0s autopkgtest [19:02:27]: starting date and time: 2024-03-16 19:02:27+0000 0s autopkgtest [19:02:27]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:02:27]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dec0rcc3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-lmertest --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-2.secgroup --name adt-noble-arm64-r-cran-lmertest-20240316-190227-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 84s autopkgtest [19:03:51]: testbed dpkg architecture: arm64 84s autopkgtest [19:03:51]: testbed apt version: 2.7.12 84s autopkgtest [19:03:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 85s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 85s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3682 kB] 86s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 86s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 86s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 86s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 86s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 86s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 86s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4006 kB] 86s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 86s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 86s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 88s Fetched 9084 kB in 2s (5328 kB/s) 88s Reading package lists... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s Calculating upgrade... 92s The following packages will be REMOVED: 92s libglib2.0-0 libssl3 92s The following NEW packages will be installed: 92s libglib2.0-0t64 libssl3t64 xdg-user-dirs 92s The following packages have been kept back: 92s curl 92s The following packages will be upgraded: 92s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 92s ubuntu-minimal ubuntu-standard 92s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 92s Need to get 4613 kB of archives. 92s After this operation, 211 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 93s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 93s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 93s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 93s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 93s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 93s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 93s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 93s Fetched 4613 kB in 1s (6415 kB/s) 94s (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 ... 74758 files and directories currently installed.) 94s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 94s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 94s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 94s udisks2 depends on libglib2.0-0 (>= 2.77.0). 94s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 94s python3-gi depends on libglib2.0-0 (>= 2.77.0). 94s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 94s netplan.io depends on libglib2.0-0 (>= 2.70.0). 94s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 94s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 94s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 94s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 94s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 94s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 94s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 94s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 94s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 94s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 94s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 94s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 94s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 94s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 94s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 94s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 94s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 94s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 94s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 94s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 94s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 94s fwupd depends on libglib2.0-0 (>= 2.79.0). 94s bolt depends on libglib2.0-0 (>= 2.56.0). 94s 94s (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 ... 74758 files and directories currently installed.) 94s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 94s Selecting previously unselected package libglib2.0-0t64:arm64. 94s (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 ... 74733 files and directories currently installed.) 94s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 94s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 94s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 94s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 94s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 94s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 94s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 94s wget depends on libssl3 (>= 3.0.0). 94s u-boot-tools depends on libssl3 (>= 3.0.0). 94s tnftp depends on libssl3 (>= 3.0.0). 94s tcpdump depends on libssl3 (>= 3.0.0). 94s systemd-resolved depends on libssl3 (>= 3.0.0). 94s systemd depends on libssl3 (>= 3.0.0). 94s sudo depends on libssl3 (>= 3.0.0). 94s sbsigntool depends on libssl3 (>= 3.0.0). 94s rsync depends on libssl3 (>= 3.0.0). 94s python3-cryptography depends on libssl3 (>= 3.0.0). 94s openssh-server depends on libssl3 (>= 3.0.10). 94s openssh-client depends on libssl3 (>= 3.0.10). 94s mtd-utils depends on libssl3 (>= 3.0.0). 94s mokutil depends on libssl3 (>= 3.0.0). 94s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 94s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 94s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 94s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 94s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 94s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 94s libnvme1 depends on libssl3 (>= 3.0.0). 94s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 94s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 94s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 94s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 94s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 94s kmod depends on libssl3 (>= 3.0.0). 94s dhcpcd-base depends on libssl3 (>= 3.0.0). 94s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 94s 94s (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 ... 74758 files and directories currently installed.) 94s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 94s Selecting previously unselected package libssl3t64:arm64. 94s (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 ... 74747 files and directories currently installed.) 94s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 94s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 94s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 94s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 94s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 94s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 94s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 94s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 94s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 94s Unpacking ubuntu-minimal (1.536) over (1.535) ... 94s Selecting previously unselected package xdg-user-dirs. 94s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 94s Unpacking xdg-user-dirs (0.18-1) ... 95s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 95s Unpacking ubuntu-standard (1.536) over (1.535) ... 95s Setting up ubuntu-minimal (1.536) ... 95s Setting up xdg-user-dirs (0.18-1) ... 95s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 95s Setting up libtirpc-common (1.3.4+ds-1.1) ... 95s Setting up ubuntu-standard (1.536) ... 95s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 95s No schema files found: doing nothing. 95s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 95s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 95s Setting up openssl (3.0.13-0ubuntu1) ... 95s Setting up readline-common (8.2-3.1) ... 95s Processing triggers for man-db (2.12.0-3) ... 95s Processing triggers for install-info (7.1-3) ... 95s Processing triggers for libc-bin (2.39-0ubuntu2) ... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 97s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 97s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 97s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 98s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 99s Reading package lists... 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s The following packages have been kept back: 100s curl 100s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 104s autopkgtest [19:04:11]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 104s autopkgtest [19:04:11]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-lmertest 107s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-lmertest 3.1-3-2 (dsc) [2223 B] 107s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-lmertest 3.1-3-2 (tar) [196 kB] 107s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-lmertest 3.1-3-2 (diff) [3500 B] 107s gpgv: Signature made Tue Oct 11 09:02:40 2022 UTC 107s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 107s gpgv: issuer "tille@debian.org" 107s gpgv: Can't check signature: No public key 107s dpkg-source: warning: cannot verify inline signature for ./r-cran-lmertest_3.1-3-2.dsc: no acceptable signature found 107s autopkgtest [19:04:14]: testing package r-cran-lmertest version 3.1-3-2 108s autopkgtest [19:04:15]: build not needed 109s autopkgtest [19:04:16]: test run-unit-test: preparing testbed 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 112s The following additional packages will be installed: 112s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 112s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libcurl4t64 112s libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 112s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 112s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 112s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 112s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 112s libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 libthai-data 112s libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 112s libxft2 libxrender1 libxss1 libxt6t64 littler node-normalize.css r-base-core 112s r-cran-backports r-cran-boot r-cran-brio r-cran-broom r-cran-callr 112s r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-desc 112s r-cran-diffobj r-cran-digest r-cran-dplyr r-cran-ellipsis 112s r-cran-estimability r-cran-evaluate r-cran-fansi r-cran-farver 112s r-cran-foreign r-cran-fs r-cran-generics r-cran-ggplot2 r-cran-glue 112s r-cran-gtable r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr 112s r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 112s r-cran-lmertest r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv 112s r-cran-minqa r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-nnet 112s r-cran-numderiv r-cran-pbkrtest r-cran-pillar r-cran-pkgbuild 112s r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise 112s r-cran-processx r-cran-ps r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 112s r-cran-rcpp r-cran-rcppeigen r-cran-rematch2 r-cran-rlang r-cran-rprojroot 112s r-cran-scales r-cran-statmod r-cran-stringi r-cran-stringr r-cran-testthat 112s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 112s r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xfun r-cran-yaml unzip 112s x11-common xdg-utils zip 112s Suggested packages: 112s fonts-mathjax-extras fonts-stix libjs-mathjax-doc tcl8.6 tk8.6 112s libjs-html5shiv elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 112s r-cran-aer r-cran-bbmle r-cran-car r-cran-cardata r-cran-caret 112s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 112s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-geepack 112s r-cran-glmnet r-cran-gmm r-cran-hmisc r-cran-irlba r-cran-interp r-cran-ks 112s r-cran-lavaan r-cran-leaps r-cran-lmtest r-cran-lsmeans r-cran-maps 112s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 112s r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg r-cran-rmarkdown 112s r-cran-robust r-cran-robustbase r-cran-rsample r-cran-sandwich r-cran-sp 112s r-cran-spdep r-cran-spatialreg r-cran-spelling r-cran-survey r-cran-survival 112s r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth r-cran-kernlab 112s r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-png r-cran-jpeg 112s r-cran-viridis r-cran-rstudioapi r-cran-markdown r-cran-magick r-cran-sf 112s r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime 112s r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-inline r-cran-bench 112s r-cran-blob r-cran-here r-cran-hms r-cran-htmltools 112s Recommended packages: 112s javascript-common r-recommended r-base-dev r-doc-html r-cran-covr 112s r-cran-cliapp r-cran-mockery r-cran-htmltools r-cran-htmlwidgets 112s r-cran-rmarkdown r-cran-rstudioapi r-cran-whoami r-cran-bench r-cran-decor 112s r-cran-lobstr r-cran-progress r-cran-gh r-cran-spelling r-cran-dbi 112s r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite 112s r-cran-unitizer r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps 112s r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart 112s r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-testit r-cran-httr 112s r-cran-r.rsp r-cran-bslib r-cran-codetools r-cran-formatr r-cran-gridsvg 112s r-cran-curl r-cran-jpeg r-cran-magick r-cran-markdown r-cran-png 112s r-cran-reticulate r-cran-rgl r-cran-sass r-cran-tikzdevice r-cran-tinytex 112s r-cran-webshot node-highlight.js r-cran-lintr r-cran-tidyverse 112s r-cran-lubridate r-cran-bitops r-cran-mathjaxr r-cran-mockr r-cran-remotes 112s r-cran-webfakes r-cran-pingr r-cran-usethis r-cran-bit64 r-cran-dichromat 112s r-cran-hms r-cran-shiny r-cran-data.table r-cran-formattable r-cran-readr 112s r-cran-pkgdown r-cran-zeallot r-cran-mime r-cran-renv r-cran-runit 112s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 112s x11-xserver-utils 112s The following packages will be REMOVED: 112s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 112s The following NEW packages will be installed: 112s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 112s fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax libblas3 112s libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 112s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 112s libjpeg8 libjs-bootstrap libjs-highlight.js libjs-jquery 112s libjs-jquery-datatables libjs-mathjax liblapack3 liblerc4 libnlopt0 112s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 112s libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 112s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc3t64 112s libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 112s libxt6t64 littler node-normalize.css r-base-core r-cran-backports 112s r-cran-boot r-cran-brio r-cran-broom r-cran-callr r-cran-cli 112s r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-desc r-cran-diffobj 112s r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-estimability 112s r-cran-evaluate r-cran-fansi r-cran-farver r-cran-foreign r-cran-fs 112s r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr 112s r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling r-cran-lattice 112s r-cran-lifecycle r-cran-littler r-cran-lme4 r-cran-lmertest r-cran-magrittr 112s r-cran-mass r-cran-matrix r-cran-mgcv r-cran-minqa r-cran-munsell 112s r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-pbkrtest 112s r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten 112s r-cran-pkgload r-cran-praise r-cran-processx r-cran-ps r-cran-purrr 112s r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen r-cran-rematch2 112s r-cran-rlang r-cran-rprojroot r-cran-scales r-cran-statmod r-cran-stringi 112s r-cran-stringr r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect 112s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr 112s r-cran-xfun r-cran-yaml unzip x11-common xdg-utils zip 112s The following packages will be upgraded: 112s curl 112s 1 upgraded, 136 newly installed, 5 to remove and 0 not upgraded. 112s Need to get 99.7 MB/99.7 MB of archives. 112s After this operation, 226 MB of additional disk space will be used. 112s Get:1 /tmp/autopkgtest.5HkFOC/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [736 B] 112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 113s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 113s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 113s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 113s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 113s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 113s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 113s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 113s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 113s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 113s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 113s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 113s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 113s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 113s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 113s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 113s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 113s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 113s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 113s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 113s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 113s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 113s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 113s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 113s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 113s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 113s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 113s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 113s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 113s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 113s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 113s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 113s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 113s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 113s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 113s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 113s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 113s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 113s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 113s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 113s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 113s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 113s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 113s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 113s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 113s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 113s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 113s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 113s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 113s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 113s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 113s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 114s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 114s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 114s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 114s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 114s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 114s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-brio arm64 1.1.4-1 [37.7 kB] 114s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 114s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 114s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 114s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 114s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 114s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 114s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 114s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 114s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 114s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 114s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 114s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 114s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 114s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 114s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 114s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 114s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 114s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 114s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 114s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 114s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 114s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 114s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 114s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ps arm64 1.7.6-1 [313 kB] 114s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-processx arm64 3.8.3-1 [345 kB] 114s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-callr all 3.7.3-2 [425 kB] 114s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 115s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 115s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-desc all 1.4.3-1 [359 kB] 115s Get:93 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB] 115s Get:94 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 115s Get:95 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-estimability all 1.4.1-1 [42.7 kB] 115s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 115s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 115s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-foreign arm64 0.8.86-1 [240 kB] 115s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 115s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 115s Get:101 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 115s Get:102 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 115s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 115s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 115s Get:105 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 115s Get:106 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 116s Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 116s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 116s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 116s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 116s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 116s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 116s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 116s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 116s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 116s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 116s Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 116s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 116s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 116s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 116s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-minqa arm64 1.2.6-1 [107 kB] 116s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 libnlopt0 arm64 2.7.1-5build2 [174 kB] 116s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgbuild all 1.4.3-1 [209 kB] 116s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rprojroot all 2.0.4-1 [124 kB] 116s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgload all 1.3.4-1 [207 kB] 116s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 116s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 116s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-waldo all 0.5.2-1build1 [120 kB] 116s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-testthat arm64 3.2.1-1 [1678 kB] 116s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nloptr arm64 2.0.3-1 [375 kB] 116s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 116s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 116s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lme4 arm64 1.1-35.1-4 [4116 kB] 116s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 116s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lmertest all 3.1-3-2 [543 kB] 116s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nnet arm64 7.3-19-2 [111 kB] 116s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pbkrtest all 0.5.2-2 [182 kB] 118s Preconfiguring packages ... 118s Fetched 99.7 MB in 4s (23.0 MB/s) 118s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 118s wget depends on libpsl5 (>= 0.16.0). 118s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 118s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 118s 118s (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 ... 74774 files and directories currently installed.) 118s Removing libpsl5:arm64 (0.21.2-1build1) ... 118s Selecting previously unselected package libpsl5t64:arm64. 118s (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 ... 74769 files and directories currently installed.) 118s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 118s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 118s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 118s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 118s (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 ... 74775 files and directories currently installed.) 118s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 119s Selecting previously unselected package libcurl4t64:arm64. 119s (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 ... 74770 files and directories currently installed.) 119s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 119s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 119s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 119s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 119s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 119s 119s (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 ... 74776 files and directories currently installed.) 119s Removing libpng16-16:arm64 (1.6.43-1) ... 119s Selecting previously unselected package libpng16-16t64:arm64. 119s (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 ... 74766 files and directories currently installed.) 119s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 119s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 119s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 119s parted depends on libreadline8 (>= 6.0). 119s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 119s gpgsm depends on libreadline8 (>= 6.0). 119s gpgconf depends on libreadline8 (>= 6.0). 119s gpg depends on libreadline8 (>= 6.0). 119s gawk depends on libreadline8 (>= 6.0). 119s fdisk depends on libreadline8 (>= 6.0). 119s 119s (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 ... 74777 files and directories currently installed.) 119s Removing libreadline8:arm64 (8.2-3) ... 119s Selecting previously unselected package libreadline8t64:arm64. 119s (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 ... 74765 files and directories currently installed.) 119s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 119s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 119s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 119s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 119s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 119s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 119s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 119s lsof depends on libtirpc3 (>= 1.0.2). 119s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 119s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 119s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 119s iproute2 depends on libtirpc3 (>= 1.0.2). 119s 119s (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 ... 74785 files and directories currently installed.) 119s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 119s Selecting previously unselected package libtirpc3t64:arm64. 119s (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 ... 74779 files and directories currently installed.) 119s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 119s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 119s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 119s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 119s Selecting previously unselected package fonts-dejavu-mono. 119s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ... 119s Unpacking fonts-dejavu-mono (2.37-8) ... 120s Selecting previously unselected package fonts-dejavu-core. 120s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ... 120s Unpacking fonts-dejavu-core (2.37-8) ... 120s Selecting previously unselected package fontconfig-config. 120s Preparing to unpack .../003-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 120s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 120s Selecting previously unselected package libfontconfig1:arm64. 120s Preparing to unpack .../004-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 120s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 120s Selecting previously unselected package fontconfig. 120s Preparing to unpack .../005-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 120s Unpacking fontconfig (2.15.0-1ubuntu1) ... 120s Selecting previously unselected package fonts-glyphicons-halflings. 120s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 120s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 120s Selecting previously unselected package fonts-mathjax. 120s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 120s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 120s Selecting previously unselected package libblas3:arm64. 120s Preparing to unpack .../008-libblas3_3.12.0-3_arm64.deb ... 120s Unpacking libblas3:arm64 (3.12.0-3) ... 121s Selecting previously unselected package libpixman-1-0:arm64. 121s Preparing to unpack .../009-libpixman-1-0_0.42.2-1_arm64.deb ... 121s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 121s Selecting previously unselected package libxcb-render0:arm64. 121s Preparing to unpack .../010-libxcb-render0_1.15-1_arm64.deb ... 121s Unpacking libxcb-render0:arm64 (1.15-1) ... 121s Selecting previously unselected package libxcb-shm0:arm64. 121s Preparing to unpack .../011-libxcb-shm0_1.15-1_arm64.deb ... 121s Unpacking libxcb-shm0:arm64 (1.15-1) ... 121s Selecting previously unselected package libxrender1:arm64. 121s Preparing to unpack .../012-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 121s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 121s Selecting previously unselected package libcairo2:arm64. 121s Preparing to unpack .../013-libcairo2_1.18.0-1_arm64.deb ... 121s Unpacking libcairo2:arm64 (1.18.0-1) ... 121s Selecting previously unselected package libdatrie1:arm64. 121s Preparing to unpack .../014-libdatrie1_0.2.13-3_arm64.deb ... 121s Unpacking libdatrie1:arm64 (0.2.13-3) ... 121s Selecting previously unselected package libdeflate0:arm64. 121s Preparing to unpack .../015-libdeflate0_1.19-1_arm64.deb ... 121s Unpacking libdeflate0:arm64 (1.19-1) ... 121s Selecting previously unselected package libgfortran5:arm64. 121s Preparing to unpack .../016-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 121s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 121s Selecting previously unselected package libgomp1:arm64. 121s Preparing to unpack .../017-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 121s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 121s Selecting previously unselected package libgraphite2-3:arm64. 121s Preparing to unpack .../018-libgraphite2-3_1.3.14-2_arm64.deb ... 121s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 122s Selecting previously unselected package libharfbuzz0b:arm64. 122s Preparing to unpack .../019-libharfbuzz0b_8.3.0-2_arm64.deb ... 122s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 122s Selecting previously unselected package x11-common. 122s Preparing to unpack .../020-x11-common_1%3a7.7+23ubuntu2_all.deb ... 122s Unpacking x11-common (1:7.7+23ubuntu2) ... 122s Selecting previously unselected package libice6:arm64. 122s Preparing to unpack .../021-libice6_2%3a1.0.10-1build2_arm64.deb ... 122s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 122s Selecting previously unselected package libjpeg-turbo8:arm64. 122s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 122s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 122s Selecting previously unselected package libjpeg8:arm64. 122s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_arm64.deb ... 122s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 122s Selecting previously unselected package libjs-bootstrap. 122s Preparing to unpack .../024-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 122s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 122s Selecting previously unselected package libjs-highlight.js. 122s Preparing to unpack .../025-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 122s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 122s Selecting previously unselected package libjs-jquery. 122s Preparing to unpack .../026-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 122s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 122s Selecting previously unselected package libjs-jquery-datatables. 122s Preparing to unpack .../027-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 122s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 122s Selecting previously unselected package liblapack3:arm64. 123s Preparing to unpack .../028-liblapack3_3.12.0-3_arm64.deb ... 123s Unpacking liblapack3:arm64 (3.12.0-3) ... 123s Selecting previously unselected package liblerc4:arm64. 123s Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 123s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 123s Selecting previously unselected package libthai-data. 123s Preparing to unpack .../030-libthai-data_0.1.29-2_all.deb ... 123s Unpacking libthai-data (0.1.29-2) ... 123s Selecting previously unselected package libthai0:arm64. 123s Preparing to unpack .../031-libthai0_0.1.29-2_arm64.deb ... 123s Unpacking libthai0:arm64 (0.1.29-2) ... 