1 0 405s recipeB:temperature195 1 0 405s recipeC:temperature195 1 0 405s recipeC:temperature185 recipeB:temperature195 405s recipeA:temperature175 0 0 405s recipeB:temperature175 0 0 405s recipeC:temperature175 0 0 405s recipeA:temperature185 0 0 405s recipeB:temperature185 0 0 405s recipeC:temperature185 1 0 405s recipeA:temperature195 0 0 405s recipeB:temperature195 0 1 405s recipeC:temperature195 0 0 405s recipeC:temperature195 405s recipeA:temperature175 0 405s recipeB:temperature175 0 405s recipeC:temperature175 0 405s recipeA:temperature185 0 405s recipeB:temperature185 0 405s recipeC:temperature185 0 405s recipeA:temperature195 0 405s recipeB:temperature195 0 405s recipeC:temperature195 1 405s 405s > show_tests(lsm7, fractions = TRUE, names = FALSE) 405s $recipe 405s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 405s [1,] 1 0 0 1/3 1/3 0 0 0 0 405s [2,] 1 1 0 1/3 1/3 1/3 0 1/3 0 405s [3,] 1 0 1 1/3 1/3 0 1/3 0 1/3 405s 405s $temperature 405s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 405s [1,] 1 1/3 fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 405s 1/3 0 0 0 0 0 0 405s [2,] 1 1/3 1/3 1 0 1/3 1/3 0 0 405s [3,] 1 1/3 1/3 0 1 0 0 1/3 1/3 405s 405s $`recipe:temperature` 405s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 405s [1,] 1 0 0 0 0 0 0 0 0 405s [2,] 1 1 0 0 0 0 0 0 0 405s [3,] 1 0 1 0 0 0 0 0 0 405s [4,] 1 0 0 1 0 0 0 0 0 405s [5,] 1 1 0 1 0 1 0 0 0 405s [6,] 1 0 1 1 0 0 1 0 0 405s [7,] 1 0 0 0 1 0 0 0 0 405s [8,] 1 1 0 0 1 0 0 1 0 405s [9,] 1 0 1 0 1 0 0 0 1 405s 405s > 405s > # Missing diagonal: 405s > cake4 <- cake 405s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 405s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 405s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 405s + (recipe == "B" & temperature == "185") | 405s + (recipe == "C" & temperature == "195") ))) 405s > # str(cake4) 405s > with(cake4, table(recipe, temperature)) 405s temperature 405s recipe 175 185 195 405s A 0 15 15 405s B 15 0 15 405s C 15 15 0 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 405s > ls_means(model) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper 405s recipeA NA NA NA NA NA NA 405s recipeB NA NA NA NA NA NA 405s recipeC NA NA NA NA NA NA 405s temperature175 NA NA NA NA NA NA 405s temperature185 NA NA NA NA NA NA 405s temperature195 NA NA NA NA NA NA 405s recipeA:temperature175 NA NA NA NA NA NA 405s recipeB:temperature175 26.8667 1.8908 53.5 14.209 23.0750 30.6584 405s recipeC:temperature175 27.9333 1.8908 53.5 14.773 24.1416 31.7250 405s recipeA:temperature185 31.5333 1.8908 53.5 16.677 27.7416 35.3250 405s recipeB:temperature185 NA NA NA NA NA NA 405s recipeC:temperature185 28.9333 1.8908 53.5 15.302 25.1416 32.7250 405s recipeA:temperature195 30.8000 1.8908 53.5 16.289 27.0083 34.5917 405s recipeB:temperature195 31.7333 1.8908 53.5 16.783 27.9416 35.5250 405s recipeC:temperature195 NA NA NA NA NA NA 405s Pr(>|t|) 405s recipeA NA 405s recipeB NA 405s recipeC NA 405s temperature175 NA 405s temperature185 NA 405s temperature195 NA 405s recipeA:temperature175 NA 405s recipeB:temperature175 < 2.2e-16 *** 405s recipeC:temperature175 < 2.2e-16 *** 405s recipeA:temperature185 < 2.2e-16 *** 405s recipeB:temperature185 NA 405s recipeC:temperature185 < 2.2e-16 *** 405s recipeA:temperature195 < 2.2e-16 *** 405s recipeB:temperature195 < 2.2e-16 *** 405s recipeC:temperature195 NA 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > 405s > 405s > ########### Various contrasts codings: 405s > 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3, 405s + contrasts = list(recipe="contr.sum", temperature="contr.helmert")) 405s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 405s > (lsm8 <- ls_means(model)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper 405s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 405s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 405s recipeC NA NA NA NA NA NA 405s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 405s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 405s temperature195 NA NA NA NA NA NA 405s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 405s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 405s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 405s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 405s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 405s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 405s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 405s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 405s recipeC:temperature195 NA NA NA NA NA NA 405s Pr(>|t|) 405s recipeA < 2.2e-16 *** 405s recipeB < 2.2e-16 *** 405s recipeC NA 405s temperature175 < 2.2e-16 *** 405s temperature185 < 2.2e-16 *** 405s temperature195 NA 405s recipeA:temperature175 < 2.2e-16 *** 405s recipeB:temperature175 < 2.2e-16 *** 405s recipeC:temperature175 < 2.2e-16 *** 405s recipeA:temperature185 < 2.2e-16 *** 405s recipeB:temperature185 < 2.2e-16 *** 405s recipeC:temperature185 < 2.2e-16 *** 405s recipeA:temperature195 < 2.2e-16 *** 405s recipeB:temperature195 < 2.2e-16 *** 405s recipeC:temperature195 NA 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > # show_tests(lsm7) 405s > # show_tests(lsm8) 405s > stopifnot( 405s + isTRUE(all.equal(lsm7, lsm8, check.attributes=FALSE, tolerance=TOL)) 405s + ) 405s > 405s > # ambient contrasts not contr.treatment: 405s > options("contrasts") 405s $contrasts 405s unordered ordered 405s "contr.treatment" "contr.poly" 405s 405s > options(contrasts = c("contr.sum", "contr.poly")) 405s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 405s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 405s > (lsm9 <- ls_means(model)) 405s Least Squares Means table: 405s 405s Estimate Std. Error df t value lower upper 405s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 405s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 405s recipeC NA NA NA NA NA NA 405s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 405s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 405s temperature195 NA NA NA NA NA NA 405s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 405s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 405s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 405s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 405s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 405s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 405s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 405s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 405s recipeC:temperature195 NA NA NA NA NA NA 405s Pr(>|t|) 405s recipeA < 2.2e-16 *** 405s recipeB < 2.2e-16 *** 405s recipeC NA 405s temperature175 < 2.2e-16 *** 405s temperature185 < 2.2e-16 *** 405s temperature195 NA 405s recipeA:temperature175 < 2.2e-16 *** 405s recipeB:temperature175 < 2.2e-16 *** 405s recipeC:temperature175 < 2.2e-16 *** 405s recipeA:temperature185 < 2.2e-16 *** 405s recipeB:temperature185 < 2.2e-16 *** 405s recipeC:temperature185 < 2.2e-16 *** 405s recipeA:temperature195 < 2.2e-16 *** 405s recipeB:temperature195 < 2.2e-16 *** 405s recipeC:temperature195 NA 405s --- 405s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 405s 405s Confidence level: 95% 405s Degrees of freedom method: Satterthwaite 405s > options(contrasts = c("contr.treatment", "contr.poly")) 405s > options("contrasts") 405s $contrasts 405s [1] "contr.treatment" "contr.poly" 405s 405s > stopifnot( 405s + isTRUE(all.equal(lsm7, lsm9, check.attributes=FALSE, tolerance=TOL)) 405s + ) 405s > 405s > 405s > 405s BEGIN TEST test_ranova_step.R 406s 406s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 406s Copyright (C) 2025 The R Foundation for Statistical Computing 406s Platform: powerpc64le-unknown-linux-gnu 406s 406s R is free software and comes with ABSOLUTELY NO WARRANTY. 406s You are welcome to redistribute it under certain conditions. 406s Type 'license()' or 'licence()' for distribution details. 406s 406s R is a collaborative project with many contributors. 406s Type 'contributors()' for more information and 406s 'citation()' on how to cite R or R packages in publications. 406s 406s Type 'demo()' for some demos, 'help()' for on-line help, or 406s 'help.start()' for an HTML browser interface to help. 406s Type 'q()' to quit R. 406s 406s > # test_ranova.R 406s > 406s > # Test functionality _before_ attaching lmerTest 406s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 406s > data("sleepstudy", package="lme4") 406s > f <- function(form, data) lmerTest::lmer(form, data=data) 406s > form <- "Reaction ~ Days + (Days|Subject)" 406s > fm <- f(form, data=sleepstudy) 408s > lmerTest::ranova(fm) 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ Days + (Days | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > lmerTest::rand(fm) 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ Days + (Days | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > lmerTest::step(fm) 408s Backward reduced random-effect table: 408s 408s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 408s 408s 408s Days in (Days | Subject) *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Backward reduced fixed-effect table: 408s Degrees of freedom method: Satterthwaite 408s 408s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 408s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Model found: 408s Reaction ~ Days + (Days | Subject) 408s > 408s > library(lmerTest) 408s Loading required package: lme4 408s Loading required package: Matrix 408s 408s Attaching package: 'lmerTest' 408s 408s The following object is masked from 'package:lme4': 408s 408s lmer 408s 408s The following object is masked from 'package:stats': 408s 408s step 408s 408s > 408s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 408s > # even in tests: 408s > assertError <- function(expr, ...) 408s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 408s > assertWarning <- function(expr, ...) 408s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 408s > 408s > TOL <- 1e-4 408s > ##################################################################### 408s > data("sleepstudy", package="lme4") 408s > 408s > # Test reduction of (Days | Subject) to (1 | Subject): 408s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 408s > (an <- rand(fm1)) # 2 df test 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ Days + (Days | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > (an <- ranova(fm1)) # 2 df test 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ Days + (Days | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > step(fm1) 408s Backward reduced random-effect table: 408s 408s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 408s 408s 408s Days in (Days | Subject) *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Backward reduced fixed-effect table: 408s Degrees of freedom method: Satterthwaite 408s 408s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 408s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Model found: 408s Reaction ~ Days + (Days | Subject) 408s > stopifnot( 408s + nrow(an) == 2L, 408s + an[2L, "Df"] == 2L 408s + ) 408s > 408s > # This test can also be achieved with anova(): 408s > fm2 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 408s > (stp <- step(fm2)) 408s Backward reduced random-effect table: 408s 408s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 408s 4 -893.23 1794.5 408s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Backward reduced fixed-effect table: 408s Degrees of freedom method: Satterthwaite 408s 408s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 408s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Model found: 408s Reaction ~ Days + (1 | Subject) 408s > get_model(stp) 408s Linear mixed model fit by REML ['lmerModLmerTest'] 408s Formula: Reaction ~ Days + (1 | Subject) 408s Data: sleepstudy 408s REML criterion at convergence: 1786.465 408s Random effects: 408s Groups Name Std.Dev. 408s Subject (Intercept) 37.12 408s Residual 30.99 408s Number of obs: 180, groups: Subject, 18 408s Fixed Effects: 408s (Intercept) Days 408s 251.41 10.47 408s > (ana <- anova(fm1, fm2, refit=FALSE)) 408s Data: sleepstudy 408s Models: 408s fm2: Reaction ~ Days + (1 | Subject) 408s fm1: Reaction ~ Days + (Days | Subject) 408s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 408s fm2 4 1794.5 1807.2 -893.23 1786.5 408s fm1 6 1755.6 1774.8 -871.81 1743.6 42.837 2 4.99e-10 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > 408s > stopifnot( 408s + all.equal(an[2L, "LRT"], ana[2L, "Chisq"], tolerance=TOL) 408s + ) 408s > 408s > # Illustrate complete.test argument: 408s > # Test removal of (Days | Subject): 408s > (an <- ranova(fm1, reduce.terms = FALSE)) # 3 df test 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ Days + (Days | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 6 -871.81 1755.6 408s (Days | Subject) 3 -946.83 1899.7 150.03 3 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > 408s > # The likelihood ratio test statistic is in this case: 408s > fm3 <- lm(Reaction ~ Days, sleepstudy) 408s > LRT <- 2*c(logLik(fm1, REML=TRUE) - logLik(fm3, REML=TRUE)) # LRT 408s > stopifnot( 408s + nrow(an) == 2L, 408s + an[2L, "Df"] == 3L, 408s + all.equal(an[2L, "LRT"], LRT, tolerance=TOL) 408s + ) 408s > 408s > ## _NULL_ model: 408s > fm <- lmer(Reaction ~ -1 + (1|Subject), sleepstudy) 408s > step(fm) 408s Backward reduced random-effect table: 408s 408s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 408s 2 -992.84 1989.7 408s (1 | Subject) 0 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Backward reduced fixed-effect table: 408s Degrees of freedom method: Satterthwaite 408s 408s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 408s 408s Model found: 408s Reaction ~ -1 + (1 | Subject) 408s > ranova(fm) 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ -1 + (1 | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 2 -992.84 1989.7 408s (1 | Subject) 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > lm1 <- lm(Reaction ~ 0, data=sleepstudy) 408s > LRT <- 2*c(logLik(fm, REML=FALSE) - logLik(lm1, REML=FALSE)) 408s > 408s > ## Tests of ML-fits agree with anova(): 408s > fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy, REML=FALSE) 408s > step(fm1) 408s Backward reduced random-effect table: 408s 408s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 408s 4 -897.04 1802.1 408s (1 | Subject) 0 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Backward reduced fixed-effect table: 408s Degrees of freedom method: Satterthwaite 408s 408s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 408s Days 0 162703 162703 1 162 170.45 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Model found: 408s Reaction ~ Days + (1 | Subject) 408s > lm2 <- lm(Reaction ~ Days, sleepstudy) 408s > (an1 <- ranova(fm1)) 408s ANOVA-like table for random-effects: Single term deletions 408s 408s Model: 408s Reaction ~ Days + (1 | Subject) 408s npar logLik AIC LRT Df Pr(>Chisq) 408s 4 -897.04 1802.1 408s (1 | Subject) 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > (an2 <- anova(fm1, lm2)) 408s Data: sleepstudy 408s Models: 408s lm2: Reaction ~ Days 408s fm1: Reaction ~ Days + (1 | Subject) 408s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 408s lm2 3 1906.3 1915.9 -950.15 1900.3 408s fm1 4 1802.1 1814.8 -897.04 1794.1 106.21 1 < 2.2e-16 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s > j <- grep("Chi Df|Df", colnames(an2)) 408s > stopifnot( 408s + all.equal(an1[2, "LRT"], an2[2, "Chisq"], tolerance=TOL), 408s + all.equal(an1[2, "Df"], an2[2, j[length(j)]], tolerance=TOL), 408s + all.equal(an1[1:2, "logLik"], an2[2:1, "logLik"], tolerance=TOL) 408s + ) 408s > ## Note that lme4 version <1.1-22 use "Chi Df" while >=1.1-22 use "Df" 408s > 408s > # Expect warnings when old (version < 3.0-0) arguments are used: 408s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 408s + type=3, fixed.calc = FALSE, lsmeans.calc = FALSE, 408s + difflsmeans.calc = TRUE, test.effs = 42, keep.e="save")) 408s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 408s + lsmeans=3)) 408s > 408s > 408s > check_nrow <- function(obj, expect_nrow) { 408s + stopifnot( 408s + is.numeric(expect_nrow), 408s + nrow(obj) == expect_nrow 408s + ) 408s + } 408s > 408s > # Statistical nonsense, but it works: 408s > fm1 <- lmer(Reaction ~ Days + (1 | Subject) + (0 + Days|Subject), sleepstudy) 408s > step(fm1) 408s Backward reduced random-effect table: 408s 408s Eliminated npar logLik AIC LRT Df 408s 5 -871.83 1753.7 408s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 408s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 408s Pr(>Chisq) 408s 408s (1 | Subject) 1.746e-06 *** 408s Days in (0 + Days | Subject) 6.076e-11 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Backward reduced fixed-effect table: 408s Degrees of freedom method: Satterthwaite 408s 408s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 408s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 408s --- 408s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 408s 408s Model found: 408s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 408s > (an <- ranova(fm1)) 409s ANOVA-like table for random-effects: Single term deletions 409s 409s Model: 409s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 409s npar logLik AIC LRT Df Pr(>Chisq) 409s 5 -871.83 1753.7 409s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 409s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s > check_nrow(an, 3) 409s > ranova(fm1, reduce.terms = FALSE) 409s ANOVA-like table for random-effects: Single term deletions 409s 409s Model: 409s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 409s npar logLik AIC LRT Df Pr(>Chisq) 409s 5 -871.83 1753.7 409s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 409s (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s > 409s > # Statistical nonsense, but it works: 409s > fm1 <- lmer(Reaction ~ Days + (0 + Days|Subject), sleepstudy) 409s > step(fm1) 409s Backward reduced random-effect table: 409s 409s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 409s 4 -883.26 1774.5 409s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 409s 409s Backward reduced fixed-effect table: 409s Degrees of freedom method: Satterthwaite 409s 409s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 409s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s 409s Model found: 409s Reaction ~ Days + (0 + Days | Subject) 409s > (an <- ranova(fm1)) # no test of non-nested models 409s ANOVA-like table for random-effects: Single term deletions 409s 409s Model: 409s Reaction ~ Days + (0 + Days | Subject) 409s npar logLik AIC LRT Df Pr(>Chisq) 409s 4 -883.26 1774.5 409s Days in (0 + Days | Subject) 4 -893.23 1794.5 19.94 0 409s > stopifnot( 409s + nrow(an) == 2L, 409s + an[2L, "Df"] == 0, 409s + all(is.na(an[2L, "Pr(>Chisq)"])) 409s + ) 409s > fm0 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 409s > step(fm0) 409s Backward reduced random-effect table: 409s 409s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 409s 4 -893.23 1794.5 409s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s 409s Backward reduced fixed-effect table: 409s Degrees of freedom method: Satterthwaite 409s 409s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 409s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s 409s Model found: 409s Reaction ~ Days + (1 | Subject) 409s > (an2 <- anova(fm1, fm0, refit=FALSE)) 409s Data: sleepstudy 409s Models: 409s fm1: Reaction ~ Days + (0 + Days | Subject) 409s fm0: Reaction ~ Days + (1 | Subject) 409s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 409s fm1 4 1774.5 1787.3 -883.26 1766.5 409s fm0 4 1794.5 1807.2 -893.23 1786.5 0 0 409s > stopifnot( 409s + (packageVersion("lme4")<="1.1.23" && an2[2L, "Pr(>Chisq)"] == 1) || 409s + is.na(an2[2L, "Pr(>Chisq)"]) 409s + ) 409s > ranova(fm1, reduce.terms = FALSE) 409s ANOVA-like table for random-effects: Single term deletions 409s 409s Model: 409s Reaction ~ Days + (0 + Days | Subject) 409s npar logLik AIC LRT Df Pr(>Chisq) 409s 4 -883.26 1774.5 409s (0 + Days | Subject) 3 -946.83 1899.7 127.14 1 < 2.2e-16 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s > 409s > fm1 <- lmer(Reaction ~ Days + (-1 + Days|Subject), sleepstudy) 409s > step(fm1) 409s Backward reduced random-effect table: 409s 409s Eliminated npar logLik AIC LRT Df 409s 4 -883.26 1774.5 409s Days in (-1 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 409s Pr(>Chisq) 409s 409s Days in (-1 + Days | Subject) 409s 409s Backward reduced fixed-effect table: 409s Degrees of freedom method: Satterthwaite 409s 409s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 409s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s 409s Model found: 409s Reaction ~ Days + (-1 + Days | Subject) 409s > (an3 <- ranova(fm1)) # no test of non-nested models 409s ANOVA-like table for random-effects: Single term deletions 409s 409s Model: 409s Reaction ~ Days + (-1 + Days | Subject) 409s npar logLik AIC LRT Df Pr(>Chisq) 409s 4 -883.26 1774.5 409s Days in (-1 + Days | Subject) 4 -893.23 1794.5 19.94 0 409s > stopifnot( 409s + all.equal(an, an3, check.attributes=FALSE, tolerance=TOL) 409s + ) 409s > 409s > # Example where comparison of non-nested models is generated 409s > fm <- lmer(Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject), sleepstudy) 409s boundary (singular) fit: see help('isSingular') 409s > step(fm) 409s Backward reduced random-effect table: 409s 409s Eliminated npar logLik AIC 409s 7 -937.05 1888.1 409s poly(Days, 2) in (0 + poly(Days, 2) | Subject) 1 5 -884.67 1779.3 409s (1 | Subject) 0 4 -938.16 1884.3 409s LRT Df Pr(>Chisq) 409s 409s poly(Days, 2) in (0 + poly(Days, 2) | Subject) -104.77 2 1 409s (1 | Subject) 106.98 1 <2e-16 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s 409s Backward reduced fixed-effect table: 409s Degrees of freedom method: Satterthwaite 409s 409s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 409s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 409s --- 409s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 409s 409s Model found: 409s Reaction ~ poly(Days, 2) + (1 | Subject) 409s > an <- ranova(fm) 409s > stopifnot( 409s + nrow(an) == 2L, 409s + an[2, "Pr(>Chisq)"] == 1 409s + ) 409s > ranova(fm, reduce.terms = FALSE) # test of nested models 409s ANOVA-like table for random-effects: Single term deletions 409s 409s Model: 409s Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject) 409s npar logLik AIC LRT Df Pr(>Chisq) 409s 7 -937.05 1888.1 409s (0 + poly(Days, 2) | Subject) 4 -938.16 1884.3 2.2153 3 0.5289 409s > 409s > # These models are nested, though: 409s > fm <- lmer(Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject), sleepstudy) 409s > step(fm) 410s Backward reduced random-effect table: 410s 410s Eliminated npar logLik AIC 410s 10 -856.40 1732.8 410s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 0 5 -884.67 1779.3 410s LRT Df Pr(>Chisq) 410s 410s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 56.524 5 6.338e-11 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Backward reduced fixed-effect table: 410s Degrees of freedom method: Satterthwaite 410s 410s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 410s poly(Days, 2) 0 24212 12106 2 16.999 23.364 1.325e-05 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Model found: 410s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 410s > ranova(fm) 410s ANOVA-like table for random-effects: Single term deletions 410s 410s Model: 410s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 410s npar logLik AIC LRT Df 410s 10 -856.40 1732.8 410s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 5 -884.67 1779.3 56.524 5 410s Pr(>Chisq) 410s 410s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 6.338e-11 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s > fm0 <- lmer(Reaction ~ poly(Days, 2) + (1 | Subject), sleepstudy) 410s > step(fm0) 410s Backward reduced random-effect table: 410s 410s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 410s 5 -884.67 1779.3 410s (1 | Subject) 0 4 -938.16 1884.3 106.98 1 < 2.2e-16 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Backward reduced fixed-effect table: 410s Degrees of freedom method: Satterthwaite 410s 410s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 410s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Model found: 410s Reaction ~ poly(Days, 2) + (1 | Subject) 410s > anova(fm0, fm, refit=FALSE) 410s Data: sleepstudy 410s Models: 410s fm0: Reaction ~ poly(Days, 2) + (1 | Subject) 410s fm: Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 410s npar AIC BIC logLik -2*log(L) Chisq Df Pr(>Chisq) 410s fm0 5 1779.3 1795.3 -884.67 1769.3 410s fm 10 1732.8 1764.7 -856.40 1712.8 56.524 5 6.338e-11 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s > ranova(fm, reduce.terms = FALSE) 410s ANOVA-like table for random-effects: Single term deletions 410s 410s Model: 410s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 410s npar logLik AIC LRT Df Pr(>Chisq) 410s 10 -856.40 1732.8 410s (1 + poly(Days, 2) | Subject) 4 -938.16 1884.3 163.51 6 < 2.2e-16 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s > 410s > # A model with ||-notation: 410s > fm1 <- lmer(Reaction ~ Days + (Days||Subject), sleepstudy) 410s > step(fm1) 410s Backward reduced random-effect table: 410s 410s Eliminated npar logLik AIC LRT Df 410s 5 -871.83 1753.7 410s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 410s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 410s Pr(>Chisq) 410s 410s (1 | Subject) 1.746e-06 *** 410s Days in (0 + Days | Subject) 6.076e-11 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Backward reduced fixed-effect table: 410s Degrees of freedom method: Satterthwaite 410s 410s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 410s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Model found: 410s Reaction ~ Days + ((1 | Subject) + (0 + Days | Subject)) 410s > ranova(fm1) 410s ANOVA-like table for random-effects: Single term deletions 410s 410s Model: 410s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 410s npar logLik AIC LRT Df Pr(>Chisq) 410s 5 -871.83 1753.7 410s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 410s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s > 410s > # What about models with nested factors? 410s > fm <- lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), 410s + data=TVbo) 410s > step(fm) 410s Backward reduced random-effect table: 410s 410s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 410s 15 -280.22 590.44 410s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 410s (1 | Assessor:TVset) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Backward reduced fixed-effect table: 410s Degrees of freedom method: Satterthwaite 410s 410s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 410s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Model found: 410s Coloursaturation ~ TVset + Picture + (1 | Assessor:TVset) + TVset:Picture 410s > (an1 <- ranova(fm)) 410s ANOVA-like table for random-effects: Single term deletions 410s 410s Model: 410s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 410s npar logLik AIC LRT Df Pr(>Chisq) 410s 15 -280.22 590.44 410s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 410s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s > 410s > fm <- lmer(Coloursaturation ~ TVset * Picture + 410s + (1|Assessor/TVset), data=TVbo) 410s > step(fm) 410s Backward reduced random-effect table: 410s 410s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 410s 15 -280.22 590.44 410s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 410s (1 | TVset:Assessor) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Backward reduced fixed-effect table: 410s Degrees of freedom method: Satterthwaite 410s 410s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 410s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 410s --- 410s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 410s 410s Model found: 410s Coloursaturation ~ TVset + Picture + (1 | TVset:Assessor) + TVset:Picture 410s > (an2 <- ranova(fm)) 411s ANOVA-like table for random-effects: Single term deletions 411s 411s Model: 411s Coloursaturation ~ TVset * Picture + (1 | TVset:Assessor) + (1 | Assessor) 411s npar logLik AIC LRT Df Pr(>Chisq) 411s 15 -280.22 590.44 411s (1 | TVset:Assessor) 14 -302.61 633.22 44.777 1 2.208e-11 *** 411s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 411s --- 411s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 411s > stopifnot( 411s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL) 411s + ) 411s > 411s > ##################################################################### 411s > # Test evaluation within functions, i.e. in other environments etc. 411s > attach(sleepstudy) 411s > fm <- lmer(Reaction ~ Days + (Days|Subject)) 411s > step(fm) 411s Backward reduced random-effect table: 411s 411s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 411s 6 -871.81 1755.6 411s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 411s 411s 411s Days in (Days | Subject) *** 411s --- 411s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 411s 411s Backward reduced fixed-effect table: 411s Degrees of freedom method: Satterthwaite 411s 411s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 411s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 411s --- 411s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 411s 411s Model found: 411s Reaction ~ Days + (Days | Subject) 411s > ranova(fm) # OK 411s ANOVA-like table for random-effects: Single term deletions 411s 411s Model: 411s Reaction ~ Days + (Days | Subject) 411s npar logLik AIC LRT Df Pr(>Chisq) 411s 6 -871.81 1755.6 411s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 411s --- 411s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 411s > detach(sleepstudy) 411s > 411s > # Evaluating in a function works: 411s > f <- function(form, data) lmer(form, data=data) 411s > form <- "Informed.liking ~ Product+Information+ 411s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 411s > fm <- f(form, data=ham) 411s > ranova(fm) 411s boundary (singular) fit: see help('isSingular') 411s ANOVA-like table for random-effects: Single term deletions 411s 411s Model: 411s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 411s npar logLik AIC LRT Df Pr(>Chisq) 411s 9 -1353.9 2725.8 411s (1 | Consumer) 8 -1355.1 2726.1 2.295 1 0.1298 411s (1 | Product:Consumer) 8 -1436.3 2888.6 164.753 1 <2e-16 *** 411s (1 | Information:Consumer) 8 -1354.5 2725.1 1.255 1 0.2626 411s --- 411s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 411s > step_res <- step(fm) 411s boundary (singular) fit: see help('isSingular') 412s > stopifnot( 412s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 412s + colnames(step_res$fixed)) 412s + ) 412s > 412s > ########################### 412s > # Evaluation in function without the formula: 412s > # Reported by Uwe Ligges 2025-01-16. 412s > f <- function(data) { 412s + lmer(Petal.Length ~ Sepal.Length + (1|Species), data=data) 412s + } 412s > 412s > res <- f(iris) 412s > ranova(res) # used to fail - now it works 412s ANOVA-like table for random-effects: Single term deletions 412s 412s Model: 412s Petal.Length ~ Sepal.Length + (1 | Species) 412s npar logLik AIC LRT Df Pr(>Chisq) 412s 4 -34.66 77.32 412s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 412s --- 412s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 412s > 412s > data <- iris 412s > ranova(res) # now it works 412s ANOVA-like table for random-effects: Single term deletions 412s 412s Model: 412s Petal.Length ~ Sepal.Length + (1 | Species) 412s npar logLik AIC LRT Df Pr(>Chisq) 412s 4 -34.66 77.32 412s (1 | Species) 3 -193.84 393.68 318.36 1 < 2.2e-16 *** 412s --- 412s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 412s > ########################### 412s > # Evaluation in function without the formula(2): 412s > # A model with ||-notation: 412s > f2 <- function(data) { 412s + lmer(Reaction ~ Days + (Days||Subject), data) 412s + } 412s > res <- f2(sleepstudy) 412s > ranova(res) 412s ANOVA-like table for random-effects: Single term deletions 412s 412s Model: 412s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 412s npar logLik AIC LRT Df Pr(>Chisq) 412s 5 -871.83 1753.7 412s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 412s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 412s --- 412s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 412s > 412s > # A model with multiple RE terms: 412s > f3 <- function(data) { 412s + lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), data) 412s + } 412s > res <- f3(TVbo) 412s > ranova(res) 412s ANOVA-like table for random-effects: Single term deletions 412s 412s Model: 412s Coloursaturation ~ TVset * Picture + (1 | Assessor:TVset) + (1 | Assessor) 412s npar logLik AIC LRT Df Pr(>Chisq) 412s 15 -280.22 590.44 412s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 412s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 412s --- 412s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 412s > ########################### 412s > 412s > # Check that step works when form is a character vector 412s > m <- lmer(form, data=ham) 412s > step_res <- step(m) 412s boundary (singular) fit: see help('isSingular') 413s > (drop1_table <- attr(step_res, "drop1")) 413s Single term deletions using Satterthwaite's method: 413s 413s Model: 413s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 413s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 413s Product 19.3466 6.4489 3 240 3.8291 0.01048 * 413s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 413s --- 413s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 413s > stopifnot( 413s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 413s + colnames(drop1_table)) 413s + ) 413s > # In version < 3.0-1.9002 attr(step_res, "drop1") picked up lme4::drop1.merMod 413s > # and returned an AIC table after the model had been update'd. 413s > 413s > ##################################################################### 413s > # Model with 2 ranef covarites: 413s > 413s > # Model of the form (x1 + x2 | gr): 413s > model <- lmer(Preference ~ sens2 + Homesize + (sens1 + sens2 | Consumer) 413s + , data=carrots) 413s boundary (singular) fit: see help('isSingular') 413s Warning message: 413s Model failed to converge with 1 negative eigenvalue: -3.1e+02 413s > step(model) 413s boundary (singular) fit: see help('isSingular') 413s Backward reduced random-effect table: 413s 413s Eliminated npar logLik AIC LRT Df 413s 10 -1874.4 3768.8 413s sens1 in (sens1 + sens2 | Consumer) 1 7 -1874.5 3762.9 0.1333 3 413s sens2 in (sens2 | Consumer) 0 5 -1878.0 3765.9 6.9944 2 413s Pr(>Chisq) 413s 413s sens1 in (sens1 + sens2 | Consumer) 0.98757 413s sens2 in (sens2 | Consumer) 0.03028 * 413s --- 413s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 413s 413s Backward reduced fixed-effect table: 413s Degrees of freedom method: Satterthwaite 413s 413s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 413s sens2 0 58.685 58.685 1 102.02 54.8236 3.888e-11 *** 413s Homesize 0 5.979 5.979 1 100.95 5.5852 0.02003 * 413s --- 413s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 413s 413s Model found: 413s Preference ~ sens2 + Homesize + (sens2 | Consumer) 413s > stopifnot( 413s + nrow(ranova(model)) == 3L, 413s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 413s + ) 413s boundary (singular) fit: see help('isSingular') 413s > 413s > # Model of the form (f1 + f2 | gr): 413s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 413s + (Gender+Homesize|Consumer), data=carrots) 413s boundary (singular) fit: see help('isSingular') 414s > step(model) 414s Backward reduced random-effect table: 414s 414s Eliminated npar logLik AIC LRT 414s 11 -1872.3 3766.5 414s Gender in (Gender + Homesize | Consumer) 1 8 -1875.1 3766.3 5.7408 414s Homesize in (Homesize | Consumer) Warning messages: 414s 0 6 -1878.4 3768.7 6.4705 414s Df Pr(>Chisq) 414s 414s Gender in (Gender + Homesize | Consumer) 3 0.12493 414s Homesize in (Homesize | Consumer) 2 0.03935 * 414s --- 414s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 414s 414s Backward reduced fixed-effect table: 414s Degrees of freedom method: Satterthwaite 414s 414s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 414s Gender 1 0.632 0.632 1 91.80 0.5686 0.45275 414s sens2 0 83.385 83.385 1 1129.09 75.0490 < 2e-16 *** 414s Homesize 0 6.212 6.212 1 97.82 5.5910 0.02003 * 414s --- 414s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 414s 414s Model found: 414s Preference ~ sens2 + Homesize + (Homesize | Consumer) 414s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 414s unable to evaluate scaled gradient 414s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 414s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 414s See ?lme4::convergence and ?lme4::troubleshooting. 414s 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 414s unable to evaluate scaled gradient 414s 4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 414s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 414s See ?lme4::convergence and ?lme4::troubleshooting. 