123s Selecting previously unselected package libpango-1.0-0:arm64. 123s Preparing to unpack .../032-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 123s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 123s Selecting previously unselected package libpangoft2-1.0-0:arm64. 123s Preparing to unpack .../033-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 123s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 123s Selecting previously unselected package libpangocairo-1.0-0:arm64. 123s Preparing to unpack .../034-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 123s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 123s Selecting previously unselected package libpaper1:arm64. 123s Preparing to unpack .../035-libpaper1_1.1.29_arm64.deb ... 123s Unpacking libpaper1:arm64 (1.1.29) ... 123s Selecting previously unselected package libpaper-utils. 123s Preparing to unpack .../036-libpaper-utils_1.1.29_arm64.deb ... 123s Unpacking libpaper-utils (1.1.29) ... 123s Selecting previously unselected package libsharpyuv0:arm64. 123s Preparing to unpack .../037-libsharpyuv0_1.3.2-0.4_arm64.deb ... 123s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 124s Selecting previously unselected package libsm6:arm64. 124s Preparing to unpack .../038-libsm6_2%3a1.2.3-1build2_arm64.deb ... 124s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 124s Selecting previously unselected package libtcl8.6:arm64. 124s Preparing to unpack .../039-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 124s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 124s Selecting previously unselected package libjbig0:arm64. 124s Preparing to unpack .../040-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 124s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 124s Selecting previously unselected package libwebp7:arm64. 124s Preparing to unpack .../041-libwebp7_1.3.2-0.4_arm64.deb ... 124s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 124s Selecting previously unselected package libtiff6:arm64. 124s Preparing to unpack .../042-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 124s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 124s Selecting previously unselected package libxft2:arm64. 124s Preparing to unpack .../043-libxft2_2.3.6-1_arm64.deb ... 124s Unpacking libxft2:arm64 (2.3.6-1) ... 124s Selecting previously unselected package libxss1:arm64. 124s Preparing to unpack .../044-libxss1_1%3a1.2.3-1build2_arm64.deb ... 124s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 124s Selecting previously unselected package libtk8.6:arm64. 124s Preparing to unpack .../045-libtk8.6_8.6.13-2_arm64.deb ... 124s Unpacking libtk8.6:arm64 (8.6.13-2) ... 124s Selecting previously unselected package libxt6t64:arm64. 124s Preparing to unpack .../046-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 124s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 124s Selecting previously unselected package zip. 124s Preparing to unpack .../047-zip_3.0-13_arm64.deb ... 124s Unpacking zip (3.0-13) ... 124s Selecting previously unselected package unzip. 124s Preparing to unpack .../048-unzip_6.0-28ubuntu3_arm64.deb ... 124s Unpacking unzip (6.0-28ubuntu3) ... 125s Selecting previously unselected package xdg-utils. 125s Preparing to unpack .../049-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 125s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 125s Selecting previously unselected package r-base-core. 125s Preparing to unpack .../050-r-base-core_4.3.3-2build1_arm64.deb ... 125s Unpacking r-base-core (4.3.3-2build1) ... 125s Selecting previously unselected package r-cran-littler. 125s Preparing to unpack .../051-r-cran-littler_0.3.19-1_arm64.deb ... 125s Unpacking r-cran-littler (0.3.19-1) ... 125s Selecting previously unselected package littler. 125s Preparing to unpack .../052-littler_0.3.19-1_all.deb ... 125s Unpacking littler (0.3.19-1) ... 125s Selecting previously unselected package node-normalize.css. 125s Preparing to unpack .../053-node-normalize.css_8.0.1-5_all.deb ... 125s Unpacking node-normalize.css (8.0.1-5) ... 125s Selecting previously unselected package r-cran-backports. 125s Preparing to unpack .../054-r-cran-backports_1.4.1-1_arm64.deb ... 125s Unpacking r-cran-backports (1.4.1-1) ... 125s Selecting previously unselected package r-cran-boot. 125s Preparing to unpack .../055-r-cran-boot_1.3-30-1_all.deb ... 125s Unpacking r-cran-boot (1.3-30-1) ... 125s Selecting previously unselected package r-cran-brio. 125s Preparing to unpack .../056-r-cran-brio_1.1.4-1_arm64.deb ... 125s Unpacking r-cran-brio (1.1.4-1) ... 126s Selecting previously unselected package r-cran-cli. 126s Preparing to unpack .../057-r-cran-cli_3.6.2-1_arm64.deb ... 126s Unpacking r-cran-cli (3.6.2-1) ... 126s Selecting previously unselected package r-cran-generics. 126s Preparing to unpack .../058-r-cran-generics_0.1.3-1_all.deb ... 126s Unpacking r-cran-generics (0.1.3-1) ... 126s Selecting previously unselected package r-cran-glue. 126s Preparing to unpack .../059-r-cran-glue_1.7.0-1_arm64.deb ... 126s Unpacking r-cran-glue (1.7.0-1) ... 126s Selecting previously unselected package r-cran-rlang. 126s Preparing to unpack .../060-r-cran-rlang_1.1.3-1_arm64.deb ... 126s Unpacking r-cran-rlang (1.1.3-1) ... 126s Selecting previously unselected package r-cran-lifecycle. 126s Preparing to unpack .../061-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 126s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 126s Selecting previously unselected package r-cran-magrittr. 126s Preparing to unpack .../062-r-cran-magrittr_2.0.3-1_arm64.deb ... 126s Unpacking r-cran-magrittr (2.0.3-1) ... 126s Selecting previously unselected package r-cran-fansi. 126s Preparing to unpack .../063-r-cran-fansi_1.0.5-1_arm64.deb ... 126s Unpacking r-cran-fansi (1.0.5-1) ... 126s Selecting previously unselected package r-cran-utf8. 126s Preparing to unpack .../064-r-cran-utf8_1.2.4-1_arm64.deb ... 126s Unpacking r-cran-utf8 (1.2.4-1) ... 126s Selecting previously unselected package r-cran-vctrs. 126s Preparing to unpack .../065-r-cran-vctrs_0.6.5-1_arm64.deb ... 126s Unpacking r-cran-vctrs (0.6.5-1) ... 126s Selecting previously unselected package r-cran-pillar. 126s Preparing to unpack .../066-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 126s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 126s Selecting previously unselected package r-cran-r6. 126s Preparing to unpack .../067-r-cran-r6_2.5.1-1_all.deb ... 126s Unpacking r-cran-r6 (2.5.1-1) ... 126s Selecting previously unselected package r-cran-pkgconfig. 126s Preparing to unpack .../068-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 126s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 126s Selecting previously unselected package r-cran-tibble. 126s Preparing to unpack .../069-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 126s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 126s Selecting previously unselected package r-cran-withr. 126s Preparing to unpack .../070-r-cran-withr_2.5.0-1_all.deb ... 126s Unpacking r-cran-withr (2.5.0-1) ... 127s Selecting previously unselected package r-cran-tidyselect. 127s Preparing to unpack .../071-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 127s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 127s Selecting previously unselected package r-cran-dplyr. 127s Preparing to unpack .../072-r-cran-dplyr_1.1.4-1_arm64.deb ... 127s Unpacking r-cran-dplyr (1.1.4-1) ... 127s Selecting previously unselected package r-cran-ellipsis. 127s Preparing to unpack .../073-r-cran-ellipsis_0.3.2-2_arm64.deb ... 127s Unpacking r-cran-ellipsis (0.3.2-2) ... 127s Selecting previously unselected package r-cran-purrr. 127s Preparing to unpack .../074-r-cran-purrr_1.0.2-1_arm64.deb ... 127s Unpacking r-cran-purrr (1.0.2-1) ... 127s Selecting previously unselected package r-cran-stringi. 127s Preparing to unpack .../075-r-cran-stringi_1.8.3-1_arm64.deb ... 127s Unpacking r-cran-stringi (1.8.3-1) ... 127s Selecting previously unselected package r-cran-stringr. 127s Preparing to unpack .../076-r-cran-stringr_1.5.1-1_all.deb ... 127s Unpacking r-cran-stringr (1.5.1-1) ... 127s Selecting previously unselected package r-cran-cpp11. 127s Preparing to unpack .../077-r-cran-cpp11_0.4.7-1_all.deb ... 127s Unpacking r-cran-cpp11 (0.4.7-1) ... 127s Selecting previously unselected package r-cran-tidyr. 127s Preparing to unpack .../078-r-cran-tidyr_1.3.1-1_arm64.deb ... 127s Unpacking r-cran-tidyr (1.3.1-1) ... 127s Selecting previously unselected package r-cran-broom. 127s Preparing to unpack .../079-r-cran-broom_1.0.5+dfsg-1_all.deb ... 127s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 127s Selecting previously unselected package r-cran-ps. 127s Preparing to unpack .../080-r-cran-ps_1.7.6-1_arm64.deb ... 127s Unpacking r-cran-ps (1.7.6-1) ... 127s Selecting previously unselected package r-cran-processx. 127s Preparing to unpack .../081-r-cran-processx_3.8.3-1_arm64.deb ... 127s Unpacking r-cran-processx (3.8.3-1) ... 127s Selecting previously unselected package r-cran-callr. 127s Preparing to unpack .../082-r-cran-callr_3.7.3-2_all.deb ... 127s Unpacking r-cran-callr (3.7.3-2) ... 127s Selecting previously unselected package r-cran-colorspace. 127s Preparing to unpack .../083-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 128s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 128s Selecting previously unselected package r-cran-crayon. 128s Preparing to unpack .../084-r-cran-crayon_1.5.2-1_all.deb ... 128s Unpacking r-cran-crayon (1.5.2-1) ... 128s Selecting previously unselected package r-cran-desc. 128s Preparing to unpack .../085-r-cran-desc_1.4.3-1_all.deb ... 128s Unpacking r-cran-desc (1.4.3-1) ... 128s Selecting previously unselected package r-cran-diffobj. 128s Preparing to unpack .../086-r-cran-diffobj_0.3.5-1_arm64.deb ... 128s Unpacking r-cran-diffobj (0.3.5-1) ... 128s Selecting previously unselected package r-cran-digest. 128s Preparing to unpack .../087-r-cran-digest_0.6.34-1_arm64.deb ... 128s Unpacking r-cran-digest (0.6.34-1) ... 128s Selecting previously unselected package r-cran-estimability. 128s Preparing to unpack .../088-r-cran-estimability_1.4.1-1_all.deb ... 128s Unpacking r-cran-estimability (1.4.1-1) ... 128s Selecting previously unselected package r-cran-evaluate. 128s Preparing to unpack .../089-r-cran-evaluate_0.23-1_all.deb ... 128s Unpacking r-cran-evaluate (0.23-1) ... 128s Selecting previously unselected package r-cran-farver. 128s Preparing to unpack .../090-r-cran-farver_2.1.1-1_arm64.deb ... 128s Unpacking r-cran-farver (2.1.1-1) ... 128s Selecting previously unselected package r-cran-foreign. 128s Preparing to unpack .../091-r-cran-foreign_0.8.86-1_arm64.deb ... 128s Unpacking r-cran-foreign (0.8.86-1) ... 128s Selecting previously unselected package r-cran-fs. 128s Preparing to unpack .../092-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 128s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 128s Selecting previously unselected package r-cran-gtable. 128s Preparing to unpack .../093-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 128s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 128s Selecting previously unselected package r-cran-isoband. 128s Preparing to unpack .../094-r-cran-isoband_0.2.7-1_arm64.deb ... 128s Unpacking r-cran-isoband (0.2.7-1) ... 128s Selecting previously unselected package r-cran-mass. 128s Preparing to unpack .../095-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 128s Unpacking r-cran-mass (7.3-60.0.1-1) ... 128s Selecting previously unselected package r-cran-lattice. 128s Preparing to unpack .../096-r-cran-lattice_0.22-5-1_arm64.deb ... 128s Unpacking r-cran-lattice (0.22-5-1) ... 128s Selecting previously unselected package r-cran-nlme. 129s Preparing to unpack .../097-r-cran-nlme_3.1.164-1_arm64.deb ... 129s Unpacking r-cran-nlme (3.1.164-1) ... 129s Selecting previously unselected package r-cran-matrix. 129s Preparing to unpack .../098-r-cran-matrix_1.6-5-1_arm64.deb ... 129s Unpacking r-cran-matrix (1.6-5-1) ... 129s Selecting previously unselected package r-cran-mgcv. 129s Preparing to unpack .../099-r-cran-mgcv_1.9-1-1_arm64.deb ... 129s Unpacking r-cran-mgcv (1.9-1-1) ... 129s Selecting previously unselected package r-cran-labeling. 129s Preparing to unpack .../100-r-cran-labeling_0.4.3-1_all.deb ... 129s Unpacking r-cran-labeling (0.4.3-1) ... 129s Selecting previously unselected package r-cran-munsell. 129s Preparing to unpack .../101-r-cran-munsell_0.5.0-2build1_all.deb ... 129s Unpacking r-cran-munsell (0.5.0-2build1) ... 129s Selecting previously unselected package r-cran-rcolorbrewer. 129s Preparing to unpack .../102-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 129s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 129s Selecting previously unselected package r-cran-viridislite. 129s Preparing to unpack .../103-r-cran-viridislite_0.4.2-2_all.deb ... 129s Unpacking r-cran-viridislite (0.4.2-2) ... 129s Selecting previously unselected package r-cran-scales. 129s Preparing to unpack .../104-r-cran-scales_1.3.0-1_all.deb ... 129s Unpacking r-cran-scales (1.3.0-1) ... 129s Selecting previously unselected package r-cran-ggplot2. 129s Preparing to unpack .../105-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 129s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 129s Selecting previously unselected package r-cran-xfun. 129s Preparing to unpack .../106-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 129s Unpacking r-cran-xfun (0.41+dfsg-1) ... 129s Selecting previously unselected package r-cran-highr. 129s Preparing to unpack .../107-r-cran-highr_0.10+dfsg-1_all.deb ... 129s Unpacking r-cran-highr (0.10+dfsg-1) ... 129s Selecting previously unselected package r-cran-jsonlite. 129s Preparing to unpack .../108-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 129s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 129s Selecting previously unselected package r-cran-yaml. 129s Preparing to unpack .../109-r-cran-yaml_2.3.8-1_arm64.deb ... 129s Unpacking r-cran-yaml (2.3.8-1) ... 129s Selecting previously unselected package libjs-mathjax. 129s Preparing to unpack .../110-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 129s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 130s Selecting previously unselected package r-cran-knitr. 130s Preparing to unpack .../111-r-cran-knitr_1.45+dfsg-1_all.deb ... 130s Unpacking r-cran-knitr (1.45+dfsg-1) ... 130s Selecting previously unselected package r-cran-pkgkitten. 130s Preparing to unpack .../112-r-cran-pkgkitten_0.2.3-1_all.deb ... 130s Unpacking r-cran-pkgkitten (0.2.3-1) ... 130s Selecting previously unselected package r-cran-rcpp. 130s Preparing to unpack .../113-r-cran-rcpp_1.0.12-1_arm64.deb ... 130s Unpacking r-cran-rcpp (1.0.12-1) ... 131s Selecting previously unselected package r-cran-minqa. 131s Preparing to unpack .../114-r-cran-minqa_1.2.6-1_arm64.deb ... 131s Unpacking r-cran-minqa (1.2.6-1) ... 131s Selecting previously unselected package libnlopt0:arm64. 131s Preparing to unpack .../115-libnlopt0_2.7.1-5build2_arm64.deb ... 131s Unpacking libnlopt0:arm64 (2.7.1-5build2) ... 131s Selecting previously unselected package r-cran-pkgbuild. 131s Preparing to unpack .../116-r-cran-pkgbuild_1.4.3-1_all.deb ... 131s Unpacking r-cran-pkgbuild (1.4.3-1) ... 131s Selecting previously unselected package r-cran-rprojroot. 131s Preparing to unpack .../117-r-cran-rprojroot_2.0.4-1_all.deb ... 131s Unpacking r-cran-rprojroot (2.0.4-1) ... 131s Selecting previously unselected package r-cran-pkgload. 131s Preparing to unpack .../118-r-cran-pkgload_1.3.4-1_all.deb ... 131s Unpacking r-cran-pkgload (1.3.4-1) ... 131s Selecting previously unselected package r-cran-praise. 131s Preparing to unpack .../119-r-cran-praise_1.0.0-4build1_all.deb ... 131s Unpacking r-cran-praise (1.0.0-4build1) ... 131s Selecting previously unselected package r-cran-rematch2. 131s Preparing to unpack .../120-r-cran-rematch2_2.1.2-2build1_all.deb ... 131s Unpacking r-cran-rematch2 (2.1.2-2build1) ... 131s Selecting previously unselected package r-cran-waldo. 131s Preparing to unpack .../121-r-cran-waldo_0.5.2-1build1_all.deb ... 131s Unpacking r-cran-waldo (0.5.2-1build1) ... 131s Selecting previously unselected package r-cran-testthat. 131s Preparing to unpack .../122-r-cran-testthat_3.2.1-1_arm64.deb ... 131s Unpacking r-cran-testthat (3.2.1-1) ... 131s Selecting previously unselected package r-cran-nloptr. 131s Preparing to unpack .../123-r-cran-nloptr_2.0.3-1_arm64.deb ... 131s Unpacking r-cran-nloptr (2.0.3-1) ... 131s Selecting previously unselected package r-cran-rcppeigen. 132s Preparing to unpack .../124-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 132s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 132s Selecting previously unselected package r-cran-statmod. 132s Preparing to unpack .../125-r-cran-statmod_1.5.0-1_arm64.deb ... 132s Unpacking r-cran-statmod (1.5.0-1) ... 132s Selecting previously unselected package r-cran-lme4. 132s Preparing to unpack .../126-r-cran-lme4_1.1-35.1-4_arm64.deb ... 132s Unpacking r-cran-lme4 (1.1-35.1-4) ... 132s Selecting previously unselected package r-cran-numderiv. 132s Preparing to unpack .../127-r-cran-numderiv_2016.8-1.1-3_all.deb ... 132s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 132s Selecting previously unselected package r-cran-lmertest. 132s Preparing to unpack .../128-r-cran-lmertest_3.1-3-2_all.deb ... 132s Unpacking r-cran-lmertest 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update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 133s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 133s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 134s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... 134s Setting up libthai0:arm64 (0.1.29-2) ... 134s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 134s Setting up curl (8.5.0-2ubuntu7) ... 134s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 134s Setting up libsm6:arm64 (2:1.2.3-1build2) ... 134s Setting up fontconfig (2.15.0-1ubuntu1) ... 136s Regenerating fonts cache... done. 136s Setting up libxft2:arm64 (2.3.6-1) ... 136s Setting up libtk8.6:arm64 (8.6.13-2) ... 136s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 136s Setting up libcairo2:arm64 (1.18.0-1) ... 136s Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... 136s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 136s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 136s Setting up r-base-core (4.3.3-2build1) ... 136s 136s Creating config file /etc/R/Renviron with new version 136s Setting up r-cran-crayon (1.5.2-1) ... 136s Setting up r-cran-labeling (0.4.3-1) ... 136s Setting up r-cran-lattice (0.22-5-1) ... 136s Setting up r-cran-ps (1.7.6-1) ... 136s Setting up r-cran-nlme (3.1.164-1) ... 136s Setting up r-cran-farver (2.1.1-1) ... 136s Setting up r-cran-viridislite (0.4.2-2) ... 136s Setting up r-cran-statmod (1.5.0-1) ... 136s Setting up r-cran-nnet (7.3-19-2) ... 136s Setting up r-cran-r6 (2.5.1-1) ... 136s Setting up r-cran-pkgkitten (0.2.3-1) ... 136s Setting up r-cran-numderiv (2016.8-1.1-3) ... 136s Setting up r-cran-magrittr (2.0.3-1) ... 136s Setting up r-cran-littler (0.3.19-1) ... 136s Setting up r-cran-fs (1.6.3+dfsg-1) ... 136s Setting up r-cran-rcpp (1.0.12-1) ... 136s Setting up r-cran-brio (1.1.4-1) ... 136s Setting up r-cran-estimability (1.4.1-1) ... 136s Setting up 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Removing autopkgtest-satdep (0) ... 152s autopkgtest [19:04:59]: test run-unit-test: [----------------------- 153s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 153s BEGIN TEST test_a_utils.R 153s 153s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 153s Copyright (C) 2024 The R Foundation for Statistical Computing 153s Platform: aarch64-unknown-linux-gnu (64-bit) 153s 153s R is free software and comes with ABSOLUTELY NO WARRANTY. 153s You are welcome to redistribute it under certain conditions. 153s Type 'license()' or 'licence()' for distribution details. 153s 153s R is a collaborative project with many contributors. 153s Type 'contributors()' for more information and 153s 'citation()' on how to cite R or R packages in publications. 153s 153s Type 'demo()' for some demos, 'help()' for on-line help, or 153s 'help.start()' for an HTML browser interface to help. 153s Type 'q()' to quit R. 153s 153s > # test_a_utils.R 153s > 153s > library(lmerTest) 153s Loading required package: lme4 153s Loading required package: Matrix 156s 156s Attaching package: 'lmerTest' 156s 156s The following object is masked from 'package:lme4': 156s 156s lmer 156s 156s The following object is masked from 'package:stats': 156s 156s step 156s 156s > 156s > # test safeDeparse() - equivalence and differences to deparse(): 156s > deparse_args <- formals(deparse) 156s > safeDeparse_args <- formals(lmerTest:::safeDeparse) 156s > stopifnot( 156s + all.equal(names(deparse_args), names(safeDeparse_args)), 156s + all.equal(deparse_args[!names(deparse_args) %in% c("control", "width.cutoff")], 156s + safeDeparse_args[!names(safeDeparse_args) %in% c("control", "width.cutoff")]), 156s + all.equal(deparse_args[["width.cutoff"]], 60L), 156s + all(eval(safeDeparse_args[["control"]]) %in% eval(deparse_args[["control"]])), 156s + all.equal(safeDeparse_args[["width.cutoff"]], 500L) 156s + ) 156s > 156s > 157s BEGIN TEST test_anova.R 157s 157s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 157s Copyright (C) 2024 The R Foundation for Statistical Computing 157s Platform: aarch64-unknown-linux-gnu (64-bit) 157s 157s R is free software and comes with ABSOLUTELY NO WARRANTY. 157s You are welcome to redistribute it under certain conditions. 157s Type 'license()' or 'licence()' for distribution details. 157s 157s R is a collaborative project with many contributors. 157s Type 'contributors()' for more information and 157s 'citation()' on how to cite R or R packages in publications. 157s 157s Type 'demo()' for some demos, 'help()' for on-line help, or 157s 'help.start()' for an HTML browser interface to help. 157s Type 'q()' to quit R. 157s 157s > # test_anova.R 157s > library(lmerTest) 157s Loading required package: lme4 157s Loading required package: Matrix 159s 159s Attaching package: 'lmerTest' 159s 159s The following object is masked from 'package:lme4': 159s 159s lmer 159s 159s The following object is masked from 'package:stats': 159s 159s step 159s 159s > 159s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 159s > # even in tests: 159s > assertError <- function(expr, ...) 159s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 159s > assertWarning <- function(expr, ...) 159s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 159s > 159s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 159s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 159s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 159s > 159s > data("sleepstudy", package="lme4") 159s > TOL <- 1e-4 159s > 159s > #################################### 159s > ## Basic anova tests 159s > #################################### 159s > 159s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 160s > 160s > ####### ddf argument: 160s > (an1 <- anova(m)) # Also testing print method. 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2 <- anova(m, ddf="Satterthwaite")) 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2b <- anova(m, ddf="Satterthwaite", type=3)) 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2c <- anova(m, ddf="Satterthwaite", type=2)) 160s Type II Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an2, tolerance=TOL) 160s + )) 160s > (an3 <- anova(m, ddf="Sat")) ## Abbreviated argument 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an3, tolerance=TOL) 160s + )) 160s > if(has_pbkrtest) { 160s + (anova(m, ddf="Kenward-Roger")) 160s + (anova(m, ddf="Kenward-Roger", type=3)) 160s + } 160s Type III Analysis of Variance Table with Kenward-Roger's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an1 <- anova(m, ddf="lme4")) 160s Analysis of Variance Table 160s npar Sum Sq Mean Sq F value 160s Days 1 30031 30031 45.853 160s > (an2 <- anova(m, ddf="lme4", type=3)) # 'type' is ignored with ddf="lme4" 160s Analysis of Variance Table 160s npar Sum Sq Mean Sq F value 160s Days 1 30031 30031 45.853 160s > stopifnot(isTRUE( 160s + all.equal(an1, an2, tolerance=TOL) 160s + )) 160s > res <- assertError(anova(m, ddf="KR")) ## Error on incorrect arg. 160s > stopifnot( 160s + grepl("'arg' should be one of ", unlist(res[[1]])$message) 160s + ) 160s > 160s > ## lme4 method: 160s > an1 <- anova(m, ddf="lme4") 160s > an2 <- anova(as(m, "lmerMod")) 160s > stopifnot(isTRUE( 160s + all.equal(an1, an2, tolerance=TOL) 160s + )) 160s > 160s > ###### type argument: 160s > (an1 <- anova(m, type="1")) # valid type arg. 160s Type I Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2 <- anova(m, type="I")) # same 160s Type I Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an2, tolerance=TOL) 160s + )) 160s > (an3 <- anova(m, type=1)) # Not strictly valid, but accepted 160s Type I Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an3, tolerance=TOL) 160s + )) 160s > 160s > (an1 <- anova(m, type="2")) # valid type arg. 160s Type II Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2 <- anova(m, type="II")) # same 160s Type II Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an2, tolerance=TOL) 160s + )) 160s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL) 160s + )) 160s > 160s > (an1 <- anova(m, type="3")) # valid type arg. 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2 <- anova(m, type="III")) # same 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an2, tolerance=TOL) 160s + )) 160s > (an3 <- anova(m, type=3)) # Not strictly valid, but accepted 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s Days 30031 30031 1 17 45.853 3.264e-06 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot(isTRUE( 160s + all.equal(an1, an3, tolerance=TOL) 160s + )) 160s > assertError(anova(m, type=0)) # Not valid arg. 160s > assertError(anova(m, type="i")) # Not valid arg. 160s > 160s > ####### Model comparison: 160s > fm <- lm(Reaction ~ Days, sleepstudy) 160s > (an <- anova(m, fm)) 160s refitting model(s) with ML (instead of REML) 160s Data: sleepstudy 160s Models: 160s fm: Reaction ~ Days 160s m: Reaction ~ Days + (Days | Subject) 160s npar AIC BIC logLik deviance Chisq Df Pr(>Chisq) 160s fm 3 1906.3 1915.9 -950.15 1900.3 160s m 6 1763.9 1783.1 -875.97 1751.9 148.35 3 < 2.2e-16 *** 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > stopifnot( 160s + nrow(an) == 2L, 160s + rownames(an)[2] == "m" 160s + ) 160s > 160s > m2 <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 160s > (an <- anova(m, m2, refit=FALSE)) 160s Data: sleepstudy 160s Models: 160s m: Reaction ~ Days + (Days | Subject) 160s m2: Reaction ~ Days + I(Days^2) + (Days | Subject) 160s npar AIC BIC logLik deviance Chisq Df Pr(>Chisq) 160s m 6 1755.6 1774.8 -871.81 1743.6 160s m2 7 1756.8 1779.2 -871.41 1742.8 0.8127 1 0.3673 160s > stopifnot( 160s + nrow(an) == 2L, 160s + rownames(an)[1] == "m" 160s + ) 160s > 160s > 160s > #################################### 160s > ## Example with factor fixef: 160s > #################################### 160s > 160s > ## 'temp' is continuous, 'temperature' an ordered factor with 6 levels 160s > data("cake", package="lme4") 160s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 160s > (an <- anova(m)) 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s recipe 4.00 2.00 2 254.02 0.0957 0.9088 160s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 160s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an_lme4 <- anova(m, ddf="lme4")) 160s Analysis of Variance Table 160s npar Sum Sq Mean Sq F value 160s recipe 2 10.39 5.20 0.2488 160s temp 1 1966.71 1966.71 94.1632 160s recipe:temp 2 1.74 0.87 0.0417 160s > 160s > if(has_pbkrtest) { 160s + (an_KR <- anova(m, ddf="Kenward-Roger")) 160s + # res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 160s + # an_lme4[, c("Sum Sq", "Mean Sq", "F value")]) 160s + # stopifnot(isTRUE(res)) 160s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 160s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 160s + stopifnot(isTRUE(res)) 160s + } 160s > stopifnot(all.equal(c(2, 1, 2), an$NumDF, tol=1e-6), 160s + all.equal(c(254.0157612, 222, 222), an$DenDF, tol=TOL)) 160s > 160s > an3 <- anova(m, type=3) 160s > an2 <- anova(m, type=2) 160s > an1 <- anova(m, type=1) 160s > 160s > ## Data is balanced, so Type II and III should be identical: 160s > ## One variable is continuous, so Type I and II/III are different: 160s > stopifnot( 160s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)), 160s + !isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=1e-8)) 160s + ) 160s > 160s > # Using an ordered factor: 160s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 160s > (an1 <- anova(m, type=1)) 160s Type I Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s recipe 10.19 5.09 2 42 0.2488 0.7809 160s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 160s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an2 <- anova(m, type=2)) 160s Type II Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s recipe 10.19 5.09 2 42 0.2488 0.7809 160s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 160s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > # Type 3 is also available with ordered factors: 160s > (an3 <- anova(m, type=3)) 160s Type III Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s recipe 10.19 5.09 2 42 0.2488 0.7809 160s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 160s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > ## Balanced data and only factors: Type I, II and III should be the same: 160s > stopifnot( 160s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 160s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)) 160s + ) 160s > 160s > (an <- anova(m, type=1)) 160s Type I Analysis of Variance Table with Satterthwaite's method 160s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 160s recipe 10.19 5.09 2 42 0.2488 0.7809 160s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 160s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 160s --- 160s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 160s > (an_lme4 <- anova(m, type=1, ddf="lme4")) 160s Analysis of Variance Table 160s npar Sum Sq Mean Sq F value 160s recipe 2 10.19 5.09 0.2488 160s temperature 5 2100.30 420.06 20.5199 160s recipe:temperature 10 205.98 20.60 1.0062 160s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 160s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 160s > stopifnot(isTRUE(res)) 160s > if(has_pbkrtest) { 160s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 160s + res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 160s + an_KR[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 160s + stopifnot(isTRUE(res)) 160s + } 161s > stopifnot(all.equal(c(2, 5, 10), an$NumDF, tolerance=TOL), 161s + all.equal(c(42, 210, 210), an$DenDF, tolerance=TOL)) 161s > 161s > ######## 161s > ## Make case with balanced unordered factors: 161s > cake2 <- cake 161s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 161s > # str(cake2) 161s > stopifnot( 161s + !is.ordered(cake2$temperature) 161s + ) 161s > m <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 161s > (an1 <- anova(m, type=1)) 161s Type I Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 10.19 5.09 2 42 0.2488 0.7809 161s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 161s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an2 <- anova(m, type=2)) 161s Type II Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 10.19 5.09 2 42 0.2488 0.7809 161s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 161s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an3 <- anova(m, type=3)) 161s Type III Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 10.19 5.09 2 42 0.2488 0.7809 161s temperature 2100.30 420.06 5 210 20.5199 <2e-16 *** 161s recipe:temperature 205.98 20.60 10 210 1.0062 0.4393 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > ## Balanced data and only factors: Type I, II, and III should be the same: 161s > stopifnot( 161s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 161s + isTRUE(all.equal(an3, an2, check.attributes=FALSE, tolerance=TOL)) 161s + ) 161s > ######## 161s > 161s > # No intercept: 161s > m <- lmer(angle ~ 0 + recipe * temp + (1|recipe:replicate), cake) 161s > (an <- anova(m, type=1)) 161s Type I Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 21442.9 7147.6 3 42 342.2200 <2e-16 *** 161s temp 1966.7 1966.7 1 222 94.1632 <2e-16 *** 161s recipe:temp 1.7 0.9 2 222 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an2 <- anova(m, type=2)) 161s Type II Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 4.48 1.49 3 254.02 0.0714 0.9752 161s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 161s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an2 <- anova(m, type=3)) 161s Type III Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 4.48 1.49 3 254.02 0.0714 0.9752 161s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 161s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > if(has_pbkrtest) 161s + (an_KR <- anova(m, ddf="Kenward-Roger")) 161s Type III Analysis of Variance Table with Kenward-Roger's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 4.48 1.49 3 254.02 0.0714 0.9752 161s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 161s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an_lme4 <- anova(m, ddf="lme4")) 161s Analysis of Variance Table 161s npar Sum Sq Mean Sq F value 161s recipe 3 21442.9 7147.6 342.2200 161s temp 1 1966.7 1966.7 94.1632 161s recipe:temp 2 1.7 0.9 0.0417 161s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 161s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 161s > stopifnot(isTRUE(res)) 161s > 161s > # ML-fit: 161s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, REML=FALSE) 161s > (an <- anova(m, type=1)) 161s Type I Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 10.99 5.49 2 45 0.2666 0.7672 161s temp 1966.71 1966.71 1 225 95.4357 <2e-16 *** 161s recipe:temp 1.74 0.87 2 225 0.0423 0.9586 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > if(has_pbkrtest) 161s + assertError(an <- anova(m, ddf="Kenward-Roger")) # KR fits should be REML 161s > (an_lme4 <- anova(m, ddf="lme4")) 161s Analysis of Variance Table 161s npar Sum Sq Mean Sq F value 161s recipe 2 10.99 5.49 0.2666 161s temp 1 1966.71 1966.71 95.4357 161s recipe:temp 2 1.74 0.87 0.0423 161s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 161s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 161s > stopifnot(isTRUE(res)) 161s > 161s > #################################### 161s > ## Using contr.sum: 161s > #################################### 161s > 161s > m <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake, 161s + contrasts = list('recipe' = "contr.sum")) 161s > (an <- anova(m, type=1)) 161s Type I Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 10.39 5.20 2 42 0.2488 0.7809 161s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 161s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an2 <- anova(m, type=2)) 161s Type II Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 4.00 2.00 2 254.02 0.0957 0.9088 161s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 161s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > (an3 <- anova(m, type=3)) 161s Type III Analysis of Variance Table with Satterthwaite's method 161s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 161s recipe 4.00 2.00 2 254.02 0.0957 0.9088 161s temp 1966.71 1966.71 1 222.00 94.1632 <2e-16 *** 161s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 161s --- 161s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 161s > stopifnot( 161s + isTRUE(all.equal(an2, an3, check.attributes=FALSE, tolerance=TOL)) 161s + ) 161s > if(has_pbkrtest) 161s + (an_KR <- anova(m, type=1, ddf="Kenward-Roger")) 162s Type I Analysis of Variance Table with Kenward-Roger's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s recipe 10.39 5.20 2 42 0.2488 0.7809 162s temp 1966.71 1966.71 1 222 94.1632 <2e-16 *** 162s recipe:temp 1.74 0.87 2 222 0.0417 0.9592 162s --- 162s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 162s > (an_lme4 <- anova(m, ddf="lme4")) 162s Analysis of Variance Table 162s npar Sum Sq Mean Sq F value 162s recipe 2 10.39 5.20 0.2488 162s temp 1 1966.71 1966.71 94.1632 162s recipe:temp 2 1.74 0.87 0.0417 162s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 162s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 162s > stopifnot(isTRUE(res)) 162s > 162s > 162s > #################################### 162s > ## Example with continuous fixef: 162s > #################################### 162s > 162s > # Example with no fixef: 162s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 162s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 162s > stopifnot(length(fixef(m)) == 0L) 162s > (an <- anova(m, type=1)) 162s Type I Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s > (an_2 <- anova(m, type=2)) 162s Type II Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s > (an_3 <- anova(m, type=3)) 162s Type III Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s > stopifnot(nrow(an) == 0L, 162s + nrow(an_2) == 0L, 162s + nrow(an_3) == 0L) 162s > # anova(m, ddf="lme4") # Bug in lme4 it seems 162s > if(has_pbkrtest) { 162s + (an_KR <- anova(m, ddf="Kenward-Roger")) 162s + stopifnot( 162s + nrow(an_KR) == 0L 162s + ) 162s + } 162s > 162s > # Example with intercept only: 162s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 162s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 162s > stopifnot(length(fixef(m)) == 1L, 162s + names(fixef(m)) == "(Intercept)") 162s > (an <- anova(m)) 162s Type III Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s > (an_2 <- anova(m, type=2)) 162s Type II Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s > (an_3 <- anova(m, type=3)) 162s Type III Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s > (an_lme4 <- anova(m, ddf="lme4")) 162s Analysis of Variance Table 162s npar Sum Sq Mean Sq F value 162s > stopifnot(nrow(an) == 0L, 162s + nrow(an_2) == 0L, 162s + nrow(an_3) == 0L, 162s + nrow(an_lme4) == 0L) 162s > if(has_pbkrtest) { 162s + (an_KR <- anova(m, ddf="Kenward-Roger")) 162s + stopifnot( 162s + nrow(an_KR) == 0L 162s + ) 162s + } 162s > 162s > # Example with 1 fixef without intercept: 162s > # for packageVersion("lme4") < 1.1.20 162s > # mOld <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy) 162s > # for packageVersion("lme4") >= 1.1.20 we need to specify the old default 162s > # optimizer to get the model to converge well enough. 