414s 5: Model failed to converge with 1 negative eigenvalue: -2.7e-04 414s > stopifnot( 414s + nrow(ranova(model)) == 3L, 414s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 414s + ) 414s > 414s > # Model of the form (-1 + f2 | gr): 414s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 414s + (Gender -1 |Consumer), data=carrots) 414s Warning messages: 414s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 414s unable to evaluate scaled gradient 414s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 414s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 414s See ?lme4::convergence and ?lme4::troubleshooting. 414s Warning message: 414s Model failed to converge with 1 negative eigenvalue: -2.0e-03 414s > step(model) 414s Backward reduced random-effect table: 414s 414s Eliminated npar logLik AIC LRT Df 414s 8 -1876.4 3768.9 414s Gender in (Gender - 1 | Consumer) 1 6 -1878.4 3768.7 3.863 2 414s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 414s Pr(>Chisq) 414s 414s Gender in (Gender - 1 | Consumer) 0.145 414s (1 | Consumer) <2e-16 *** 414s --- 414s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 414s 414s Backward reduced fixed-effect table: 414s Degrees of freedom method: Satterthwaite 414s 414s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 414s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 414s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 414s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 414s --- 414s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 414s 414s Model found: 414s Preference ~ sens2 + Homesize + (1 | Consumer) 414s > an1 <- ranova(model) 415s > an1b <- ranova(model, reduce.terms = FALSE) 415s > 415s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 415s + (0 + Gender|Consumer), data=carrots) 415s Warning message: 415s Model failed to converge with 1 negative eigenvalue: -2.0e-03 415s > step(model) 415s Backward reduced random-effect table: 415s 415s Eliminated npar logLik AIC LRT Df 415s 8 -1876.4 3768.9 415s Gender in (0 + Gender | Consumer) 1 6 -1878.4 3768.7 3.863 2 415s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 415s Pr(>Chisq) 415s 415s Gender in (0 + Gender | Consumer) 0.145 415s (1 | Consumer) <2e-16 *** 415s --- 415s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 415s 415s Backward reduced fixed-effect table: 415s Degrees of freedom method: Satterthwaite 415s 415s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 415s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 415s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 415s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 415s --- 415s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 415s 415s Model found: 415s Preference ~ sens2 + Homesize + (1 | Consumer) 415s > an2 <- ranova(model) 415s > an2b <- ranova(model, reduce.terms = FALSE) 415s > 415s > stopifnot( 415s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL), 415s + all.equal(an1b, an2b, check.attributes=FALSE, tolerance=TOL) 415s + ) 415s > 415s > ####### Polynomial terms: 415s > model <- lmer(Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer), 415s + data=carrots) 415s > (an <- ranova(model)) 415s Warning message: 415s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 415s Model failed to converge with max|grad| = 0.00377852 (tol = 0.002, component 1) 415s See ?lme4::convergence and ?lme4::troubleshooting. 415s ANOVA-like table for random-effects: Single term deletions 415s 415s Model: 415s Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer) 415s npar logLik AIC LRT Df 415s 10 -1874.1 3768.2 415s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 5 -1879.9 3769.7 11.551 5 415s Pr(>Chisq) 415s 415s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0.04148 * 415s --- 415s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 415s > step(model) 416s Backward reduced random-effect table: 416s 416s Eliminated npar logLik AIC 416s 10 -1874.1 3768.2 416s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0 5 -1879.9 3769.7 416s LRT Df Pr(>Chisq) 416s 416s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 11.551 5 0.04148 * 416s --- 416s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 416s 416s Backward reduced fixed-effect table: 416s Degrees of freedom method: Satterthwaite 416s 416s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 416s Gender 1 1.188 1.188 1 101.02 1.1264 0.2911 416s sens2 0 53.452 53.452 1 114.59 50.6805 1.017e-10 *** 416s --- 416s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 416s 416s Model found: 416s Preference ~ sens2 + (poly(sens2, 2) | Consumer) 416s > 416s > model <- lmer(Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer), 416s + data=carrots) 416s boundary (singular) fit: see help('isSingular') 416s > (an2 <- ranova(model)) 416s boundary (singular) fit: see help('isSingular') 416s ANOVA-like table for random-effects: Single term deletions 416s 416s Model: 416s Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer) 416s npar logLik AIC LRT Df 416s 10 -1874.1 3768.2 416s sens2 in (sens2 + I(sens2^2) | Consumer) 7 -1879.8 3773.5 11.3667 3 416s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 7 -1876.5 3767.0 4.8784 3 416s Pr(>Chisq) 416s 416s sens2 in (sens2 + I(sens2^2) | Consumer) 0.0099 ** 416s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 0.1809 416s --- 416s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 416s > step(model) 416s boundary (singular) fit: see help('isSingular') 417s Backward reduced random-effect table: 417s 417s Eliminated npar logLik AIC 417s 10 -1874.1 3768.2 417s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 1 7 -1876.5 3767.0 417s sens2 in (sens2 | Consumer) 0 5 -1879.9 3769.7 417s LRT Df Pr(>Chisq) 417s 417s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 4.8784 3 0.18092 417s sens2 in (sens2 | Consumer) 6.6735 2 0.03555 * 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Backward reduced fixed-effect table: 417s Degrees of freedom method: Satterthwaite 417s 417s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 417s Gender 1 1.211 1.211 1 101.02 1.1309 0.2901 417s sens2 0 58.688 58.688 1 102.01 54.8276 3.883e-11 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Model found: 417s Preference ~ sens2 + (sens2 | Consumer) 417s > stopifnot( 417s + nrow(an) == 2L, 417s + an[2L, "Df"] == 5L, 417s + nrow(an2) == 3L, 417s + all(an2[2:3, "Df"] == 3L) 417s + ) 417s > 417s > ######## Functions of terms in random effects: 417s > model <- lmer(Preference ~ sens2 + Gender + (log(10+sens2) | Consumer), 417s + data=carrots) 417s > ranova(model) # Works 417s ANOVA-like table for random-effects: Single term deletions 417s 417s Model: 417s Preference ~ sens2 + Gender + (log(10 + sens2) | Consumer) 417s npar logLik AIC LRT Df 417s 7 -1875.3 3764.6 417s log(10 + sens2) in (log(10 + sens2) | Consumer) 5 -1879.9 3769.7 9.0854 2 417s Pr(>Chisq) 417s 417s log(10 + sens2) in (log(10 + sens2) | Consumer) 0.01064 * 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s > step(model) 417s Backward reduced random-effect table: 417s 417s Eliminated npar logLik AIC 417s 7 -1875.3 3764.6 417s log(10 + sens2) in (log(10 + sens2) | Consumer) 0 5 -1879.9 3769.7 417s LRT Df Pr(>Chisq) 417s 417s log(10 + sens2) in (log(10 + sens2) | Consumer) 9.0854 2 0.01064 * 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Backward reduced fixed-effect table: 417s Degrees of freedom method: Satterthwaite 417s 417s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 417s Gender 1 1.200 1.200 1 101.02 1.1295 0.2904 417s sens2 0 54.185 54.185 1 109.20 51.0018 1.083e-10 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Model found: 417s Preference ~ sens2 + (log(10 + sens2) | Consumer) 417s > 417s > ##################################################################### 417s > 417s > # Missing values changes the number of observations in use: 417s > m <- lmer(Preference ~ sens2 + Homesize + 417s + (1 |Consumer:Income), data=carrots) 417s > assertError(step(m)) 417s > ans <- try(ranova(m), silent = TRUE) 417s > stopifnot( 417s + inherits(ans, "try-error"), 417s + grepl("number of rows in use has changed", ans) 417s + ) 417s > 417s > ## Removing missing values solves the problem: 417s > m2 <- lmer(Preference ~ sens2 + Homesize + 417s + (1 |Consumer:Income), data=carrots[complete.cases(carrots), ]) 417s > ranova(m2) # Works 417s ANOVA-like table for random-effects: Single term deletions 417s 417s Model: 417s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 417s npar logLik AIC LRT Df Pr(>Chisq) 417s 5 -1752.0 3513.9 417s (1 | Consumer:Income) 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s > step(m2) 417s Backward reduced random-effect table: 417s 417s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 417s 5 -1752.0 3513.9 417s (1 | Consumer:Income) 0 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Backward reduced fixed-effect table: 417s Degrees of freedom method: Satterthwaite 417s 417s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 417s sens2 0 77.308 77.308 1 1058.49 69.7915 < 2.2e-16 *** 417s Homesize 0 8.569 8.569 1 95.23 7.7355 0.006527 ** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s 417s Model found: 417s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 417s > 417s > ## Including the variable with missing values (Income) among the fixed effects 417s > ## also solves the problem: 417s > m <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 417s + (1 |Consumer:Income), data=carrots) 417s > ranova(m) 417s ANOVA-like table for random-effects: Single term deletions 417s 417s Model: 417s Preference ~ sens2 + Homesize + Income + (1 | Consumer:Income) 417s npar logLik AIC LRT Df Pr(>Chisq) 417s 8 -1766.0 3547.9 417s (1 | Consumer:Income) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 417s --- 417s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 417s > step(m) 418s Backward reduced random-effect table: 418s 418s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 418s 8 -1766.0 3547.9 418s (1 | Consumer:Income) 0 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 418s --- 418s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 418s 418s Backward reduced fixed-effect table: 418s Degrees of freedom method: Satterthwaite 418s 418s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 418s Income 1 3.567 1.189 3 91.92 1.0627 0.368918 418s sens2 0 78.191 78.191 1 1062.96 69.8919 < 2.2e-16 *** 418s Homesize 0 7.983 7.983 1 94.93 7.1355 0.008894 ** 418s --- 418s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 418s 418s Model found: 418s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 418s > 418s > # Missing values in a an insignificant fixed effect causes the an error in step: 418s > m0 <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 418s + (1 |Consumer), data=carrots) 418s > ranova(m0) 418s ANOVA-like table for random-effects: Single term deletions 418s 418s Model: 418s Preference ~ sens2 + Homesize + Income + (1 | Consumer) 418s npar logLik AIC LRT Df Pr(>Chisq) 418s 8 -1766.0 3547.9 418s (1 | Consumer) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 418s --- 418s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 418s > ans <- try(step(m0), silent = TRUE) 418s > stopifnot( 418s + inherits(ans, "try-error"), 418s + grepl("number of rows in use has changed", ans) 418s + ) 418s > 418s > # Check that step still works for linear models (etc.) 418s > flm <- lm(Coloursaturation ~ TVset * Picture, data=TVbo) 418s > res <- step(flm, trace=0) 418s > stopifnot( 418s + inherits(res, "lm") 418s + ) 418s > 418s > ##################### Using reduce and keep args: 418s > # Fit a model to the ham dataset: 418s > m <- lmer(Informed.liking ~ Product*Information+ 418s + (1|Consumer) + (1|Product:Consumer) 418s + + (1|Information:Consumer), data=ham) 418s > 418s > # Backward elimination using terms with default alpha-levels: 418s > (step_res <- step(m)) 418s boundary (singular) fit: see help('isSingular') 418s Backward reduced random-effect table: 418s 418s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 418s 12 -1352.0 2728.1 418s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 418s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 418s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 418s 418s 418s (1 | Information:Consumer) 418s (1 | Consumer) . 418s (1 | Product:Consumer) *** 418s --- 418s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 418s 418s Backward reduced fixed-effect table: 418s Degrees of freedom method: Satterthwaite 418s 418s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 418s Product:Information 1 10.3873 3.4624 3 320 2.0765 0.10321 418s Product 0 19.3466 6.4489 3 240 3.8291 0.01048 * 418s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 418s --- 418s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 418s 418s Model found: 418s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 418s > 418s > (step_res <- step(m, reduce.random = FALSE)) 419s boundary (singular) fit: see help('isSingular') 419s Backward reduced random-effect table: 419s 419s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 419s 12 -1352.0 2728.1 419s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 419s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 419s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 419s 419s 419s (1 | Consumer) 419s (1 | Product:Consumer) *** 419s (1 | Information:Consumer) 419s --- 419s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 419s 419s Backward reduced fixed-effect table: 419s Degrees of freedom method: Satterthwaite 419s 419s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 419s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 419s Information 2 5.3335 5.3335 1 80 3.3414 0.07129 . 419s Product 0 18.3361 6.1120 3 240 3.8291 0.01048 * 419s --- 419s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 419s 419s Model found: 419s Informed.liking ~ Product + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 419s > (step_res <- step(m, reduce.fixed = FALSE)) 419s boundary (singular) fit: see help('isSingular') 419s Backward reduced random-effect table: 419s 419s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 419s 12 -1352.0 2728.1 419s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 419s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 419s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 419s 419s 419s (1 | Information:Consumer) 419s (1 | Consumer) . 419s (1 | Product:Consumer) *** 419s --- 419s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 419s 419s Backward reduced fixed-effect table: 419s Degrees of freedom method: Satterthwaite 419s 419s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 419s Product:Information 0 10.387 3.4624 3 320 2.0765 0.1032 419s 419s Model found: 419s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + Product:Information 419s > (step_res <- step(m, reduce.fixed = FALSE, reduce.random = FALSE)) 420s boundary (singular) fit: see help('isSingular') 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 12 -1352.0 2728.1 420s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 420s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 420s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 420s 420s 420s (1 | Consumer) 420s (1 | Product:Consumer) *** 420s (1 | Information:Consumer) 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 420s > 420s > (step_res <- step(m, reduce.random = FALSE, keep="Information")) 420s boundary (singular) fit: see help('isSingular') 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 12 -1352.0 2728.1 420s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 420s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 420s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 420s 420s 420s (1 | Consumer) 420s (1 | Product:Consumer) *** 420s (1 | Information:Consumer) 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 420s Product 0 18.3363 6.1121 3 240 3.8292 0.01048 * 420s Information 0 5.3335 5.3335 1 80 3.3414 0.07129 . 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 420s > (step_res <- step(m, reduce.random = FALSE, keep="Product:Information")) 420s boundary (singular) fit: see help('isSingular') 420s Backward reduced random-effect table: 420s 420s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 420s 12 -1352.0 2728.1 420s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 420s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 420s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 420s 420s 420s (1 | Consumer) 420s (1 | Product:Consumer) *** 420s (1 | Information:Consumer) 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Backward reduced fixed-effect table: 420s Degrees of freedom method: Satterthwaite 420s 420s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 420s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 420s --- 420s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 420s 420s Model found: 420s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 420s > 420s > 420s > ########################### 420s > ## Test that `step` works even if all random terms are reduced away: 420s > set.seed(101) 420s > test <- data.frame(TM = factor(rep(rep(c("org","min"),each=3),3)), 420s + dep = runif(18,0,20), 420s + ind = runif(18,0,7), 420s + dorp = factor(rep(1:3,each=6))) 420s > full.model <- lmer(dep ~ TM + ind + (1 | dorp), data=test) 420s > res <- step(full.model) 420s > # res$random 420s > # res$fixed 420s > # attr(res, "model") 420s > # attr(res, "drop1") 420s > 420s > 420s > 420s BEGIN TEST test_re_covar_structures.R 420s 420s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 420s Copyright (C) 2025 The R Foundation for Statistical Computing 420s Platform: powerpc64le-unknown-linux-gnu 420s 420s R is free software and comes with ABSOLUTELY NO WARRANTY. 420s You are welcome to redistribute it under certain conditions. 420s Type 'license()' or 'licence()' for distribution details. 420s 420s R is a collaborative project with many contributors. 420s Type 'contributors()' for more information and 420s 'citation()' on how to cite R or R packages in publications. 420s 420s Type 'demo()' for some demos, 'help()' for on-line help, or 420s 'help.start()' for an HTML browser interface to help. 420s Type 'q()' to quit R. 420s 421s > # test_re_covar_structure.R 421s > library(lmerTest) 421s Loading required package: lme4 421s Loading required package: Matrix 423s 423s Attaching package: 'lmerTest' 423s 423s The following object is masked from 'package:lme4': 423s 423s lmer 423s 423s > 423s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 423s > # even in tests: 423s > assertError <- function(expr, ...) 423s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 423s The following object is masked from 'package:stats': 423s 423s step 423s 423s > assertWarning <- function(expr, ...) 423s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 423s > 423s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 423s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 423s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 423s > 423s > data("sleepstudy", package="lme4") 423s > TOL <- 1e-4 423s > 423s > #################################### 423s > ## Test that lmerMod objects can be coerced to lmerModLmerTest and 423s > ## that the deviance function can be evaluated with expected results 423s > #################################### 423s > 423s > 423s > #################################### 423s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 423s > ## - simple sleepstudy data (random coefficient) 423s > #################################### 423s > 423s > has_pkgs <- requireNamespace("utils", quietly = TRUE) && 423s + requireNamespace("lme4", quietly = TRUE) && 423s + requireNamespace("pbkrtest", quietly = TRUE) && 423s + getRversion() >= "3.3.3" 423s > is_lme4_2_0_0 <- utils::packageVersion("lme4") >= "2.0.0" 423s > 423s > if(has_pkgs && is_lme4_2_0_0) { 423s + 423s + ## From the examples of ?`Covariance-class`: 423s + ## Unstructured 423s + fm1.us <- lmer(Reaction ~ Days + us(Days | Subject), sleepstudy) 423s + ## Diagional 423s + fm1.diag <- lmer(Reaction ~ Days + diag(Days | Subject), sleepstudy) 423s + fm1.diag.hom <- lmer(Reaction ~ Days + diag(Days | Subject, hom = TRUE), 423s + sleepstudy) 423s + ## Compound symmetry 423s + fm1.cs <- lmer(Reaction ~ Days + cs(1 + Days | Subject), sleepstudy) 423s + fm1.cs.hom <- lmer(Reaction ~ Days + cs(1 + Days | Subject, hom = TRUE), 423s + sleepstudy) 423s + ## Auto-regressive order 1 423s + sleepstudy$Daysf <- factor(sleepstudy$Days, ordered = TRUE) 423s + fm1.ar1 <- lmer(Reaction ~ Daysf + ar1(0 + Daysf | Subject, hom = TRUE), 423s + sleepstudy, REML = TRUE) 423s + 423s + ## Also adding a double-vertical-bar model (though not from 423s + ## 'Covariance-class' examples): 423s + fm1.bv <- lmer(Reaction ~ Days + (Days || Subject), sleepstudy) 423s + 423s + 423s + ltmodels <- namedList(fm1.us, 423s + fm1.diag, 423s + fm1.diag.hom, 423s + fm1.cs, 423s + fm1.cs.hom, 423s + fm1.ar1, 423s + fm1.bv) 423s + ## Run various methods on all models: 423s + for(model in ltmodels) { 423s + # model <- ltmodels[[5]] 423s + print(model) 423s + print(summary(model)) 423s + # model 423s + # summary(model) 423s + L <- diag(c(0, rep(1, length(fixef(model)) -1))) 423s + contest(model, L, joint = TRUE) 423s + contest(model, L[2, ], joint = FALSE) 423s + (an <- anova(model)) ## ddf is Satterthwaite 423s + anova(model, ddf = "Ken") 423s + anova(model, ddf="lme4") 423s + anova(model, type="I") 423s + anova(model, type="II") 423s + anova(model, type="III") 423s + show_tests(an) 423s + drop1(model) 423s + ranova(model) 423s + ranova(model, reduce.terms = FALSE) 423s + step(model) 423s + (lsm <- ls_means(model)) 423s + show_tests(lsm) 423s + (dlsm <- difflsmeans(model)) 423s + show_tests(dlsm) 423s + } 423s + } 423s > 423s > #################################### 423s > ## Basic tests of new (lme4 >= 2.0.0) covariance structure 423s > ## - Unbalanced categorical dataset with multiple RE terms 423s > #################################### 423s > 423s > 423s > 423s > 423s > 423s BEGIN TEST test_summary.R 423s 423s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 423s Copyright (C) 2025 The R Foundation for Statistical Computing 423s Platform: powerpc64le-unknown-linux-gnu 423s 423s R is free software and comes with ABSOLUTELY NO WARRANTY. 423s You are welcome to redistribute it under certain conditions. 423s Type 'license()' or 'licence()' for distribution details. 423s 423s R is a collaborative project with many contributors. 423s Type 'contributors()' for more information and 423s 'citation()' on how to cite R or R packages in publications. 423s 423s Type 'demo()' for some demos, 'help()' for on-line help, or 423s 'help.start()' for an HTML browser interface to help. 423s Type 'q()' to quit R. 423s 423s > # test_summary.R 423s > 423s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 423s > # even in tests: 423s > assertError <- function(expr, ...) 423s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 423s > assertWarning <- function(expr, ...) 423s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 423s > 423s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 423s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 423s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 425s > 425s > library(lmerTest) 425s Loading required package: lme4 425s Loading required package: Matrix 425s 425s Attaching package: 'lmerTest' 425s 425s The following object is masked from 'package:lme4': 425s 425s lmer 425s 425s The following object is masked from 'package:stats': 425s 425s step 425s 425s > 425s > data("sleepstudy", package="lme4") 425s > data("cake", package="lme4") 425s > 425s > # Fit basic model and compute summary: 425s > fm <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) 425s > (sfm <- summary(fm)) 425s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 425s lmerModLmerTest] 425s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 425s Data: sleepstudy 425s 425s REML criterion at convergence: 1743.7 425s 425s Scaled residuals: 425s Min 1Q Median 3Q Max 425s -3.9626 -0.4625 0.0204 0.4653 5.1860 425s 425s Random effects: 425s Groups Name Variance Std.Dev. 425s Subject (Intercept) 627.57 25.051 425s Subject.1 Days 35.86 5.988 425s Residual 653.58 25.565 425s Number of obs: 180, groups: Subject, 18 425s 425s Fixed effects: 425s Estimate Std. Error df t value Pr(>|t|) 425s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 425s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 425s --- 425s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 425s 425s Correlation of Fixed Effects: 425s (Intr) 425s Days -0.184 425s > 425s > ## Test class: 425s > stopifnot(all( 425s + class(sfm) == c("summary.lmerModLmerTest", "summary.merMod"), 425s + all(c("df", "Pr(>|t|)") %in% colnames(coef(sfm))) 425s + )) 425s > stopifnot(class(summary(fm, ddf="lme4")) == "summary.merMod") 425s > 425s > ## Test coefficient table names: 425s > mat <- coef(summary(fm)) 425s > stopifnot(all( # colnames 425s + colnames(mat) == c("Estimate", "Std. Error", "df", "t value", "Pr(>|t|)") 425s + )) 425s > stopifnot(all( # rownames 425s + names(fixef(fm)) == rownames(mat) 425s + )) 425s > 425s > ## Test pass of 'correlation' argument to lme4:::summary.merMod: 425s > x <- capture.output(summary(fm)) 425s > x_nocor <- capture.output(summary(fm, correlation=FALSE)) 425s > txt <- "Correlation of Fixed Effects:" 425s > stopifnot( 425s + any(grep(txt, x)), 425s + !any(grepl(txt, x_nocor)) 425s + ) 425s > 425s > # Test warning with unrecognized arguments (caught by lme4:::summary.merMod): 425s > assertWarning(summary(fm, false_arg=FALSE)) 425s > 425s > ## Test pass of extra arguments to lme4:::print.summary.merMod: 425s > x <- capture.output(print(summary(fm), signif.stars=TRUE)) 425s > x_nocor <- capture.output(print(summary(fm), signif.stars=FALSE)) 425s > txt <- "Signif. codes:" 425s > stopifnot( 425s + any(grep(txt, x)), 425s + !any(grepl(txt, x_nocor)) 425s + ) 425s > 425s > ####### ddf argument: 425s > (an1 <- summary(fm)) # Also testing print method. 425s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 425s lmerModLmerTest] 425s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 425s Data: sleepstudy 425s 425s REML criterion at convergence: 1743.7 425s 425s Scaled residuals: 425s Min 1Q Median 3Q Max 425s -3.9626 -0.4625 0.0204 0.4653 5.1860 425s 425s Random effects: 425s Groups Name Variance Std.Dev. 425s Subject (Intercept) 627.57 25.051 425s Subject.1 Days 35.86 5.988 425s Residual 653.58 25.565 425s Number of obs: 180, groups: Subject, 18 425s 425s Fixed effects: 425s Estimate Std. Error df t value Pr(>|t|) 425s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 425s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 425s --- 425s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 425s 425s Correlation of Fixed Effects: 425s (Intr) 425s Days -0.184 425s > (an2 <- summary(fm, ddf="Satterthwaite")) 425s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 425s lmerModLmerTest] 425s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 425s Data: sleepstudy 425s 425s REML criterion at convergence: 1743.7 425s 425s Scaled residuals: 425s Min 1Q Median 3Q Max 425s -3.9626 -0.4625 0.0204 0.4653 5.1860 425s 425s Random effects: 425s Groups Name Variance Std.Dev. 425s Subject (Intercept) 627.57 25.051 425s Subject.1 Days 35.86 5.988 425s Residual 653.58 25.565 425s Number of obs: 180, groups: Subject, 18 425s 425s Fixed effects: 425s Estimate Std. Error df t value Pr(>|t|) 425s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 425s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 425s --- 425s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 425s 425s Correlation of Fixed Effects: 425s (Intr) 425s Days -0.184 425s > stopifnot(isTRUE( 425s + all.equal(an1, an2) 425s + )) 425s > (an3 <- summary(fm, ddf="Sat")) ## Abbreviated argument 425s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 425s lmerModLmerTest] 425s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 425s Data: sleepstudy 425s 425s REML criterion at convergence: 1743.7 425s 425s Scaled residuals: 425s Min 1Q Median 3Q Max 425s -3.9626 -0.4625 0.0204 0.4653 5.1860 425s 425s Random effects: 425s Groups Name Variance Std.Dev. 425s Subject (Intercept) 627.57 25.051 425s Subject.1 Days 35.86 5.988 425s Residual 653.58 25.565 425s Number of obs: 180, groups: Subject, 18 425s 425s Fixed effects: 425s Estimate Std. Error df t value Pr(>|t|) 425s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 425s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 425s --- 425s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 425s 425s Correlation of Fixed Effects: 425s (Intr) 425s Days -0.184 425s > stopifnot(isTRUE( 425s + all.equal(an1, an3) 425s + )) 425s > (summary(fm, ddf="lme4")) 425s Linear mixed model fit by REML ['lmerMod'] 425s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 425s Data: sleepstudy 425s 425s REML criterion at convergence: 1743.7 425s 425s Scaled residuals: 425s Min 1Q Median 3Q Max 425s -3.9626 -0.4625 0.0204 0.4653 5.1860 425s 425s Random effects: 425s Groups Name Variance Std.Dev. 425s Subject (Intercept) 627.57 25.051 425s Subject.1 Days 35.86 5.988 425s Residual 653.58 25.565 425s Number of obs: 180, groups: Subject, 18 425s 425s Fixed effects: 425s Estimate Std. Error t value 425s (Intercept) 251.405 6.885 36.513 425s Days 10.467 1.560 6.712 425s 425s Correlation of Fixed Effects: 425s (Intr) 425s Days -0.184 425s > if(has_pbkrtest) { 425s + (summary(fm, ddf="Kenward-Roger")) 425s + assertError(summary(fm, ddf="KR")) ## Error on incorrect arg. 425s + } 425s > 425s > ## lme4 method: 425s > an1 <- summary(fm, ddf="lme4") 425s > an2 <- summary(as(fm, "lmerMod")) 425s > stopifnot(isTRUE( 425s + all.equal(an1, an2) 425s + )) 425s > 425s > 425s > # Test printed output 425s > # - Satterthwaite 425s > x <- capture.output(sfm) # equal to output of 'print(sfm)' 425s > txt <- c("lmerModLmerTest", "t-tests use Satterthwaite's method", 425s + "df", "t value", "Pr(>|t|)") 425s > stopifnot(all( 425s + sapply(txt, function(text) any(grepl(text, x))) 425s + )) 425s > 425s > # Test printed output 425s > # - KR 425s > if(has_pbkrtest) { 425s + (sfm <- summary(fm, ddf="Kenward-Roger")) 425s + x <- capture.output(sfm) 425s + txt <- c("lmerModLmerTest", "t-tests use Kenward-Roger's method", 425s + "df", "t value", "Pr(>|t|)") 425s + stopifnot(all( 425s + sapply(txt, function(text) any(grepl(text, x))) 425s + )) 425s + } 425s > 425s > #################################### 425s > ## Test 'boundary' fixef structures: 425s > #################################### 425s > 425s > # Example with no fixef: 425s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 425s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 425s > stopifnot(length(fixef(m)) == 0L) 425s > stopifnot( 425s + nrow(coef(summary(m))) == 0L, 425s + nrow(coef(summary(m, ddf="lme4"))) == 0L 425s + ) 425s > if(has_pbkrtest){ 425s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 0L) 425s + } 425s > 425s > # Example with intercept only: 425s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 426s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 426s > stopifnot(length(fixef(m)) == 1L, 426s + names(fixef(m)) == "(Intercept)") 426s > stopifnot( 426s + nrow(coef(summary(m))) == 1L, 426s + nrow(coef(summary(m, ddf="lme4"))) == 1L 426s + ) 426s > if(has_pbkrtest){ 426s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 1L) 426s + } 426s > 426s > # Example with >1 fixef without intercept: 426s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 426s Warning message: 426s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 426s Model failed to converge with max|grad| = 0.00492394 (tol = 0.002, component 1) 426s See ?lme4::convergence and ?lme4::troubleshooting. 426s > stopifnot(length(fixef(m)) == 2L, 426s + names(fixef(m)) == c("Days", "I(Days^2)")) 426s > stopifnot( 426s + nrow(coef(summary(m))) == 2L, 426s + nrow(coef(summary(m, ddf="lme4"))) == 2L 426s + ) 426s > if(has_pbkrtest){ 426s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 2L) 426s + } 426s > 426s > 426s BEGIN TEST test_zerovar.R 426s 426s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 426s Copyright (C) 2025 The R Foundation for Statistical Computing 426s Platform: powerpc64le-unknown-linux-gnu 426s 426s R is free software and comes with ABSOLUTELY NO WARRANTY. 426s You are welcome to redistribute it under certain conditions. 426s Type 'license()' or 'licence()' for distribution details. 426s 426s R is a collaborative project with many contributors. 426s Type 'contributors()' for more information and 426s 'citation()' on how to cite R or R packages in publications. 426s 426s Type 'demo()' for some demos, 'help()' for on-line help, or 426s 'help.start()' for an HTML browser interface to help. 426s Type 'q()' to quit R. 426s 426s > # test_zerovar.R 426s > 426s > library(lmerTest) 426s Loading required package: lme4 426s Loading required package: Matrix 428s 428s Attaching package: 'lmerTest' 428s 428s The following object is masked from 'package:lme4': 428s 428s lmer 428s 428s The following object is masked from 'package:stats': 428s 428s step 428s 428s > data("sleepstudy", package="lme4") 428s > 428s > # Baseline fit: 428s > m0 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy, 428s + control=lmerControl(optimizer="bobyqa")) 428s > ## default optimizer does not converge proporly 428s > m0 428s Linear mixed model fit by REML ['lmerModLmerTest'] 428s Formula: Reaction ~ Days + (Days | Subject) 428s Data: sleepstudy 428s REML criterion at convergence: 1743.628 428s Random effects: 428s Groups Name Std.Dev. Corr 428s Subject (Intercept) 24.740 428s Days 5.922 0.07 428s Residual 25.592 428s Number of obs: 180, groups: Subject, 18 428s Fixed Effects: 428s (Intercept) Days 428s 251.41 10.47 428s > (an0 <- anova(m0)) 428s Type III Analysis of Variance Table with Satterthwaite's method 428s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 428s Days 30031 30031 1 17 45.853 3.264e-06 *** 428s --- 428s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 428s > 428s > # Make a fit with a zero variance estimate: 428s > n <- nrow(sleepstudy) 428s > g <- factor(rep(1:2, c(n - 10, 10))) 428s > m <- lmer(Reaction ~ Days + (Days | Subject) + (1|g), sleepstudy, 428s + control=lmerControl(optimizer="bobyqa")) 428s boundary (singular) fit: see help('isSingular') 428s > m 428s Linear mixed model fit by REML ['lmerModLmerTest'] 428s Formula: Reaction ~ Days + (Days | Subject) + (1 | g) 428s Data: sleepstudy 428s REML criterion at convergence: 1743.628 428s Random effects: 428s Groups Name Std.Dev. Corr 428s Subject (Intercept) 24.740 428s Days 5.922 0.07 428s g (Intercept) 0.000 428s Residual 25.592 428s Number of obs: 180, groups: Subject, 18; g, 2 428s Fixed Effects: 428s (Intercept) Days 428s 251.41 10.47 428s optimizer (bobyqa) convergence code: 0 (OK) ; 0 optimizer warnings; 1 lme4 warnings 428s > (an <- anova(m)) 428s Type III Analysis of Variance Table with Satterthwaite's method 428s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 428s Days 30031 30031 1 17 45.853 3.264e-06 *** 428s --- 428s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 428s > 428s > # check that fit has a zero variance 428s > vc <- as.data.frame(VarCorr(m)) 428s > stopifnot(isTRUE( 428s + all.equal(0, vc[vc$grp == "g", "sdcor"], tolerance=1e-4) 428s + )) 428s > # The hessian/vcov is actually positive definite: 428s > stopifnot(isTRUE( 428s + all(eigen(m@vcov_varpar, only.values = TRUE)$values > 0) 428s + )) 428s > 428s > # Check that ANOVA tables are the same: 428s > stopifnot(isTRUE( 428s + all.equal(an0[, 1:5], an[, 1:5], tolerance=1e-4) 428s + )) 428s > 428s > stopifnot(isTRUE( # Equality of summary tables 428s + all.equal(coef(summary(m0)), coef(summary(m)), tolerance=1e-4) 428s + )) 428s > stopifnot(isTRUE( # Equality of lme4-anova tables 428s + all.equal(anova(m0, ddf="lme4"), anova(m, ddf="lme4"), tolerance=1e-4) 428s + )) 428s > 428s > 428s BEGIN TEST zlmerTest_zeroDenom.R 428s 428s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 428s Copyright (C) 2025 The R Foundation for Statistical Computing 428s Platform: powerpc64le-unknown-linux-gnu 428s 428s R is free software and comes with ABSOLUTELY NO WARRANTY. 428s You are welcome to redistribute it under certain conditions. 428s Type 'license()' or 'licence()' for distribution details. 428s 428s R is a collaborative project with many contributors. 428s Type 'contributors()' for more information and 428s 'citation()' on how to cite R or R packages in publications. 