162s > m <- lmer(Reaction ~ Days - 1 + (Days | Subject), sleepstudy, 162s + control=lmerControl(optimizer="bobyqa")) 162s > # m <- lmer(Reaction ~ 0 + Days + (Days | Subject), sleepstudy) # alternative 162s > stopifnot(length(fixef(m)) == 1L, 162s + names(fixef(m)) == "Days") 162s > (an <- anova(m)) 162s Type III Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s Days 93564 93564 1 17 142.86 1.069e-09 *** 162s --- 162s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 162s > (an_2 <- anova(m, type=2)) 162s Type II Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s Days 93564 93564 1 17 142.86 1.069e-09 *** 162s --- 162s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 162s > (an_3 <- anova(m, type=3)) 162s Type III Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s Days 93564 93564 1 17 142.86 1.069e-09 *** 162s --- 162s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 162s > (an_lme4 <- anova(m, ddf="lme4")) 162s Analysis of Variance Table 162s npar Sum Sq Mean Sq F value 162s Days 1 93564 93564 142.86 162s > stopifnot(nrow(an) == 1L, 162s + nrow(an_2) == 1L, 162s + nrow(an_3) == 1L, 162s + nrow(an_lme4) == 1L) 162s > if(has_pbkrtest) { 162s + (an_KR <- anova(m, ddf="Kenward-Roger")) 162s + stopifnot( 162s + nrow(an_KR) == 1L 162s + ) 162s + } 162s > 162s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 162s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 162s > stopifnot(isTRUE(res)) 162s > stopifnot(isTRUE(all.equal( 162s + c(1, 17), unname(unlist(an[, c("NumDF", "DenDF")])), tolerance=TOL 162s + ))) 162s > 162s > # Example with >1 fixef without intercept: 162s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 162s > stopifnot(length(fixef(m)) == 2L, 162s + names(fixef(m)) == c("Days", "I(Days^2)")) 162s > (an <- anova(m)) 162s Type III Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s Days 22138.3 22138.3 1 69.047 33.9451 1.64e-07 *** 162s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 162s --- 162s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 162s > (an_2 <- anova(m, type=2)) 162s Type II Analysis of Variance Table with Satterthwaite's method 162s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 162s Days 22138.3 22138.3 1 69.047 33.9451 1.64e-07 *** 162s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 162s --- 162s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 162s > (an_3 <- anova(m, type=3)) 163s Type III Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s Days 22138.3 22138.3 1 69.047 33.9451 1.64e-07 *** 163s I(Days^2) 744.7 744.7 1 143.679 1.1419 0.287 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an_lme4 <- anova(m, ddf="lme4")) 163s Analysis of Variance Table 163s npar Sum Sq Mean Sq F value 163s Days 1 93162 93162 142.8476 163s I(Days^2) 1 745 745 1.1419 163s > stopifnot(nrow(an) == 2L, 163s + nrow(an_3) == 2L, 163s + nrow(an_lme4) == 2L) 163s > if(has_pbkrtest) { 163s + (an_KR <- anova(m, ddf="Kenward-Roger")) 163s + stopifnot( 163s + nrow(an_KR) == 2L 163s + ) 163s + } 163s > # Here is a diff in SSQ which doesn't seem well-defined anyway... 163s > # SSQ for I(Days^2) agree though. 163s > # t-statistics also agree: 163s > coef(summary(m)) 163s Estimate Std. Error df t value Pr(>|t|) 163s Days 15.8883551 2.7270320 69.04683 5.826244 1.639902e-07 163s I(Days^2) 0.2795482 0.2616035 143.67928 1.068595 2.870442e-01 163s > Lmat <- diag(length(fixef(m))) 163s > lmerTest:::rbindall(lapply(1:nrow(Lmat), function(i) contest1D(m, Lmat[i, ]))) 163s Estimate Std. Error df t value Pr(>|t|) 163s 1 15.8883551 2.7270320 69.04683 5.826244 1.639902e-07 163s 2 0.2795482 0.2616035 143.67928 1.068595 2.870442e-01 163s > 163s > # Example with >1 fixef and intercept: 163s > m <- lmer(Reaction ~ Days + I(Days^2) + (Days | Subject), sleepstudy) 163s > stopifnot(length(fixef(m)) == 3L) 163s > (an <- anova(m, type=1)) 163s Type I Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s Days 29894.8 29894.8 1 17 45.8530 3.264e-06 *** 163s I(Days^2) 1079.5 1079.5 1 143 1.6558 0.2003 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an_2 <- anova(m, type=2)) 163s Type II Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 163s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an_3 <- anova(m, type=3)) 163s Type III Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 163s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an_lme4 <- anova(m, ddf="lme4")) 163s Analysis of Variance Table 163s npar Sum Sq Mean Sq F value 163s Days 1 29894.8 29894.8 45.8530 163s I(Days^2) 1 1079.5 1079.5 1.6558 163s > res <- all.equal(an[, c("Sum Sq", "Mean Sq", "F value")], 163s + an_lme4[, c("Sum Sq", "Mean Sq", "F value")], tolerance=TOL) 163s > stopifnot(isTRUE(res)) 163s > 163s > if(has_pbkrtest) { 163s + (an_KR <- anova(m, ddf="Kenward-Roger")) 163s + res <- all.equal(an_3[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], 163s + an_KR[, c("Sum Sq", "Mean Sq", "DenDF", "F value")], tolerance=TOL) 163s + stopifnot(isTRUE(res)) 163s + } 163s > 163s > ## FIXME: Test the use of refit arg to lme4:::anova.merMod 163s > 163s > ############################## 163s > # Test that type III anova is the same regardless of contrast coding: 163s > # 3 x 3 factorial with missing diagonal 163s > data("cake", package="lme4") 163s > cake4 <- cake 163s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 163s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 163s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 163s + (recipe == "B" & temperature == "185") | 163s + (recipe == "C" & temperature == "195") ))) 163s > str(cake4) 163s 'data.frame': 90 obs. of 5 variables: 163s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 2 2 2 2 ... 163s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 2 2 3 3 1 1 2 2 ... 163s $ temperature: Factor w/ 3 levels "175","185","195": 2 3 1 3 1 2 2 3 1 3 ... 163s $ angle : int 46 47 39 51 46 44 29 35 35 47 ... 163s $ temp : num 185 195 175 195 175 185 185 195 175 195 ... 163s > with(cake4, table(recipe, temperature)) 163s temperature 163s recipe 175 185 195 163s A 0 15 15 163s B 15 0 15 163s C 15 15 0 163s > # load_all(r2path) 163s > 163s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 163s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 163s > fm2 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 163s + contrasts=list(recipe="contr.sum", temperature="contr.SAS")) 163s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 163s > fm3 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 163s + contrasts=list(recipe="contr.sum", temperature="contr.poly")) 163s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 163s > fm4 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4, 163s + contrasts=list(recipe=contr.helmert, temperature="contr.poly")) 163s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 163s > (an1 <- anova(fm1)) 163s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 163s Interpret type III hypotheses with care. 163s Type III Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s recipe 2.282 1.141 2 45.888 0.0871 0.916766 163s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 163s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an2 <- anova(fm2)) 163s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 163s Interpret type III hypotheses with care. 163s Type III Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s recipe 2.282 1.141 2 45.888 0.0871 0.916766 163s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 163s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an3 <- anova(fm3)) 163s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 163s Interpret type III hypotheses with care. 163s Type III Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s recipe 2.282 1.141 2 45.888 0.0871 0.916766 163s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 163s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > (an4 <- anova(fm4)) 163s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 163s Interpret type III hypotheses with care. 163s Type III Analysis of Variance Table with Satterthwaite's method 163s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 163s recipe 2.282 1.141 2 45.888 0.0871 0.916766 163s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 163s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 163s --- 163s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 163s > options("contrasts") 163s $contrasts 163s unordered ordered 163s "contr.treatment" "contr.poly" 163s 163s > options(contrasts = c("contr.sum", "contr.poly")) 163s > fm5 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 164s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 164s > (an5 <- anova(fm5)) 164s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 164s Interpret type III hypotheses with care. 164s Type III Analysis of Variance Table with Satterthwaite's method 164s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 164s recipe 2.282 1.141 2 45.888 0.0871 0.916766 164s temperature 136.267 68.133 2 42.000 5.1998 0.009602 ** 164s recipe:temperature 52.900 52.900 1 42.000 4.0372 0.050963 . 164s --- 164s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 164s > options(contrasts = c("contr.treatment", "contr.poly")) 164s > options("contrasts") 164s $contrasts 164s [1] "contr.treatment" "contr.poly" 164s 164s > stopifnot( 164s + isTRUE(all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL)), 164s + isTRUE(all.equal(an1, an3, check.attributes=FALSE, tolerance=TOL)), 164s + isTRUE(all.equal(an1, an4, check.attributes=FALSE, tolerance=TOL)), 164s + isTRUE(all.equal(an1, an5, check.attributes=FALSE, tolerance=TOL)) 164s + ) 164s > 164s > 164s BEGIN TEST test_compare_sas.R 164s 164s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 164s Copyright (C) 2024 The R Foundation for Statistical Computing 164s Platform: aarch64-unknown-linux-gnu (64-bit) 164s 164s R is free software and comes with ABSOLUTELY NO WARRANTY. 164s You are welcome to redistribute it under certain conditions. 164s Type 'license()' or 'licence()' for distribution details. 164s 164s R is a collaborative project with many contributors. 164s Type 'contributors()' for more information and 164s 'citation()' on how to cite R or R packages in publications. 164s 164s Type 'demo()' for some demos, 'help()' for on-line help, or 164s 'help.start()' for an HTML browser interface to help. 164s Type 'q()' to quit R. 164s 164s > # test_compare_sas.R 164s > library(lmerTest) 164s Loading required package: lme4 164s Loading required package: Matrix 167s 167s Attaching package: 'lmerTest' 167s 167s The following object is masked from 'package:lme4': 167s 167s lmer 167s 167s The following object is masked from 'package:stats': 167s 167s step 167s 167s > 167s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 167s > # even in tests: 167s > assertError <- function(expr, ...) 167s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 167s > assertWarning <- function(expr, ...) 167s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 167s > 167s > ##################################################################### 167s > 167s > 167s > # Use contrasts to get particular estimates for the summary table: 167s > l <- list(Frequency="contr.SAS", Income="contr.SAS") 167s > m.carrots <- lmer(Preference ~ sens2*Frequency*Income 167s + +(1+sens2|Consumer), data=carrots, contrasts=l) 167s fixed-effect model matrix is rank deficient so dropping 12 columns / coefficients 167s > an.m <- anova(m.carrots) 167s 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. 167s Interpret type III hypotheses with care. 167s > 167s > TOL <- 1e-4 167s > TOL2 <- 1e-5 167s > # with 4 decimals should agree with SAS output 167s > # numbers before decimals should agree with SAS output 167s > stopifnot( 167s + all.equal(an.m[,"Pr(>F)"], 167s + c(2e-5, 0.15512, 0.06939, 0.08223, 0.52459, 0.03119, 0.48344), 167s + tolerance = TOL), 167s + all.equal(round(an.m$DenDF), c(83, 83, 83, 83, 83, 83, 83)) 167s + ) 167s > 167s > sm <- summary(m.carrots) 167s > stopifnot( 167s + isTRUE(all.equal(sm$coefficients[,"Pr(>|t|)"], 167s + c(1e-10, 0.005061, 0.6865554, 0.342613, 0.129157, 167s + 0.088231, 0.846000, 0.354472, 0.526318, 0.020646, 0.010188, 167s + 0.031242, 0.055356, 0.694689, 0.099382, 0.28547, 167s + 0.977774, 0.855653, 0.427737, 0.321086, 0.417465 , 0.204385, 0.784437, 167s + 0.681434, 0.106180, 0.149122, 0.390870, 0.273686), tolerance=TOL, 167s + check.attributes = FALSE)) 167s + ) 167s > 167s > # Takes too long to run: 167s > # if(requireNamespace("pbkrtest", quietly = TRUE)) { 167s > # sm.kr <- summary(m.carrots, ddf = "Kenward-Roger") 167s > # 167s > # ## coefficients for Sat and KR agree in this example 167s > # # cbind(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"]) 167s > # all.equal(sm$coefficients[,"Pr(>|t|)"], sm.kr$coefficients[,"Pr(>|t|)"], 167s > # tol=TOL) 167s > # } 167s > 167s > ################################################################################ 167s > ## checking lsmeans and difflsmeans 167s > ## compare with SAS output 167s > m <- lmer(Informed.liking ~ Product*Information*Gender 167s + + (1|Product:Consumer) + (1|Consumer) , data=ham) 168s > 168s > 168s > lsm <- lsmeansLT(m, which = "Product") 168s > # head(lsm) 168s > 168s > stopifnot( 168s + isTRUE(all.equal(lsm[, "Estimate"], c(5.8084, 5.1012, 6.0909, 5.9256), 168s + tol=TOL, check.attributes = FALSE)), 168s + isTRUE(all.equal(round(lsm[, "t value"], 2), c(24.93, 21.89, 26.14, 25.43), tolerance=TOL, 168s + check.attributes = FALSE)), 168s + isTRUE(all.equal(lsm[, "lower"], c(5.3499, 4.6428, 5.6324, 5.4672), tolerance=TOL, 168s + check.attributes = FALSE)), 168s + isTRUE(all.equal(lsm[, "upper"], c(6.2668, 5.5597, 6.5493, 6.3840), tolerance=TOL, 168s + check.attributes = FALSE)) 168s + ) 168s > 168s > ################################################################################ 168s > # Not actually 'hard-coded' tests versus SAS results... 168s > 168s > m.carrots <- lmer(Preference ~ 0 + sens2 + Homesize + 168s + (1+sens2 | Consumer), data=carrots, 168s + control=lmerControl(optimizer="bobyqa")) 168s > summary(m.carrots) 168s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 168s lmerModLmerTest] 168s Formula: Preference ~ 0 + sens2 + Homesize + (1 + sens2 | Consumer) 168s Data: carrots 168s Control: lmerControl(optimizer = "bobyqa") 168s 168s REML criterion at convergence: 3748.9 168s 168s Scaled residuals: 168s Min 1Q Median 3Q Max 168s -3.5322 -0.5571 0.0308 0.6297 2.8552 168s 168s Random effects: 168s Groups Name Variance Std.Dev. Corr 168s Consumer (Intercept) 0.195168 0.44178 168s sens2 0.002779 0.05271 0.18 168s Residual 1.070441 1.03462 168s Number of obs: 1233, groups: Consumer, 103 168s 168s Fixed effects: 168s Estimate Std. Error df t value Pr(>|t|) 168s sens2 7.068e-02 9.545e-03 1.020e+02 7.404 3.89e-11 *** 168s Homesize1 4.910e+00 7.056e-02 1.013e+02 69.586 < 2e-16 *** 168s Homesize3 4.661e+00 7.850e-02 1.013e+02 59.374 < 2e-16 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s 168s Correlation of Fixed Effects: 168s sens2 Homsz1 168s Homesize1 0.061 168s Homesize3 0.055 0.003 168s > 168s > (an.1 <- anova(m.carrots, type=1)) 168s Type I Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s sens2 60.5 60.5 1 102.01 56.539 2.211e-11 *** 168s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an.3 <- anova(m.carrots)) 168s Type III Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s sens2 58.7 58.7 1 102.01 54.821 3.892e-11 *** 168s Homesize 8927.2 4463.6 2 101.31 4169.863 < 2.2e-16 *** 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an.lme4 <- anova(m.carrots, ddf = "lme4")) # difference in SSQ MS and F-values 168s Analysis of Variance Table 168s npar Sum Sq Mean Sq F value 168s sens2 1 0.0 0.0 0.0122 168s Homesize 2 8927.2 4463.6 4169.8634 168s > # Is this a problem with lme4? 168s > # fm <- lm(Preference ~ 0 + sens2 + Homesize, data=carrots) 168s > # anova(fm) 168s > # coef(summary(fm)) 168s > # Here the F value is a little greater than the squared t-value (as expected) 168s > 168s > stopifnot(all.equal(an.1[, "F value"], c(56.5394, 4169.87), tolerance = TOL2), 168s + all.equal(an.3[, "F value"], c(54.8206, 4169.87), tolerance = TOL2)) 168s > 168s > 168s > ################################################################################ 168s > # Check exmaple from GLM SAS report 168s > 168s > ### example from the paper GLM SAS 101 report 168s > a <- factor(c(1,1,1,2,2,2,2,2,1,2)) 168s > b <- factor(c(1,1,2,1,2,2,2,2,2,1)) 168s > f=factor(c(1,2,1,2,1,2,1,2,1,2)) 168s > y <- c(12,14,11,20,17,23,35,46,15,16) 168s > dd <- data.frame(a=a, b=b, y=y, f=f) 168s > 168s > ## check type 2 is order independent 168s > model <- lmer(y ~ a*b + (1|f), data=dd) 168s boundary (singular) fit: see help('isSingular') 168s > model2 <- lmer(y ~ b*a + (1|f), data=dd) 168s boundary (singular) fit: see help('isSingular') 168s > (an <- anova(model, type=2)) 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s a 336.00 336.00 1 6 3.9013 0.09566 . 168s b 114.33 114.33 1 6 1.3275 0.29308 168s a:b 85.75 85.75 1 6 0.9956 0.35689 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > (an2 <- anova(model2, type=2)) 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s b 114.33 114.33 1 6 1.3275 0.29308 168s a 336.00 336.00 1 6 3.9013 0.09566 . 168s b:a 85.75 85.75 1 6 0.9956 0.35689 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > stopifnot( 168s + isTRUE(all.equal(an,an2[c(2,1,3),], check.attributes = FALSE, tolerance=TOL2)) 168s + ) 168s > 168s > ## check the results are the same as from SAS proc mixed 168s > stopifnot( 168s + isTRUE(all.equal(an[,"F value"], c(3.90131, 1.32753, 0.99565), tolerance=TOL2)) 168s + ) 168s > ################################################################################ 168s > ## Check type II and III anova tables versus SAS 168s > 168s > m.carrots <- lmer(Preference ~ sens2*Homesize 168s + +(1+sens2|Consumer), data=carrots) 168s > (ancar <- anova(m.carrots, type=2)) 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s sens2 58.697 58.697 1 101.02 54.8339 4.042e-11 *** 168s Homesize 5.526 5.526 1 100.99 5.1621 0.02521 * 168s sens2:Homesize 1.103 1.103 1 101.02 1.0303 0.31251 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > 168s > stopifnot( 168s + isTRUE(all.equal(ancar[,"F value"], c(54.8361, 5.16138, 1.03035), tolerance = TOL)) 168s + ) 168s > 168s > m <- lmer(Informed.liking ~ Product*Age 168s + + (1|Consumer) , data=ham) 168s > (an <- anova(m, type=2)) 168s Type II Analysis of Variance Table with Satterthwaite's method 168s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 168s Product 32.498 10.8327 3 561 2.4814 0.06014 . 168s Age 0.024 0.0235 1 79 0.0054 0.94168 168s Product:Age 19.442 6.4808 3 561 1.4845 0.21772 168s --- 168s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 168s > 168s > stopifnot( 168s + isTRUE(all.equal(an[,"F value"], c(2.48135, .005387, 1.48451), tolerance = TOL2)) 168s + ) 168s > 168s > 168s > fm <- lmer(Preference ~ sens2*Homesize*sens1 + (1|Product), 168s + data=carrots) 169s > (ant2 <- anova(fm, type=2)) 169s Type II Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s sens2 21.0228 21.0228 1 7.97 16.4832 0.0036583 ** 169s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 169s sens1 0.6709 0.6709 1 7.98 0.5260 0.4889911 169s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 169s sens2:sens1 0.1372 0.1372 1 7.98 0.1076 0.7513796 169s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 169s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > (ant3 <- anova(fm, type=3)) 169s Type III Analysis of Variance Table with Satterthwaite's method 169s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 169s sens2 21.5710 21.5710 1 8.02 16.9130 0.0033602 ** 169s Homesize 17.8570 17.8570 1 1217.01 14.0010 0.0001912 *** 169s sens1 0.6136 0.6136 1 8.03 0.4811 0.5074890 169s sens2:Homesize 1.5068 1.5068 1 1216.99 1.1814 0.2772780 169s sens2:sens1 0.0946 0.0946 1 8.02 0.0742 0.7922017 169s Homesize:sens1 0.4275 0.4275 1 1217.00 0.3352 0.5627339 169s sens2:Homesize:sens1 1.3512 1.3512 1 1216.99 1.0595 0.3035426 169s --- 169s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 169s > 169s > stopifnot( 169s + isTRUE(all.equal(ant2[,"F value"], 169s + c(16.4842, 14.0010, .526076, 1.18144, 169s + .107570, .335177, 1.05946), tolerance = TOL)), 169s + isTRUE(all.equal(ant3[,"F value"], 169s + c(16.9140, 14.0010,.481148, 1.18144, 169s + .074201, .335177, 1.05946), tolerance = TOL)) 169s + ) 169s > 169s > ################################################################################ 169s > 169s > 169s > 169s BEGIN TEST test_contest1D.R 169s 169s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 169s Copyright (C) 2024 The R Foundation for Statistical Computing 169s Platform: aarch64-unknown-linux-gnu (64-bit) 169s 169s R is free software and comes with ABSOLUTELY NO WARRANTY. 169s You are welcome to redistribute it under certain conditions. 169s Type 'license()' or 'licence()' for distribution details. 169s 169s R is a collaborative project with many contributors. 169s Type 'contributors()' for more information and 169s 'citation()' on how to cite R or R packages in publications. 169s 169s Type 'demo()' for some demos, 'help()' for on-line help, or 169s 'help.start()' for an HTML browser interface to help. 169s Type 'q()' to quit R. 169s 169s > # test_contest1D.R 169s > library(lmerTest) 169s Loading required package: lme4 169s Loading required package: Matrix 172s 172s Attaching package: 'lmerTest' 172s 172s The following object is masked from 'package:lme4': 172s 172s lmer 172s 172s The following object is masked from 'package:stats': 172s 172s step 172s 172s > 172s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 172s > # even in tests: 172s > assertError <- function(expr, ...) 172s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 172s > assertWarning <- function(expr, ...) 172s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 172s > 172s > TOL <- 1e-4 172s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 172s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 172s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 172s > 172s > data("sleepstudy", package="lme4") 172s > 172s > #################################### 172s > ## Tests of contest1D 172s > #################################### 172s > 172s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 172s + sleepstudy) 172s > # Basic tests: 172s > L <- c(0, 1, 0) 172s > contest1D(fm, L) 172s Estimate Std. Error df t value Pr(>|t|) 172s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 172s > contest1D(fm, L, confint = TRUE) 172s Estimate Std. Error df t value lower upper Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 173s > contest1D(fm, L, confint = TRUE, level=0.99) 173s Estimate Std. Error df t value lower upper Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 173s > if(has_pbkrtest) 173s + contest1D(fm, L, ddf="Kenward-Roger") 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 173s > 173s > # Test too long L 173s > assertError(contest1D(fm, c(0, 1, 1, 1))) 173s > 173s > # Test too short L 173s > assertError(contest1D(fm, c(0, 1))) 173s > 173s > # Test matrix L 173s > contest1D(fm, matrix(L, nrow=1)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 173s > contest1D(fm, matrix(L, ncol=1)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 173s > assertError(contest1D(fm, matrix(c(0, 1), ncol=1))) 173s > assertError(contest1D(fm, matrix(c(0, 1, 0, 0), nrow=1))) 173s > L <- matrix(numeric(0L), ncol=3) 173s > assertError(contest1D(fm, L)) # "empty" matrix 173s > assertError(contest1D(fm, matrix(1, ncol=3, nrow=2))) 173s > 173s > # Test list L 173s > assertError(contest1D(fm, list(c(0, 1, 0)))) 173s > 173s > # Test equivalence to coef(summary(fm)): 173s > Lmat <- diag(length(fixef(fm))) 173s > (coef_mat <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 173s + contest1D(fm, Lmat[i, ])))) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 255.4493728 7.5663677 26.22939 33.761163 3.810058e-23 173s 2 7.4340850 2.8242827 114.99433 2.632203 9.648080e-03 173s 3 0.3370223 0.2616475 144.63110 1.288078 1.997759e-01 173s > (coef_mat_lme4 <- coef(summary(fm, ddf="lme4"))) 173s Estimate Std. Error t value 173s (Intercept) 255.4493728 7.5663677 33.761163 173s Days 7.4340850 2.8242827 2.632203 173s I(Days^2) 0.3370223 0.2616475 1.288078 173s > rownames(coef_mat) <- rownames(coef_mat_lme4) 173s > stopifnot(isTRUE( 173s + all.equal(as.data.frame(coef_mat_lme4), 173s + coef_mat[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 173s + )) 173s > 173s > if(has_pbkrtest) { 173s + (coef_mat_KR <- lmerTest:::rbindall(lapply(1:ncol(Lmat), function(i) 173s + contest1D(fm, Lmat[i, ], ddf="Kenward-Roger")))) 173s + rownames(coef_mat_KR) <- rownames(coef_mat_lme4) 173s + stopifnot(isTRUE( 173s + all.equal(as.data.frame(coef_mat_lme4), 173s + coef_mat_KR[, c("Estimate", "Std. Error", "t value")], tolerance=TOL) 173s + )) 173s + } 173s > # Test of 0-length beta 173s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 173s + sleepstudy) 173s > stopifnot(length(fixef(fm1)) == 0L) 173s > if(has_pbkrtest) { 173s + (ans <- contest1D(fm1, numeric(0L), ddf="Kenward-Roger")) 173s + stopifnot(nrow(ans) == 0L) 173s + } 173s > 173s > ## Test rhs argument: 173s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 173s > contest1D(fm, L=cbind(0, 1)) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 16.99998 6.771481 3.263824e-06 173s > contest1D(fm, L=cbind(0, 1), rhs=10) 173s Estimate Std. Error df t value Pr(>|t|) 173s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 173s > if(has_pbkrtest) { 173s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger") 173s + contest1D(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 173s + } 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 10.46729 1.54579 17 0.302296 0.7660937 174s > 174s > contest1D(fm, L=c(0, 1), rhs = 10.467) 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 10.46729 1.54579 16.99998 0.0001849926 0.9998546 174s > 174s > (ct1 <- contest1D(fm, L=cbind(c(0, 1)), rhs = 10)) 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 10.46729 1.54579 16.99998 0.302296 0.7660937 174s > (ct2 <- contestMD(fm, L=rbind(c(0, 1)), rhs = 10)) 174s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 174s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 174s > stopifnot( 174s + isTRUE(all.equal(ct1[, "t value"]^2, ct2[, "F value"], tolerance=1e-6)) 174s + ) 174s > 174s > ## Test 'lmerMod' method: 174s > fm <- lme4::lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 174s + sleepstudy) 174s > # Basic tests: 174s > L <- c(0, 1, 0) 174s > contest1D(fm, L) 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 7.434085 2.824283 114.9943 2.632203 0.00964808 174s > contest1D(fm, L, confint = TRUE) 174s Estimate Std. Error df t value lower upper Pr(>|t|) 174s 1 7.434085 2.824283 114.9943 2.632203 1.839722 13.02845 0.00964808 174s > contest1D(fm, L, confint = TRUE, level=0.99) 174s Estimate Std. Error df t value lower upper Pr(>|t|) 174s 1 7.434085 2.824283 114.9943 2.632203 0.03655396 14.83162 0.00964808 174s > if(has_pbkrtest) 174s + contest1D(fm, L, ddf="Kenward-Roger") 174s Estimate Std. Error df t value Pr(>|t|) 174s 1 7.434085 2.824283 115.5148 2.632203 0.009642692 174s > 174s > 174s BEGIN TEST test_contestMD.R 174s 174s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 174s Copyright (C) 2024 The R Foundation for Statistical Computing 174s Platform: aarch64-unknown-linux-gnu (64-bit) 174s 174s R is free software and comes with ABSOLUTELY NO WARRANTY. 174s You are welcome to redistribute it under certain conditions. 174s Type 'license()' or 'licence()' for distribution details. 174s 174s R is a collaborative project with many contributors. 174s Type 'contributors()' for more information and 174s 'citation()' on how to cite R or R packages in publications. 174s 174s Type 'demo()' for some demos, 'help()' for on-line help, or 174s 'help.start()' for an HTML browser interface to help. 174s Type 'q()' to quit R. 174s 174s > # test_contestMD.R 174s > library(lmerTest) 174s Loading required package: lme4 174s Loading required package: Matrix 177s > 177s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 177s > # even in tests: 177s > assertError <- function(expr, ...) 177s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 177s > assertWarning <- function(expr, ...) 