428s 428s Type 'demo()' for some demos, 'help()' for on-line help, or 428s 'help.start()' for an HTML browser interface to help. 428s Type 'q()' to quit R. 428s 428s > library(lmerTest) 428s Loading required package: lme4 428s Loading required package: Matrix 430s 430s Attaching package: 'lmerTest' 430s 430s The following object is masked from 'package:lme4': 430s 430s lmer 430s 430s The following object is masked from 'package:stats': 430s 430s step 430s 430s > 430s > # Read in data set 430s > load(system.file("testdata","potdata.RData", package="lmerTest")) 430s > 430s > # Mixed model 430s > lmerout <- lmer(biomass ~ CO2*nutrients + (1|chamber),data=potdata) 431s > summary(lmerout) 431s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 431s lmerModLmerTest] 431s Formula: biomass ~ CO2 * nutrients + (1 | chamber) 431s Data: potdata 431s 431s REML criterion at convergence: 49.2 431s 431s Scaled residuals: 431s Min 1Q Median 3Q Max 431s -1.4159 -0.5588 0.0000 0.5588 1.4159 431s 431s Random effects: 431s Groups Name Variance Std.Dev. 431s chamber (Intercept) 0.2437 0.4936 431s Residual 1.5797 1.2568 431s Number of obs: 24, groups: chamber, 4 431s 431s Fixed effects: 431s Estimate Std. Error df t value Pr(>|t|) 431s (Intercept) 12.8500 0.9548 11.0163 13.458 3.49e-08 *** 431s CO2675 2.0000 1.3503 11.0163 1.481 0.166595 431s nutrients2 7.3500 1.2568 10.0000 5.848 0.000162 *** 431s nutrients3 10.4500 1.2568 10.0000 8.314 8.39e-06 *** 431s nutrients4 18.6500 1.2568 10.0000 14.839 3.88e-08 *** 431s nutrients5 25.0500 1.2568 10.0000 19.931 2.22e-09 *** 431s nutrients6 29.0000 1.2568 10.0000 23.074 5.28e-10 *** 431s CO2675:nutrients2 -0.5000 1.7775 10.0000 -0.281 0.784214 431s CO2675:nutrients3 1.9000 1.7775 10.0000 1.069 0.310218 431s CO2675:nutrients4 3.4500 1.7775 10.0000 1.941 0.080949 . 431s CO2675:nutrients5 5.9000 1.7775 10.0000 3.319 0.007756 ** 431s CO2675:nutrients6 5.2500 1.7775 10.0000 2.954 0.014444 * 431s --- 431s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 431s 431s Correlation of Fixed Effects: 431s (Intr) CO2675 ntrnt2 ntrnt3 ntrnt4 ntrnt5 ntrnt6 CO2675:2 CO2675:3 431s CO2675 -0.707 431s nutrients2 -0.658 0.465 431s nutrients3 -0.658 0.465 0.500 431s nutrients4 -0.658 0.465 0.500 0.500 431s nutrients5 -0.658 0.465 0.500 0.500 0.500 431s nutrients6 -0.658 0.465 0.500 0.500 0.500 0.500 431s CO2675:ntr2 0.465 -0.658 -0.707 -0.354 -0.354 -0.354 -0.354 431s CO2675:ntr3 0.465 -0.658 -0.354 -0.707 -0.354 -0.354 -0.354 0.500 431s CO2675:ntr4 0.465 -0.658 -0.354 -0.354 -0.707 -0.354 -0.354 0.500 0.500 431s CO2675:ntr5 0.465 -0.658 -0.354 -0.354 -0.354 -0.707 -0.354 0.500 0.500 431s CO2675:ntr6 0.465 -0.658 -0.354 -0.354 -0.354 -0.354 -0.707 0.500 0.500 431s CO2675:4 CO2675:5 431s CO2675 431s nutrients2 431s nutrients3 431s nutrients4 431s nutrients5 431s nutrients6 431s CO2675:ntr2 431s CO2675:ntr3 431s CO2675:ntr4 431s CO2675:ntr5 0.500 431s CO2675:ntr6 0.500 0.500 431s > 431s > an.sat <- anova(lmerout) 431s > anova(lmerout, ddf="lme4") 431s Analysis of Variance Table 431s npar Sum Sq Mean Sq F value 431s CO2 1 67.86 67.86 42.9589 431s nutrients 5 3050.44 610.09 386.2129 431s CO2:nutrients 5 35.47 7.09 4.4906 431s > TOL <- 1e-5 431s > stopifnot(isTRUE(all.equal( 431s + an.sat[,"DenDF"], c(2, 10, 10), tolerance=TOL 431s + ))) 431s > 431s > stopifnot(isTRUE( 431s + all.equal(an.sat[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569), tolerance=TOL) 431s + )) 431s > 431s > # if(require(pbkrtest)) 431s > # an.kr <- anova(lmerout, ddf="Kenward-Roger") 431s > # 431s > # TOL <- 1e-7 431s > # stopifnot(all.equal(an.kr[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569) , 431s > # tol=TOL), 431s > # all.equal(an.kr[,"DenDF"], 431s > # c(2, 10, 10) , tol=TOL), 431s > # TRUE) 431s > 431s autopkgtest [23:34:04]: test run-unit-test: -----------------------] 431s run-unit-test PASS 431s autopkgtest [23:34:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 432s autopkgtest [23:34:05]: test pkg-r-autopkgtest: preparing testbed 451s Creating nova instance adt-resolute-ppc64el-r-cran-lmertest-20260209-232653-juju-7f2275-prod-proposed-migration-environment-20-b22c053d-8cce-4bc5-9e34-e9aadc2be1a4 from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)... 594s autopkgtest [23:36:47]: testbed dpkg architecture: ppc64el 594s autopkgtest [23:36:47]: testbed apt version: 3.1.15 594s autopkgtest [23:36:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 594s autopkgtest [23:36:47]: testbed release detected to be: resolute 595s autopkgtest [23:36:48]: updating testbed package index (apt update) 595s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 595s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 595s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 595s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 595s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 595s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 600s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 600s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB] 600s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB] 603s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB] 604s Fetched 3774 kB in 8s (445 kB/s) 604s Reading package lists... 605s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 605s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 605s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 605s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 606s Reading package lists... 606s Reading package lists... 606s Building dependency tree... 606s Reading state information... 606s Calculating upgrade... 606s The following packages will be upgraded: 606s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 606s libip6tc2 libxtables12 wget 606s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 606s Need to get 3125 kB of archives. 606s After this operation, 78.8 kB of additional disk space will be used. 606s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB] 607s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB] 607s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB] 607s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB] 607s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB] 610s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB] 610s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB] 610s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB] 610s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB] 610s dpkg-preconfigure: unable to re-open stdin: No such file or directory 610s Fetched 3125 kB in 4s (884 kB/s) 611s (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 ... 122003 files and directories currently installed.) 611s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ... 611s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 611s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ... 611s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 611s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ... 611s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 611s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ... 611s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 611s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ... 611s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 612s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 612s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 612s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ... 612s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 612s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 612s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 612s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ... 612s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 612s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ... 612s Setting up wget (1.25.0-2ubuntu4) ... 612s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ... 612s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ... 612s Setting up dracut-install (109-11ubuntu1) ... 612s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ... 612s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 612s Setting up iptables (1.8.11-2ubuntu3) ... 612s Setting up iproute2 (6.18.0-1ubuntu1) ... 612s Processing triggers for man-db (2.13.1-1build1) ... 614s Processing triggers for install-info (7.2-5) ... 614s Processing triggers for libc-bin (2.42-2ubuntu4) ... 614s autopkgtest [23:37:07]: upgrading testbed (apt dist-upgrade and autopurge) 614s Reading package lists... 615s Building dependency tree... 615s Reading state information... 615s Calculating upgrade... 615s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 615s Reading package lists... 615s Building dependency tree... 615s Reading state information... 615s Solving dependencies... 615s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 617s Reading package lists... 618s Building dependency tree... 618s Reading state information... 618s Solving dependencies... 618s The following NEW packages will be installed: 618s build-essential cpp cpp-15 cpp-15-powerpc64le-linux-gnu 618s cpp-powerpc64le-linux-gnu dctrl-tools fontconfig fontconfig-config 618s fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax 618s g++ g++-15 g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15 618s gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-15 618s gfortran-15-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 618s icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 618s libcairo2 libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 618s libfontconfig1 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 618s libgraphite2-3 libharfbuzz0b libice6 libicu-dev libisl23 libitm1 libjbig0 618s libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 618s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 618s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 618s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 618s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 618s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 618s libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 618s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 618s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 618s libzstd-dev linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf 618s pkgconf-bin r-base-core r-base-dev r-cran-backports r-cran-boot r-cran-broom 618s r-cran-cli r-cran-colorspace r-cran-cowplot r-cran-cpp11 r-cran-curl 618s r-cran-deriv r-cran-doby r-cran-dplyr r-cran-evaluate r-cran-fansi 618s r-cran-farver r-cran-forecast r-cran-fracdiff r-cran-generics r-cran-ggplot2 618s r-cran-glue r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite 618s r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler 618s r-cran-lme4 r-cran-lmertest r-cran-lmtest r-cran-magrittr r-cran-mass 618s r-cran-matrix r-cran-microbenchmark r-cran-minqa r-cran-modelr r-cran-nlme 618s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-pbkrtest r-cran-pillar 618s r-cran-pkgconfig r-cran-pkgkitten r-cran-purrr r-cran-quadprog 618s r-cran-quantmod r-cran-r6 r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp 618s r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rdpack r-cran-reformulas 618s r-cran-rlang r-cran-s7 r-cran-scales r-cran-statmod r-cran-stringi 618s r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timedate 618s r-cran-tseries r-cran-ttr r-cran-urca r-cran-utf8 r-cran-vctrs 618s r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xts r-cran-yaml 618s r-cran-zoo rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev 618s 0 upgraded, 190 newly installed, 0 to remove and 0 not upgraded. 618s Need to get 220 MB of archives. 618s After this operation, 658 MB of additional disk space will be used. 618s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc-dev-bin ppc64el 2.42-2ubuntu4 [23.9 kB] 618s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el linux-libc-dev ppc64el 6.19.0-3.3 [1832 kB] 621s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcrypt-dev ppc64el 1:4.5.1-1 [162 kB] 621s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el rpcsvc-proto ppc64el 1.4.3-1build1 [84.2 kB] 621s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc6-dev ppc64el 2.42-2ubuntu4 [2080 kB] 624s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB] 626s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB] 626s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [11.4 MB] 648s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-12ubuntu1 [1038 B] 648s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B] 648s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB] 648s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-12ubuntu1 [49.0 kB] 648s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 648s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-12ubuntu1 [32.2 kB] 648s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-12ubuntu1 [3006 kB] 666s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-12ubuntu1 [1374 kB] 669s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-12ubuntu1 [2729 kB] 676s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-12ubuntu1 [1231 kB] 678s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-12ubuntu1 [160 kB] 678s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-12ubuntu1 [1670 kB] 681s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [22.4 MB] 719s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-12ubuntu1 [530 kB] 720s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B] 720s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B] 720s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-12ubuntu1 [2747 kB] 725s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [13.0 MB] 757s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-12ubuntu1 [25.3 kB] 757s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B] 757s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B] 757s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B] 757s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el dctrl-tools ppc64el 2.24-3build4 [108 kB] 757s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 757s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 759s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 759s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 759s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 759s Get:37 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 759s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 763s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 764s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran-15-dev ppc64el 15.2.0-12ubuntu1 [651 kB] 765s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [12.3 MB] 788s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15 ppc64el 15.2.0-12ubuntu1 [18.1 kB] 788s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1020 B] 788s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran ppc64el 4:15.2.0-4ubuntu1 [1166 B] 788s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el icu-devtools ppc64el 78.2-1ubuntu1 [246 kB] 788s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 788s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas-dev ppc64el 3.12.1-7ubuntu1 [306 kB] 788s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbz2-dev ppc64el 1.0.8-6build2 [50.0 kB] 788s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 788s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 788s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 788s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 788s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 789s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 790s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB] 790s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate-dev ppc64el 1.23-2build1 [71.8 kB] 790s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 790s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 791s Get:59 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 791s Get:60 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 791s Get:61 http://ftpmaster.internal/ubuntu resolute/main ppc64el libicu-dev ppc64el 78.2-1ubuntu1 [13.3 MB] 813s Get:62 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB] 813s Get:63 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-4ubuntu3 [358 kB] 813s Get:64 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 813s Get:65 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 813s Get:66 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 814s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 814s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 814s Get:69 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 814s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 814s Get:71 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 818s Get:72 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack-dev ppc64el 3.12.1-7ubuntu1 [6357 kB] 831s Get:73 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 831s Get:74 http://ftpmaster.internal/ubuntu resolute/main ppc64el libncurses-dev ppc64el 6.6+20251231-1 [505 kB] 831s Get:75 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 832s Get:76 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 832s Get:77 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 832s Get:78 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 832s Get:79 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 832s Get:80 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 832s Get:81 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 832s Get:82 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-16-0 ppc64el 10.46-1 [292 kB] 832s Get:83 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-32-0 ppc64el 10.46-1 [275 kB] 832s Get:84 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-posix3 ppc64el 10.46-1 [7334 B] 832s Get:85 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-dev ppc64el 10.46-1 [937 kB] 833s Get:86 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpkgconf3 ppc64el 1.8.1-4build1 [37.9 kB] 833s Get:87 http://ftpmaster.internal/ubuntu resolute/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu2 [903 kB] 835s Get:88 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpng-dev ppc64el 1.6.54-1 [326 kB] 835s Get:89 http://ftpmaster.internal/ubuntu resolute/main ppc64el libreadline-dev ppc64el 8.3-3 [252 kB] 835s Get:90 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 835s Get:91 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB] 835s Get:92 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 837s Get:93 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 837s Get:94 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 837s Get:95 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 837s Get:96 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 837s Get:97 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 837s Get:98 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 839s Get:99 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 839s Get:100 http://ftpmaster.internal/ubuntu resolute/main ppc64el libzstd-dev ppc64el 1.5.7+dfsg-3 [528 kB] 840s Get:101 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-normalize.css