177s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 177s > 177s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 177s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 177s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 177s 177s Attaching package: 'lmerTest' 177s 177s The following object is masked from 'package:lme4': 177s 177s lmer 177s 177s The following object is masked from 'package:stats': 177s 177s step 177s 177s > 177s > data("sleepstudy", package="lme4") 177s > 177s > #################################### 177s > ## Tests of contestMD 177s > #################################### 177s > 177s > fm <- lmer(Reaction ~ Days + I(Days^2) + (1|Subject) + (0+Days|Subject), 177s + sleepstudy) 177s > # Basic tests: 177s > L <- diag(3L) 177s > contestMD(fm, L) 177s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 177s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 177s > 177s > # Tests of ddf arg: 177s > contestMD(fm, L, ddf="Sat") 177s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 177s 1 990089.3 330029.8 3 42.15441 507.24 4.351211e-33 177s > if(has_pbkrtest) 177s + contestMD(fm, L, ddf="Kenward-Roger") 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 990089.3 330029.8 3 38.84733 490.1937 6.706733e-31 178s > assertError(contestMD(fm, L, ddf="sat")) # Invalid ddf arg. 178s > 178s > # Tests of simple 2-df test: 178s > (ans <- contestMD(fm, L[2:3, ], ddf="Sat")) 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 30399.15 15199.57 2 54.40752 23.36102 4.744897e-08 178s > stopifnot(nrow(ans) == 1L, 178s + ans$NumDF == 2L) 178s > if(has_pbkrtest) { 178s + (ans <- contestMD(fm, L[2:3, ], ddf="Kenward-Roger")) 178s + stopifnot(nrow(ans) == 1L, 178s + ans$NumDF == 2L) 178s + } 178s > 178s > # Tests of simple 1-df test: 178s > (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Sat")) 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 178s > stopifnot(nrow(ans) == 1L, 178s + ans$NumDF == 1L) 178s > if(has_pbkrtest) { 178s + (ans <- contestMD(fm, L[3, , drop=FALSE], ddf="Kenward-Roger")) 178s + stopifnot(nrow(ans) == 1L, 178s + ans$NumDF == 1L) 178s + } 178s > 178s > # Test of vector input: 178s > (ans <- contestMD(fm, L[3, ], ddf="Sat")) # OK since length(L[3, ]) == length(fixef(fm)) 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 1079.503 1079.503 1 144.6311 1.659144 0.1997759 178s > stopifnot(nrow(ans) == 1L, 178s + ans$NumDF == 1L) 178s > assertError(contestMD(fm, c(1, 0))) # L is too short 178s > assertError(contestMD(fm, c(1, 0, 1, 1))) # L is too long 178s > 178s > # Test of list input: 178s > assertError(contestMD(fm, list(L[3, , drop=FALSE]), ddf="Sat")) # Need L to be a matrix 178s > 178s > # zero-row L's are allowed (if ncol(L) is correct): 178s > ans1 <- contestMD(fm, L[0, , drop=FALSE], ddf="Sat") 178s > stopifnot(nrow(ans1) == 0L) 178s > if(has_pbkrtest) { 178s + ans2 <- contestMD(fm, L[0, , drop=FALSE], ddf="Kenward-Roger") 178s + stopifnot(nrow(ans2) == 0L) 178s + } 178s > 178s > # Test wrong ncol(L): 178s > assertError(contestMD(fm, L[2:3, 2:3])) # need ncol(L) == length(fixef(fm)) 178s > 178s > # row-rank deficient L are allowed: 178s > L <- rbind(c(1, 0, 1), 178s + c(0, 1, 0), 178s + c(1, -1, 1)) 178s > ans <- contestMD(fm, L) 178s > stopifnot(nrow(L) == 3L, 178s + qr(L)$rank == 2, 178s + ans$NumDF == 2) 178s > if(has_pbkrtest) { 178s + ans_KR <- contestMD(fm, L, ddf="Kenward-Roger") 178s + stopifnot(ans_KR$NumDF == 2) 178s + } 178s > 178s > # Test of 0-length beta 178s > fm1 <- lmer(Reaction ~ 0 + (1|Subject) + (0+Days|Subject), 178s + sleepstudy) 178s > stopifnot(length(fixef(fm1)) == 0L) 178s > L <- numeric(0L) 178s > (ans <- contestMD(fm1, L)) 178s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s <0 rows> (or 0-length row.names) 178s > stopifnot(nrow(ans) == 0L) 178s > L <- matrix(numeric(0L), ncol=0L) 178s > (ans <- contestMD(fm1, L)) 178s [1] Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s <0 rows> (or 0-length row.names) 178s > stopifnot(nrow(ans) == 0L) 178s > 178s > 178s > ## rhs argument: 178s > data("cake", package="lme4") 178s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 178s > (L <- diag(length(fixef(model)))[2:3, ]) 178s [,1] [,2] [,3] [,4] [,5] [,6] 178s [1,] 0 1 0 0 0 0 178s [2,] 0 0 1 0 0 0 178s > (an <- anova(model, type="marginal")) 178s Marginal Analysis of Variance Table with Satterthwaite's method 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s recipe 4.00 2.00 2 254.02 0.0957 0.9088 178s temp 620.24 620.24 1 222.00 29.6961 1.339e-07 *** 178s recipe:temp 1.74 0.87 2 222.00 0.0417 0.9592 178s --- 178s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 178s > 178s > ct <- contestMD(model, L, rhs = 0) 178s > ct2 <- contestMD(model, L, rhs = c(2, 2)) 178s > stopifnot( 178s + isTRUE(all.equal(ct[1, ], an[1, ], check.attributes=FALSE, tolerance=1e-6)), 178s + ct[, "F value"] < ct2[, "F value"] 178s + ) 178s > 178s > L2 <- rbind(L, L[1, ] + L[2, ]) # rank deficient! 178s > contestMD(model, L2, rhs = c(0, 0, 0)) # no warning 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 3.996684 1.998342 2 254.0158 0.09567796 0.9087894 178s > assertWarning(contestMD(model, L2, rhs = c(2, 2, 2))) # warning since L2 is rank def. 178s > if(has_pbkrtest) 178s + assertWarning(contestMD(model, L2, rhs = c(2, 2, 2), ddf="Kenward-Roger")) 178s > 178s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 178s > contestMD(fm, L=cbind(0, 1)) 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 178s > contestMD(fm, L=cbind(0, 1), rhs=10) 178s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 178s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 178s > if(has_pbkrtest) { 178s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 178s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 178s + } 179s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 179s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 179s > 179s > 179s > ## Test 'lmerMod' method: 179s > fm <- lme4::lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 179s > contestMD(fm, L=cbind(0, 1)) 179s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 179s 1 30030.94 30030.94 1 16.99998 45.85296 3.263824e-06 179s > contestMD(fm, L=cbind(0, 1), rhs=10) 179s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 179s 1 59.85028 59.85028 1 16.99998 0.09138285 0.7660937 179s > if(has_pbkrtest) { 179s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger") 179s + contestMD(fm, L=cbind(0, 1), ddf="Kenward-Roger", rhs=10) 179s + } 179s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 179s 1 59.85028 59.85028 1 17 0.09138285 0.7660937 179s > 179s BEGIN TEST test_contrast_utils.R 180s 180s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 180s Copyright (C) 2024 The R Foundation for Statistical Computing 180s Platform: aarch64-unknown-linux-gnu (64-bit) 180s 180s R is free software and comes with ABSOLUTELY NO WARRANTY. 180s You are welcome to redistribute it under certain conditions. 180s Type 'license()' or 'licence()' for distribution details. 180s 180s R is a collaborative project with many contributors. 180s Type 'contributors()' for more information and 180s 'citation()' on how to cite R or R packages in publications. 180s 180s Type 'demo()' for some demos, 'help()' for on-line help, or 180s 'help.start()' for an HTML browser interface to help. 180s Type 'q()' to quit R. 180s 180s > # test_contrast_utils.R 180s > 180s > library(lmerTest) 180s Loading required package: lme4 180s Loading required package: Matrix 182s 182s Attaching package: 'lmerTest' 182s 182s The following object is masked from 'package:lme4': 182s 182s lmer 182s 182s The following object is masked from 'package:stats': 182s 182s step 182s 182s > 182s > ########## 182s > # Test that a message is printed if some cells have zero data: 182s > # Missing a single cell: 182s > data("cake", package="lme4") 182s > cake4 <- cake 182s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 182s > cake4 <- droplevels(subset(cake4, !(recipe == "A" & temperature == "175") )) 182s > with(cake4, table(recipe, temperature)) 182s temperature 182s recipe 175 185 195 205 215 225 182s A 0 15 15 15 15 15 182s B 15 15 15 15 15 15 182s C 15 15 15 15 15 15 182s > 182s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 182s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 182s > an <- anova(fm1) 182s Missing cells for: recipeA:temperature175. 182s Interpret type III hypotheses with care. 182s > txt <- capture.output(an <- anova(fm1), type = "message") 182s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 182s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 182s > 182s > ########## 182s > # Test that a message is printed if some cells have zero data: 182s > # Missing diagonal: 182s > cake4 <- cake 182s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 182s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 182s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 182s + (recipe == "B" & temperature == "185") | 182s + (recipe == "C" & temperature == "195") ))) 182s > cake4$temp0 <- cake4$temp - mean(cake4$temp) 182s > with(cake4, table(recipe, temperature)) 182s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 182s temperature 182s recipe 175 185 195 182s A 0 15 15 182s B 15 0 15 182s C 15 15 0 182s > 182s > fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 182s > an <- anova(fm1) 182s Missing cells for: recipeA:temperature175, recipeB:temperature185, recipeC:temperature195. 182s Interpret type III hypotheses with care. 182s > txt <- capture.output(an <- anova(fm1), type = "message") 182s > stopifnot(length(grep("Missing cells for:", txt)) > 0, 182s + length(grep("Interpret type III hypotheses with care.", txt)) > 0) 182s > 182s > ########## 182s > # Test that a message is NOT printed with centered covariates: 182s > fm1 <- lmer(angle ~ recipe * temp0 + (1|recipe:replicate), cake4) 182s > an <- anova(fm1) 182s > txt <- capture.output(an <- anova(fm1), type = "message") 182s > stopifnot(length(grep("Missing cells for:", txt)) == 0, 182s + length(grep("Interpret type III hypotheses with care.", txt)) == 0) 182s > # Note: in many cases a message would not be printed anyway because the 182s > # columns sums in the rdX design matrix would not be exactly zero but just a 182s > # small number very close to zero. 182s > 182s > 182s > 182s > 182s BEGIN TEST test_drop1.R 182s 182s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 182s Copyright (C) 2024 The R Foundation for Statistical Computing 182s Platform: aarch64-unknown-linux-gnu (64-bit) 182s 182s R is free software and comes with ABSOLUTELY NO WARRANTY. 182s You are welcome to redistribute it under certain conditions. 182s Type 'license()' or 'licence()' for distribution details. 182s 182s R is a collaborative project with many contributors. 182s Type 'contributors()' for more information and 182s 'citation()' on how to cite R or R packages in publications. 182s 182s Type 'demo()' for some demos, 'help()' for on-line help, or 182s 'help.start()' for an HTML browser interface to help. 182s Type 'q()' to quit R. 182s 182s > # test_drop1.R 182s > 182s > library(lmerTest) 182s Loading required package: lme4 182s Loading required package: Matrix 185s 185s Attaching package: 'lmerTest' 185s 185s The following object is masked from 'package:lme4': 185s 185s lmer 185s 185s The following object is masked from 'package:stats': 185s 185s step 185s 185s > 185s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 185s > # even in tests: 185s > assertError <- function(expr, ...) 185s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 185s > assertWarning <- function(expr, ...) 185s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 185s > 185s > TOL <- 1e-4 185s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 185s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 185s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 185s > 185s > data("sleepstudy", package="lme4") 185s > 185s > ######### Basic usage 185s > 185s > data("cake", package="lme4") 185s > cake2 <- cake 185s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 185s > fm <- lmer(angle ~ recipe + temperature + (1|recipe:replicate), cake2) 185s > (an1 <- drop1(fm)) 185s Single term deletions using Satterthwaite's method: 185s 185s Model: 185s angle ~ recipe + temperature + (1 | recipe:replicate) 185s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 185s recipe 10.19 5.09 2 42 0.2488 0.7809 185s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 185s --- 185s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 185s > (an2 <- drop1(fm, force_get_contrasts = TRUE)) 185s Single term deletions using Satterthwaite's method: 185s 185s Model: 185s angle ~ recipe + temperature + (1 | recipe:replicate) 185s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 185s recipe 10.19 5.09 2 42 0.2488 0.7809 185s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 185s --- 185s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 185s > drop1(fm, ddf="lme4", test="Chi") 185s Single term deletions 185s 185s Model: 185s angle ~ recipe + temperature + (1 | recipe:replicate) 185s npar AIC LRT Pr(Chi) 185s 1709.6 185s recipe 2 1706.1 0.530 0.7672 185s temperature 5 1785.7 86.106 <2e-16 *** 185s --- 185s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 185s > if(has_pbkrtest) 185s + drop1(fm, ddf="Kenward-Roger") 185s Single term deletions using Kenward-Roger's method: 185s 185s Model: 185s angle ~ recipe + temperature + (1 | recipe:replicate) 185s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 185s recipe 10.19 5.09 2 42 0.2488 0.7809 185s temperature 2100.30 420.06 5 220 20.5141 <2e-16 *** 185s --- 185s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 185s > 185s > tests1 <- show_tests(an1) 185s > tests2 <- show_tests(an2) 185s > 185s > stopifnot( 185s + # Tests are the same: 185s + isTRUE(all.equal(an1, an2, check.attributes = FALSE, tolerance=TOL)), 185s + # But contrast matrices are not: 185s + all(!mapply(function(x, y) isTRUE(all.equal(x, y)), tests1, tests2)) 185s + ) 185s > 185s > fm <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 185s > drop1(fm) 185s Single term deletions using Satterthwaite's method: 185s 185s Model: 185s angle ~ recipe * temperature + (1 | recipe:replicate) 185s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 185s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 185s > drop1(fm, ddf="lme4") 185s Single term deletions 185s 185s Model: 185s angle ~ recipe * temperature + (1 | recipe:replicate) 185s npar AIC 185s 1719.0 185s recipe:temperature 10 1709.6 185s > if(has_pbkrtest) 185s + drop1(fm, ddf="Kenward-Roger") 185s Single term deletions using Kenward-Roger's method: 185s 185s Model: 185s angle ~ recipe * temperature + (1 | recipe:replicate) 185s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 185s recipe:temperature 205.98 20.598 10 210 1.0062 0.4393 185s > 185s > # Incorrect arguments: 185s > assertError(drop1(fm, scope="recipe")) # Correct Error 185s > assertError(drop1(fm, scope=3)) # Correct Error 185s > assertError(drop1(fm, scope=list("recipe"))) # Correct Error 185s > 185s > # Polynomial terms: 185s > 185s > fm <- lmer(Reaction ~ 0 + (Days|Subject), sleepstudy) 186s > (an0 <- drop1(fm)) # No fixef! 186s Single term deletions using Satterthwaite's method: 186s 186s Model: 186s Reaction ~ 0 + (Days | Subject) 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s > fm <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 186s > (an1 <- drop1(fm)) 186s Single term deletions using Satterthwaite's method: 186s 186s Model: 186s Reaction ~ Days + (Days | Subject) 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s Days 30031 30031 1 17 45.853 3.264e-06 *** 186s --- 186s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 186s > fm <- lmer(Reaction ~ Days + I(Days^2) + (Days|Subject), sleepstudy) 186s > (an2 <- (drop1(fm))) 186s Single term deletions using Satterthwaite's method: 186s 186s Model: 186s Reaction ~ Days + I(Days^2) + (Days | Subject) 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s Days 4534.5 4534.5 1 114.43 6.9551 0.00952 ** 186s I(Days^2) 1079.5 1079.5 1 143.00 1.6558 0.20026 186s --- 186s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 186s > fm <- lmer(Reaction ~ poly(Days, 2) + (Days|Subject), sleepstudy) 186s > (an3 <- drop1(fm)) 186s Single term deletions using Satterthwaite's method: 186s 186s Model: 186s Reaction ~ poly(Days, 2) + (Days | Subject) 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s poly(Days, 2) 30974 15487 2 29.115 23.754 7.625e-07 *** 186s --- 186s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 186s > stopifnot( 186s + nrow(an0) == 0L, 186s + nrow(an1) == 1L, 186s + nrow(an2) == 2L, 186s + nrow(an3) == 1L 186s + ) 186s > 186s > # Consider a rank-deficient design matrix: 186s > fm <- lmer(angle ~ recipe + temp + temperature + (1|recipe:replicate), cake) 186s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 186s > # Here temp accounts for the linear effect of temperature, and 186s > # temperature is an (ordered) factor that accounts for the remaining 186s > # variation between temperatures (4 df). 186s > (an4 <- drop1(fm)) 186s Single term deletions using Satterthwaite's method: 186s 186s Model: 186s angle ~ recipe + temp + temperature + (1 | recipe:replicate) 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s recipe 10.189 5.094 2 42 0.2488 0.7809 186s temp 186s temperature 133.595 33.399 4 220 1.6311 0.1674 186s > # While temperature is in the model, we cannot test the effect of dropping 186s > # temp. After removing temperature we can test the effect of dropping temp: 186s > (an5 <- drop1(update(fm, ~.-temperature))) 186s Single term deletions using Satterthwaite's method: 186s 186s Model: 186s angle ~ recipe + temp + (1 | recipe:replicate) 186s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 186s recipe 10.3 5.15 2 42 0.2488 0.7809 186s temp 1966.7 1966.71 1 224 94.9759 <2e-16 *** 186s --- 186s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 186s > 186s > stopifnot( 186s + nrow(an4) == 3, 186s + rownames(an4)[2] == "temp", 186s + all(is.na(an4[2, ])), 186s + all(!is.na(an4[-2, ])), 186s + all(rownames(an5) == c("recipe", "temp")) 186s + ) 186s > 186s > 186s > 186s > 186s BEGIN TEST test_legacy.R 186s 186s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 186s Copyright (C) 2024 The R Foundation for Statistical Computing 186s Platform: aarch64-unknown-linux-gnu (64-bit) 186s 186s R is free software and comes with ABSOLUTELY NO WARRANTY. 186s You are welcome to redistribute it under certain conditions. 186s Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 186s 186s Type 'demo()' for some demos, 'help()' for on-line help, or 186s 'help.start()' for an HTML browser interface to help. 186s Type 'q()' to quit R. 186s 186s > # test_legacy.R 186s > library(lmerTest) 186s Loading required package: lme4 186s Loading required package: Matrix 188s 188s Attaching package: 'lmerTest' 188s 188s The following object is masked from 'package:lme4': 188s 188s lmer 188s 188s The following object is masked from 'package:stats': 188s 188s step 188s 188s > TOL <- 1e-4 188s > ##################################################################### 188s > 188s > # Read in data set 188s > load(system.file("testdata", "legacy_fits.RData", package="lmerTest")) 188s > # Generated with the following code using lmerTest version 2.0-37.9002 188s > # 188s > # library("lmerTest") 188s > # packageVersion("lmerTest") 188s > # fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 188s > # (an1 <- anova(fm1)) 188s > # (sfm1 <- summary(fm1)) 188s > # 188s > # fm2 <- lmer(Informed.liking ~ Product + Information + Gender + 188s > # (1|Product:Consumer) , data=ham) 188s > # (an2 <- anova(fm2)) 188s > # (sfm2 <- summary(fm2)) 188s > # 188s > # save(fm1, an1, sfm1, fm2, an2, sfm2, 188s > # file="~/GitHub/lmerTestR/package/inst/testdata/legacy_fits.RData") 188s > 188s > 188s > ####################################### 188s > ### Check that arguments for merModLmerTest and lmerModLmerTest methods match up: 188s > 188s > stopifnot( 188s + isTRUE(all.equal(formals(lmerTest:::anova.merModLmerTest), 188s + formals(lmerTest:::anova.lmerModLmerTest))), 188s + isTRUE(all.equal(formals(lmerTest:::summary.merModLmerTest), 188s + formals(lmerTest:::summary.lmerModLmerTest))), 188s + isTRUE(all.equal(formals(lmerTest:::drop1.merModLmerTest), 188s + formals(lmerTest:::drop1.lmerModLmerTest))), 188s + isTRUE(all.equal(formals(lmerTest:::step.merModLmerTest), 188s + formals(lmerTest:::step.lmerModLmerTest))), 188s + isTRUE(all.equal(formals(lmerTest:::ls_means.merModLmerTest), 188s + formals(lmerTest:::ls_means.lmerModLmerTest))), 188s + isTRUE(all.equal(formals(lmerTest:::difflsmeans.merModLmerTest), 188s + formals(lmerTest:::difflsmeans.lmerModLmerTest)))) 188s > 188s > 188s > ####################################### 188s > ## Tests for fm1: 188s > 188s > an1new <- anova(fm1) 188s > sfm1new <- summary(fm1) 188s > 188s > stopifnot( 188s + isTRUE(all.equal(an1new, an1, check.attributes=FALSE, tol=TOL)), 188s + isTRUE(all.equal(coef(sfm1new), coef(sfm1), tol=TOL)) 188s + ) 188s > 188s > contest(fm1, c(0, 1)) 188s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 188s 1 30031.01 30031.01 1 17 45.853 3.26379e-06 188s > contest(fm1, c(0, 1), joint=FALSE) 188s Estimate Std. Error df t value lower upper Pr(>|t|) 188s 1 10.46729 1.545789 17 6.771485 7.205956 13.72862 3.26379e-06 188s > drop1(fm1) 189s Single term deletions using Satterthwaite's method: 189s 189s Model: 189s Reaction ~ Days + (Days | Subject) 189s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 189s Days 30031 30031 1 17 45.853 3.264e-06 *** 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s > ranova(fm1) 189s ANOVA-like table for random-effects: Single term deletions 189s 189s Model: 189s Reaction ~ Days + (Days | Subject) 189s npar logLik AIC LRT Df Pr(>Chisq) 189s 6 -871.81 1755.6 189s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s > step(fm1) 189s Backward reduced random-effect table: 189s 189s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 189s 6 -871.81 1755.6 189s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 189s 189s 189s Days in (Days | Subject) *** 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s 189s Backward reduced fixed-effect table: 189s Degrees of freedom method: Satterthwaite 189s 189s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 189s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s 189s Model found: 189s Reaction ~ Days + (Days | Subject) 189s > 189s > fm1new <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, 189s + control=lmerControl(optimizer="bobyqa")) 189s > stopifnot( 189s + isTRUE(all.equal(drop1(fm1), drop1(fm1new), tol=TOL)), 189s + isTRUE(all.equal(ranova(fm1), ranova(fm1new), tol=TOL)), 189s + isTRUE(all.equal(contest(fm1, c(0, 1)), contest(fm1new, c(0, 1)), tol=TOL)), 189s + isTRUE(all.equal(contest(fm1, c(0, 1), joint=FALSE), 189s + contest(fm1new, c(0, 1), joint=FALSE), tol=TOL)) 189s + ) 189s > 189s > # Test that lme4 methods work: 189s > coef(fm1) 189s $Subject 189s (Intercept) Days 189s 308 253.6637 19.6662579 189s 309 211.0065 1.8475828 189s 310 212.4449 5.0184061 189s 330 275.0956 5.6529547 189s 331 273.6653 7.3973914 189s 332 260.4446 10.1951153 189s 333 268.2455 10.2436615 189s 334 244.1725 11.5418620 189s 335 251.0714 -0.2848731 189s 337 286.2955 19.0955699 189s 349 226.1950 11.6407002 189s 350 238.3351 17.0814910 189s 351 255.9829 7.4520288 189s 352 272.2687 14.0032993 189s 369 254.6806 11.3395026 189s 370 225.7922 15.2897506 189s 371 252.2121 9.4791309 189s 372 263.7196 11.7513157 189s 189s attr(,"class") 189s [1] "coef.mer" 189s > fixef(fm1) 189s (Intercept) Days 189s 251.40510 10.46729 189s > resid(fm1) 189s 1 2 3 4 5 6 189s -4.1036703 -14.6252282 -42.1955860 8.7773561 24.5231982 62.6951403 189s 7 8 9 10 11 12 189s 10.5425825 -101.1788754 19.5915667 35.6935088 11.7273721 -7.5883107 189s 13 14 15 16 17 18 189s -11.7238935 -11.8422762 -10.6807590 -4.2826418 -8.4617246 -6.2124074 189s 19 20 21 22 23 24 189s -1.4914902 9.6794271 -13.3909590 -23.1310650 11.8383289 5.3415228 189s 25 26 27 28 29 30 189s -3.2110832 -17.0789893 -7.1344953 8.1773986 8.4203926 -10.0952135 189s 31 32 33 34 35 36 189s 46.4469967 19.6516420 -2.5450126 -6.9214673 -11.9101220 -5.7748766 189s 37 38 39 40 41 42 189s -28.7737313 3.5950141 -14.9697406 28.0765048 13.9425924 3.9373010 189s 43 44 45 46 47 48 189s 13.3605097 24.2578183 13.0224270 -17.3335644 -27.9746558 9.3706529 189s 49 50 51 52 53 54 189s -39.0975385 31.3392701 -25.5840308 -27.8279461 -7.8735614 18.7388233 189s 55 56 57 58 59 60 189s 16.2378080 -1.4226073 132.5465774 15.0206621 -11.7052532 -98.3362685 189s 61 62 63 64 65 66 189s 15.5968640 11.0658025 -11.9635591 0.8331794 -12.0491821 18.7026564 189s 67 68 69 70 71 72 189s 2.3189949 8.8887334 -16.8348282 1.6043103 21.3005744 20.4868123 189s 73 74 75 76 77 78 189s -23.8915497 -24.1258118 -11.3155738 -17.6906358 -7.8988979 6.5573401 189s 79 80 81 82 83 84 189s -0.7605219 29.2497160 -9.4631090 23.1606642 3.9890373 20.5853104 189s 85 86 87 88 89 90 189s 1.5199836 4.9891567 -3.9098701 -13.7662970 -13.0383239 -11.2609507 189s 91 92 93 94 95 96 189s 26.0711443 8.4147744 -32.8753955 2.5400346 3.0546647 10.0651947 189s 97 98 99 100 101 102 189s 3.3912248 -3.2721451 16.8042850 0.7611151 9.9082056 -7.5189947 189s 103 104 105 106 107 108 189s -10.5507949 -6.1950951 -22.0474953 -14.6240955 -14.4743957 0.4221041 189s 109 110 111 112 113 114 189s 16.9600039 20.6838037 17.9616518 -11.9623391 -16.2935301 -34.0525210 189s 115 116 117 118 119 120 189s -37.7446120 5.9820971 38.6204061 5.0128151 19.5001242 -3.0158668 189s 121 122 123 124 125 126 189s -5.4564400 36.6226312 -0.9930976 2.2500737 -13.9636551 11.3905161 189s 127 128 129 130 131 132 189s -12.9485127 -41.5516414 5.9426298 24.5143010 -50.5915973 11.9219034 189s 133 134 135 136 137 138 189s 26.6032041 32.5769048 20.4583056 10.5435063 -1.8618930 -9.8591922 189s 139 140 141 142 143 144 189s -8.6544915 -9.7566908 17.2429421 2.4168396 -20.1171630 -11.0424656 189s 145 146 147 148 149 150 189s 14.7836319 5.8354293 -24.5822732 14.0658242 -5.1165783 9.7770191 189s 151 152 153 154 155 156 189s -0.5282354 -6.5584860 -17.4709366 -31.1884871 -19.4139377 41.9527117 189s 157 158 159 160 161 162 189s -36.3826389 14.7650105 17.0527600 8.8288094 17.6682554 10.7515245 189s 163 164 165 166 167 168 189s 6.7284937 1.1399628 -10.9581681 -15.0957989 -49.8211298 -13.9354607 189s 169 170 171 172 173 174 189s 22.7355085 31.9448776 5.6920558 -1.9969599 10.3745244 11.6580087 189s 175 176 177 178 179 180 189s -23.5523070 7.1313773 0.2542616 -2.7589541 11.4115302 -5.3578855 189s > 189s > ####################################### 189s > ## Tests for fm2: 189s > an2new <- anova(fm2) 189s > sfm2new <- summary(fm2) 189s > 189s > stopifnot( 189s + isTRUE(all.equal(an2new, an2, check.attributes=FALSE, tol=TOL)), 189s + isTRUE(all.equal(coef(sfm2new), coef(sfm2), tol=TOL)) 189s + ) 189s > 189s > drop1(fm2) 189s Single term deletions using Satterthwaite's method: 189s 189s Model: 189s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 189s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 189s Product 17.6984 5.8995 3 319 3.5029 0.01577 * 189s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 189s Gender 1.8634 1.8634 1 319 1.1064 0.29366 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s > ranova(fm2) 189s ANOVA-like table for random-effects: Single term deletions 189s 189s Model: 189s Informed.liking ~ Product + Information + Gender + (1 | Product:Consumer) 189s npar logLik AIC LRT Df Pr(>Chisq) 189s 8 -1356.1 2728.2 189s (1 | Product:Consumer) 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s > ls_means(fm2) 189s Least Squares Means table: 189s 189s Estimate Std. Error df t value lower upper Pr(>|t|) 189s Product1 5.80713 0.23223 319.0 25.006 5.35025 6.26402 < 2.2e-16 *** 189s Product2 5.10343 0.23223 319.0 21.976 4.64654 5.56032 < 2.2e-16 *** 189s Product3 6.09108 0.23223 319.0 26.229 5.63420 6.54797 < 2.2e-16 *** 189s Product4 5.92442 0.23223 319.0 25.511 5.46753 6.38131 < 2.2e-16 *** 189s Information1 5.63121 0.12682 437.8 44.404 5.38196 5.88046 < 2.2e-16 *** 189s Information2 5.83183 0.12682 437.8 45.986 5.58258 6.08107 < 2.2e-16 *** 189s Gender1 5.85366 0.16320 319.0 35.868 5.53257 6.17475 < 2.2e-16 *** 189s Gender2 5.60937 0.16523 319.0 33.949 5.28430 5.93445 < 2.2e-16 *** 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s 189s Confidence level: 95% 189s Degrees of freedom method: Satterthwaite 189s > difflsmeans(fm2) 189s Least Squares Means table: 189s 189s Estimate Std. Error df t value lower 189s Product1 - Product2 7.0370e-01 3.2841e-01 319 2.1428 5.7578e-02 189s Product1 - Product3 -2.8395e-01 3.2841e-01 319 -0.8646 -9.3008e-01 189s Product1 - Product4 -1.1728e-01 3.2841e-01 319 -0.3571 -7.6341e-01 189s Product2 - Product3 -9.8765e-01 3.2841e-01 319 -3.0074 -1.6338e+00 189s Product2 - Product4 -8.2099e-01 3.2841e-01 319 -2.4999 -1.4671e+00 189s Product3 - Product4 1.6667e-01 3.2841e-01 319 0.5075 -4.7946e-01 189s Information1 - Information2 -2.0062e-01 1.0196e-01 323 -1.9676 -4.0121e-01 189s Gender1 - Gender2 2.4428e-01 2.3224e-01 319 1.0519 -2.1263e-01 189s upper Pr(>|t|) 189s Product1 - Product2 1.3498e+00 0.032890 * 189s Product1 - Product3 3.6218e-01 0.387898 189s Product1 - Product4 5.2884e-01 0.721234 189s Product2 - Product3 -3.4153e-01 0.002845 ** 189s Product2 - Product4 -1.7486e-01 0.012926 * 189s Product3 - Product4 8.1279e-01 0.612159 189s Information1 - Information2 -2.6433e-05 0.049970 * 189s Gender1 - Gender2 7.0120e-01 0.293660 189s --- 189s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 189s 189s Confidence level: 95% 189s Degrees of freedom method: Satterthwaite 189s > nbeta <- length(fixef(fm2)) 189s > L <- diag(nbeta) 189s > L[1:4, ] <- 0 189s > contest(fm2, L) 189s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 189s 1 8.383419 4.19171 2 320.9875 2.488919 0.08460028 189s > contest(fm2, diag(nbeta), joint=FALSE) 189s Estimate Std. Error df t value lower upper 189s 1 5.8289672 0.2639677 343.6884 22.0821233 5.309772e+00 6.34816269 189s 2 -0.7037037 0.3284114 319.0000 -2.1427506 -1.349830e+00 -0.05757783 189s 3 0.2839506 0.3284114 319.0000 0.8646187 -3.621753e-01 0.93007650 189s 4 0.1172840 0.3284114 319.0000 0.3571251 -5.288419e-01 0.76340983 189s 5 0.2006173 0.1019607 323.0000 1.9675949 2.643318e-05 0.40120813 189s 6 -0.2442835 0.2322396 319.0000 -1.0518599 -7.011983e-01 0.21263128 189s Pr(>|t|) 189s 1 6.753245e-68 189s 2 3.288952e-02 189s 3 3.878978e-01 189s 4 7.212343e-01 189s 5 4.997000e-02 189s 6 2.936600e-01 189s > step(fm2) 190s Backward reduced random-effect table: 190s 190s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 190s 8 -1356.1 2728.2 190s (1 | Product:Consumer) 0 7 -1454.7 2923.4 197.19 1 < 2.2e-16 *** 190s --- 190s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 190s 190s Backward reduced fixed-effect table: 190s Degrees of freedom method: Satterthwaite 190s 190s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 190s Gender 1 1.8634 1.8634 1 319 1.1064 0.29366 190s Product 0 17.6926 5.8975 3 320 3.5018 0.01579 * 190s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 190s --- 190s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 190s 190s Model found: 190s Informed.liking ~ Product + Information + (1 | Product:Consumer) 190s > 190s > fm2new <- lmer(Informed.liking ~ Product + Information + Gender + 190s + (1|Product:Consumer), data=ham) 190s > stopifnot( 190s + isTRUE(all.equal(drop1(fm2), drop1(fm2new), tol=TOL)), 190s + isTRUE(all.equal(ranova(fm2), ranova(fm2new), tol=TOL)), 190s + isTRUE(all.equal(ls_means(fm2), ls_means(fm2new), tol=TOL)), 190s + isTRUE(all.equal(difflsmeans(fm2), difflsmeans(fm2new), tol=TOL)) 190s + ) 190s > 190s > # Test that lme4 methods work: 190s > coef(fm2) 190s $`Product:Consumer` 190s (Intercept) Product2 Product3 Product4 Information2 Gender2 190s 1:1 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:2 5.276027 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:3 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:4 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:5 4.468805 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:6 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:7 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:8 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:9 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:10 5.482447 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:11 8.504912 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:12 3.661584 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:13 7.697691 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:14 8.101302 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:15 4.675225 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:16 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:17 7.096889 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:18 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:19 8.307721 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:20 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:21 6.693279 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:22 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:23 6.486859 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:24 7.500500 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:25 5.078836 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:26 7.294080 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:29 4.872416 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:30 6.083248 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:31 6.289668 -0.7037037 0.2839506 0.117284 0.2006173 -0.2442835 190s 1:32 7.697691 -0.7037037 0.2839506 0.117284 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0.56464608 -0.63597120 1.08586242 -0.11475486 -0.89370421 0.90567850 190s 487 488 489 490 491 492 190s 0.54203624 -0.65858105 1.37186743 -1.82874985 1.08586242 -0.11475486 190s 493 494 495 496 497 498 190s -0.29731489 0.50206783 0.54203624 -0.65858105 0.49950005 0.29888276 190s 499 500 501 502 503 504 190s -0.73234482 0.06703790 0.07725652 -1.12336076 -0.48700303 -0.68762031 190s 505 506 507 508 509 510 190s -0.83896460 0.96041812 2.10391580 -2.09670148 -2.87565083 1.92373189 190s 511 512 513 514 515 516 190s 2.13842556 -2.06219172 0.11394275 -0.08667453 1.03876977 -0.16184751 190s 517 518 519 520 521 522 190s 0.84837111 -0.35224618 -0.31227776 0.48710495 1.95020337 -1.25041391 190s 523 524 525 526 527 528 190s -0.87803081 -0.07864810 -0.85759745 -1.05821473 2.54203624 -2.65858105 190s 529 530 531 532 533 534 190s -0.62813257 0.17125015 0.48947310 0.28885581 -0.70092557 1.09845715 190s 535 536 537 538 539 540 190s 0.33120421 0.13058692 -0.24257527 0.55680744 -1.28164149 0.51774123 190s 541 542 543 544 545 546 190s -0.06842948 -1.26904676 -0.66879579 1.13058692 1.92116411 -2.27945318 190s 547 548 549 550 551 552 190s 0.03876977 0.83815249 0.63753908 0.43692179 -0.10144573 -0.30206302 190s 553 554 555 556 557 558 190s -1.61007918 0.18930353 0.87503039 0.67441311 0.68463173 0.48401444 190s 559 560 561 562 563 564 190s 0.13842556 -0.06219172 -0.24257527 0.55680744 -0.70330555 1.09607717 190s 565 566 567 568 569 570 190s 0.68463173 0.48401444 0.71676150 0.51614422 -0.67522522 0.12415750 190s 571 572 573 574 575 576 190s 0.82793774 0.62732046 -0.51913280 -0.71975009 0.47689021 0.27627292 190s 577 578 579 580 581 582 190s -2.62813257 2.17125015 -0.31774826 1.48163446 -2.89370421 2.90567850 190s 583 584 585 586 587 588 190s 0.71676150 0.51614422 -2.01368986 0.78569286 -0.31774826 1.48163446 190s 589 590 591 592 593 594 190s 0.29907443 0.09845715 0.71676150 0.51614422 0.92116411 -1.27945318 190s 595 596 597 598 599 600 190s -1.34678752 1.45259519 0.63753908 0.43692179 0.47689021 0.27627292 190s 601 602 603 604 605 606 190s -0.04979663 0.74958609 0.48947310 0.28885581 -0.27926151 -0.47987879 190s 607 608 609 610 611 612 190s 0.13842556 -0.06219172 -0.04979663 0.74958609 1.89308377 -1.30753351 190s 613 614 615 616 617 618 190s 0.93157052 -2.26904676 -0.84352105 -0.04413834 0.11394275 -0.08667453 190s 619 620 621 622 623 624 190s -0.32873414 -0.52935142 -0.92274348 -0.12336076 -1.69783506 1.10154766 190s 625 626 627 628 629 630 190s 2.35381405 -1.84680323 1.27864107 0.07802378 1.49185308 -0.70876420 190s 631 632 633 634 635 636 190s 0.13842556 -0.06219172 -2.86800386 1.93137885 -2.34678752 2.45259519 190s 637 638 639 640 641 642 190s -1.13357551 0.66580721 1.09133291 -1.10928437 0.51755343 -0.68306385 190s 643 644 645 646 647 648 190s 0.24960180 0.04898452 -1.94079686 1.85858585 0.30216494 -0.89845234 190s > 190s > 190s BEGIN TEST test_lmer.R 190s 190s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 190s Copyright (C) 2024 The R Foundation for Statistical Computing 190s Platform: aarch64-unknown-linux-gnu (64-bit) 190s 190s R is free software and comes with ABSOLUTELY NO WARRANTY. 