all 8.0.1-5.1 [10.4 kB] 840s Get:102 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB] 840s Get:103 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 840s Get:104 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 840s Get:105 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 895s Get:106 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblzma-dev ppc64el 5.8.2-2 [210 kB] 895s Get:107 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf-bin ppc64el 1.8.1-4build1 [22.7 kB] 895s Get:108 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf ppc64el 1.8.1-4build1 [16.8 kB] 895s Get:109 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtirpc-dev ppc64el 1.3.6+ds-1 [223 kB] 895s Get:110 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-dev all 4.5.2-1ubuntu2 [1880 B] 895s Get:111 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pkg-r-autopkgtest all 20250812 [6158 B] 895s Get:112 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-backports ppc64el 1.5.0-2 [122 kB] 895s Get:113 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-boot all 1.3-32-1 [636 kB] 896s Get:114 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB] 901s Get:115 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-generics all 0.1.4-1 [84.0 kB] 901s Get:116 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB] 901s Get:117 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB] 906s Get:118 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 906s Get:119 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 906s Get:120 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB] 907s Get:121 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 910s Get:122 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 910s Get:123 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB] 910s Get:124 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB] 912s Get:125 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 912s Get:126 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB] 913s Get:127 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB] 913s Get:128 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyselect ppc64el 1.2.1+dfsg-1 [222 kB] 913s Get:129 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dplyr ppc64el 1.1.4-4 [1542 kB] 916s Get:130 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-purrr ppc64el 1.0.4-1 [555 kB] 917s Get:131 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringi ppc64el 1.8.4-1build2 [947 kB] 919s Get:132 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB] 920s Get:133 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB] 920s Get:134 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB] 922s Get:135 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 925s Get:136 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-colorspace ppc64el 2.1-1+dfsg-1 [1570 kB] 927s Get:137 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 928s Get:138 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 930s Get:139 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-s7 ppc64el 0.2.0-1 [330 kB] 930s Get:140 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB] 933s Get:141 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 933s Get:142 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 933s Get:143 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB] 935s Get:144 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB] 936s Get:145 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 948s Get:146 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 949s Get:147 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-curl ppc64el 7.0.0+dfsg-1 [205 kB] 949s Get:148 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-deriv all 4.2.0-1 [154 kB] 949s Get:149 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fracdiff ppc64el 1.5-3-1 [118 kB] 949s Get:150 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lattice ppc64el 0.22-7-1 [1366 kB] 951s Get:151 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-zoo ppc64el 1.8-15-1 [1028 kB] 953s Get:152 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lmtest ppc64el 0.9.40-1build1 [401 kB] 953s Get:153 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nnet ppc64el 7.3-20-1 [119 kB] 953s Get:154 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB] 953s Get:155 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 953s Get:156 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB] 956s Get:157 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-timedate ppc64el 4052.112-1 [1299 kB] 959s Get:158 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quadprog ppc64el 1.5-8-1build2 [38.8 kB] 959s Get:159 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xts ppc64el 0.14.1-1 [1209 kB] 961s Get:160 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ttr ppc64el 0.24.4-1 [516 kB] 961s Get:161 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-jsonlite ppc64el 1.9.1+dfsg-1 [452 kB] 962s Get:162 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quantmod all 0.4.28-1 [1037 kB] 964s Get:163 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tseries ppc64el 0.10-59-3 [390 kB] 964s Get:164 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB] 968s Get:165 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-urca ppc64el 1.3-4-1build1 [1056 kB] 970s Get:166 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpparmadillo ppc64el 15.2.3-1-1 [935 kB] 971s Get:167 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-forecast ppc64el 8.23.0-1 [1598 kB] 974s Get:168 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 976s Get:169 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 985s Get:170 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-modelr all 0.1.11-1 [195 kB] 985s Get:171 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-microbenchmark ppc64el 1.5.0-1 [67.9 kB] 985s Get:172 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-doby all 4.7.1-3 [4741 kB] 993s Get:173 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-evaluate all 1.0.5-1 [117 kB] 993s Get:174 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xfun ppc64el 0.55+dfsg-1 [589 kB] 994s Get:175 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB] 994s Get:176 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB] 994s Get:177 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 1006s Get:178 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-knitr all 1.51+dfsg-1 [847 kB] 1008s Get:179 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-minqa ppc64el 1.2.8-1 [141 kB] 1008s Get:180 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libnlopt0 ppc64el 2.7.1-7ubuntu1 [292 kB] 1008s Get:181 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nloptr ppc64el 2.2.1-2 [251 kB] 1008s Get:182 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rbibutils ppc64el 2.3-1 [1047 kB] 1010s Get:183 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rdpack all 2.6.3-1 [636 kB] 1011s Get:184 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-reformulas all 0.4.4-1 [151 kB] 1011s Get:185 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcppeigen ppc64el 0.3.4.0.2-1 [1477 kB] 1014s Get:186 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-statmod ppc64el 1.5.0-1 [298 kB] 1014s Get:187 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lme4 ppc64el 1.1-38-1 [4220 kB] 1022s Get:188 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 1022s Get:189 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lmertest all 3.2-0-1 [535 kB] 1023s Get:190 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pbkrtest all 0.5.5-1 [217 kB] 1023s Preconfiguring packages ... 1023s Fetched 220 MB in 6min 45s (543 kB/s) 1023s Selecting previously unselected package libc-dev-bin. 1023s (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 ... 122006 files and directories currently installed.) 1023s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_ppc64el.deb ... 1023s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 1023s Selecting previously unselected package linux-libc-dev:ppc64el. 1023s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_ppc64el.deb ... 1023s Unpacking linux-libc-dev:ppc64el (6.19.0-3.3) ... 1024s Selecting previously unselected package libcrypt-dev:ppc64el. 1024s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_ppc64el.deb ... 1024s Unpacking libcrypt-dev:ppc64el (1:4.5.1-1) ... 1024s Selecting previously unselected package rpcsvc-proto. 1024s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_ppc64el.deb ... 1024s Unpacking rpcsvc-proto (1.4.3-1build1) ... 1024s Selecting previously unselected package libc6-dev:ppc64el. 1024s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_ppc64el.deb ... 1024s Unpacking libc6-dev:ppc64el (2.42-2ubuntu4) ... 1024s Selecting previously unselected package libisl23:ppc64el. 1024s Preparing to unpack .../005-libisl23_0.27-1build1_ppc64el.deb ... 1024s Unpacking libisl23:ppc64el (0.27-1build1) ... 1024s Selecting previously unselected package libmpc3:ppc64el. 1024s Preparing to unpack .../006-libmpc3_1.3.1-2_ppc64el.deb ... 1024s Unpacking libmpc3:ppc64el (1.3.1-2) ... 1024s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu. 1024s Preparing to unpack .../007-cpp-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package cpp-15. 1024s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 1024s Preparing to unpack .../009-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1024s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1024s Selecting previously unselected package cpp. 1024s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1024s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1024s Selecting previously unselected package libcc1-0:ppc64el. 1024s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libgomp1:ppc64el. 1024s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libitm1:ppc64el. 1024s Preparing to unpack .../013-libitm1_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libitm1:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libasan8:ppc64el. 1024s Preparing to unpack .../014-libasan8_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libasan8:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package liblsan0:ppc64el. 1024s Preparing to unpack .../015-liblsan0_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking liblsan0:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libtsan2:ppc64el. 1024s Preparing to unpack .../016-libtsan2_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libtsan2:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libubsan1:ppc64el. 1024s Preparing to unpack .../017-libubsan1_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libubsan1:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libquadmath0:ppc64el. 1024s Preparing to unpack .../018-libquadmath0_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package libgcc-15-dev:ppc64el. 1024s Preparing to unpack .../019-libgcc-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1024s Selecting previously unselected package gcc-15-powerpc64le-linux-gnu. 1024s Preparing to unpack .../020-gcc-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 1024s Unpacking gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package gcc-15. 1025s Preparing to unpack .../021-gcc-15_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 1025s Preparing to unpack .../022-gcc-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1025s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1025s Selecting previously unselected package gcc. 1025s Preparing to unpack .../023-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1025s Unpacking gcc (4:15.2.0-4ubuntu1) ... 1025s Selecting previously unselected package libstdc++-15-dev:ppc64el. 1025s Preparing to unpack .../024-libstdc++-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package g++-15-powerpc64le-linux-gnu. 1025s Preparing to unpack .../025-g++-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package g++-15. 1025s Preparing to unpack .../026-g++-15_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking g++-15 (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package g++-powerpc64le-linux-gnu. 1025s Preparing to unpack .../027-g++-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1025s Unpacking g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1025s Selecting previously unselected package g++. 1025s Preparing to unpack .../028-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1025s Unpacking g++ (4:15.2.0-4ubuntu1) ... 1025s Selecting previously unselected package build-essential. 1025s Preparing to unpack .../029-build-essential_12.12ubuntu2_ppc64el.deb ... 1025s Unpacking build-essential (12.12ubuntu2) ... 1025s Selecting previously unselected package dctrl-tools. 1025s Preparing to unpack .../030-dctrl-tools_2.24-3build4_ppc64el.deb ... 1025s Unpacking dctrl-tools (2.24-3build4) ... 1025s Selecting previously unselected package fonts-dejavu-mono. 1025s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8build1_all.deb ... 1025s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1025s Selecting previously unselected package fonts-dejavu-core. 1025s Preparing to unpack .../032-fonts-dejavu-core_2.37-8build1_all.deb ... 1025s Unpacking fonts-dejavu-core (2.37-8build1) ... 1025s Selecting previously unselected package fontconfig-config. 1025s Preparing to unpack .../033-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 1025s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 1025s Selecting previously unselected package libfontconfig1:ppc64el. 1025s Preparing to unpack .../034-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 1025s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 1025s Selecting previously unselected package fontconfig. 1025s Preparing to unpack .../035-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 1025s Unpacking fontconfig (2.17.1-3ubuntu1) ... 1025s Selecting previously unselected package fonts-glyphicons-halflings. 1025s Preparing to unpack .../036-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 1025s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 1025s Selecting previously unselected package fonts-mathjax. 1025s Preparing to unpack .../037-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 1025s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 1025s Selecting previously unselected package libgfortran5:ppc64el. 1025s Preparing to unpack .../038-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package libgfortran-15-dev:ppc64el. 1025s Preparing to unpack .../039-libgfortran-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1025s Selecting previously unselected package gfortran-15-powerpc64le-linux-gnu. 1025s Preparing to unpack .../040-gfortran-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 1025s Unpacking gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1026s Selecting previously unselected package gfortran-15. 1026s Preparing to unpack .../041-gfortran-15_15.2.0-12ubuntu1_ppc64el.deb ... 1026s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 1026s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 1026s Preparing to unpack .../042-gfortran-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1026s Unpacking gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1026s Selecting previously unselected package gfortran. 1026s Preparing to unpack .../043-gfortran_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 1026s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 1026s Selecting previously unselected package icu-devtools. 1026s Preparing to unpack .../044-icu-devtools_78.2-1ubuntu1_ppc64el.deb ... 1026s Unpacking icu-devtools (78.2-1ubuntu1) ... 1026s Selecting previously unselected package libblas3:ppc64el. 1026s Preparing to unpack .../045-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 1026s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 1026s Selecting previously unselected package libblas-dev:ppc64el. 1026s Preparing to unpack .../046-libblas-dev_3.12.1-7ubuntu1_ppc64el.deb ... 1026s Unpacking libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 1026s Selecting previously unselected package libbz2-dev:ppc64el. 1026s Preparing to unpack .../047-libbz2-dev_1.0.8-6build2_ppc64el.deb ... 1026s Unpacking libbz2-dev:ppc64el (1.0.8-6build2) ... 1026s Selecting previously unselected package libpixman-1-0:ppc64el. 1026s Preparing to unpack .../048-libpixman-1-0_0.46.4-1_ppc64el.deb ... 1026s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 1026s Selecting previously unselected package libxcb-render0:ppc64el. 1026s Preparing to unpack .../049-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 1026s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 1026s Selecting previously unselected package libxcb-shm0:ppc64el. 1026s Preparing to unpack .../050-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 1026s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 1026s Selecting previously unselected package libxrender1:ppc64el. 1026s Preparing to unpack .../051-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 1026s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 1026s Selecting previously unselected package libcairo2:ppc64el. 1026s Preparing to unpack .../052-libcairo2_1.18.4-3_ppc64el.deb ... 1026s Unpacking libcairo2:ppc64el (1.18.4-3) ... 1026s Selecting previously unselected package libdatrie1:ppc64el. 1026s Preparing to unpack .../053-libdatrie1_0.2.14-1_ppc64el.deb ... 1026s Unpacking libdatrie1:ppc64el (0.2.14-1) ... 1026s Selecting previously unselected package libdeflate0:ppc64el. 1026s Preparing to unpack .../054-libdeflate0_1.23-2build1_ppc64el.deb ... 1026s Unpacking libdeflate0:ppc64el (1.23-2build1) ... 1026s Selecting previously unselected package libdeflate-dev:ppc64el. 1026s Preparing to unpack .../055-libdeflate-dev_1.23-2build1_ppc64el.deb ... 1026s Unpacking libdeflate-dev:ppc64el (1.23-2build1) ... 1026s Selecting previously unselected package libgraphite2-3:ppc64el. 1026s Preparing to unpack .../056-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ... 1026s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 1026s Selecting previously unselected package libharfbuzz0b:ppc64el. 1026s Preparing to unpack .../057-libharfbuzz0b_12.3.2-1_ppc64el.deb ... 1026s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ... 1026s Selecting previously unselected package x11-common. 1026s Preparing to unpack .../058-x11-common_1%3a7.7+24ubuntu1_all.deb ... 1026s Unpacking x11-common (1:7.7+24ubuntu1) ... 