190s You are welcome to redistribute it under certain conditions. 190s Type 'license()' or 'licence()' for distribution details. 190s 190s R is a collaborative project with many contributors. 190s Type 'contributors()' for more information and 190s 'citation()' on how to cite R or R packages in publications. 190s 190s Type 'demo()' for some demos, 'help()' for on-line help, or 190s 'help.start()' for an HTML browser interface to help. 190s Type 'q()' to quit R. 190s 190s > # test_lmer.R 190s > 190s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 190s > data("sleepstudy", package="lme4") 190s > f <- function(form, data) lmerTest::lmer(form, data=data) 190s > form <- "Reaction ~ Days + (Days|Subject)" 190s > fm <- f(form, data=sleepstudy) 192s > anova(fm) 192s Type III Analysis of Variance Table with Satterthwaite's method 192s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 193s Days 30031 30031 1 17 45.853 3.264e-06 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s > summary(fm) 193s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 193s lmerModLmerTest] 193s Formula: form 193s Data: data 193s 193s REML criterion at convergence: 1743.6 193s 193s Scaled residuals: 193s Min 1Q Median 3Q Max 193s -3.9536 -0.4634 0.0231 0.4634 5.1793 193s 193s Random effects: 193s Groups Name Variance Std.Dev. Corr 193s Subject (Intercept) 612.10 24.741 193s Days 35.07 5.922 0.07 193s Residual 654.94 25.592 193s Number of obs: 180, groups: Subject, 18 193s 193s Fixed effects: 193s Estimate Std. Error df t value Pr(>|t|) 193s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 193s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Correlation of Fixed Effects: 193s (Intr) 193s Days -0.138 193s > 193s > # cf. GitHub issue #2: 193s > test <- function() { 193s + tmp <- sleepstudy 193s + m <- lmerTest::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 193s + summary(m) 193s + } 193s > test() 193s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 193s lmerModLmerTest] 193s Formula: Reaction ~ Days + (Days | Subject) 193s Data: tmp 193s 193s REML criterion at convergence: 1743.6 193s 193s Scaled residuals: 193s Min 1Q Median 3Q Max 193s -3.9536 -0.4634 0.0231 0.4634 5.1793 193s 193s Random effects: 193s Groups Name Variance Std.Dev. Corr 193s Subject (Intercept) 612.10 24.741 193s Days 35.07 5.922 0.07 193s Residual 654.94 25.592 193s Number of obs: 180, groups: Subject, 18 193s 193s Fixed effects: 193s Estimate Std. Error df t value Pr(>|t|) 193s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 193s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Correlation of Fixed Effects: 193s (Intr) 193s Days -0.138 193s > test <- function() { 193s + tmp <- sleepstudy 193s + m <- lme4::lmer(Reaction ~ Days + (Days | Subject), data = tmp) 193s + if(requireNamespace("lmerTest", quietly = TRUE)) { 193s + summary(lmerTest::as_lmerModLmerTest(m)) 193s + } 193s + } 193s > test() 193s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 193s lmerModLmerTest] 193s Formula: Reaction ~ Days + (Days | Subject) 193s Data: tmp 193s 193s REML criterion at convergence: 1743.6 193s 193s Scaled residuals: 193s Min 1Q Median 3Q Max 193s -3.9536 -0.4634 0.0231 0.4634 5.1793 193s 193s Random effects: 193s Groups Name Variance Std.Dev. Corr 193s Subject (Intercept) 612.10 24.741 193s Days 35.07 5.922 0.07 193s Residual 654.94 25.592 193s Number of obs: 180, groups: Subject, 18 193s 193s Fixed effects: 193s Estimate Std. Error df t value Pr(>|t|) 193s (Intercept) 251.405 6.825 17.000 36.838 < 2e-16 *** 193s Days 10.467 1.546 17.000 6.771 3.26e-06 *** 193s --- 193s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 193s 193s Correlation of Fixed Effects: 193s (Intr) 193s Days -0.138 193s > 193s > library(lmerTest) 193s Loading required package: lme4 193s Loading required package: Matrix 193s 193s Attaching package: 'lmerTest' 193s 193s The following object is masked from 'package:lme4': 193s 193s lmer 193s 193s The following object is masked from 'package:stats': 193s 193s step 193s 193s > 193s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 193s > # even in tests: 193s > assertError <- function(expr, ...) 193s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 193s > assertWarning <- function(expr, ...) 193s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 193s > 193s > TOL <- 1e-4 193s > 193s > ##################################################################### 193s > # Check that lme4::lmer and lmerTest::lmer have the same arguments 193s > 193s > lmer_args <- formals(lme4::lmer) 193s > names(lmer_args) 193s [1] "formula" "data" "REML" "control" "start" 193s [6] "verbose" "subset" "weights" "na.action" "offset" 193s [11] "contrasts" "devFunOnly" 193s > lmerTest_args <- formals(lmerTest::lmer) 193s > seq_args <- seq_along(lmerTest_args) 193s > if(packageVersion("lme4") > '1.1.21') { 193s + stopifnot( 193s + all.equal(names(lmer_args), names(lmerTest_args)), 193s + all.equal(lmer_args, lmerTest_args) 193s + ) 193s + } else { # Older versions of 'lme4' has a "..." argument: 193s + stopifnot( 193s + all.equal(names(lmer_args)[seq_args], names(lmerTest_args[seq_args])), 193s + all.equal(lmer_args[seq_args], lmerTest_args[seq_args]) 193s + ) 193s + } 193s > 193s > ##################################################################### 193s > # Test evaluation of update inside a function: 193s > myupdate <- function(m, ...) { 193s + update(m, ...) 193s + } 193s > 193s > data("sleepstudy", package="lme4") 193s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 193s > tmp <- sleepstudy 193s > rm(sleepstudy) 193s > fmA <- update(fm1, data = tmp) # works 193s > fmB <- myupdate(fm1, data = tmp) # also works 193s > # Same except for 'call': 193s > fmB@call <- fmA@call 193s > stopifnot(isTRUE(all.equal(fmA, fmB, tolerance=TOL))) 193s > # Based on bug-report by Henrik Singmann, github issue #3 193s > 193s > ##################################################################### 193s > # Test update when formula is a character vector: 193s > 193s > form <- "Informed.liking ~ Product+Information+ 193s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 193s > m <- lmer(form, data=ham) 193s > class(m) 193s [1] "lmerModLmerTest" 193s attr(,"package") 193s [1] "lmerTest" 193s > class(update(m, ~.- Product)) 193s [1] "lmerModLmerTest" 193s attr(,"package") 193s [1] "lmerTest" 193s > stopifnot(inherits(update(m, ~.- Product), "lmerModLmerTest")) 193s > 193s > # In version < 3.0-1.9002 class(update(m, ~.- Product)) was "lmerMod" 193s > ##################################################################### 193s > # Test error message from as_lmerModLmerTest: 193s > data("sleepstudy", package="lme4") 193s > myfit <- function(formula, data) { 193s + lme4::lmer(formula = formula, data = data) 193s + } 193s > fm2 <- myfit(Reaction ~ Days + (Days|Subject), sleepstudy) 193s > m <- assertError(as_lmerModLmerTest(fm2)) 193s > stopifnot( 193s + grepl("Unable to extract deviance function from model fit", m[[1]], fixed=TRUE) 193s + ) 193s > 193s > ##################################################################### 193s > # Check that devFunOnly argument works: 193s > data("sleepstudy", package="lme4") 193s > fun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = TRUE) 193s > stopifnot(is.function(fun) && names(formals(fun)[1]) == "theta") 193s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 194s > fun <- update(fm1, devFunOnly=TRUE) 194s > stopifnot(is.function(fun) && names(formals(fun)[1]) == "theta") 194s > # devFunOnly = FALSE: 194s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFunOnly = FALSE) 194s > stopifnot(inherits(notfun, "lmerModLmerTest")) 194s > # Partial matching: 194s > notfun <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy, devFun = FALSE) 194s > stopifnot(inherits(notfun, "lmerModLmerTest")) 194s > 194s > ##################################################################### 194s > # Use of as_lmerModLmerTest 194s > data("sleepstudy", package="lme4") 194s > m <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 194s > bm <- lmerTest:::as_lmerModLmerTest(m) 194s > stopifnot( 194s + inherits(bm, "lmerModLmerTest"), 194s + !inherits(m, "lmerModLmerTest"), 194s + inherits(bm, "lmerMod"), 194s + all(c("vcov_varpar", "Jac_list", "vcov_beta", "sigma") %in% slotNames(bm)) 194s + ) 194s > 194s > ##################################################################### 194s > # Update method 194s > 194s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 194s > m1 <- update(m, ~.-Days) 194s > m2 <- lmer(Reaction ~ (Days | Subject), sleepstudy) 194s > 194s > stopifnot( 194s + inherits(m, "lmerModLmerTest"), 194s + inherits(m1, "lmerModLmerTest"), 194s + inherits(m2, "lmerModLmerTest"), 194s + all.equal(m1, m2, tolerance=1e-6) 194s + ) 194s > 194s > 194s BEGIN TEST test_lmerTest_paper.R 194s 194s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 194s Copyright (C) 2024 The R Foundation for Statistical Computing 194s Platform: aarch64-unknown-linux-gnu (64-bit) 194s 194s R is free software and comes with ABSOLUTELY NO WARRANTY. 194s You are welcome to redistribute it under certain conditions. 194s Type 'license()' or 'licence()' for distribution details. 194s 194s R is a collaborative project with many contributors. 194s Type 'contributors()' for more information and 194s 'citation()' on how to cite R or R packages in publications. 194s 194s Type 'demo()' for some demos, 'help()' for on-line help, or 194s 'help.start()' for an HTML browser interface to help. 194s Type 'q()' to quit R. 194s 194s > # test_lmerTest_paper.R 194s > 194s > library(lmerTest) 194s Loading required package: lme4 194s Loading required package: Matrix 196s 196s Attaching package: 'lmerTest' 196s 196s The following object is masked from 'package:lme4': 196s 196s lmer 196s 196s The following object is masked from 'package:stats': 196s 196s step 196s 196s > 196s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 196s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 196s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 196s > 196s > # Read in data set 196s > load(system.file("testdata","test_paper_objects.RData", package="lmerTest")) 196s > 196s > # Evaluate code from paper: 196s > ## Section 8.2: 196s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + (1 | Assessor) + 196s + (1 | Assessor:TVset) + (1 | Assessor:Picture), data = TVbo, 196s + control=lmerControl(optimizer="bobyqa")) 197s > 197s > (an8.2 <- anova(tv)) 197s Type III Analysis of Variance Table with Satterthwaite's method 197s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 197s TVset 1.765 0.8825 2 14 0.2437 0.7869818 197s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 197s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > 197s > if(has_pbkrtest) 197s + (ankr8.2 <- anova(tv, type=2, ddf="Kenward-Roger")) 197s Type II Analysis of Variance Table with Kenward-Roger's method 197s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 197s TVset 1.765 0.8825 2 14 0.2437 0.7869818 197s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 197s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 197s --- 197s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 197s > 197s > ## Section 8.3: 197s > m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 197s + (1 | Product), data=carrots, 197s + control=lmerControl(optimizer="bobyqa")) 197s boundary (singular) fit: see help('isSingular') 198s > (sum8.3 <- coef(summary(m.carrots))) 198s Estimate Std. Error df t value Pr(>|t|) 198s (Intercept) 4.79911155 0.07529214 20.721910 63.7398768 2.918945e-25 198s sens1 0.01082919 0.01502840 9.168029 0.7205818 4.891315e-01 198s sens2 0.07064553 0.01727799 10.944477 4.0887589 1.812020e-03 198s > 198s > ## Section 8.4: 198s > tv <- lmer(Sharpnessofmovement ~ TVset * Picture + 198s + (1 | Assessor:TVset) + (1 | Assessor:Picture) + 198s + (1 | Assessor:Picture:TVset) + (1 | Repeat) + (1 | Repeat:Picture) + 198s + (1 | Repeat:TVset) + (1 | Repeat:TVset:Picture) + (1 | Assessor), 198s + data = TVbo, 198s + control=lmerControl(optimizer="bobyqa")) 198s boundary (singular) fit: see help('isSingular') 198s > st <- step(tv) 198s boundary (singular) fit: see help('isSingular') 199s boundary (singular) fit: see help('isSingular') 199s boundary (singular) fit: see help('isSingular') 200s boundary (singular) fit: see help('isSingular') 200s boundary (singular) fit: see help('isSingular') 201s boundary (singular) fit: see help('isSingular') 201s boundary (singular) fit: see help('isSingular') 201s boundary (singular) fit: see help('isSingular') 202s boundary (singular) fit: see help('isSingular') 202s boundary (singular) fit: see help('isSingular') 202s boundary (singular) fit: see help('isSingular') 202s boundary (singular) fit: see help('isSingular') 203s boundary (singular) fit: see help('isSingular') 203s boundary (singular) fit: see help('isSingular') 203s boundary (singular) fit: see help('isSingular') 203s boundary (singular) fit: see help('isSingular') 204s boundary (singular) fit: see help('isSingular') 204s boundary (singular) fit: see help('isSingular') 204s boundary (singular) fit: see help('isSingular') 204s boundary (singular) fit: see help('isSingular') 205s boundary (singular) fit: see help('isSingular') 205s boundary (singular) fit: see help('isSingular') 205s boundary (singular) fit: see help('isSingular') 205s boundary (singular) fit: see help('isSingular') 205s boundary (singular) fit: see help('isSingular') 205s boundary (singular) fit: see help('isSingular') 206s boundary (singular) fit: see help('isSingular') 206s boundary (singular) fit: see help('isSingular') 206s boundary (singular) fit: see help('isSingular') 206s boundary (singular) fit: see help('isSingular') 206s boundary (singular) fit: see help('isSingular') 206s boundary (singular) fit: see help('isSingular') 207s boundary (singular) fit: see help('isSingular') 207s > (elim_tab_random8.4 <- st$random) 207s Backward reduced random-effect table: 207s 207s Eliminated npar logLik AIC LRT Df 207s 21 -412.70 867.41 207s (1 | Assessor:Picture:TVset) 1 20 -412.70 865.41 0.0000 1 207s (1 | Repeat) 2 19 -412.70 863.41 0.0000 1 207s (1 | Repeat:Picture) 3 18 -412.70 861.41 0.0000 1 207s (1 | Repeat:TVset) 4 17 -412.70 859.41 0.0000 1 207s (1 | Repeat:TVset:Picture) 5 16 -412.70 857.41 0.0000 1 207s (1 | Assessor:TVset) 0 15 -414.10 858.20 2.7891 1 207s (1 | Assessor:Picture) 0 15 -418.88 867.76 12.3473 1 207s (1 | Assessor) 0 15 -416.44 862.88 7.4698 1 207s Pr(>Chisq) 207s 207s (1 | Assessor:Picture:TVset) 1.0000000 207s (1 | Repeat) 1.0000000 207s (1 | Repeat:Picture) 1.0000000 207s (1 | Repeat:TVset) 0.9999997 207s (1 | Repeat:TVset:Picture) 0.9999997 207s (1 | Assessor:TVset) 0.0949061 . 207s (1 | Assessor:Picture) 0.0004416 *** 207s (1 | Assessor) 0.0062742 ** 207s --- 207s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 207s > (elim_tab_fixed8.4 <- st$fixed) 207s Backward reduced fixed-effect table: 207s Degrees of freedom method: Satterthwaite 207s 207s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 207s TVset:Picture 0 90.767 15.128 6 138 4.1777 0.0006845 *** 207s --- 207s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 207s > (an8.4 <- anova(get_model(st))) 207s Type III Analysis of Variance Table with Satterthwaite's method 207s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 207s TVset 1.765 0.8825 2 14 0.2437 0.7869818 207s Picture 51.857 17.2857 3 21 4.7735 0.0108785 * 207s TVset:Picture 90.767 15.1279 6 138 4.1777 0.0006845 *** 207s --- 207s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 207s > 207s > ## Section 8.5: 207s > # L <- matrix(0, ncol = 12, nrow = 6) 207s > # L[1, 7] <- L[2, 8] <- L[3, 9] <- L[4, 10] <- L[5, 11] <- L[6, 12] <- 1 207s > L <- cbind(array(0, dim=c(6, 6)), diag(6)) 207s > (con1_8.5 <- calcSatterth(tv, L)) 207s $denom 207s [1] 138 207s 207s $Fstat 207s [,1] 207s [1,] 4.177655 207s 207s $pvalue 207s [,1] 207s [1,] 0.0006844793 207s 207s $ndf 207s [1] 6 207s 207s > (con2_8.5 <- contest(tv, L)) 207s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 207s 1 90.76719 15.12786 6 138 4.177655 0.0006844793 207s > 207s > ## Section C: 207s > # m.carrots <- lmer(Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + 207s > # (1 | product), data = carrots) 207s > # step(m.carrots, reduce.fixed = FALSE) 207s > (ran_C <- ranova(m.carrots)) 207s boundary (singular) fit: see help('isSingular') 208s boundary (singular) fit: see help('isSingular') 208s ANOVA-like table for random-effects: Single term deletions 208s 208s Model: 208s Preference ~ sens1 + sens2 + (1 + sens1 + sens2 | Consumer) + (1 | Product) 208s npar logLik AIC LRT Df 208s 11 -1869.7 3761.5 208s sens1 in (1 + sens1 + sens2 | Consumer) 8 -1870.7 3757.3 1.8274 3 208s sens2 in (1 + sens1 + sens2 | Consumer) 8 -1874.5 3765.0 9.5464 3 208s (1 | Product) 10 -1878.7Warning message: 208s Model failed to converge with 1 negative eigenvalue: -1.6e+03 208s 3777.4 17.9080 1 208s Pr(>Chisq) 208s 208s sens1 in (1 + sens1 + sens2 | Consumer) 0.60899 208s sens2 in (1 + sens1 + sens2 | Consumer) 0.02284 * 208s (1 | Product) 2.318e-05 *** 208s --- 208s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 208s > 208s > # Compare to validated outputs: 208s > TOL <- 1e-4 208s > stopifnot( 208s + isTRUE(all.equal(an8.2_save, an8.2, check.attributes = FALSE, tolerance=TOL)), 208s + isTRUE(all.equal(sum8.3_save, sum8.3, check.attributes = FALSE, tolerance=TOL)), 208s + isTRUE(all.equal(elim_tab_random8.4_save, elim_tab_random8.4, 208s + check.attributes = FALSE, tolerance=TOL)), 208s + isTRUE(all.equal(elim_tab_fixed8.4_save, elim_tab_fixed8.4, 208s + check.attributes = FALSE, tolerance=TOL)), 208s + isTRUE(all.equal(an8.4_save, an8.4, check.attributes = FALSE, tolerance=TOL)), 208s + isTRUE(all.equal(con1_8.5_save, con1_8.5, check.attributes = FALSE, tolerance=TOL)), 208s + isTRUE(all.equal(con2_8.5_save, con2_8.5, check.attributes = FALSE, tolerance=TOL)) 208s + ) 208s > if(has_pbkrtest) { 208s + stopifnot( 208s + isTRUE(all.equal(ankr8.2_save, ankr8.2, check.attributes = FALSE, tolerance=TOL)) 208s + ) 208s + } 208s > 208s > 209s BEGIN TEST test_ls_means.R 209s 209s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 209s Copyright (C) 2024 The R Foundation for Statistical Computing 209s Platform: aarch64-unknown-linux-gnu (64-bit) 209s 209s R is free software and comes with ABSOLUTELY NO WARRANTY. 209s You are welcome to redistribute it under certain conditions. 209s Type 'license()' or 'licence()' for distribution details. 209s 209s R is a collaborative project with many contributors. 209s Type 'contributors()' for more information and 209s 'citation()' on how to cite R or R packages in publications. 209s 209s Type 'demo()' for some demos, 'help()' for on-line help, or 209s 'help.start()' for an HTML browser interface to help. 209s Type 'q()' to quit R. 209s 209s > # test_lsmeans.R 209s > 209s > library(lmerTest) 209s Loading required package: lme4 209s Loading required package: Matrix 211s 211s Attaching package: 'lmerTest' 211s 211s The following object is masked from 'package:lme4': 211s 211s lmer 211s 211s The following object is masked from 'package:stats': 211s 211s step 211s 211s > 211s > TOL <- 1e-4 211s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 211s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 211s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 211s > 211s > ########### Basic model structures: 211s > 211s > # Factor * covariate: 211s > data("cake", package="lme4") 211s > model <- lmer(angle ~ recipe * temp + (1|recipe:replicate), cake) 211s > (lsm <- ls_means(model)) 211s Least Squares Means table: 211s 211s Estimate Std. Error df t value lower upper Pr(>|t|) 211s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 211s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 211s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 211s --- 211s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 211s 211s Confidence level: 95% 211s Degrees of freedom method: Satterthwaite 211s > stopifnot( 211s + nrow(lsm) == 3L, 211s + ncol(lsm) == 7L, 211s + # Balanced, so LS-means equal raw means: 211s + isTRUE(all.equal(c(with(cake, tapply(angle, recipe, mean))), lsm[, "Estimate"], 211s + check.attributes=FALSE, tolerance=TOL)) 211s + ) 211s > 211s > # Pairwise differences of LS-means: 211s > plsm <- ls_means(model, pairwise = TRUE) 211s > plsm2 <- difflsmeans(model) 211s > C <- as.matrix(lmerTest:::get_pairs(rownames(lsm))) 211s > stopifnot( 211s + isTRUE(all.equal(plsm, plsm2, tolerance=TOL)), 211s + isTRUE(all.equal(plsm[, "Estimate"], c(lsm[, "Estimate"] %*% C), 211s + check.attributes=FALSE, tolerance=TOL)) 211s + ) 211s > 211s > # Contrasts vectors: 211s > show_tests(lsm) 211s $recipe 211s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 211s recipeA 1 0 0 200 0 0 211s recipeB 1 1 0 200 200 0 211s recipeC 1 0 1 200 0 200 211s 211s > show_tests(plsm) 211s $recipe 211s (Intercept) recipeB recipeC temp recipeB:temp recipeC:temp 211s recipeA - recipeB 0 -1 0 0 -200 0 211s recipeA - recipeC 0 0 -1 0 0 -200 211s recipeB - recipeC 0 1 -1 0 200 -200 211s 211s > 211s > # Factor * Ordered: 211s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake) 211s > (lsm2 <- ls_means(model)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper 212s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 212s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 212s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 212s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 212s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 212s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 212s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 212s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 212s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 212s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 212s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 212s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 212s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 212s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 212s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 212s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 212s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 212s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 212s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 212s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 212s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 212s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 212s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 212s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 212s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 212s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 212s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 212s Pr(>|t|) 212s recipeA < 2.2e-16 *** 212s recipeB < 2.2e-16 *** 212s recipeC < 2.2e-16 *** 212s temperature175 < 2.2e-16 *** 212s temperature185 < 2.2e-16 *** 212s temperature195 < 2.2e-16 *** 212s temperature205 < 2.2e-16 *** 212s temperature215 < 2.2e-16 *** 212s temperature225 < 2.2e-16 *** 212s recipeA:temperature175 < 2.2e-16 *** 212s recipeB:temperature175 < 2.2e-16 *** 212s recipeC:temperature175 < 2.2e-16 *** 212s recipeA:temperature185 < 2.2e-16 *** 212s recipeB:temperature185 < 2.2e-16 *** 212s recipeC:temperature185 < 2.2e-16 *** 212s recipeA:temperature195 < 2.2e-16 *** 212s recipeB:temperature195 < 2.2e-16 *** 212s recipeC:temperature195 < 2.2e-16 *** 212s recipeA:temperature205 < 2.2e-16 *** 212s recipeB:temperature205 < 2.2e-16 *** 212s recipeC:temperature205 < 2.2e-16 *** 212s recipeA:temperature215 < 2.2e-16 *** 212s recipeB:temperature215 < 2.2e-16 *** 212s recipeC:temperature215 < 2.2e-16 *** 212s recipeA:temperature225 < 2.2e-16 *** 212s recipeB:temperature225 < 2.2e-16 *** 212s recipeC:temperature225 < 2.2e-16 *** 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > stopifnot( 212s + nrow(lsm2) == 3 + 6 + 3*6, 212s + ncol(lsm) == 7L, 212s + # Balanced, so LS-means equal raw means: 212s + isTRUE(all.equal(lsm[1:3, ], lsm2[1:3, ], 212s + check.attributes=FALSE, tolerance=TOL)) 212s + ) 212s > 212s > 212s > # Factor * Factor: 212s > cake2 <- cake 212s > cake2$temperature <- factor(cake2$temperature, ordered = FALSE) 212s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 212s > (lsm3 <- ls_means(model)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper 212s recipeA 33.1222 1.7368 42.0 19.070 29.6172 36.6273 212s recipeB 31.6444 1.7368 42.0 18.220 28.1394 35.1495 212s recipeC 31.6000 1.7368 42.0 18.194 28.0949 35.1051 212s temperature175 27.9778 1.1767 77.4 23.776 25.6349 30.3207 212s temperature185 29.9556 1.1767 77.4 25.457 27.6127 32.2985 212s temperature195 31.4222 1.1767 77.4 26.704 29.0793 33.7651 212s temperature205 32.1778 1.1767 77.4 27.346 29.8349 34.5207 212s temperature215 35.8444 1.1767 77.4 30.462 33.5015 38.1873 212s temperature225 35.3556 1.1767 77.4 30.046 33.0127 37.6985 212s recipeA:temperature175 29.1333 2.0381 77.4 14.294 25.0753 33.1913 212s recipeB:temperature175 26.8667 2.0381 77.4 13.182 22.8087 30.9247 212s recipeC:temperature175 27.9333 2.0381 77.4 13.706 23.8753 31.9913 212s recipeA:temperature185 31.5333 2.0381 77.4 15.472 27.4753 35.5913 212s recipeB:temperature185 29.4000 2.0381 77.4 14.425 25.3420 33.4580 212s recipeC:temperature185 28.9333 2.0381 77.4 14.196 24.8753 32.9913 212s recipeA:temperature195 30.8000 2.0381 77.4 15.112 26.7420 34.8580 212s recipeB:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 212s recipeC:temperature195 31.7333 2.0381 77.4 15.570 27.6753 35.7913 212s recipeA:temperature205 33.5333 2.0381 77.4 16.453 29.4753 37.5913 212s recipeB:temperature205 32.1333 2.0381 77.4 15.766 28.0753 36.1913 212s recipeC:temperature205 30.8667 2.0381 77.4 15.145 26.8087 34.9247 212s recipeA:temperature215 38.6667 2.0381 77.4 18.972 34.6087 42.7247 212s recipeB:temperature215 34.4667 2.0381 77.4 16.911 30.4087 38.5247 212s recipeC:temperature215 34.4000 2.0381 77.4 16.878 30.3420 38.4580 212s recipeA:temperature225 35.0667 2.0381 77.4 17.206 31.0087 39.1247 212s recipeB:temperature225 35.2667 2.0381 77.4 17.304 31.2087 39.3247 212s recipeC:temperature225 35.7333 2.0381 77.4 17.533 31.6753 39.7913 212s Pr(>|t|) 212s recipeA < 2.2e-16 *** 212s recipeB < 2.2e-16 *** 212s recipeC < 2.2e-16 *** 212s temperature175 < 2.2e-16 *** 212s temperature185 < 2.2e-16 *** 212s temperature195 < 2.2e-16 *** 212s temperature205 < 2.2e-16 *** 212s temperature215 < 2.2e-16 *** 212s temperature225 < 2.2e-16 *** 212s recipeA:temperature175 < 2.2e-16 *** 212s recipeB:temperature175 < 2.2e-16 *** 212s recipeC:temperature175 < 2.2e-16 *** 212s recipeA:temperature185 < 2.2e-16 *** 212s recipeB:temperature185 < 2.2e-16 *** 212s recipeC:temperature185 < 2.2e-16 *** 212s recipeA:temperature195 < 2.2e-16 *** 212s recipeB:temperature195 < 2.2e-16 *** 212s recipeC:temperature195 < 2.2e-16 *** 212s recipeA:temperature205 < 2.2e-16 *** 212s recipeB:temperature205 < 2.2e-16 *** 212s recipeC:temperature205 < 2.2e-16 *** 212s recipeA:temperature215 < 2.2e-16 *** 212s recipeB:temperature215 < 2.2e-16 *** 212s recipeC:temperature215 < 2.2e-16 *** 212s recipeA:temperature225 < 2.2e-16 *** 212s recipeB:temperature225 < 2.2e-16 *** 212s recipeC:temperature225 < 2.2e-16 *** 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > stopifnot( 212s + isTRUE(all.equal(lsm2, lsm3, check.attributes=FALSE, tolerance=TOL)) 212s + ) 212s > 212s > # Covariate (only): 212s > data("sleepstudy", package="lme4") 212s > m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 212s > (lsm <- ls_means(m)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper Pr(>|t|) 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > stopifnot( 212s + nrow(lsm) == 0L, 212s + ncol(lsm) == 7L 212s + ) 212s > 212s > # No fixef: 212s > m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) 212s > (lsm <- ls_means(m)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper Pr(>|t|) 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > stopifnot( 212s + nrow(lsm) == 0L, 212s + ncol(lsm) == 7L 212s + ) 212s > 212s > ########### Arguments and options: 212s > 212s > # which 212s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake2) 212s > (lsm4 <- ls_means(model, which = "recipe")) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper Pr(>|t|) 212s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 212s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 212s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > stopifnot( 212s + nrow(lsm4) == 3L, 212s + ncol(lsm4) == 7L, 212s + isTRUE(all.equal(lsm3[1:3, ], lsm4, check.attributes=FALSE, tolerance=TOL)) 212s + ) 212s > 212s > # KR: 212s > if(has_pbkrtest) 212s + (lsm5 <- ls_means(model, which = "recipe", ddf = "Kenward-Roger")) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper Pr(>|t|) 212s recipeA 33.1222 1.7368 42 19.070 29.6172 36.6273 < 2.2e-16 *** 212s recipeB 31.6444 1.7368 42 18.220 28.1394 35.1495 < 2.2e-16 *** 212s recipeC 31.6000 1.7368 42 18.194 28.0949 35.1051 < 2.2e-16 *** 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Kenward-Roger 212s > 212s > # level: 212s > (lsm6 <- ls_means(model, which = "recipe", level=0.99)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper Pr(>|t|) 212s recipeA 33.1222 1.7368 42 19.070 28.4361 37.8083 < 2.2e-16 *** 212s recipeB 31.6444 1.7368 42 18.220 26.9584 36.3305 < 2.2e-16 *** 212s recipeC 31.6000 1.7368 42 18.194 26.9139 36.2861 < 2.2e-16 *** 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 99% 212s Degrees of freedom method: Satterthwaite 212s > 212s > stopifnot( 212s + all(lsm6[, "lower"] < lsm4[, "lower"]), 212s + all(lsm6[, "upper"] > lsm4[, "upper"]) 212s + ) 212s > 212s > 212s > 212s > ########### Missing cels -> unestimable contrasts: 212s > 212s > # Missing cell: 212s > cake3 <- cake 212s > cake3$temperature <- factor(cake3$temperature, ordered=FALSE) 212s > cake3 <- droplevels(subset(cake3, temperature %in% levels(cake3$temperature)[1:3])) 212s > cake3 <- droplevels(subset(cake3, !(recipe == "C" & temperature == "195") )) 212s > str(cake3) 212s 'data.frame': 120 obs. of 5 variables: 212s $ replicate : Factor w/ 15 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 2 2 ... 212s $ recipe : Factor w/ 3 levels "A","B","C": 1 1 1 2 2 2 3 3 1 1 ... 212s $ temperature: Factor w/ 3 levels "175","185","195": 1 2 3 1 2 3 1 2 1 2 ... 212s $ angle : int 42 46 47 39 46 51 46 44 47 29 ... 212s $ temp : num 175 185 195 175 185 195 175 185 175 185 ... 212s > with(cake3, table(recipe, temperature)) 212s temperature 212s recipe 175 185 195 212s A 15 15 15 212s B 15 15 15 212s C 15 15 0 212s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 212s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 212s > (lsm7 <- ls_means(model)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper 212s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 212s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 212s recipeC NA NA NA NA NA NA 212s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 212s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 212s temperature195 NA NA NA NA NA NA 212s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 212s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 212s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 212s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 212s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 212s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 212s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 212s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 212s recipeC:temperature195 NA NA NA NA NA NA 212s Pr(>|t|) 212s recipeA < 2.2e-16 *** 212s recipeB < 2.2e-16 *** 212s recipeC NA 212s temperature175 < 2.2e-16 *** 212s temperature185 < 2.2e-16 *** 212s temperature195 NA 212s recipeA:temperature175 < 2.2e-16 *** 212s recipeB:temperature175 < 2.2e-16 *** 212s recipeC:temperature175 < 2.2e-16 *** 212s recipeA:temperature185 < 2.2e-16 *** 212s recipeB:temperature185 < 2.2e-16 *** 212s recipeC:temperature185 < 2.2e-16 *** 212s recipeA:temperature195 < 2.2e-16 *** 212s recipeB:temperature195 < 2.2e-16 *** 212s recipeC:temperature195 NA 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > 212s > # Using show_tests with options: 212s > show_tests(lsm7, fractions = TRUE) 212s $recipe 212s (Intercept) recipeB recipeC temperature185 temperature195 212s recipeA 1 0 0 1/3 1/3 212s recipeB 1 1 0 1/3 1/3 212s recipeC 1 0 1 1/3 1/3 212s recipeB:temperature185 recipeC:temperature185 recipeB:temperature195 212s recipeA 0 0 0 212s recipeB 1/3 0 1/3 212s recipeC 0 1/3 0 212s recipeC:temperature195 212s recipeA 0 212s recipeB 0 212s recipeC 1/3 212s 212s $temperature 212s (Intercept) recipeB recipeC temperature185 temperature195 212s temperature175 1 1/3 1/3 0 0 212s temperature185 1 1/3 1/3 1 0 212s temperature195 1 1/3 1/3 0 1 212s recipeB:temperature185 recipeC:temperature185 212s temperature175 0 0 212s temperature185 1/3 1/3 212s temperature195 0 0 212s recipeB:temperature195 recipeC:temperature195 212s temperature175 0 0 212s temperature185 0 0 212s temperature195 1/3 1/3 212s 212s $`recipe:temperature` 212s (Intercept) recipeB recipeC temperature185 212s recipeA:temperature175 1 0 0 0 212s recipeB:temperature175 1 1 0 0 212s recipeC:temperature175 1 0 1 0 212s recipeA:temperature185 1 0 0 1 212s recipeB:temperature185 1 1 0 1 212s recipeC:temperature185 1 0 1 1 212s recipeA:temperature195 1 0 0 0 212s recipeB:temperature195 1 1 0 0 212s recipeC:temperature195 1 0 1 0 212s temperature195 recipeB:temperature185 212s recipeA:temperature175 0 0 212s recipeB:temperature175 0 0 212s recipeC:temperature175 0 0 212s recipeA:temperature185 0 0 212s recipeB:temperature185 0 1 212s recipeC:temperature185 0 0 212s recipeA:temperature195 1 0 212s recipeB:temperature195 1 0 212s recipeC:temperature195 1 0 212s recipeC:temperature185 recipeB:temperature195 212s recipeA:temperature175 0 0 212s recipeB:temperature175 0 0 212s recipeC:temperature175 0 0 212s recipeA:temperature185 0 0 212s recipeB:temperature185 0 0 212s recipeC:temperature185 1 0 212s recipeA:temperature195 0 0 212s recipeB:temperature195 0 1 212s recipeC:temperature195 0 0 212s recipeC:temperature195 212s recipeA:temperature175 0 212s recipeB:temperature175 0 212s recipeC:temperature175 0 212s recipeA:temperature185 0 212s recipeB:temperature185 0 212s recipeC:temperature185 0 212s recipeA:temperature195 0 212s recipeB:temperature195 0 212s recipeC:temperature195 1 212s 212s > show_tests(lsm7, fractions = TRUE, names = FALSE) 212s $recipe 212s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 212s [1,] 1 0 0 1/3 1/3 0 0 0 0 212s [2,] 1 1 0 1/3 1/3 1/3 0 1/3 0 212s [3,] 1 0 1 1/3 1/3 0 1/3 0 1/3 212s 212s $temperature 212s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 212s [1,] 1 1/3 1/3 0 0 0 0 0 0 212s [2,] 1 1/3 1/3 1 0 1/3 1/3 0 0 212s [3,] 1 1/3 1/3 0 1 0 0 1/3 1/3 212s 212s $`recipe:temperature` 212s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] 212s [1,] 1 0 0 0 0 0 0 0 0 212s [2,] 1 1 0 0 0 0 0 0 0 212s [3,] 1 0 1 0 0 0 0 0 0 212s [4,] 1 0 0 1 0 0 0 0 0 212s [5,] 1 1 0 1 0 1 0 0 0 212s [6,] 1 0 1 1 0 0 1 0 0 212s [7,] 1 0 0 0 1 0 0 0 0 212s [8,] 1 1 0 0 1 0 0 1 0 212s [9,] 1 0 1 0 1 0 0 0 1 212s 212s > 212s > # Missing diagonal: 212s > cake4 <- cake 212s > cake4$temperature <- factor(cake4$temperature, ordered=FALSE) 212s > cake4 <- droplevels(subset(cake4, temperature %in% levels(cake4$temperature)[1:3])) 212s > cake4 <- droplevels(subset(cake4, !((recipe == "A" & temperature == "175") | 212s + (recipe == "B" & temperature == "185") | 212s + (recipe == "C" & temperature == "195") ))) 212s > # str(cake4) 212s > with(cake4, table(recipe, temperature)) 212s temperature 212s recipe 175 185 195 212s A 0 15 15 212s B 15 0 15 212s C 15 15 0 212s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake4) 212s fixed-effect model matrix is rank deficient so dropping 3 columns / coefficients 212s > ls_means(model) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper 212s recipeA NA NA NA NA NA NA 212s recipeB NA NA NA NA NA NA 212s recipeC NA NA NA NA NA NA 212s temperature175 NA NA NA NA NA NA 212s temperature185 NA NA NA NA NA NA 212s temperature195 NA NA NA NA NA NA 212s recipeA:temperature175 NA NA NA NA NA NA 212s recipeB:temperature175 26.8667 1.8908 53.5 14.209 23.0750 30.6584 212s recipeC:temperature175 27.9333 1.8908 53.5 14.773 24.1416 31.7250 212s recipeA:temperature185 31.5333 1.8908 53.5 16.677 27.7416 35.3250 212s recipeB:temperature185 NA NA NA NA NA NA 212s recipeC:temperature185 28.9333 1.8908 53.5 15.302 25.1416 32.7250 212s recipeA:temperature195 30.8000 1.8908 53.5 16.289 27.0083 34.5917 212s recipeB:temperature195 31.7333 1.8908 53.5 16.783 27.9416 35.5250 212s recipeC:temperature195 NA NA NA NA NA NA 212s Pr(>|t|) 212s recipeA NA 212s recipeB NA 212s recipeC NA 212s temperature175 NA 212s temperature185 NA 212s temperature195 NA 212s recipeA:temperature175 NA 212s recipeB:temperature175 < 2.2e-16 *** 212s recipeC:temperature175 < 2.2e-16 *** 212s recipeA:temperature185 < 2.2e-16 *** 212s recipeB:temperature185 NA 212s recipeC:temperature185 < 2.2e-16 *** 212s recipeA:temperature195 < 2.2e-16 *** 212s recipeB:temperature195 < 2.2e-16 *** 212s recipeC:temperature195 NA 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > 212s > 212s > ########### Various contrasts codings: 212s > 212s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3, 212s + contrasts = list(recipe="contr.sum", temperature="contr.helmert")) 212s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 212s > (lsm8 <- ls_means(model)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper 212s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 212s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 212s recipeC NA NA NA NA NA NA 212s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 212s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 212s temperature195 NA NA NA NA NA NA 212s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 212s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 212s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 212s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 212s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 212s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 212s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 212s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 212s recipeC:temperature195 NA NA NA NA NA NA 212s Pr(>|t|) 212s recipeA < 2.2e-16 *** 212s recipeB < 2.2e-16 *** 212s recipeC NA 212s temperature175 < 2.2e-16 *** 212s temperature185 < 2.2e-16 *** 212s temperature195 NA 212s recipeA:temperature175 < 2.2e-16 *** 212s recipeB:temperature175 < 2.2e-16 *** 212s recipeC:temperature175 < 2.2e-16 *** 212s recipeA:temperature185 < 2.2e-16 *** 212s recipeB:temperature185 < 2.2e-16 *** 212s recipeC:temperature185 < 2.2e-16 *** 212s recipeA:temperature195 < 2.2e-16 *** 212s recipeB:temperature195 < 2.2e-16 *** 212s recipeC:temperature195 NA 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > # show_tests(lsm7) 212s > # show_tests(lsm8) 212s > stopifnot( 212s + isTRUE(all.equal(lsm7, lsm8, check.attributes=FALSE, tolerance=TOL)) 212s + ) 212s > 212s > # ambient contrasts not contr.treatment: 212s > options("contrasts") 212s $contrasts 212s unordered ordered 212s "contr.treatment" "contr.poly" 212s 212s > options(contrasts = c("contr.sum", "contr.poly")) 212s > model <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake3) 212s fixed-effect model matrix is rank deficient so dropping 1 column / coefficient 212s > (lsm9 <- ls_means(model)) 212s Least Squares Means table: 212s 212s Estimate Std. Error df t value lower upper 212s recipeA 30.4889 1.7407 40.3 17.515 26.9716 34.0062 212s recipeB 29.3333 1.7407 40.3 16.851 25.8160 32.8506 212s recipeC NA NA NA NA NA NA 212s temperature175 27.9778 1.1016 57.2 25.398 25.7720 30.1835 212s temperature185 29.9556 1.1016 57.2 27.193 27.7498 32.1613 212s temperature195 NA NA NA NA NA NA 212s recipeA:temperature175 29.1333 1.9080 57.2 15.269 25.3129 32.9538 212s recipeB:temperature175 26.8667 1.9080 57.2 14.081 23.0462 30.6871 212s recipeC:temperature175 27.9333 1.9080 57.2 14.640 24.1129 31.7538 212s recipeA:temperature185 31.5333 1.9080 57.2 16.527 27.7129 35.3538 212s recipeB:temperature185 29.4000 1.9080 57.2 15.409 25.5795 33.2205 212s recipeC:temperature185 28.9333 1.9080 57.2 15.164 25.1129 32.7538 212s recipeA:temperature195 30.8000 1.9080 57.2 16.143 26.9795 34.6205 212s recipeB:temperature195 31.7333 1.9080 57.2 16.632 27.9129 35.5538 212s recipeC:temperature195 NA NA NA NA NA NA 212s Pr(>|t|) 212s recipeA < 2.2e-16 *** 212s recipeB < 2.2e-16 *** 212s recipeC NA 212s temperature175 < 2.2e-16 *** 212s temperature185 < 2.2e-16 *** 212s temperature195 NA 212s recipeA:temperature175 < 2.2e-16 *** 212s recipeB:temperature175 < 2.2e-16 *** 212s recipeC:temperature175 < 2.2e-16 *** 212s recipeA:temperature185 < 2.2e-16 *** 212s recipeB:temperature185 < 2.2e-16 *** 212s recipeC:temperature185 < 2.2e-16 *** 212s recipeA:temperature195 < 2.2e-16 *** 212s recipeB:temperature195 < 2.2e-16 *** 212s recipeC:temperature195 NA 212s --- 212s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 212s 212s Confidence level: 95% 212s Degrees of freedom method: Satterthwaite 212s > options(contrasts = c("contr.treatment", "contr.poly")) 212s > options("contrasts") 212s $contrasts 212s [1] "contr.treatment" "contr.poly" 212s 212s > stopifnot( 212s + isTRUE(all.equal(lsm7, lsm9, check.attributes=FALSE, tolerance=TOL)) 212s + ) 212s > 212s > 212s > 212s BEGIN TEST test_ranova_step.R 213s 213s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 213s Copyright (C) 2024 The R Foundation for Statistical Computing 213s Platform: aarch64-unknown-linux-gnu (64-bit) 213s 213s R is free software and comes with ABSOLUTELY NO WARRANTY. 213s You are welcome to redistribute it under certain conditions. 213s Type 'license()' or 'licence()' for distribution details. 213s 213s R is a collaborative project with many contributors. 213s Type 'contributors()' for more information and 213s 'citation()' on how to cite R or R packages in publications. 213s 213s Type 'demo()' for some demos, 'help()' for on-line help, or 213s 'help.start()' for an HTML browser interface to help. 213s Type 'q()' to quit R. 213s 213s > # test_ranova.R 213s > 213s > # Test functionality _before_ attaching lmerTest 213s > stopifnot(!"lmerTest" %in% .packages()) # ensure that lmerTest is NOT attached 213s > data("sleepstudy", package="lme4") 213s > f <- function(form, data) lmerTest::lmer(form, data=data) 213s > form <- "Reaction ~ Days + (Days|Subject)" 213s > fm <- f(form, data=sleepstudy) 215s > lmerTest::ranova(fm) 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ Days + (Days | Subject) 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > lmerTest::rand(fm) 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ Days + (Days | Subject) 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > lmerTest::step(fm) 215s Backward reduced random-effect table: 215s 215s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 215s 215s 215s Days in (Days | Subject) *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Backward reduced fixed-effect table: 215s Degrees of freedom method: Satterthwaite 215s 215s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 215s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s Loading required package: lme4 215s Loading required package: Matrix 215s 215s Model found: 215s Reaction ~ Days + (Days | Subject) 215s > 215s > library(lmerTest) 215s 215s Attaching package: 'lmerTest' 215s 215s The following object is masked from 'package:lme4': 215s 215s lmer 215s 215s The following object is masked from 'package:stats': 215s 215s step 215s 215s > 215s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 215s > # even in tests: 215s > assertError <- function(expr, ...) 215s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 215s > assertWarning <- function(expr, ...) 215s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 215s > 215s > TOL <- 1e-4 215s > ##################################################################### 215s > data("sleepstudy", package="lme4") 215s > 215s > # Test reduction of (Days | Subject) to (1 | Subject): 215s > fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) 215s > (an <- rand(fm1)) # 2 df test 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ Days + (Days | Subject) 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > (an <- ranova(fm1)) # 2 df test 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ Days + (Days | Subject) 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > step(fm1) 215s Backward reduced random-effect table: 215s 215s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 215s 215s 215s Days in (Days | Subject) *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Backward reduced fixed-effect table: 215s Degrees of freedom method: Satterthwaite 215s 215s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 215s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Model found: 215s Reaction ~ Days + (Days | Subject) 215s > stopifnot( 215s + nrow(an) == 2L, 215s + an[2L, "Df"] == 2L 215s + ) 215s > 215s > # This test can also be achieved with anova(): 215s > fm2 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 215s > (stp <- step(fm2)) 215s Backward reduced random-effect table: 215s 215s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 215s 4 -893.23 1794.5 215s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Backward reduced fixed-effect table: 215s Degrees of freedom method: Satterthwaite 215s 215s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 215s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Model found: 215s Reaction ~ Days + (1 | Subject) 215s > get_model(stp) 215s Linear mixed model fit by REML ['lmerModLmerTest'] 215s Formula: Reaction ~ Days + (1 | Subject) 215s Data: sleepstudy 215s REML criterion at convergence: 1786.465 215s Random effects: 215s Groups Name Std.Dev. 215s Subject (Intercept) 37.12 215s Residual 30.99 215s Number of obs: 180, groups: Subject, 18 215s Fixed Effects: 215s (Intercept) Days 215s 251.41 10.47 215s > (ana <- anova(fm1, fm2, refit=FALSE)) 215s Data: sleepstudy 215s Models: 215s fm2: Reaction ~ Days + (1 | Subject) 215s fm1: Reaction ~ Days + (Days | Subject) 215s npar AIC BIC logLik deviance Chisq Df Pr(>Chisq) 215s fm2 4 1794.5 1807.2 -893.23 1786.5 215s fm1 6 1755.6 1774.8 -871.81 1743.6 42.837 2 4.99e-10 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > 215s > stopifnot( 215s + all.equal(an[2L, "LRT"], ana[2L, "Chisq"], tolerance=TOL) 215s + ) 215s > 215s > # Illustrate complete.test argument: 215s > # Test removal of (Days | Subject): 215s > (an <- ranova(fm1, reduce.terms = FALSE)) # 3 df test 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ Days + (Days | Subject) 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 6 -871.81 1755.6 215s (Days | Subject) 3 -946.83 1899.7 150.03 3 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > 215s > # The likelihood ratio test statistic is in this case: 215s > fm3 <- lm(Reaction ~ Days, sleepstudy) 215s > LRT <- 2*c(logLik(fm1, REML=TRUE) - logLik(fm3, REML=TRUE)) # LRT 215s > stopifnot( 215s + nrow(an) == 2L, 215s + an[2L, "Df"] == 3L, 215s + all.equal(an[2L, "LRT"], LRT, tolerance=TOL) 215s + ) 215s > 215s > ## _NULL_ model: 215s > fm <- lmer(Reaction ~ -1 + (1|Subject), sleepstudy) 215s > step(fm) 215s Backward reduced random-effect table: 215s 215s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 215s 2 -992.84 1989.7 215s (1 | Subject) 0 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Backward reduced fixed-effect table: 215s Degrees of freedom method: Satterthwaite 215s 215s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 215s 215s Model found: 215s Reaction ~ -1 + (1 | Subject) 215s > ranova(fm) 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ (1 | Subject) - 1 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 2 -992.84 1989.7 215s (1 | Subject) 1 -1284.32 2570.7 582.97 1 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > lm1 <- lm(Reaction ~ 0, data=sleepstudy) 215s > LRT <- 2*c(logLik(fm, REML=FALSE) - logLik(lm1, REML=FALSE)) 215s > 215s > ## Tests of ML-fits agree with anova(): 215s > fm1 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy, REML=FALSE) 215s > step(fm1) 215s Backward reduced random-effect table: 215s 215s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 215s 4 -897.04 1802.1 215s (1 | Subject) 0 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Backward reduced fixed-effect table: 215s Degrees of freedom method: Satterthwaite 215s 215s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 215s Days 0 162703 162703 1 162 170.45 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s 215s Model found: 215s Reaction ~ Days + (1 | Subject) 215s > lm2 <- lm(Reaction ~ Days, sleepstudy) 215s > (an1 <- ranova(fm1)) 215s ANOVA-like table for random-effects: Single term deletions 215s 215s Model: 215s Reaction ~ Days + (1 | Subject) 215s npar logLik AIC LRT Df Pr(>Chisq) 215s 4 -897.04 1802.1 215s (1 | Subject) 3 -950.15 1906.3 106.21 1 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > (an2 <- anova(fm1, lm2)) 215s Data: sleepstudy 215s Models: 215s lm2: Reaction ~ Days 215s fm1: Reaction ~ Days + (1 | Subject) 215s npar AIC BIC logLik deviance Chisq Df Pr(>Chisq) 215s lm2 3 1906.3 1915.9 -950.15 1900.3 215s fm1 4 1802.1 1814.8 -897.04 1794.1 106.21 1 < 2.2e-16 *** 215s --- 215s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 215s > j <- grep("Chi Df|Df", colnames(an2)) 215s > stopifnot( 215s + all.equal(an1[2, "LRT"], an2[2, "Chisq"], tolerance=TOL), 215s + all.equal(an1[2, "Df"], an2[2, j[length(j)]], tolerance=TOL), 215s + all.equal(an1[1:2, "logLik"], an2[2:1, "logLik"], tolerance=TOL) 215s + ) 215s > ## Note that lme4 version <1.1-22 use "Chi Df" while >=1.1-22 use "Df" 215s > 215s > # Expect warnings when old (version < 3.0-0) arguments are used: 215s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 215s + type=3, fixed.calc = FALSE, lsmeans.calc = FALSE, 215s + difflsmeans.calc = TRUE, test.effs = 42, keep.e="save")) 216s > assertWarning(step(fm, reduce.fixed = FALSE, reduce.random = FALSE, 216s + lsmeans=3)) 216s > 216s > 216s > check_nrow <- function(obj, expect_nrow) { 216s + stopifnot( 216s + is.numeric(expect_nrow), 216s + nrow(obj) == expect_nrow 216s + ) 216s + } 216s > 216s > # Statistical nonsense, but it works: 216s > fm1 <- lmer(Reaction ~ Days + (1 | Subject) + (0 + Days|Subject), sleepstudy) 216s > step(fm1) 216s Backward reduced random-effect table: 216s 216s Eliminated npar logLik AIC LRT Df 216s 5 -871.83 1753.7 216s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 216s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 216s Pr(>Chisq) 216s 216s (1 | Subject) 1.746e-06 *** 216s Days in (0 + Days | Subject) 6.076e-11 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Backward reduced fixed-effect table: 216s Degrees of freedom method: Satterthwaite 216s 216s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 216s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Model found: 216s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 216s > (an <- ranova(fm1)) 216s ANOVA-like table for random-effects: Single term deletions 216s 216s Model: 216s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 216s npar logLik AIC LRT Df Pr(>Chisq) 216s 5 -871.83 1753.7 216s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 216s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s > check_nrow(an, 3) 216s > ranova(fm1, reduce.terms = FALSE) 216s ANOVA-like table for random-effects: Single term deletions 216s 216s Model: 216s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 216s npar logLik AIC LRT Df Pr(>Chisq) 216s 5 -871.83 1753.7 216s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 216s (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s > 216s > # Statistical nonsense, but it works: 216s > fm1 <- lmer(Reaction ~ Days + (0 + Days|Subject), sleepstudy) 216s > step(fm1) 216s Backward reduced random-effect table: 216s 216s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 216s 4 -883.26 1774.5 216s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 216s 216s Backward reduced fixed-effect table: 216s Degrees of freedom method: Satterthwaite 216s 216s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 216s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Model found: 216s Reaction ~ Days + (0 + Days | Subject) 216s > (an <- ranova(fm1)) # no test of non-nested models 216s ANOVA-like table for random-effects: Single term deletions 216s 216s Model: 216s Reaction ~ Days + (0 + Days | Subject) 216s npar logLik AIC LRT Df Pr(>Chisq) 216s 4 -883.26 1774.5 216s Days in (0 + Days | Subject) 4 -893.23 1794.5 19.94 0 216s > stopifnot( 216s + nrow(an) == 2L, 216s + an[2L, "Df"] == 0, 216s + all(is.na(an[2L, "Pr(>Chisq)"])) 216s + ) 216s > fm0 <- lmer(Reaction ~ Days + (1|Subject), sleepstudy) 216s > step(fm0) 216s Backward reduced random-effect table: 216s 216s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 216s 4 -893.23 1794.5 216s (1 | Subject) 0 3 -946.83 1899.7 107.2 1 < 2.2e-16 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Backward reduced fixed-effect table: 216s Degrees of freedom method: Satterthwaite 216s 216s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 216s Days 0 162703 162703 1 161 169.4 < 2.2e-16 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Model found: 216s Reaction ~ Days + (1 | Subject) 216s > (an2 <- anova(fm1, fm0, refit=FALSE)) 216s Data: sleepstudy 216s Models: 216s fm1: Reaction ~ Days + (0 + Days | Subject) 216s fm0: Reaction ~ Days + (1 | Subject) 216s npar AIC BIC logLik deviance Chisq Df Pr(>Chisq) 216s fm1 4 1774.5 1787.3 -883.26 1766.5 216s fm0 4 1794.5 1807.2 -893.23 1786.5 0 0 216s > stopifnot( 216s + (packageVersion("lme4")<="1.1.23" && an2[2L, "Pr(>Chisq)"] == 1) || 216s + is.na(an2[2L, "Pr(>Chisq)"]) 216s + ) 216s > ranova(fm1, reduce.terms = FALSE) 216s ANOVA-like table for random-effects: Single term deletions 216s 216s Model: 216s Reaction ~ Days + (0 + Days | Subject) 216s npar logLik AIC LRT Df Pr(>Chisq) 216s 4 -883.26 1774.5 216s (0 + Days | Subject) 3 -946.83 1899.7 127.14 1 < 2.2e-16 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s > 216s > fm1 <- lmer(Reaction ~ Days + (-1 + Days|Subject), sleepstudy) 216s > step(fm1) 216s Backward reduced random-effect table: 216s 216s Eliminated npar logLik AIC LRT Df 216s 4 -883.26 1774.5 216s Days in (-1 + Days | Subject) 0 4 -893.23 1794.5 19.94 0 216s Pr(>Chisq) 216s 216s Days in (-1 + Days | Subject) 216s 216s Backward reduced fixed-effect table: 216s Degrees of freedom method: Satterthwaite 216s 216s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 216s Days 0 26395 26395 1 21.679 31.347 1.32e-05 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Model found: 216s Reaction ~ Days + (-1 + Days | Subject) 216s > (an3 <- ranova(fm1)) # no test of non-nested models 216s ANOVA-like table for random-effects: Single term deletions 216s 216s Model: 216s Reaction ~ Days + (-1 + Days | Subject) 216s npar logLik AIC LRT Df Pr(>Chisq) 216s 4 -883.26 1774.5 216s Days in (-1 + Days | Subject) 4 -893.23 1794.5 19.94 0 216s > stopifnot( 216s + all.equal(an, an3, check.attributes=FALSE, tolerance=TOL) 216s + ) 216s > 216s > # Example where comparison of non-nested models is generated 216s > fm <- lmer(Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject), sleepstudy) 216s boundary (singular) fit: see help('isSingular') 216s > step(fm) 216s Backward reduced random-effect table: 216s 216s Eliminated npar logLik AIC 216s 7 -937.05 1888.1 216s poly(Days, 2) in (0 + poly(Days, 2) | Subject) 1 5 -884.67 1779.3 216s (1 | Subject) 0 4 -938.16 1884.3 216s LRT Df Pr(>Chisq) 216s 216s poly(Days, 2) in (0 + poly(Days, 2) | Subject) -104.77 2 1 216s (1 | Subject) 106.98 1 <2e-16 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Backward reduced fixed-effect table: 216s Degrees of freedom method: Satterthwaite 216s 216s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 216s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 216s --- 216s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 216s 216s Model found: 216s Reaction ~ poly(Days, 2) + (1 | Subject) 216s > an <- ranova(fm) 217s > stopifnot( 217s + nrow(an) == 2L, 217s + an[2, "Pr(>Chisq)"] == 1 217s + ) 217s > ranova(fm, reduce.terms = FALSE) # test of nested models 217s ANOVA-like table for random-effects: Single term deletions 217s 217s Model: 217s Reaction ~ poly(Days, 2) + (0 + poly(Days, 2) | Subject) 217s npar logLik AIC LRT Df Pr(>Chisq) 217s 7 -937.05 1888.1 217s (0 + poly(Days, 2) | Subject) 4 -938.16 1884.3 2.2153 3 0.5289 217s > 217s > # These models are nested, though: 217s > fm <- lmer(Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject), sleepstudy) 217s > step(fm) 217s Backward reduced random-effect table: 217s 217s Eliminated npar logLik AIC 217s 10 -856.40 1732.8 217s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 0 5 -884.67 1779.3 217s LRT Df Pr(>Chisq) 217s 217s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 56.524 5 6.338e-11 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Backward reduced fixed-effect table: 217s Degrees of freedom method: Satterthwaite 217s 217s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 217s poly(Days, 2) 0 24213 12106 2 16.998 23.363 1.326e-05 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Model found: 217s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 217s > ranova(fm) 217s ANOVA-like table for random-effects: Single term deletions 217s 217s Model: 217s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 217s npar logLik AIC LRT Df 217s 10 -856.40 1732.8 217s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 5 -884.67 1779.3 56.524 5 217s Pr(>Chisq) 217s 217s poly(Days, 2) in (1 + poly(Days, 2) | Subject) 6.338e-11 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s > fm0 <- lmer(Reaction ~ poly(Days, 2) + (1 | Subject), sleepstudy) 217s > step(fm0) 217s Backward reduced random-effect table: 217s 217s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 217s 5 -884.67 1779.3 217s (1 | Subject) 0 4 -938.16 1884.3 106.98 1 < 2.2e-16 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Backward reduced fixed-effect table: 217s Degrees of freedom method: Satterthwaite 217s 217s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 217s poly(Days, 2) 0 163782 81891 2 160 85.329 < 2.2e-16 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Model found: 217s Reaction ~ poly(Days, 2) + (1 | Subject) 217s > anova(fm0, fm, refit=FALSE) 217s Data: sleepstudy 217s Models: 217s fm0: Reaction ~ poly(Days, 2) + (1 | Subject) 217s fm: Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 217s npar AIC BIC logLik deviance Chisq Df Pr(>Chisq) 217s fm0 5 1779.3 1795.3 -884.67 1769.3 217s fm 10 1732.8 1764.7 -856.40 1712.8 56.524 5 6.338e-11 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s > ranova(fm, reduce.terms = FALSE) 217s ANOVA-like table for random-effects: Single term deletions 217s 217s Model: 217s Reaction ~ poly(Days, 2) + (1 + poly(Days, 2) | Subject) 217s npar logLik AIC LRT Df Pr(>Chisq) 217s 10 -856.40 1732.8 217s (1 + poly(Days, 2) | Subject) 4 -938.16 1884.3 163.51 6 < 2.2e-16 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s > 217s > # A model with ||-notation: 217s > fm1 <- lmer(Reaction ~ Days + (Days||Subject), sleepstudy) 217s > step(fm1) 217s Backward reduced random-effect table: 217s 217s Eliminated npar logLik AIC LRT Df 217s 5 -871.83 1753.7 217s (1 | Subject) 0 4 -883.26 1774.5 22.856 1 217s Days in (0 + Days | Subject) 0 4 -893.23 1794.5 42.796 1 217s Pr(>Chisq) 217s 217s (1 | Subject) 1.746e-06 *** 217s Days in (0 + Days | Subject) 6.076e-11 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Backward reduced fixed-effect table: 217s Degrees of freedom method: Satterthwaite 217s 217s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 217s Days 0 29442 29442 1 18.156 45.046 2.594e-06 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Model found: 217s Reaction ~ Days + ((1 | Subject) + (0 + Days | Subject)) 217s > ranova(fm1) 217s ANOVA-like table for random-effects: Single term deletions 217s 217s Model: 217s Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 217s npar logLik AIC LRT Df Pr(>Chisq) 217s 5 -871.83 1753.7 217s (1 | Subject) 4 -883.26 1774.5 22.856 1 1.746e-06 *** 217s Days in (0 + Days | Subject) 4 -893.23 1794.5 42.796 1 6.076e-11 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s > 217s > # What about models with nested factors? 217s > fm <- lmer(Coloursaturation ~ TVset*Picture + (1|Assessor:TVset) + (1|Assessor), 217s + data=TVbo) 217s > step(fm) 217s Backward reduced random-effect table: 217s 217s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 217s 15 -280.22 590.44 217s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 217s (1 | Assessor:TVset) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Backward reduced fixed-effect table: 217s Degrees of freedom method: Satterthwaite 217s 217s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 217s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s Model found: 217s Coloursaturation ~ TVset + Picture + (1 | Assessor:TVset) + TVset:Picture 217s > (an1 <- ranova(fm)) 217s ANOVA-like table for random-effects: Single term deletions 217s 217s Model: 217s Coloursaturation ~ TVset + Picture + (1 | Assessor:TVset) + (1 | Assessor) + TVset:Picture 217s npar logLik AIC LRT Df Pr(>Chisq) 217s 15 -280.22 590.44 217s (1 | Assessor:TVset) 14 -302.61 633.22 44.777 1 2.208e-11 *** 217s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s > 217s > fm <- lmer(Coloursaturation ~ TVset * Picture + 217s + (1|Assessor/TVset), data=TVbo) 217s > step(fm) 218s Backward reduced random-effect table: 218s 218s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 218s 15 -280.22 590.44 218s (1 | Assessor) 1 14 -280.27 588.53 0.090 1 0.7643 218s (1 | TVset:Assessor) 0 13 -312.24 650.47 63.941 1 1.282e-15 *** 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s 218s Backward reduced fixed-effect table: 218s Degrees of freedom method: Satterthwaite 218s 218s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 218s TVset:Picture 0 13.8 2.2999 6 159 2.6761 0.01679 * 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s 218s Model found: 218s Coloursaturation ~ TVset + Picture + (1 | TVset:Assessor) + TVset:Picture 218s > (an2 <- ranova(fm)) 218s ANOVA-like table for random-effects: Single term deletions 218s 218s Model: 218s Coloursaturation ~ TVset + Picture + (1 | TVset:Assessor) + (1 | Assessor) + TVset:Picture 218s npar logLik AIC LRT Df Pr(>Chisq) 218s 15 -280.22 590.44 218s (1 | TVset:Assessor) 14 -302.61 633.22 44.777 1 2.208e-11 *** 218s (1 | Assessor) 14 -280.27 588.53 0.090 1 0.7643 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s > stopifnot( 218s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL) 218s + ) 218s > 218s > ##################################################################### 218s > # Test evaluation within functions, i.e. in other environments etc. 218s > attach(sleepstudy) 218s > fm <- lmer(Reaction ~ Days + (Days|Subject)) 218s > step(fm) 218s Backward reduced random-effect table: 218s 218s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 218s 6 -871.81 1755.6 218s Days in (Days | Subject) 0 4 -893.23 1794.5 42.837 2 4.99e-10 218s 218s 218s Days in (Days | Subject) *** 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s 218s Backward reduced fixed-effect table: 218s Degrees of freedom method: Satterthwaite 218s 218s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 218s Days 0 30031 30031 1 17 45.853 3.264e-06 *** 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s 218s Model found: 218s Reaction ~ Days + (Days | Subject) 218s > ranova(fm) # OK 218s ANOVA-like table for random-effects: Single term deletions 218s 218s Model: 218s Reaction ~ Days + (Days | Subject) 218s npar logLik AIC LRT Df Pr(>Chisq) 218s 6 -871.81 1755.6 218s Days in (Days | Subject) 4 -893.23 1794.5 42.837 2 4.99e-10 *** 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s > detach(sleepstudy) 218s > 218s > # Evaluating in a function works: 218s > f <- function(form, data) lmer(form, data=data) 218s > form <- "Informed.liking ~ Product+Information+ 218s + (1|Consumer) + (1|Product:Consumer) + (1|Information:Consumer)" 218s > fm <- f(form, data=ham) 218s > ranova(fm) 218s boundary (singular) fit: see help('isSingular') 218s ANOVA-like table for random-effects: Single term deletions 218s 218s Model: 218s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 218s npar logLik AIC LRT Df Pr(>Chisq) 218s 9 -1353.9 2725.8 218s (1 | Consumer) 8 -1355.1 2726.1 2.295 1 0.1298 218s (1 | Product:Consumer) 8 -1436.3 2888.6 164.753 1 <2e-16 *** 218s (1 | Information:Consumer) 8 -1354.5 2725.1 1.255 1 0.2626 218s --- 218s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 218s > step_res <- step(fm) 218s boundary (singular) fit: see help('isSingular') 219s > stopifnot( 219s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 219s + colnames(step_res$fixed)) 219s + ) 219s > 219s > # Check that step works when form is a character vector 219s > m <- lmer(form, data=ham) 219s > step_res <- step(m) 219s boundary (singular) fit: see help('isSingular') 219s > (drop1_table <- attr(step_res, "drop1")) 219s Single term deletions using Satterthwaite's method: 219s 219s Model: 219s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 219s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 219s Product 19.3466 6.4489 3 240 3.8291 0.01048 * 219s Information 6.5201 6.5201 1 323 3.8714 0.04997 * 219s --- 219s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 219s > stopifnot( 219s + all(c("Sum Sq", "Mean Sq", "NumDF", "DenDF", "F value", "Pr(>F)") %in% 219s + colnames(drop1_table)) 219s + ) 219s > # In version < 3.0-1.9002 attr(step_res, "drop1") picked up lme4::drop1.merMod 219s > # and returned an AIC table after the model had been update'd. 219s > 219s > ##################################################################### 219s > # Model with 2 ranef covarites: 219s > 219s > # Model of the form (x1 + x2 | gr): 219s > model <- lmer(Preference ~ sens2 + Homesize + (sens1 + sens2 | Consumer) 219s + , data=carrots) 219s boundary (singular) fit: see help('isSingular') 220s Warning message: 220s Model failed to converge with 1 negative eigenvalue: -3.1e+02 220s > step(model) 220s boundary (singular) fit: see help('isSingular') 220s Backward reduced random-effect table: 220s 220s Eliminated npar logLik AIC LRT Df 220s 10 -1874.4 3768.8 220s sens1 in (sens1 + sens2 | Consumer) 1 7 -1874.5 3762.9 0.1333 3 220s sens2 in (sens2 | Consumer) 0 5 -1878.0 3765.9 6.9944 2 220s Pr(>Chisq) 220s 220s sens1 in (sens1 + sens2 | Consumer) 0.98757 220s sens2 in (sens2 | Consumer) 0.03028 * 220s --- 220s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 220s 220s Backward reduced fixed-effect table: 220s Degrees of freedom method: Satterthwaite 220s 220s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 220s sens2 0 58.685 58.685 1 102.02 54.8236 3.888e-11 *** 220s Homesize 0 5.979 5.979 1 100.95 5.5852 0.02003 * 220s --- 220s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 220s 220s Model found: 220s Preference ~ sens2 + Homesize + (sens2 | Consumer) 220s > stopifnot( 220s + nrow(ranova(model)) == 3L, 220s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 220s + ) 220s boundary (singular) fit: see help('isSingular') 220s > 220s > # Model of the form (f1 + f2 | gr): 220s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 220s + (Gender+Homesize|Consumer), data=carrots) 220s boundary (singular) fit: see help('isSingular') 220s > step(model) 221s Backward reduced random-effect table: 221s 221s Warning messages: 221s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 221s unable to evaluate scaled gradient 221s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 221s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 221s 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 221s Model is nearly unidentifiable: large eigenvalue ratio 221s - Rescale variables? 