1026s Selecting previously unselected package libice6:ppc64el. 1026s Preparing to unpack .../059-libice6_2%3a1.1.1-1build1_ppc64el.deb ... 1026s Unpacking libice6:ppc64el (2:1.1.1-1build1) ... 1026s Selecting previously unselected package libicu-dev:ppc64el. 1026s Preparing to unpack .../060-libicu-dev_78.2-1ubuntu1_ppc64el.deb ... 1026s Unpacking libicu-dev:ppc64el (78.2-1ubuntu1) ... 1026s Selecting previously unselected package libjpeg-turbo8:ppc64el. 1026s Preparing to unpack .../061-libjpeg-turbo8_2.1.5-4ubuntu3_ppc64el.deb ... 1026s Unpacking libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 1026s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 1026s Preparing to unpack .../062-libjpeg-turbo8-dev_2.1.5-4ubuntu3_ppc64el.deb ... 1026s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 1026s Selecting previously unselected package libjpeg8:ppc64el. 1026s Preparing to unpack .../063-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 1026s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 1026s Selecting previously unselected package libjpeg8-dev:ppc64el. 1026s Preparing to unpack .../064-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 1026s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 1026s Selecting previously unselected package libjpeg-dev:ppc64el. 1026s Preparing to unpack .../065-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 1026s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 1026s Selecting previously unselected package libjs-bootstrap. 1026s Preparing to unpack .../066-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 1026s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 1026s Selecting previously unselected package libjs-highlight.js. 1026s Preparing to unpack .../067-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 1026s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 1027s Selecting previously unselected package libjs-jquery. 1027s Preparing to unpack .../068-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 1027s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1027s Selecting previously unselected package libjs-jquery-datatables. 1027s Preparing to unpack .../069-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 1027s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1027s Selecting previously unselected package liblapack3:ppc64el. 1027s Preparing to unpack .../070-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ... 1027s Unpacking liblapack3:ppc64el (3.12.1-7ubuntu1) ... 1027s Selecting previously unselected package liblapack-dev:ppc64el. 1027s Preparing to unpack .../071-liblapack-dev_3.12.1-7ubuntu1_ppc64el.deb ... 1027s Unpacking liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 1027s Selecting previously unselected package liblerc4:ppc64el. 1027s Preparing to unpack .../072-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ... 1027s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 1027s Selecting previously unselected package libncurses-dev:ppc64el. 1027s Preparing to unpack .../073-libncurses-dev_6.6+20251231-1_ppc64el.deb ... 1027s Unpacking libncurses-dev:ppc64el (6.6+20251231-1) ... 1027s Selecting previously unselected package libthai-data. 1027s Preparing to unpack .../074-libthai-data_0.1.30-1_all.deb ... 1027s Unpacking libthai-data (0.1.30-1) ... 1027s Selecting previously unselected package libthai0:ppc64el. 1027s Preparing to unpack .../075-libthai0_0.1.30-1_ppc64el.deb ... 1027s Unpacking libthai0:ppc64el (0.1.30-1) ... 1027s Selecting previously unselected package libpango-1.0-0:ppc64el. 1027s Preparing to unpack .../076-libpango-1.0-0_1.57.0-1_ppc64el.deb ... 1027s Unpacking libpango-1.0-0:ppc64el (1.57.0-1) ... 1027s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 1027s Preparing to unpack .../077-libpangoft2-1.0-0_1.57.0-1_ppc64el.deb ... 1027s Unpacking libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 1027s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 1027s Preparing to unpack .../078-libpangocairo-1.0-0_1.57.0-1_ppc64el.deb ... 1027s Unpacking libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 1027s Selecting previously unselected package libpaper2:ppc64el. 1027s Preparing to unpack .../079-libpaper2_2.2.5-0.3build1_ppc64el.deb ... 1027s Unpacking libpaper2:ppc64el (2.2.5-0.3build1) ... 1027s Selecting previously unselected package libpaper-utils. 1027s Preparing to unpack .../080-libpaper-utils_2.2.5-0.3build1_ppc64el.deb ... 1027s Unpacking libpaper-utils (2.2.5-0.3build1) ... 1027s Selecting previously unselected package libpcre2-16-0:ppc64el. 1027s Preparing to unpack .../081-libpcre2-16-0_10.46-1_ppc64el.deb ... 1027s Unpacking libpcre2-16-0:ppc64el (10.46-1) ... 1027s Selecting previously unselected package libpcre2-32-0:ppc64el. 1027s Preparing to unpack .../082-libpcre2-32-0_10.46-1_ppc64el.deb ... 1027s Unpacking libpcre2-32-0:ppc64el (10.46-1) ... 1027s Selecting previously unselected package libpcre2-posix3:ppc64el. 1027s Preparing to unpack .../083-libpcre2-posix3_10.46-1_ppc64el.deb ... 1027s Unpacking libpcre2-posix3:ppc64el (10.46-1) ... 1027s Selecting previously unselected package libpcre2-dev:ppc64el. 1027s Preparing to unpack .../084-libpcre2-dev_10.46-1_ppc64el.deb ... 1027s Unpacking libpcre2-dev:ppc64el (10.46-1) ... 1027s Selecting previously unselected package libpkgconf3:ppc64el. 1027s Preparing to unpack .../085-libpkgconf3_1.8.1-4build1_ppc64el.deb ... 1027s Unpacking libpkgconf3:ppc64el (1.8.1-4build1) ... 1027s Selecting previously unselected package zlib1g-dev:ppc64el. 1027s Preparing to unpack .../086-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_ppc64el.deb ... 1027s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1027s Selecting previously unselected package libpng-dev:ppc64el. 1027s Preparing to unpack .../087-libpng-dev_1.6.54-1_ppc64el.deb ... 1027s Unpacking libpng-dev:ppc64el (1.6.54-1) ... 1027s Selecting previously unselected package libreadline-dev:ppc64el. 1027s Preparing to unpack .../088-libreadline-dev_8.3-3_ppc64el.deb ... 1027s Unpacking libreadline-dev:ppc64el (8.3-3) ... 1027s Selecting previously unselected package libsharpyuv0:ppc64el. 1027s Preparing to unpack .../089-libsharpyuv0_1.5.0-0.1build1_ppc64el.deb ... 1027s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 1027s Selecting previously unselected package libsm6:ppc64el. 1027s Preparing to unpack .../090-libsm6_2%3a1.2.6-1build1_ppc64el.deb ... 1027s Unpacking libsm6:ppc64el (2:1.2.6-1build1) ... 1027s Selecting previously unselected package libtcl8.6:ppc64el. 1027s Preparing to unpack .../091-libtcl8.6_8.6.17+dfsg-1build1_ppc64el.deb ... 1027s Unpacking libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 1027s Selecting previously unselected package libjbig0:ppc64el. 1027s Preparing to unpack .../092-libjbig0_2.1-6.1ubuntu3_ppc64el.deb ... 1027s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu3) ... 1027s Selecting previously unselected package libwebp7:ppc64el. 1027s Preparing to unpack .../093-libwebp7_1.5.0-0.1build1_ppc64el.deb ... 1027s Unpacking libwebp7:ppc64el (1.5.0-0.1build1) ... 1027s Selecting previously unselected package libtiff6:ppc64el. 1027s Preparing to unpack .../094-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ... 1027s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ... 1027s Selecting previously unselected package libxft2:ppc64el. 1027s Preparing to unpack .../095-libxft2_2.3.6-1build2_ppc64el.deb ... 1027s Unpacking libxft2:ppc64el (2.3.6-1build2) ... 1027s Selecting previously unselected package libxss1:ppc64el. 1027s Preparing to unpack .../096-libxss1_1%3a1.2.3-1build4_ppc64el.deb ... 1027s Unpacking libxss1:ppc64el (1:1.2.3-1build4) ... 1027s Selecting previously unselected package libtk8.6:ppc64el. 1027s Preparing to unpack .../097-libtk8.6_8.6.17-1_ppc64el.deb ... 1027s Unpacking libtk8.6:ppc64el (8.6.17-1) ... 1027s Selecting previously unselected package libxt6t64:ppc64el. 1027s Preparing to unpack .../098-libxt6t64_1%3a1.2.1-1.3_ppc64el.deb ... 1027s Unpacking libxt6t64:ppc64el (1:1.2.1-1.3) ... 1027s Selecting previously unselected package libzstd-dev:ppc64el. 1027s Preparing to unpack .../099-libzstd-dev_1.5.7+dfsg-3_ppc64el.deb ... 1027s Unpacking libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 1027s Selecting previously unselected package node-normalize.css. 1027s Preparing to unpack .../100-node-normalize.css_8.0.1-5.1_all.deb ... 1027s Unpacking node-normalize.css (8.0.1-5.1) ... 1027s Selecting previously unselected package zip. 1027s Preparing to unpack .../101-zip_3.0-15ubuntu3_ppc64el.deb ... 1027s Unpacking zip (3.0-15ubuntu3) ... 1027s Selecting previously unselected package unzip. 1027s Preparing to unpack .../102-unzip_6.0-29ubuntu1_ppc64el.deb ... 1027s Unpacking unzip (6.0-29ubuntu1) ... 1028s Selecting previously unselected package xdg-utils. 1028s Preparing to unpack .../103-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1028s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1028s Selecting previously unselected package r-base-core. 1028s Preparing to unpack .../104-r-base-core_4.5.2-1ubuntu2_ppc64el.deb ... 1028s Unpacking r-base-core (4.5.2-1ubuntu2) ... 1028s Selecting previously unselected package liblzma-dev:ppc64el. 1028s Preparing to unpack .../105-liblzma-dev_5.8.2-2_ppc64el.deb ... 1028s Unpacking liblzma-dev:ppc64el (5.8.2-2) ... 1028s Selecting previously unselected package pkgconf-bin. 1028s Preparing to unpack .../106-pkgconf-bin_1.8.1-4build1_ppc64el.deb ... 1028s Unpacking pkgconf-bin (1.8.1-4build1) ... 1028s Selecting previously unselected package pkgconf:ppc64el. 1028s Preparing to unpack .../107-pkgconf_1.8.1-4build1_ppc64el.deb ... 1028s Unpacking pkgconf:ppc64el (1.8.1-4build1) ... 1028s Selecting previously unselected package libtirpc-dev:ppc64el. 1028s Preparing to unpack .../108-libtirpc-dev_1.3.6+ds-1_ppc64el.deb ... 1028s Unpacking libtirpc-dev:ppc64el (1.3.6+ds-1) ... 1028s Selecting previously unselected package r-base-dev. 1028s Preparing to unpack .../109-r-base-dev_4.5.2-1ubuntu2_all.deb ... 1028s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 1028s Selecting previously unselected package pkg-r-autopkgtest. 1028s Preparing to unpack .../110-pkg-r-autopkgtest_20250812_all.deb ... 1028s Unpacking pkg-r-autopkgtest (20250812) ... 1028s Selecting previously unselected package r-cran-backports. 1028s Preparing to unpack .../111-r-cran-backports_1.5.0-2_ppc64el.deb ... 1028s Unpacking r-cran-backports (1.5.0-2) ... 1028s Selecting previously unselected package r-cran-boot. 1028s Preparing to unpack .../112-r-cran-boot_1.3-32-1_all.deb ... 1028s Unpacking r-cran-boot (1.3-32-1) ... 1028s Selecting previously unselected package r-cran-cli. 1028s Preparing to unpack .../113-r-cran-cli_3.6.4-1_ppc64el.deb ... 1028s Unpacking r-cran-cli (3.6.4-1) ... 1028s Selecting previously unselected package r-cran-generics. 1028s Preparing to unpack .../114-r-cran-generics_0.1.4-1_all.deb ... 1028s Unpacking r-cran-generics (0.1.4-1) ... 1028s Selecting previously unselected package r-cran-glue. 1028s Preparing to unpack .../115-r-cran-glue_1.8.0-1_ppc64el.deb ... 1028s Unpacking r-cran-glue (1.8.0-1) ... 1028s Selecting previously unselected package r-cran-rlang. 1028s Preparing to unpack .../116-r-cran-rlang_1.1.5-3_ppc64el.deb ... 1028s Unpacking r-cran-rlang (1.1.5-3) ... 1028s Selecting previously unselected package r-cran-lifecycle. 1028s Preparing to unpack .../117-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 1028s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 1029s Selecting previously unselected package r-cran-magrittr. 1029s Preparing to unpack .../118-r-cran-magrittr_2.0.3-1_ppc64el.deb ... 1029s Unpacking r-cran-magrittr (2.0.3-1) ... 1029s Selecting previously unselected package r-cran-utf8. 1029s Preparing to unpack .../119-r-cran-utf8_1.2.4-1_ppc64el.deb ... 1029s Unpacking r-cran-utf8 (1.2.4-1) ... 1029s Selecting previously unselected package r-cran-vctrs. 1029s Preparing to unpack .../120-r-cran-vctrs_0.6.5-1_ppc64el.deb ... 1029s Unpacking r-cran-vctrs (0.6.5-1) ... 1029s Selecting previously unselected package r-cran-pillar. 1029s Preparing to unpack .../121-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 1029s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 1029s Selecting previously unselected package r-cran-r6. 1029s Preparing to unpack .../122-r-cran-r6_2.6.1-1_all.deb ... 1029s Unpacking r-cran-r6 (2.6.1-1) ... 1029s Selecting previously unselected package r-cran-fansi. 1029s Preparing to unpack .../123-r-cran-fansi_1.0.6-2_ppc64el.deb ... 1029s Unpacking r-cran-fansi (1.0.6-2) ... 1029s Selecting previously unselected package r-cran-pkgconfig. 1029s Preparing to unpack .../124-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 1029s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 1029s Selecting previously unselected package r-cran-tibble. 1029s Preparing to unpack .../125-r-cran-tibble_3.2.1+dfsg-3_ppc64el.deb ... 1029s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 1029s Selecting previously unselected package r-cran-withr. 1029s Preparing to unpack .../126-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1029s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1029s Selecting previously unselected package r-cran-tidyselect. 1029s Preparing to unpack .../127-r-cran-tidyselect_1.2.1+dfsg-1_ppc64el.deb ... 1029s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 1029s Selecting previously unselected package r-cran-dplyr. 1029s Preparing to unpack .../128-r-cran-dplyr_1.1.4-4_ppc64el.deb ... 1029s Unpacking r-cran-dplyr (1.1.4-4) ... 1029s Selecting previously unselected package r-cran-purrr. 1029s Preparing to unpack .../129-r-cran-purrr_1.0.4-1_ppc64el.deb ... 1029s Unpacking r-cran-purrr (1.0.4-1) ... 1029s Selecting previously unselected package r-cran-stringi. 1029s Preparing to unpack .../130-r-cran-stringi_1.8.4-1build2_ppc64el.deb ... 1029s Unpacking r-cran-stringi (1.8.4-1build2) ... 1029s Selecting previously unselected package r-cran-stringr. 1029s Preparing to unpack .../131-r-cran-stringr_1.5.1-1_all.deb ... 1029s Unpacking r-cran-stringr (1.5.1-1) ... 1029s Selecting previously unselected package r-cran-cpp11. 1029s Preparing to unpack .../132-r-cran-cpp11_0.5.3-1_all.deb ... 1029s Unpacking r-cran-cpp11 (0.5.3-1) ... 1029s Selecting previously unselected package r-cran-tidyr. 1029s Preparing to unpack .../133-r-cran-tidyr_1.3.1-1_ppc64el.deb ... 1029s Unpacking r-cran-tidyr (1.3.1-1) ... 1029s Selecting previously unselected package r-cran-broom. 1029s Preparing to unpack .../134-r-cran-broom_1.0.12+dfsg-1_all.deb ... 1029s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 1029s Selecting previously unselected package r-cran-colorspace. 1029s Preparing to unpack .../135-r-cran-colorspace_2.1-1+dfsg-1_ppc64el.deb ... 1029s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 1029s Selecting previously unselected package r-cran-gtable. 1029s Preparing to unpack .../136-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1029s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 1029s Selecting previously unselected package r-cran-isoband. 1029s Preparing to unpack .../137-r-cran-isoband_0.2.7-1_ppc64el.deb ... 1029s Unpacking r-cran-isoband (0.2.7-1) ... 1029s Selecting previously unselected package r-cran-s7. 1029s Preparing to unpack .../138-r-cran-s7_0.2.0-1_ppc64el.deb ... 1029s Unpacking r-cran-s7 (0.2.0-1) ... 1029s Selecting previously unselected package r-cran-farver. 1029s Preparing to unpack .../139-r-cran-farver_2.1.2-1_ppc64el.deb ... 1029s Unpacking r-cran-farver (2.1.2-1) ... 1029s Selecting previously unselected package r-cran-labeling. 1029s Preparing to unpack .../140-r-cran-labeling_0.4.3-1_all.deb ... 1029s Unpacking r-cran-labeling (0.4.3-1) ... 1029s Selecting previously unselected package r-cran-rcolorbrewer. 1029s Preparing to unpack .../141-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 1029s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 1029s Selecting previously unselected package r-cran-viridislite. 1029s Preparing to unpack .../142-r-cran-viridislite_0.4.3-1_all.deb ... 1029s Unpacking r-cran-viridislite (0.4.3-1) ... 1029s Selecting previously unselected package r-cran-scales. 1029s Preparing to unpack .../143-r-cran-scales_1.4.0-1_all.deb ... 1029s Unpacking r-cran-scales (1.4.0-1) ... 1029s Selecting previously unselected package r-cran-ggplot2. 1029s Preparing to unpack .../144-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 1029s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 1029s Selecting previously unselected package r-cran-cowplot. 1029s Preparing to unpack .../145-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 1029s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 1029s Selecting previously unselected package r-cran-curl. 1029s Preparing to unpack .../146-r-cran-curl_7.0.0+dfsg-1_ppc64el.deb ... 1029s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 1029s Selecting previously unselected package r-cran-deriv. 1029s Preparing to unpack .../147-r-cran-deriv_4.2.0-1_all.deb ... 1029s Unpacking r-cran-deriv (4.2.0-1) ... 1029s Selecting previously unselected package r-cran-fracdiff. 1029s Preparing to unpack .../148-r-cran-fracdiff_1.5-3-1_ppc64el.deb ... 1029s Unpacking r-cran-fracdiff (1.5-3-1) ... 1029s Selecting previously unselected package r-cran-lattice. 1029s Preparing to unpack .../149-r-cran-lattice_0.22-7-1_ppc64el.deb ... 1029s Unpacking r-cran-lattice (0.22-7-1) ... 1029s Selecting previously unselected package r-cran-zoo. 1030s Preparing to unpack .../150-r-cran-zoo_1.8-15-1_ppc64el.deb ... 1030s Unpacking r-cran-zoo (1.8-15-1) ... 1030s Selecting previously unselected package r-cran-lmtest. 1030s Preparing to unpack .../151-r-cran-lmtest_0.9.40-1build1_ppc64el.deb ... 1030s Unpacking r-cran-lmtest (0.9.40-1build1) ... 1030s Selecting previously unselected package r-cran-nnet. 1030s Preparing to unpack .../152-r-cran-nnet_7.3-20-1_ppc64el.deb ... 1030s Unpacking r-cran-nnet (7.3-20-1) ... 1030s Selecting previously unselected package r-cran-littler. 1030s Preparing to unpack .../153-r-cran-littler_0.3.22-1_ppc64el.deb ... 1030s Unpacking r-cran-littler (0.3.22-1) ... 1030s Selecting previously unselected package r-cran-pkgkitten. 1030s Preparing to unpack .../154-r-cran-pkgkitten_0.2.4-1_all.deb ... 1030s Unpacking r-cran-pkgkitten (0.2.4-1) ... 1030s Selecting previously unselected package r-cran-rcpp. 1030s Preparing to unpack .../155-r-cran-rcpp_1.1.0-1_ppc64el.deb ... 1030s Unpacking r-cran-rcpp (1.1.0-1) ... 1030s Selecting previously unselected package r-cran-timedate. 