221s 4: Model failed to converge with 1 negative eigenvalue: -2.7e-04 221s Eliminated npar logLik AIC LRT 221s 11 -1872.3 3766.5 221s Gender in (Gender + Homesize | Consumer) 1 8 -1875.1 3766.3 5.7408 221s Homesize in (Homesize | Consumer) 0 6 -1878.4 3768.7 6.4705 221s Df Pr(>Chisq) 221s 221s Gender in (Gender + Homesize | Consumer) 3 0.12493 221s Homesize in (Homesize | Consumer) 2 0.03935 * 221s --- 221s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 221s 221s Backward reduced fixed-effect table: 221s Degrees of freedom method: Satterthwaite 221s 221s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 221s Gender 1 0.632 0.632 1 91.80 0.5686 0.45275 221s sens2 0 83.385 83.385 1 1129.09 75.0490 < 2e-16 *** 221s Homesize 0 6.212 6.212 1 97.82 5.5910 0.02003 * 221s --- 221s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 221s 221s Model found: 221s Preference ~ sens2 + Homesize + (Homesize | Consumer) 221s > stopifnot( 221s + nrow(ranova(model)) == 3L, 221s + nrow(ranova(model, reduce.terms = FALSE)) == 2L 221s + ) 221s > 221s > # Model of the form (-1 + f2 | gr): 221s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 221s + (Gender -1 |Consumer), data=carrots) 221s Warning messages: 221s 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 221s unable to evaluate scaled gradient 221s 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 221s Model failed to converge: degenerate Hessian with 1 negative eigenvalues 221s Warning message: 221s Model failed to converge with 1 negative eigenvalue: -2.4e-03 221s > step(model) 221s Backward reduced random-effect table: 221s 221s Eliminated npar logLik AIC LRT Df 221s 8 -1876.4 3768.9 221s Gender in (Gender - 1 | Consumer) 1 6 -1878.4 3768.7 3.863 2 221s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 221s Pr(>Chisq) 221s 221s Gender in (Gender - 1 | Consumer) 0.145 221s (1 | Consumer) <2e-16 *** 221s --- 221s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 221s 221s Backward reduced fixed-effect table: 221s Degrees of freedom method: Satterthwaite 221s 221s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 221s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 221s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 221s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 221s --- 221s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 221s 221s Model found: 221s Preference ~ sens2 + Homesize + (1 | Consumer) 221s > an1 <- ranova(model) 221s > an1b <- ranova(model, reduce.terms = FALSE) 221s > 221s > model <- lmer(Preference ~ sens2 + Homesize + Gender + 221s + (0 + Gender|Consumer), data=carrots) 222s > step(model) 222s Warning message: 222s Model failed to converge with 1 negative eigenvalue: -2.4e-03 222s Backward reduced random-effect table: 222s 222s Eliminated npar logLik AIC LRT Df 222s 8 -1876.4 3768.9 222s Gender in (0 + Gender | Consumer) 1 6 -1878.4 3768.7 3.863 2 222s (1 | Consumer) 0 5 -1917.2 3844.5 77.714 1 222s Pr(>Chisq) 222s 222s Gender in (0 + Gender | Consumer) 0.145 222s (1 | Consumer) <2e-16 *** 222s --- 222s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 222s 222s Backward reduced fixed-effect table: 222s Degrees of freedom method: Satterthwaite 222s 222s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 222s Gender 1 1.879 1.879 1 99.98 1.6909 0.19647 222s sens2 0 83.363 83.363 1 1129.00 75.0256 < 2e-16 *** 222s Homesize 0 5.729 5.729 1 100.97 5.1557 0.02529 * 222s --- 222s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 222s 222s Model found: 222s Preference ~ sens2 + Homesize + (1 | Consumer) 222s > an2 <- ranova(model) 222s > an2b <- ranova(model, reduce.terms = FALSE) 222s > 222s > stopifnot( 222s + all.equal(an1, an2, check.attributes=FALSE, tolerance=TOL), 222s + all.equal(an1b, an2b, check.attributes=FALSE, tolerance=TOL) 222s + ) 222s > 222s > ####### Polynomial terms: 222s > model <- lmer(Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer), 222s + data=carrots) 222s > (an <- ranova(model)) 222s ANOVA-like table for random-effects: Single term deletions 222s 222s Model: 222s Preference ~ sens2 + Gender + (poly(sens2, 2) | Consumer) 222s npar logLik AIC LRT Df 222s 10 -1874.1 3768.2 222s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 5 -1879.9 3769.7 11.552 5 222s Pr(>Chisq) 222s 222s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0.04147 * 222s --- 222s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 222s > step(model) 223s Backward reduced random-effect table: 223s 223s Eliminated npar logLik AIC 223s 10 -1874.1 3768.2 223s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 0 5 -1879.9 3769.7 223s LRT Df Pr(>Chisq) 223s 223s poly(sens2, 2) in (poly(sens2, 2) | Consumer) 11.552 5 0.04147 * 223s --- 223s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 223s 223s Backward reduced fixed-effect table: 223s Degrees of freedom method: Satterthwaite 223s 223s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 223s Gender 1 1.188 1.188 1 101.03 1.1263 0.2911 223s sens2 0 53.447 53.447 1 114.58 50.6761 1.019e-10 *** 223s --- 223s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 223s 223s Model found: 223s Preference ~ sens2 + (poly(sens2, 2) | Consumer) 223s > 223s > model <- lmer(Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer), 223s + data=carrots) 223s > (an2 <- ranova(model)) 223s Warning message: 223s In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : 223s Model failed to converge with max|grad| = 0.0311907 (tol = 0.002, component 1) 223s boundary (singular) fit: see help('isSingular') 223s ANOVA-like table for random-effects: Single term deletions 223s 223s Model: 223s Preference ~ sens2 + Gender + (sens2 + I(sens2^2) | Consumer) 223s npar logLik AIC LRT Df 223s 10 -1874.1 3768.2 223s sens2 in (sens2 + I(sens2^2) | Consumer) 7 -1879.8 3773.5 11.3656 3 223s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 7 -1876.5 3767.0 4.8774 3 223s Pr(>Chisq) 223s 223s sens2 in (sens2 + I(sens2^2) | Consumer) 0.009905 ** 223s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 0.180999 223s --- 223s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 223s > step(model) 223s boundary (singular) fit: see help('isSingular') 224s Backward reduced random-effect table: 224s 224s Eliminated npar logLik AIC 224s 10 -1874.1 3768.2 224s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 1 7 -1876.5 3767.0 224s sens2 in (sens2 | Consumer) 0 5 -1879.9 3769.7 224s LRT Df Pr(>Chisq) 224s 224s I(sens2^2) in (sens2 + I(sens2^2) | Consumer) 4.8774 3 0.18100 224s sens2 in (sens2 | Consumer) 6.6735 2 0.03555 * 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Backward reduced fixed-effect table: 224s Degrees of freedom method: Satterthwaite 224s 224s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 224s Gender 1 1.211 1.211 1 101.02 1.1309 0.2901 224s sens2 0 58.688 58.688 1 102.01 54.8276 3.883e-11 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Model found: 224s Preference ~ sens2 + (sens2 | Consumer) 224s > stopifnot( 224s + nrow(an) == 2L, 224s + an[2L, "Df"] == 5L, 224s + nrow(an2) == 3L, 224s + all(an2[2:3, "Df"] == 3L) 224s + ) 224s > 224s > ######## Functions of terms in random effects: 224s > model <- lmer(Preference ~ sens2 + Gender + (log(10+sens2) | Consumer), 224s + data=carrots) 224s > ranova(model) # Works 224s ANOVA-like table for random-effects: Single term deletions 224s 224s Model: 224s Preference ~ sens2 + Gender + (log(10 + sens2) | Consumer) 224s npar logLik AIC LRT Df 224s 7 -1875.3 3764.6 224s log(10 + sens2) in (log(10 + sens2) | Consumer) 5 -1879.9 3769.7 9.0854 2 224s Pr(>Chisq) 224s 224s log(10 + sens2) in (log(10 + sens2) | Consumer) 0.01064 * 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s > step(model) 224s Backward reduced random-effect table: 224s 224s Eliminated npar logLik AIC 224s 7 -1875.3 3764.6 224s log(10 + sens2) in (log(10 + sens2) | Consumer) 0 5 -1879.9 3769.7 224s LRT Df Pr(>Chisq) 224s 224s log(10 + sens2) in (log(10 + sens2) | Consumer) 9.0854 2 0.01064 * 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Backward reduced fixed-effect table: 224s Degrees of freedom method: Satterthwaite 224s 224s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 224s Gender 1 1.200 1.200 1 101.03 1.1296 0.2904 224s sens2 0 54.184 54.184 1 109.20 51.0011 1.083e-10 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Model found: 224s Preference ~ sens2 + (log(10 + sens2) | Consumer) 224s > 224s > ##################################################################### 224s > 224s > # Missing values changes the number of observations in use: 224s > m <- lmer(Preference ~ sens2 + Homesize + 224s + (1 |Consumer:Income), data=carrots) 224s > assertError(step(m)) 224s > ans <- try(ranova(m), silent = TRUE) 224s > stopifnot( 224s + inherits(ans, "try-error"), 224s + grepl("number of rows in use has changed", ans) 224s + ) 224s > 224s > ## Removing missing values solves the problem: 224s > m2 <- lmer(Preference ~ sens2 + Homesize + 224s + (1 |Consumer:Income), data=carrots[complete.cases(carrots), ]) 224s > ranova(m2) # Works 224s ANOVA-like table for random-effects: Single term deletions 224s 224s Model: 224s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 224s npar logLik AIC LRT Df Pr(>Chisq) 224s 5 -1752.0 3513.9 224s (1 | Consumer:Income) 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s > step(m2) 224s Backward reduced random-effect table: 224s 224s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 224s 5 -1752.0 3513.9 224s (1 | Consumer:Income) 0 4 -1778.6 3565.2 53.272 1 2.904e-13 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Backward reduced fixed-effect table: 224s Degrees of freedom method: Satterthwaite 224s 224s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 224s sens2 0 77.308 77.308 1 1058.49 69.7915 < 2.2e-16 *** 224s Homesize 0 8.569 8.569 1 95.23 7.7355 0.006527 ** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Model found: 224s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 224s > 224s > ## Including the variable with missing values (Income) among the fixed effects 224s > ## also solves the problem: 224s > m <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 224s + (1 |Consumer:Income), data=carrots) 224s > ranova(m) 224s ANOVA-like table for random-effects: Single term deletions 224s 224s Model: 224s Preference ~ sens2 + Homesize + Income + (1 | Consumer:Income) 224s npar logLik AIC LRT Df Pr(>Chisq) 224s 8 -1766.0 3547.9 224s (1 | Consumer:Income) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s > step(m) 224s Backward reduced random-effect table: 224s 224s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 224s 8 -1766.0 3547.9 224s (1 | Consumer:Income) 0 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Backward reduced fixed-effect table: 224s Degrees of freedom method: Satterthwaite 224s 224s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 224s Income 1 3.567 1.189 3 91.92 1.0627 0.368918 224s sens2 0 78.191 78.191 1 1062.96 69.8919 < 2.2e-16 *** 224s Homesize 0 7.983 7.983 1 94.93 7.1355 0.008894 ** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s 224s Model found: 224s Preference ~ sens2 + Homesize + (1 | Consumer:Income) 224s > 224s > # Missing values in a an insignificant fixed effect causes the an error in step: 224s > m0 <- lmer(Preference ~ sens2 + Homesize + Income + #(1 + sens2 | Consumer) + 224s + (1 |Consumer), data=carrots) 224s > ranova(m0) 224s ANOVA-like table for random-effects: Single term deletions 224s 224s Model: 224s Preference ~ sens2 + Homesize + Income + (1 | Consumer) 224s npar logLik AIC LRT Df Pr(>Chisq) 224s 8 -1766.0 3547.9 224s (1 | Consumer) 7 -1791.1 3596.3 50.395 1 1.257e-12 *** 224s --- 224s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 224s > ans <- try(step(m0), silent = TRUE) 224s > stopifnot( 224s + inherits(ans, "try-error"), 224s + grepl("number of rows in use has changed", ans) 224s + ) 224s > 224s > # Check that step still works for linear models (etc.) 224s > flm <- lm(Coloursaturation ~ TVset * Picture, data=TVbo) 224s > res <- step(flm, trace=0) 224s > stopifnot( 224s + inherits(res, "lm") 224s + ) 224s > 224s > ##################### Using reduce and keep args: 224s > # Fit a model to the ham dataset: 224s > m <- lmer(Informed.liking ~ Product*Information+ 224s + (1|Consumer) + (1|Product:Consumer) 224s + + (1|Information:Consumer), data=ham) 224s > 224s > # Backward elimination using terms with default alpha-levels: 224s > (step_res <- step(m)) 225s boundary (singular) fit: see help('isSingular') 225s Backward reduced random-effect table: 225s 225s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 225s 12 -1352.0 2728.1 225s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 225s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 225s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 225s 225s 225s (1 | Information:Consumer) 225s (1 | Consumer) . 225s (1 | Product:Consumer) *** 225s --- 225s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 225s 225s Backward reduced fixed-effect table: 225s Degrees of freedom method: Satterthwaite 225s 225s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 225s Product:Information 1 10.3873 3.4624 3 320 2.0765 0.10321 225s Product 0 19.3466 6.4489 3 240 3.8291 0.01048 * 225s Information 0 6.5201 6.5201 1 323 3.8714 0.04997 * 225s --- 225s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 225s 225s Model found: 225s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) 225s > 225s > (step_res <- step(m, reduce.random = FALSE)) 225s boundary (singular) fit: see help('isSingular') 225s Backward reduced random-effect table: 225s 225s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 225s 12 -1352.0 2728.1 225s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 225s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 225s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 225s 225s 225s (1 | Consumer) 225s (1 | Product:Consumer) *** 225s (1 | Information:Consumer) 225s --- 225s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 225s 225s Backward reduced fixed-effect table: 225s Degrees of freedom method: Satterthwaite 225s 225s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 225s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 225s Information 2 5.3335 5.3335 1 80 3.3414 0.07129 . 226s Product 0 18.3361 6.1120 3 240 3.8291 0.01048 * 226s --- 226s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 226s 226s Model found: 226s Informed.liking ~ Product + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 226s > (step_res <- step(m, reduce.fixed = FALSE)) 226s boundary (singular) fit: see help('isSingular') 226s Backward reduced random-effect table: 226s 226s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 226s 12 -1352.0 2728.1 226s (1 | Information:Consumer) 1 11 -1352.8 2727.5 1.444 1 0.22952 226s (1 | Consumer) 0 10 -1354.4 2728.7 3.184 1 0.07437 226s (1 | Product:Consumer) 0 10 -1435.0 2890.0 164.443 1 < 2e-16 226s 226s 226s (1 | Information:Consumer) 226s (1 | Consumer) . 226s (1 | Product:Consumer) *** 226s --- 226s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 226s 226s Backward reduced fixed-effect table: 226s Degrees of freedom method: Satterthwaite 226s 226s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 226s Product:Information 0 10.387 3.4624 3 320 2.0765 0.1032 226s 226s Model found: 226s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + Product:Information 226s > (step_res <- step(m, reduce.fixed = FALSE, reduce.random = FALSE)) 226s boundary (singular) fit: see help('isSingular') 226s Backward reduced random-effect table: 226s 226s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 226s 12 -1352.0 2728.1 226s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 226s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 226s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 226s 226s 226s (1 | Consumer) 226s (1 | Product:Consumer) *** 226s (1 | Information:Consumer) 226s --- 226s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 226s 226s Backward reduced fixed-effect table: 226s Degrees of freedom method: Satterthwaite 226s 226s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 226s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 226s --- 226s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 226s 226s Model found: 226s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 226s > 226s > (step_res <- step(m, reduce.random = FALSE, keep="Information")) 226s boundary (singular) fit: see help('isSingular') 227s Backward reduced random-effect table: 227s 227s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 227s 12 -1352.0 2728.1 227s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 227s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 227s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 227s 227s 227s (1 | Consumer) 227s (1 | Product:Consumer) *** 227s (1 | Information:Consumer) 227s --- 227s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 227s 227s Backward reduced fixed-effect table: 227s Degrees of freedom method: Satterthwaite 227s 227s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 227s Product:Information 1 10.3873 3.4624 3 240 2.2014 0.08855 . 227s Product 0 18.3363 6.1121 3 240 3.8292 0.01048 * 227s Information 0 5.3335 5.3335 1 80 3.3414 0.07129 . 227s --- 227s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 227s 227s Model found: 227s Informed.liking ~ Product + Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 227s > (step_res <- step(m, reduce.random = FALSE, keep="Product:Information")) 227s boundary (singular) fit: see help('isSingular') 227s Backward reduced random-effect table: 227s 227s Eliminated npar logLik AIC LRT Df Pr(>Chisq) 227s 12 -1352.0 2728.1 227s (1 | Consumer) 0 11 -1353.2 2728.3 2.252 1 0.1335 227s (1 | Product:Consumer) 0 11 -1435.0 2892.0 165.887 1 <2e-16 227s (1 | Information:Consumer) 0 11 -1352.8 2727.5 1.444 1 0.2295 227s 227s 227s (1 | Consumer) 227s (1 | Product:Consumer) *** 227s (1 | Information:Consumer) 227s --- 227s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 227s 227s Backward reduced fixed-effect table: 227s Degrees of freedom method: Satterthwaite 227s 227s Eliminated Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 227s Product:Information 0 10.387 3.4624 3 240 2.2014 0.08855 . 227s --- 227s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 227s 227s Model found: 227s Informed.liking ~ Product * Information + (1 | Consumer) + (1 | Product:Consumer) + (1 | Information:Consumer) 227s > 227s > 227s > ########################### 227s > ## Test that `step` works even if all random terms are reduced away: 227s > set.seed(101) 227s > test <- data.frame(TM = factor(rep(rep(c("org","min"),each=3),3)), 227s + dep = runif(18,0,20), 227s + ind = runif(18,0,7), 227s + dorp = factor(rep(1:3,each=6))) 227s > full.model <- lmer(dep ~ TM + ind + (1 | dorp), data=test) 227s > res <- step(full.model) 227s > # res$random 227s > # res$fixed 227s > # attr(res, "model") 227s > # attr(res, "drop1") 227s > 227s > 227s > 227s BEGIN TEST test_summary.R 227s 227s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 227s Copyright (C) 2024 The R Foundation for Statistical Computing 227s Platform: aarch64-unknown-linux-gnu (64-bit) 227s 227s R is free software and comes with ABSOLUTELY NO WARRANTY. 227s You are welcome to redistribute it under certain conditions. 227s Type 'license()' or 'licence()' for distribution details. 227s 227s R is a collaborative project with many contributors. 227s Type 'contributors()' for more information and 227s 'citation()' on how to cite R or R packages in publications. 227s 227s Type 'demo()' for some demos, 'help()' for on-line help, or 227s 'help.start()' for an HTML browser interface to help. 227s Type 'q()' to quit R. 227s 227s > # test_summary.R 227s > 227s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 227s > # even in tests: 227s > assertError <- function(expr, ...) 227s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 227s > assertWarning <- function(expr, ...) 227s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 227s > 227s > # Kenward-Roger only available with pbkrtest and only then validated in R >= 3.3.3 227s > # (faulty results for R < 3.3.3 may be due to unstated dependencies in pbkrtest) 227s > has_pbkrtest <- requireNamespace("pbkrtest", quietly = TRUE) && getRversion() >= "3.3.3" 229s > 229s > library(lmerTest) 229s Loading required package: lme4 229s Loading required package: Matrix 229s 229s Attaching package: 'lmerTest' 229s 229s The following object is masked from 'package:lme4': 229s 229s lmer 229s 229s The following object is masked from 'package:stats': 229s 229s step 229s 229s > 229s > data("sleepstudy", package="lme4") 229s > data("cake", package="lme4") 229s > 229s > # Fit basic model and compute summary: 229s > fm <- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) 229s > (sfm <- summary(fm)) 229s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 229s lmerModLmerTest] 229s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 229s Data: sleepstudy 229s 229s REML criterion at convergence: 1743.7 229s 229s Scaled residuals: 229s Min 1Q Median 3Q Max 229s -3.9626 -0.4625 0.0204 0.4653 5.1860 229s 229s Random effects: 229s Groups Name Variance Std.Dev. 229s Subject (Intercept) 627.57 25.051 229s Subject.1 Days 35.86 5.988 229s Residual 653.58 25.565 229s Number of obs: 180, groups: Subject, 18 229s 229s Fixed effects: 229s Estimate Std. Error df t value Pr(>|t|) 229s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 229s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 229s --- 229s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 229s 229s Correlation of Fixed Effects: 229s (Intr) 229s Days -0.184 229s > 229s > ## Test class: 229s > stopifnot(all( 229s + class(sfm) == c("summary.lmerModLmerTest", "summary.merMod"), 229s + all(c("df", "Pr(>|t|)") %in% colnames(coef(sfm))) 229s + )) 229s > stopifnot(class(summary(fm, ddf="lme4")) == "summary.merMod") 229s > 229s > ## Test coefficient table names: 229s > mat <- coef(summary(fm)) 229s > stopifnot(all( # colnames 229s + colnames(mat) == c("Estimate", "Std. Error", "df", "t value", "Pr(>|t|)") 229s + )) 229s > stopifnot(all( # rownames 229s + names(fixef(fm)) == rownames(mat) 229s + )) 229s > 229s > ## Test pass of 'correlation' argument to lme4:::summary.merMod: 229s > x <- capture.output(summary(fm)) 229s > x_nocor <- capture.output(summary(fm, correlation=FALSE)) 229s > txt <- "Correlation of Fixed Effects:" 229s > stopifnot( 229s + any(grep(txt, x)), 229s + !any(grepl(txt, x_nocor)) 229s + ) 229s > 229s > # Test warning with unrecognized arguments (caught by lme4:::summary.merMod): 229s > assertWarning(summary(fm, false_arg=FALSE)) 229s > 229s > ## Test pass of extra arguments to lme4:::print.summary.merMod: 229s > x <- capture.output(print(summary(fm), signif.stars=TRUE)) 229s > x_nocor <- capture.output(print(summary(fm), signif.stars=FALSE)) 229s > txt <- "Signif. codes:" 229s > stopifnot( 229s + any(grep(txt, x)), 229s + !any(grepl(txt, x_nocor)) 229s + ) 229s > 229s > ####### ddf argument: 229s > (an1 <- summary(fm)) # Also testing print method. 229s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 229s lmerModLmerTest] 229s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 229s Data: sleepstudy 229s 229s REML criterion at convergence: 1743.7 229s 229s Scaled residuals: 229s Min 1Q Median 3Q Max 229s -3.9626 -0.4625 0.0204 0.4653 5.1860 229s 229s Random effects: 229s Groups Name Variance Std.Dev. 229s Subject (Intercept) 627.57 25.051 229s Subject.1 Days 35.86 5.988 229s Residual 653.58 25.565 229s Number of obs: 180, groups: Subject, 18 229s 229s Fixed effects: 229s Estimate Std. Error df t value Pr(>|t|) 229s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 229s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 229s --- 229s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 229s 229s Correlation of Fixed Effects: 229s (Intr) 229s Days -0.184 229s > (an2 <- summary(fm, ddf="Satterthwaite")) 229s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 229s lmerModLmerTest] 229s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 229s Data: sleepstudy 229s 229s REML criterion at convergence: 1743.7 229s 229s Scaled residuals: 229s Min 1Q Median 3Q Max 229s -3.9626 -0.4625 0.0204 0.4653 5.1860 229s 229s Random effects: 229s Groups Name Variance Std.Dev. 229s Subject (Intercept) 627.57 25.051 229s Subject.1 Days 35.86 5.988 229s Residual 653.58 25.565 229s Number of obs: 180, groups: Subject, 18 229s 229s Fixed effects: 229s Estimate Std. Error df t value Pr(>|t|) 229s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 229s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 229s --- 229s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 229s 229s Correlation of Fixed Effects: 229s (Intr) 229s Days -0.184 229s > stopifnot(isTRUE( 229s + all.equal(an1, an2) 229s + )) 229s > (an3 <- summary(fm, ddf="Sat")) ## Abbreviated argument 229s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 229s lmerModLmerTest] 229s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 229s Data: sleepstudy 229s 229s REML criterion at convergence: 1743.7 229s 229s Scaled residuals: 229s Min 1Q Median 3Q Max 229s -3.9626 -0.4625 0.0204 0.4653 5.1860 229s 229s Random effects: 229s Groups Name Variance Std.Dev. 229s Subject (Intercept) 627.57 25.051 229s Subject.1 Days 35.86 5.988 229s Residual 653.58 25.565 229s Number of obs: 180, groups: Subject, 18 229s 229s Fixed effects: 229s Estimate Std. Error df t value Pr(>|t|) 229s (Intercept) 251.405 6.885 18.156 36.513 < 2e-16 *** 229s Days 10.467 1.560 18.156 6.712 2.59e-06 *** 229s --- 229s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 229s 229s Correlation of Fixed Effects: 229s (Intr) 229s Days -0.184 229s > stopifnot(isTRUE( 229s + all.equal(an1, an3) 229s + )) 229s > (summary(fm, ddf="lme4")) 229s Linear mixed model fit by REML ['lmerMod'] 229s Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject) 229s Data: sleepstudy 229s 229s REML criterion at convergence: 1743.7 229s 229s Scaled residuals: 229s Min 1Q Median 3Q Max 229s -3.9626 -0.4625 0.0204 0.4653 5.1860 229s 229s Random effects: 229s Groups Name Variance Std.Dev. 229s Subject (Intercept) 627.57 25.051 229s Subject.1 Days 35.86 5.988 229s Residual 653.58 25.565 229s Number of obs: 180, groups: Subject, 18 229s 229s Fixed effects: 229s Estimate Std. Error t value 229s (Intercept) 251.405 6.885 36.513 229s Days 10.467 1.560 6.712 229s 229s Correlation of Fixed Effects: 229s (Intr) 229s Days -0.184 229s > if(has_pbkrtest) { 229s + (summary(fm, ddf="Kenward-Roger")) 229s + assertError(summary(fm, ddf="KR")) ## Error on incorrect arg. 229s + } 230s > 230s > ## lme4 method: 230s > an1 <- summary(fm, ddf="lme4") 230s > an2 <- summary(as(fm, "lmerMod")) 230s > stopifnot(isTRUE( 230s + all.equal(an1, an2) 230s + )) 230s > 230s > 230s > # Test printed output 230s > # - Satterthwaite 230s > x <- capture.output(sfm) # equal to output of 'print(sfm)' 230s > txt <- c("lmerModLmerTest", "t-tests use Satterthwaite's method", 230s + "df", "t value", "Pr(>|t|)") 230s > stopifnot(all( 230s + sapply(txt, function(text) any(grepl(text, x))) 230s + )) 230s > 230s > # Test printed output 230s > # - KR 230s > if(has_pbkrtest) { 230s + (sfm <- summary(fm, ddf="Kenward-Roger")) 230s + x <- capture.output(sfm) 230s + txt <- c("lmerModLmerTest", "t-tests use Kenward-Roger's method", 230s + "df", "t value", "Pr(>|t|)") 230s + stopifnot(all( 230s + sapply(txt, function(text) any(grepl(text, x))) 230s + )) 230s + } 230s > 230s > #################################### 230s > ## Test 'boundary' fixef structures: 230s > #################################### 230s > 230s > # Example with no fixef: 230s > m <- lmer(Reaction ~ -1 + (Days | Subject), sleepstudy) 230s > # m <- lmer(Reaction ~ 0 + (Days | Subject), sleepstudy) # alternative 230s > stopifnot(length(fixef(m)) == 0L) 230s > stopifnot( 230s + nrow(coef(summary(m))) == 0L, 230s + nrow(coef(summary(m, ddf="lme4"))) == 0L 230s + ) 230s > if(has_pbkrtest){ 230s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 0L) 230s + } 230s > 230s > # Example with intercept only: 230s > m <- lmer(Reaction ~ (Days | Subject), sleepstudy) 230s > # m <- lmer(Reaction ~ 1 + (Days | Subject), sleepstudy) # alternative 230s > stopifnot(length(fixef(m)) == 1L, 230s + names(fixef(m)) == "(Intercept)") 230s > stopifnot( 230s + nrow(coef(summary(m))) == 1L, 230s + nrow(coef(summary(m, ddf="lme4"))) == 1L 230s + ) 230s > if(has_pbkrtest){ 230s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 1L) 230s + } 230s > 230s > # Example with >1 fixef without intercept: 230s > m <- lmer(Reaction ~ Days - 1 + I(Days^2) + (Days | Subject), sleepstudy) 230s > stopifnot(length(fixef(m)) == 2L, 230s + names(fixef(m)) == c("Days", "I(Days^2)")) 230s > stopifnot( 230s + nrow(coef(summary(m))) == 2L, 230s + nrow(coef(summary(m, ddf="lme4"))) == 2L 230s + ) 230s > if(has_pbkrtest){ 230s + stopifnot(nrow(coef(summary(m, ddf="Kenward-Roger"))) == 2L) 230s + } 230s > 230s > 230s BEGIN TEST test_zerovar.R 230s 230s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 230s Copyright (C) 2024 The R Foundation for Statistical Computing 230s Platform: aarch64-unknown-linux-gnu (64-bit) 230s 230s R is free software and comes with ABSOLUTELY NO WARRANTY. 230s You are welcome to redistribute it under certain conditions. 230s Type 'license()' or 'licence()' for distribution details. 230s 230s R is a collaborative project with many contributors. 230s Type 'contributors()' for more information and 230s 'citation()' on how to cite R or R packages in publications. 230s 230s Type 'demo()' for some demos, 'help()' for on-line help, or 230s 'help.start()' for an HTML browser interface to help. 230s Type 'q()' to quit R. 230s 230s > # test_zerovar.R 230s > 230s > library(lmerTest) 230s Loading required package: lme4 230s Loading required package: Matrix 232s 232s Attaching package: 'lmerTest' 232s 232s The following object is masked from 'package:lme4': 232s 232s lmer 232s 232s The following object is masked from 'package:stats': 232s 232s step 232s 232s > data("sleepstudy", package="lme4") 232s > 232s > # Baseline fit: 232s > m0 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy, 232s + control=lmerControl(optimizer="bobyqa")) 232s > ## default optimizer does not converge proporly 232s > m0 232s Linear mixed model fit by REML ['lmerModLmerTest'] 232s Formula: Reaction ~ Days + (Days | Subject) 232s Data: sleepstudy 232s REML criterion at convergence: 1743.628 232s Random effects: 232s Groups Name Std.Dev. Corr 232s Subject (Intercept) 24.740 232s Days 5.922 0.07 232s Residual 25.592 232s Number of obs: 180, groups: Subject, 18 232s Fixed Effects: 232s (Intercept) Days 232s 251.41 10.47 232s > (an0 <- anova(m0)) 232s Type III Analysis of Variance Table with Satterthwaite's method 232s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 232s Days 30031 30031 1 17 45.853 3.264e-06 *** 232s --- 232s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 232s > 232s > # Make a fit with a zero variance estimate: 232s > n <- nrow(sleepstudy) 232s > g <- factor(rep(1:2, c(n - 10, 10))) 232s > m <- lmer(Reaction ~ Days + (Days | Subject) + (1|g), sleepstudy, 232s + control=lmerControl(optimizer="bobyqa")) 232s boundary (singular) fit: see help('isSingular') 232s > m 232s Linear mixed model fit by REML ['lmerModLmerTest'] 232s Formula: Reaction ~ Days + (Days | Subject) + (1 | g) 232s Data: sleepstudy 232s REML criterion at convergence: 1743.628 232s Random effects: 232s Groups Name Std.Dev. Corr 232s Subject (Intercept) 24.740 232s Days 5.922 0.07 232s g (Intercept) 0.000 232s Residual 25.592 232s Number of obs: 180, groups: Subject, 18; g, 2 232s Fixed Effects: 232s (Intercept) Days 232s 251.41 10.47 232s optimizer (bobyqa) convergence code: 0 (OK) ; 0 optimizer warnings; 1 lme4 warnings 232s > (an <- anova(m)) 232s Type III Analysis of Variance Table with Satterthwaite's method 232s Sum Sq Mean Sq NumDF DenDF F value Pr(>F) 232s Days 30031 30031 1 17 45.853 3.264e-06 *** 232s --- 232s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 232s > 232s > # check that fit has a zero variance 232s > vc <- as.data.frame(VarCorr(m)) 232s > stopifnot(isTRUE( 232s + all.equal(0, vc[vc$grp == "g", "sdcor"], tolerance=1e-4) 232s + )) 232s > # The hessian/vcov is actually positive definite: 232s > stopifnot(isTRUE( 232s + all(eigen(m@vcov_varpar, only.values = TRUE)$values > 0) 232s + )) 232s > 232s > # Check that ANOVA tables are the same: 232s > stopifnot(isTRUE( 232s + all.equal(an0[, 1:5], an[, 1:5], tolerance=1e-4) 232s + )) 232s > 232s > stopifnot(isTRUE( # Equality of summary tables 232s + all.equal(coef(summary(m0)), coef(summary(m)), tolerance=1e-4) 232s + )) 232s > stopifnot(isTRUE( # Equality of lme4-anova tables 232s + all.equal(anova(m0, ddf="lme4"), anova(m, ddf="lme4"), tolerance=1e-4) 232s + )) 232s > 232s > 232s BEGIN TEST zlmerTest_zeroDenom.R 232s 232s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 232s Copyright (C) 2024 The R Foundation for Statistical Computing 232s Platform: aarch64-unknown-linux-gnu (64-bit) 232s 232s R is free software and comes with ABSOLUTELY NO WARRANTY. 232s You are welcome to redistribute it under certain conditions. 232s Type 'license()' or 'licence()' for distribution details. 232s 232s R is a collaborative project with many contributors. 232s Type 'contributors()' for more information and 232s 'citation()' on how to cite R or R packages in publications. 232s 232s Type 'demo()' for some demos, 'help()' for on-line help, or 232s 'help.start()' for an HTML browser interface to help. 232s Type 'q()' to quit R. 232s 232s > library(lmerTest) 232s Loading required package: lme4 232s Loading required package: Matrix 234s > 234s > # Read in data set 234s > load(system.file("testdata","potdata.RData", package="lmerTest")) 234s > 234s > # Mixed model 234s > lmerout <- lmer(biomass ~ CO2*nutrients + (1|chamber),data=potdata) 234s 234s Attaching package: 'lmerTest' 234s 234s The following object is masked from 'package:lme4': 234s 234s lmer 234s 234s The following object is masked from 'package:stats': 234s 234s step 234s 234s > summary(lmerout) 234s Linear mixed model fit by REML. t-tests use Satterthwaite's method [ 234s lmerModLmerTest] 234s Formula: biomass ~ CO2 * nutrients + (1 | chamber) 234s Data: potdata 234s 234s REML criterion at convergence: 49.2 234s 234s Scaled residuals: 234s Min 1Q Median 3Q Max 234s -1.4159 -0.5588 0.0000 0.5588 1.4159 234s 234s Random effects: 234s Groups Name Variance Std.Dev. 234s chamber (Intercept) 0.2437 0.4936 234s Residual 1.5797 1.2568 234s Number of obs: 24, groups: chamber, 4 234s 234s Fixed effects: 234s Estimate Std. Error df t value Pr(>|t|) 234s (Intercept) 12.8500 0.9548 11.0163 13.458 3.49e-08 *** 234s CO2675 2.0000 1.3503 11.0163 1.481 0.166595 234s nutrients2 7.3500 1.2568 10.0000 5.848 0.000162 *** 234s nutrients3 10.4500 1.2568 10.0000 8.314 8.39e-06 *** 234s nutrients4 18.6500 1.2568 10.0000 14.839 3.88e-08 *** 234s nutrients5 25.0500 1.2568 10.0000 19.931 2.22e-09 *** 234s nutrients6 29.0000 1.2568 10.0000 23.074 5.28e-10 *** 234s CO2675:nutrients2 -0.5000 1.7775 10.0000 -0.281 0.784214 234s CO2675:nutrients3 1.9000 1.7775 10.0000 1.069 0.310218 234s CO2675:nutrients4 3.4500 1.7775 10.0000 1.941 0.080949 . 