1030s Preparing to unpack .../156-r-cran-timedate_4052.112-1_ppc64el.deb ... 1030s Unpacking r-cran-timedate (4052.112-1) ... 1030s Selecting previously unselected package r-cran-quadprog. 1030s Preparing to unpack .../157-r-cran-quadprog_1.5-8-1build2_ppc64el.deb ... 1030s Unpacking r-cran-quadprog (1.5-8-1build2) ... 1030s Selecting previously unselected package r-cran-xts. 1030s Preparing to unpack .../158-r-cran-xts_0.14.1-1_ppc64el.deb ... 1030s Unpacking r-cran-xts (0.14.1-1) ... 1030s Selecting previously unselected package r-cran-ttr. 1030s Preparing to unpack .../159-r-cran-ttr_0.24.4-1_ppc64el.deb ... 1030s Unpacking r-cran-ttr (0.24.4-1) ... 1030s Selecting previously unselected package r-cran-jsonlite. 1030s Preparing to unpack .../160-r-cran-jsonlite_1.9.1+dfsg-1_ppc64el.deb ... 1030s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 1030s Selecting previously unselected package r-cran-quantmod. 1030s Preparing to unpack .../161-r-cran-quantmod_0.4.28-1_all.deb ... 1030s Unpacking r-cran-quantmod (0.4.28-1) ... 1030s Selecting previously unselected package r-cran-tseries. 1030s Preparing to unpack .../162-r-cran-tseries_0.10-59-3_ppc64el.deb ... 1030s Unpacking r-cran-tseries (0.10-59-3) ... 1030s Selecting previously unselected package r-cran-nlme. 1030s Preparing to unpack .../163-r-cran-nlme_3.1.168-1_ppc64el.deb ... 1030s Unpacking r-cran-nlme (3.1.168-1) ... 1030s Selecting previously unselected package r-cran-urca. 1030s Preparing to unpack .../164-r-cran-urca_1.3-4-1build1_ppc64el.deb ... 1030s Unpacking r-cran-urca (1.3-4-1build1) ... 1030s Selecting previously unselected package r-cran-rcpparmadillo. 1030s Preparing to unpack .../165-r-cran-rcpparmadillo_15.2.3-1-1_ppc64el.deb ... 1030s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 1030s Selecting previously unselected package r-cran-forecast. 1030s Preparing to unpack .../166-r-cran-forecast_8.23.0-1_ppc64el.deb ... 1030s Unpacking r-cran-forecast (8.23.0-1) ... 1030s Selecting previously unselected package r-cran-mass. 1030s Preparing to unpack .../167-r-cran-mass_7.3-65-1_ppc64el.deb ... 1030s Unpacking r-cran-mass (7.3-65-1) ... 1030s Selecting previously unselected package r-cran-matrix. 1030s Preparing to unpack .../168-r-cran-matrix_1.7-4-1_ppc64el.deb ... 1030s Unpacking r-cran-matrix (1.7-4-1) ... 1030s Selecting previously unselected package r-cran-modelr. 1030s Preparing to unpack .../169-r-cran-modelr_0.1.11-1_all.deb ... 1030s Unpacking r-cran-modelr (0.1.11-1) ... 1030s Selecting previously unselected package r-cran-microbenchmark. 1030s Preparing to unpack .../170-r-cran-microbenchmark_1.5.0-1_ppc64el.deb ... 1030s Unpacking r-cran-microbenchmark (1.5.0-1) ... 1030s Selecting previously unselected package r-cran-doby. 1030s Preparing to unpack .../171-r-cran-doby_4.7.1-3_all.deb ... 1030s Unpacking r-cran-doby (4.7.1-3) ... 1030s Selecting previously unselected package r-cran-evaluate. 1030s Preparing to unpack .../172-r-cran-evaluate_1.0.5-1_all.deb ... 1030s Unpacking r-cran-evaluate (1.0.5-1) ... 1030s Selecting previously unselected package r-cran-xfun. 1030s Preparing to unpack .../173-r-cran-xfun_0.55+dfsg-1_ppc64el.deb ... 1030s Unpacking r-cran-xfun (0.55+dfsg-1) ... 1030s Selecting previously unselected package r-cran-highr. 1030s Preparing to unpack .../174-r-cran-highr_0.11+dfsg-1_all.deb ... 1030s Unpacking r-cran-highr (0.11+dfsg-1) ... 1030s Selecting previously unselected package r-cran-yaml. 1031s Preparing to unpack .../175-r-cran-yaml_2.3.10-1_ppc64el.deb ... 1031s Unpacking r-cran-yaml (2.3.10-1) ... 1031s Selecting previously unselected package libjs-mathjax. 1031s Preparing to unpack .../176-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 1031s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 1031s Selecting previously unselected package r-cran-knitr. 1031s Preparing to unpack .../177-r-cran-knitr_1.51+dfsg-1_all.deb ... 1031s Unpacking r-cran-knitr (1.51+dfsg-1) ... 1031s Selecting previously unselected package r-cran-minqa. 1031s Preparing to unpack .../178-r-cran-minqa_1.2.8-1_ppc64el.deb ... 1031s Unpacking r-cran-minqa (1.2.8-1) ... 1031s Selecting previously unselected package libnlopt0:ppc64el. 1031s Preparing to unpack .../179-libnlopt0_2.7.1-7ubuntu1_ppc64el.deb ... 1031s Unpacking libnlopt0:ppc64el (2.7.1-7ubuntu1) ... 1031s Selecting previously unselected package r-cran-nloptr. 1031s Preparing to unpack .../180-r-cran-nloptr_2.2.1-2_ppc64el.deb ... 1031s Unpacking r-cran-nloptr (2.2.1-2) ... 1031s Selecting previously unselected package r-cran-rbibutils. 1031s Preparing to unpack .../181-r-cran-rbibutils_2.3-1_ppc64el.deb ... 1031s Unpacking r-cran-rbibutils (2.3-1) ... 1031s Selecting previously unselected package r-cran-rdpack. 1031s Preparing to unpack .../182-r-cran-rdpack_2.6.3-1_all.deb ... 1031s Unpacking r-cran-rdpack (2.6.3-1) ... 1031s Selecting previously unselected package r-cran-reformulas. 1031s Preparing to unpack .../183-r-cran-reformulas_0.4.4-1_all.deb ... 1031s Unpacking r-cran-reformulas (0.4.4-1) ... 1031s Selecting previously unselected package r-cran-rcppeigen. 1031s Preparing to unpack .../184-r-cran-rcppeigen_0.3.4.0.2-1_ppc64el.deb ... 1031s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 1031s Selecting previously unselected package r-cran-statmod. 1031s Preparing to unpack .../185-r-cran-statmod_1.5.0-1_ppc64el.deb ... 1031s Unpacking r-cran-statmod (1.5.0-1) ... 1031s Selecting previously unselected package r-cran-lme4. 1031s Preparing to unpack .../186-r-cran-lme4_1.1-38-1_ppc64el.deb ... 1031s Unpacking r-cran-lme4 (1.1-38-1) ... 1031s Selecting previously unselected package r-cran-numderiv. 1031s Preparing to unpack .../187-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 1031s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 1031s Selecting previously unselected package r-cran-lmertest. 1031s Preparing to unpack .../188-r-cran-lmertest_3.2-0-1_all.deb ... 1031s Unpacking r-cran-lmertest (3.2-0-1) ... 1031s Selecting previously unselected package r-cran-pbkrtest. 1031s Preparing to unpack .../189-r-cran-pbkrtest_0.5.5-1_all.deb ... 1031s Unpacking r-cran-pbkrtest (0.5.5-1) ... 1032s Setting up libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ... 1032s Setting up libpixman-1-0:ppc64el (0.46.4-1) ... 1032s Setting up libsharpyuv0:ppc64el (1.5.0-0.1build1) ... 1032s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 1032s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ... 1032s Setting up libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 1032s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 1032s Setting up libxrender1:ppc64el (1:0.9.12-1) ... 1032s Setting up libdatrie1:ppc64el (0.2.14-1) ... 1032s Setting up libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 1032s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 1032s Setting up unzip (6.0-29ubuntu1) ... 1032s Setting up x11-common (1:7.7+24ubuntu1) ... 1032s Setting up libdeflate0:ppc64el (1.23-2build1) ... 1032s Setting up linux-libc-dev:ppc64el (6.19.0-3.3) ... 1032s Setting up libnlopt0:ppc64el (2.7.1-7ubuntu1) ... 1032s Setting up libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 1032s Setting up libgomp1:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libjbig0:ppc64el (2.1-6.1ubuntu3) ... 1032s Setting up libpcre2-16-0:ppc64el (10.46-1) ... 1032s Setting up zip (3.0-15ubuntu3) ... 1032s Setting up libpcre2-32-0:ppc64el (10.46-1) ... 1032s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ... 1032s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 1032s Setting up libtirpc-dev:ppc64el (1.3.6+ds-1) ... 1032s Setting up libpkgconf3:ppc64el (1.8.1-4build1) ... 1032s Setting up rpcsvc-proto (1.4.3-1build1) ... 1032s Setting up libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up fonts-dejavu-mono (2.37-8build1) ... 1032s Setting up libmpc3:ppc64el (1.3.1-2) ... 1032s Setting up libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ... 1032s Setting up icu-devtools (78.2-1ubuntu1) ... 1032s Setting up fonts-dejavu-core (2.37-8build1) ... 1032s Setting up pkgconf-bin (1.8.1-4build1) ... 1032s Setting up libjpeg-turbo8:ppc64el (2.1.5-4ubuntu3) ... 1032s Setting up libgfortran5:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libwebp7:ppc64el (1.5.0-0.1build1) ... 1032s Setting up liblzma-dev:ppc64el (5.8.2-2) ... 1032s Setting up libubsan1:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libpcre2-posix3:ppc64el (10.46-1) ... 1032s Setting up libjs-highlight.js (10.7.3+dfsg-2) ... 1032s Setting up libcrypt-dev:ppc64el (1:4.5.1-1) ... 1032s Setting up libasan8:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libharfbuzz0b:ppc64el (12.3.2-1) ... 1032s Setting up libthai-data (0.1.30-1) ... 1032s Setting up libxss1:ppc64el (1:1.2.3-1build4) ... 1032s Setting up libpaper2:ppc64el (2.2.5-0.3build1) ... 1032s Setting up libtsan2:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1032s Setting up libisl23:ppc64el (0.27-1build1) ... 1032s Setting up libc-dev-bin (2.42-2ubuntu4) ... 1032s Setting up libdeflate-dev:ppc64el (1.23-2build1) ... 1032s Setting up node-normalize.css (8.0.1-5.1) ... 1032s Setting up xdg-utils (1.2.1-2ubuntu2) ... 1032s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1032s Setting up libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up liblsan0:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 1032s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 1032s Setting up dctrl-tools (2.24-3build4) ... 1032s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 1032s Setting up libitm1:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 1032s Setting up libice6:ppc64el (2:1.1.1-1build1) ... 1032s Setting up liblapack3:ppc64el (3.12.1-7ubuntu1) ... 1032s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 1032s Setting up libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 1032s Setting up libpaper-utils (2.2.5-0.3build1) ... 1032s Setting up libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1032s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1032s Setting up pkgconf:ppc64el (1.8.1-4build1) ... 1032s Setting up libthai0:ppc64el (0.1.30-1) ... 1032s Setting up cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1032s Setting up liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 1032s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 1032s Setting up cpp-15 (15.2.0-12ubuntu1) ... 1032s Setting up libtiff6:ppc64el (4.7.0-3ubuntu3) ... 1032s Setting up libc6-dev:ppc64el (2.42-2ubuntu4) ... 1032s Setting up libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 1032s Setting up libsm6:ppc64el (2:1.2.6-1build1) ... 1032s Setting up libicu-dev:ppc64el (78.2-1ubuntu1) ... 1032s Setting up cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1032s Setting up libbz2-dev:ppc64el (1.0.8-6build2) ... 1032s Setting up fontconfig (2.17.1-3ubuntu1) ... 1034s Regenerating fonts cache... done. 1034s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 1034s Setting up libxft2:ppc64el (2.3.6-1build2) ... 1034s Setting up libncurses-dev:ppc64el (6.6+20251231-1) ... 1034s Setting up libpcre2-dev:ppc64el (10.46-1) ... 1034s Setting up gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1034s Setting up libtk8.6:ppc64el (8.6.17-1) ... 1034s Setting up libpango-1.0-0:ppc64el (1.57.0-1) ... 1034s Setting up libreadline-dev:ppc64el (8.3-3) ... 1034s Setting up libcairo2:ppc64el (1.18.4-3) ... 1034s Setting up gcc-15 (15.2.0-12ubuntu1) ... 1034s Setting up libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 1034s Setting up gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1034s Setting up libxt6t64:ppc64el (1:1.2.1-1.3) ... 1034s Setting up gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1034s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1034s Setting up cpp (4:15.2.0-4ubuntu1) ... 1034s Setting up libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 1034s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 1034s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 1034s Setting up libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 1034s Setting up g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 1034s Setting up libpng-dev:ppc64el (1.6.54-1) ... 1034s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 1034s Setting up gcc (4:15.2.0-4ubuntu1) ... 1034s Setting up gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1034s Setting up r-base-core (4.5.2-1ubuntu2) ... 1035s Creating config file /etc/R/Renviron with new version 1035s Setting up r-cran-labeling (0.4.3-1) ... 1035s Setting up r-cran-lattice (0.22-7-1) ... 1035s Setting up r-cran-nlme (3.1.168-1) ... 1035s Setting up r-cran-farver (2.1.2-1) ... 1035s Setting up r-cran-viridislite (0.4.3-1) ... 1035s Setting up r-cran-statmod (1.5.0-1) ... 1035s Setting up r-cran-nnet (7.3-20-1) ... 1035s Setting up r-cran-r6 (2.6.1-1) ... 1035s Setting up r-cran-pkgkitten (0.2.4-1) ... 1035s Setting up r-cran-numderiv (2016.8-1.1-3build1) ... 1035s Setting up g++-15 (15.2.0-12ubuntu1) ... 1035s Setting up r-cran-magrittr (2.0.3-1) ... 1035s Setting up r-cran-microbenchmark (1.5.0-1) ... 1035s Setting up r-cran-quadprog (1.5-8-1build2) ... 1035s Setting up g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 1035s Setting up r-cran-littler (0.3.22-1) ... 1035s Setting up r-cran-rcpp (1.1.0-1) ... 1035s Setting up r-cran-curl (7.0.0+dfsg-1) ... 1035s Setting up r-cran-nloptr (2.2.1-2) ... 1035s Setting up r-cran-boot (1.3-32-1) ... 1035s Setting up r-cran-rlang (1.1.5-3) ... 1035s Setting up r-cran-xfun (0.55+dfsg-1) ... 1035s Setting up r-cran-urca (1.3-4-1build1) ... 1035s Setting up r-cran-withr (3.0.2+dfsg-1) ... 1035s Setting up r-cran-backports (1.5.0-2) ... 1035s Setting up r-cran-deriv (4.2.0-1) ... 1035s Setting up r-cran-generics (0.1.4-1) ... 1035s Setting up r-cran-yaml (2.3.10-1) ... 1035s Setting up r-cran-evaluate (1.0.5-1) ... 1035s Setting up r-cran-timedate (4052.112-1) ... 1035s Setting up r-cran-highr (0.11+dfsg-1) ... 1035s Setting up r-cran-fansi (1.0.6-2) ... 1035s Setting up r-cran-mass (7.3-65-1) ... 1035s Setting up r-cran-glue (1.8.0-1) ... 1035s Setting up r-cran-fracdiff (1.5-3-1) ... 1035s Setting up r-cran-cli (3.6.4-1) ... 1035s Setting up gfortran (4:15.2.0-4ubuntu1) ... 1035s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1035s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 1035s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 1035s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 1035s Setting up r-cran-rbibutils (2.3-1) ... 1035s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 1035s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 1035s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 1035s Setting up r-cran-utf8 (1.2.4-1) ... 1035s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 1035s Setting up r-cran-stringi (1.8.4-1build2) ... 1035s Setting up r-cran-s7 (0.2.0-1) ... 1035s Setting up r-cran-cpp11 (0.5.3-1) ... 1035s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 1035s Setting up r-cran-isoband (0.2.7-1) ... 1035s Setting up r-cran-scales (1.4.0-1) ... 1035s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 1035s Setting up r-cran-zoo (1.8-15-1) ... 1035s Setting up r-cran-matrix (1.7-4-1) ... 1035s Setting up r-cran-knitr (1.51+dfsg-1) ... 1035s Setting up g++ (4:15.2.0-4ubuntu1) ... 1035s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1035s Setting up r-cran-lmtest (0.9.40-1build1) ... 1035s Setting up build-essential (12.12ubuntu2) ... 1035s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 1035s Setting up r-cran-vctrs (0.6.5-1) ... 1035s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 1035s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 1035s Setting up r-cran-minqa (1.2.8-1) ... 1035s Setting up r-base-dev (4.5.2-1ubuntu2) ... 1035s Setting up r-cran-stringr (1.5.1-1) ... 1035s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ... 1035s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 1035s Setting up r-cran-xts (0.14.1-1) ... 1035s Setting up r-cran-rdpack (2.6.3-1) ... 1035s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 1035s Setting up r-cran-purrr (1.0.4-1) ... 1035s Setting up pkg-r-autopkgtest (20250812) ... 1035s Setting up r-cran-dplyr (1.1.4-4) ... 1035s Setting up r-cran-reformulas (0.4.4-1) ... 1035s Setting up r-cran-ttr (0.24.4-1) ... 1035s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 1035s Setting up r-cran-lme4 (1.1-38-1) ... 1035s Setting up r-cran-lmertest (3.2-0-1) ... 1035s Setting up r-cran-tidyr (1.3.1-1) ... 1035s Setting up r-cran-quantmod (0.4.28-1) ... 1035s Setting up r-cran-tseries (0.10-59-3) ... 1035s Setting up r-cran-broom (1.0.12+dfsg-1) ... 1035s Setting up r-cran-forecast (8.23.0-1) ... 1035s Setting up r-cran-modelr (0.1.11-1) ... 1035s Setting up r-cran-doby (4.7.1-3) ... 1035s Setting up r-cran-pbkrtest (0.5.5-1) ... 1035s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1035s Processing triggers for man-db (2.13.1-1build1) ... 1036s Processing triggers for install-info (7.2-5) ... 1038s autopkgtest [23:44:11]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1038s autopkgtest [23:44:11]: test pkg-r-autopkgtest: [----------------------- 1038s Test: Try to load the R library lmerTest 1038s 1038s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1038s Copyright (C) 2025 The R Foundation for Statistical Computing 1038s Platform: powerpc64le-unknown-linux-gnu 1038s 1038s R is free software and comes with ABSOLUTELY NO WARRANTY. 1038s You are welcome to redistribute it under certain conditions. 1038s Type 'license()' or 'licence()' for distribution details. 1038s 1038s R is a collaborative project with many contributors. 1038s Type 'contributors()' for more information and 1038s 'citation()' on how to cite R or R packages in publications. 1038s 1038s Type 'demo()' for some demos, 'help()' for on-line help, or 1038s 'help.start()' for an HTML browser interface to help. 1038s Type 'q()' to quit R. 1038s 1038s > library('lmerTest') 1038s Loading required package: lme4 1038s Loading required package: Matrix 1040s 1040s Attaching package: ‘lmerTest’ 1040s 1040s > 1040s The following object is masked from ‘package:lme4’: 1040s 1040s lmer 1040s 1040s The following object is masked from ‘package:stats’: 1040s 1040s step 1040s 1040s autopkgtest [23:44:13]: test pkg-r-autopkgtest: -----------------------] 1041s autopkgtest [23:44:14]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1041s pkg-r-autopkgtest PASS 1041s autopkgtest [23:44:14]: @@@@@@@@@@@@@@@@@@@@ summary 1041s run-unit-test PASS 1041s pkg-r-autopkgtest PASS