234s CO2675:nutrients5 5.9000 1.7775 10.0000 3.319 0.007756 ** 234s CO2675:nutrients6 5.2500 1.7775 10.0000 2.954 0.014444 * 234s --- 234s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 234s 234s Correlation of Fixed Effects: 234s (Intr) CO2675 ntrnt2 ntrnt3 ntrnt4 ntrnt5 ntrnt6 CO2675:2 CO2675:3 234s CO2675 -0.707 234s nutrients2 -0.658 0.465 234s nutrients3 -0.658 0.465 0.500 234s nutrients4 -0.658 0.465 0.500 0.500 234s nutrients5 -0.658 0.465 0.500 0.500 0.500 234s nutrients6 -0.658 0.465 0.500 0.500 0.500 0.500 234s CO2675:ntr2 0.465 -0.658 -0.707 -0.354 -0.354 -0.354 -0.354 234s CO2675:ntr3 0.465 -0.658 -0.354 -0.707 -0.354 -0.354 -0.354 0.500 234s CO2675:ntr4 0.465 -0.658 -0.354 -0.354 -0.707 -0.354 -0.354 0.500 0.500 234s CO2675:ntr5 0.465 -0.658 -0.354 -0.354 -0.354 -0.707 -0.354 0.500 0.500 234s CO2675:ntr6 0.465 -0.658 -0.354 -0.354 -0.354 -0.354 -0.707 0.500 0.500 234s CO2675:4 CO2675:5 234s CO2675 234s nutrients2 234s nutrients3 234s nutrients4 234s nutrients5 234s nutrients6 234s CO2675:ntr2 234s CO2675:ntr3 234s CO2675:ntr4 234s CO2675:ntr5 0.500 234s CO2675:ntr6 0.500 0.500 234s > 234s > an.sat <- anova(lmerout) 234s > anova(lmerout, ddf="lme4") 234s Analysis of Variance Table 234s npar Sum Sq Mean Sq F value 234s CO2 1 67.86 67.86 42.9589 234s nutrients 5 3050.44 610.09 386.2129 234s CO2:nutrients 5 35.47 7.09 4.4906 234s > TOL <- 1e-5 234s > stopifnot(isTRUE(all.equal( 234s + an.sat[,"DenDF"], c(2, 10, 10), tolerance=TOL 234s + ))) 234s > 234s > stopifnot(isTRUE( 234s + all.equal(an.sat[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569), tolerance=TOL) 234s + )) 234s > 234s > # if(require(pbkrtest)) 234s > # an.kr <- anova(lmerout, ddf="Kenward-Roger") 234s > # 234s > # TOL <- 1e-7 234s > # stopifnot(all.equal(an.kr[,"Pr(>F)"], c(0.0224955602, 1e-11, 0.020905569) , 234s > # tol=TOL), 234s > # all.equal(an.kr[,"DenDF"], 234s > # c(2, 10, 10) , tol=TOL), 234s > # TRUE) 234s > 235s autopkgtest [19:06:22]: test run-unit-test: -----------------------] 236s run-unit-test PASS 236s autopkgtest [19:06:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 236s autopkgtest [19:06:23]: test pkg-r-autopkgtest: preparing testbed 344s autopkgtest [19:08:11]: testbed dpkg architecture: arm64 344s autopkgtest [19:08:11]: testbed apt version: 2.7.12 344s autopkgtest [19:08:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 344s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 345s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 345s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3682 kB] 345s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 345s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 345s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 345s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 345s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 345s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 345s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4006 kB] 345s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 345s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 345s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 347s Fetched 9084 kB in 2s (5447 kB/s) 347s Reading package lists... 350s Reading package lists... 350s Building dependency tree... 350s Reading state information... 350s Calculating upgrade... 351s The following packages will be REMOVED: 351s libglib2.0-0 libssl3 351s The following NEW packages will be installed: 351s libglib2.0-0t64 libssl3t64 xdg-user-dirs 351s The following packages have been kept back: 351s curl 351s The following packages will be upgraded: 351s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 351s ubuntu-minimal ubuntu-standard 351s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 351s Need to get 4613 kB of archives. 351s After this operation, 211 kB of additional disk space will be used. 351s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 351s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 351s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 351s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 352s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 352s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 352s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 352s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 352s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 352s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 352s Fetched 4613 kB in 1s (6547 kB/s) 352s (Reading database ... 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(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 ... 74758 files and directories currently installed.) 353s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 353s Selecting previously unselected package libssl3t64:arm64. 353s (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 ... 74747 files and directories currently installed.) 353s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 353s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 353s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 353s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 353s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ... 353s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 353s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ... 353s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 353s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ... 353s Unpacking ubuntu-minimal (1.536) over (1.535) ... 353s Selecting previously unselected package xdg-user-dirs. 353s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ... 353s Unpacking xdg-user-dirs (0.18-1) ... 353s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ... 353s Unpacking ubuntu-standard (1.536) over (1.535) ... 353s Setting up ubuntu-minimal (1.536) ... 353s Setting up xdg-user-dirs (0.18-1) ... 353s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 353s Setting up libtirpc-common (1.3.4+ds-1.1) ... 353s Setting up ubuntu-standard (1.536) ... 353s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 353s No schema files found: doing nothing. 353s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 353s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 353s Setting up openssl (3.0.13-0ubuntu1) ... 353s Setting up readline-common (8.2-3.1) ... 353s Processing triggers for man-db (2.12.0-3) ... 354s Processing triggers for install-info (7.1-3) ... 354s Processing triggers for libc-bin (2.39-0ubuntu2) ... 354s Reading package lists... 355s Building dependency tree... 355s Reading state information... 355s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 356s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 356s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 356s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 356s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 357s Reading package lists... 357s Reading package lists... 358s Building dependency tree... 358s Reading state information... 358s Calculating upgrade... 358s The following packages have been kept back: 358s curl 359s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 359s Reading package lists... 359s Building dependency tree... 359s Reading state information... 359s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 363s Reading package lists... 364s Building dependency tree... 364s Reading state information... 364s Starting pkgProblemResolver with broken count: 0 364s Starting 2 pkgProblemResolver with broken count: 0 364s Done 365s The following additional packages will be installed: 365s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 365s curl dctrl-tools fontconfig fontconfig-config fonts-dejavu-core 365s fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax g++ g++-13 365s g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 365s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 365s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 365s libasan8 libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 365s libcairo2 libcc1-0 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 365s libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1 365s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 365s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 365s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 365s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 365s libncurses-dev libnlopt0 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 365s libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 365s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 365s libpng16-16t64 libpsl5t64 libreadline-dev libreadline8t64 libsharpyuv0 365s libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 365s libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7 365s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 365s linux-libc-dev littler node-normalize.css pkg-config pkg-r-autopkgtest 365s pkgconf pkgconf-bin r-base-core r-base-dev r-cran-backports r-cran-boot 365s r-cran-brio r-cran-broom r-cran-callr r-cran-cli r-cran-colorspace 365s r-cran-cpp11 r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest 365s r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 365s r-cran-fs r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 365s r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling 365s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 r-cran-lmertest 365s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-minqa 365s r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-numderiv r-cran-pbkrtest 365s r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten 365s r-cran-pkgload r-cran-praise r-cran-processx r-cran-ps r-cran-purrr 365s r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen r-cran-rematch2 365s r-cran-rlang r-cran-rprojroot r-cran-scales r-cran-statmod r-cran-stringi 365s r-cran-stringr r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect 365s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr 365s r-cran-xfun r-cran-yaml rpcsvc-proto unzip x11-common xdg-utils zip 365s zlib1g-dev 365s Suggested packages: 365s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 365s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 365s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 365s liblapack-doc glibc-doc icu-doc fonts-mathjax-extras fonts-stix 365s libjs-mathjax-doc liblzma-doc ncurses-doc readline-doc libstdc++-13-doc 365s tcl8.6 tk8.6 libjs-html5shiv elpa-ess r-doc-info | r-doc-pdf r-mathlib 365s r-base-html texlive-base texlive-latex-base texlive-plain-generic 365s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 365s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 365s r-cran-bbmle r-cran-car r-cran-cardata r-cran-caret r-cran-cluster 365s r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 r-cran-emmeans 365s r-cran-epir r-cran-gam r-cran-gee r-cran-geepack r-cran-glmnet r-cran-gmm 365s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-ks r-cran-lavaan r-cran-leaps 365s r-cran-lmtest r-cran-lsmeans r-cran-maps r-cran-mclust r-cran-metafor 365s r-cran-modeldata r-cran-multcomp r-cran-network r-cran-nnet r-cran-ordinal 365s r-cran-plm r-cran-psych r-cran-quantreg r-cran-rmarkdown r-cran-robust 365s r-cran-robustbase r-cran-rsample r-cran-sandwich r-cran-sp r-cran-spdep 365s r-cran-spatialreg r-cran-spelling r-cran-survey r-cran-survival 365s r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth r-cran-kernlab 365s r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-png r-cran-jpeg 365s r-cran-viridis r-cran-rstudioapi r-cran-markdown r-cran-magick r-cran-sf 365s r-cran-getopt r-cran-bit64 r-cran-dbi r-cran-formattable r-cran-nanotime 365s r-cran-palmerpenguins r-cran-units r-cran-vdiffr r-cran-inline r-cran-bench 365s r-cran-blob r-cran-here r-cran-hms r-cran-htmltools 365s Recommended packages: 365s bzip2-doc manpages manpages-dev libc-devtools javascript-common libpng-tools 365s r-recommended r-doc-html r-cran-covr r-cran-cliapp r-cran-mockery 365s r-cran-htmltools r-cran-htmlwidgets r-cran-rmarkdown r-cran-rstudioapi 365s r-cran-whoami r-cran-bench r-cran-decor r-cran-lobstr r-cran-progress 365s r-cran-gh r-cran-spelling r-cran-dbi r-cran-dbplyr r-cran-rmysql 365s r-cran-rpostgresql r-cran-rsqlite r-cran-unitizer r-cran-hexbin r-cran-hmisc 365s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 365s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 365s r-cran-testit r-cran-httr r-cran-r.rsp r-cran-bslib r-cran-codetools 365s r-cran-formatr r-cran-gridsvg r-cran-curl r-cran-jpeg r-cran-magick 365s r-cran-markdown r-cran-png r-cran-reticulate r-cran-rgl r-cran-sass 365s r-cran-tikzdevice r-cran-tinytex r-cran-webshot node-highlight.js 365s r-cran-lintr r-cran-tidyverse r-cran-foreign r-cran-nnet r-cran-estimability 365s r-cran-lubridate r-cran-bitops r-cran-mathjaxr r-cran-mockr r-cran-remotes 365s r-cran-webfakes r-cran-pingr r-cran-usethis r-cran-bit64 r-cran-dichromat 365s r-cran-hms r-cran-shiny r-cran-data.table r-cran-formattable r-cran-readr 365s r-cran-pkgdown r-cran-zeallot r-cran-mime r-cran-renv r-cran-runit 365s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 365s x11-xserver-utils 365s The following packages will be REMOVED: 365s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 365s The following NEW packages will be installed: 365s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 365s cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config 365s fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax 365s g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-13 365s gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 365s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 365s libasan8 libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 365s libcairo2 libcc1-0 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 365s libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1 365s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 365s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 365s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 365s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 365s libncurses-dev libnlopt0 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 365s libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 365s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 365s libpng16-16t64 libpsl5t64 libreadline-dev libreadline8t64 libsharpyuv0 365s libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0 libtiff6 365s libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7 365s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 365s linux-libc-dev littler node-normalize.css pkg-config pkg-r-autopkgtest 365s pkgconf pkgconf-bin r-base-core r-base-dev r-cran-backports r-cran-boot 365s r-cran-brio r-cran-broom r-cran-callr r-cran-cli r-cran-colorspace 365s r-cran-cpp11 r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest 365s r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver 365s r-cran-fs r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 365s r-cran-highr r-cran-isoband r-cran-jsonlite r-cran-knitr r-cran-labeling 365s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 r-cran-lmertest 365s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-minqa 365s r-cran-munsell r-cran-nlme r-cran-nloptr r-cran-numderiv r-cran-pbkrtest 365s r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten 365s r-cran-pkgload r-cran-praise r-cran-processx r-cran-ps r-cran-purrr 365s r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen r-cran-rematch2 365s r-cran-rlang r-cran-rprojroot r-cran-scales r-cran-statmod r-cran-stringi 365s r-cran-stringr r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect 365s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr 365s r-cran-xfun r-cran-yaml rpcsvc-proto unzip x11-common xdg-utils zip 365s zlib1g-dev 365s The following packages will be upgraded: 365s curl 365s 1 upgraded, 194 newly installed, 5 to remove and 0 not upgraded. 365s Need to get 192 MB/192 MB of archives. 365s After this operation, 568 MB of additional disk space will be used. 365s Get:1 /tmp/autopkgtest.5HkFOC/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 365s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 365s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 365s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 365s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 365s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 365s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 365s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 365s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 365s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 365s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 365s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 365s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 365s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 365s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 365s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 365s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 366s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 366s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 366s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 366s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 366s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 366s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 366s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 366s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 366s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 366s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 366s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 366s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 366s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 366s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 367s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 367s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 367s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 367s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 367s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 367s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 367s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 367s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 367s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 367s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 367s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 367s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 367s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 367s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 367s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 367s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 367s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 367s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 367s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 367s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 367s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 367s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 367s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 367s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 367s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 367s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 367s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 367s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 367s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 367s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 367s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 367s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 367s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 367s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 367s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 367s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 367s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 367s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 367s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 368s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 368s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 368s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 368s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 368s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 368s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 368s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 368s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 368s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 368s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 368s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 368s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 368s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 368s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 368s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 368s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 368s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 368s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 368s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 368s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 368s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 368s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 368s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 368s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 368s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 368s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 368s Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 368s Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 368s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 368s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 368s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 368s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 368s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 368s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 368s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 368s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 368s Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 369s Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 369s Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 369s Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 369s Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 369s Get:112 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 369s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 369s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 369s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 369s Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 369s Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 369s Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 369s Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 370s Get:120 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 370s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 370s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 370s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-boot all 1.3-30-1 [619 kB] 370s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-brio arm64 1.1.4-1 [37.7 kB] 370s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 370s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 370s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 370s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 370s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 370s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 370s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 370s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 370s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 370s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 370s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 370s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 370s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 370s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 370s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 370s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 370s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 370s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 370s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 370s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 370s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 370s Get:146 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 370s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 370s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ps arm64 1.7.6-1 [313 kB] 370s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-processx arm64 3.8.3-1 [345 kB] 370s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-callr all 3.7.3-2 [425 kB] 370s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 370s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB] 370s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-desc all 1.4.3-1 [359 kB] 370s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB] 370s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB] 370s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-evaluate all 0.23-1 [90.2 kB] 370s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 370s Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fs arm64 1.6.3+dfsg-1 [227 kB] 370s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 370s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 370s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 370s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 370s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 370s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 371s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 371s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 371s Get:167 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 371s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 371s Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 371s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 371s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 371s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xfun arm64 0.41+dfsg-1 [415 kB] 371s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 371s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB] 371s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB] 371s Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 371s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 371s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 371s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 371s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-minqa arm64 1.2.6-1 [107 kB] 371s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 libnlopt0 arm64 2.7.1-5build2 [174 kB] 371s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgbuild all 1.4.3-1 [209 kB] 371s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rprojroot all 2.0.4-1 [124 kB] 371s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgload all 1.3.4-1 [207 kB] 371s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 371s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rematch2 all 2.1.2-2build1 [46.5 kB] 371s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-waldo all 0.5.2-1build1 [120 kB] 371s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-testthat arm64 3.2.1-1 [1678 kB] 371s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nloptr arm64 2.0.3-1 [375 kB] 371s Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcppeigen arm64 0.3.3.9.4-1 [1180 kB] 371s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 371s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lme4 arm64 1.1-35.1-4 [4116 kB] 371s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 371s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lmertest all 3.1-3-2 [543 kB] 371s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pbkrtest all 0.5.2-2 [182 kB] 373s Preconfiguring packages ... 373s Fetched 192 MB in 7s (28.0 MB/s) 373s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 373s wget depends on libpsl5 (>= 0.16.0). 373s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 373s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 373s 373s (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 ... 74774 files and directories currently installed.) 373s Removing libpsl5:arm64 (0.21.2-1build1) ... 373s Selecting previously unselected package libpsl5t64:arm64. 373s (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 ... 74769 files and directories currently installed.) 373s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 373s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 373s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 373s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 373s (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 ... 74775 files and directories currently installed.) 373s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 373s Selecting previously unselected package libcurl4t64:arm64. 373s (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 ... 74770 files and directories currently installed.) 373s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 373s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 373s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 373s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 373s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 373s 373s (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 ... 74776 files and directories currently installed.) 373s Removing libpng16-16:arm64 (1.6.43-1) ... 373s Selecting previously unselected package libpng16-16t64:arm64. 373s (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 ... 74766 files and directories currently installed.) 373s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 373s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 373s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 373s parted depends on libreadline8 (>= 6.0). 373s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 373s gpgsm depends on libreadline8 (>= 6.0). 373s gpgconf depends on libreadline8 (>= 6.0). 373s gpg depends on libreadline8 (>= 6.0). 373s gawk depends on libreadline8 (>= 6.0). 373s fdisk depends on libreadline8 (>= 6.0). 373s 373s (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 ... 74777 files and directories currently installed.) 373s Removing libreadline8:arm64 (8.2-3) ... 373s Selecting previously unselected package libreadline8t64:arm64. 373s (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 ... 74765 files and directories currently installed.) 373s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 374s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 374s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 374s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 374s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 374s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 374s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 374s lsof depends on libtirpc3 (>= 1.0.2). 374s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 374s libnss-nisplus:arm64 depends on libtirpc3 (>= 1.0.2). 374s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 374s iproute2 depends on libtirpc3 (>= 1.0.2). 374s 374s (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 ... 74785 files and directories currently installed.) 374s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 374s Selecting previously unselected package libtirpc3t64:arm64. 374s (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 ... 74779 files and directories currently installed.) 374s Preparing to unpack .../000-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 374s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 374s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 374s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 374s Selecting previously unselected package libc-dev-bin. 374s Preparing to unpack .../001-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 374s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 374s Selecting previously unselected package linux-libc-dev:arm64. 374s Preparing to unpack .../002-linux-libc-dev_6.8.0-11.11_arm64.deb ... 374s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 374s Selecting previously unselected package libcrypt-dev:arm64. 374s Preparing to unpack .../003-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 374s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 374s Selecting previously unselected package libtirpc-dev:arm64. 374s Preparing to unpack .../004-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 374s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 374s Selecting previously unselected package libnsl-dev:arm64. 374s Preparing to unpack .../005-libnsl-dev_1.3.0-3_arm64.deb ... 374s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 374s Selecting previously unselected package rpcsvc-proto. 374s Preparing to unpack .../006-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 374s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 374s Selecting previously unselected package libc6-dev:arm64. 374s Preparing to unpack .../007-libc6-dev_2.39-0ubuntu2_arm64.deb ... 374s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 374s Selecting previously unselected package libisl23:arm64. 374s Preparing to unpack .../008-libisl23_0.26-3_arm64.deb ... 374s Unpacking libisl23:arm64 (0.26-3) ... 374s Selecting previously unselected package libmpc3:arm64. 374s Preparing to unpack .../009-libmpc3_1.3.1-1_arm64.deb ... 374s Unpacking libmpc3:arm64 (1.3.1-1) ... 374s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 374s Preparing to unpack .../010-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 374s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 375s Selecting previously unselected package cpp-13. 375s Preparing to unpack .../011-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 375s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 375s Selecting previously unselected package cpp-aarch64-linux-gnu. 375s Preparing to unpack .../012-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 375s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 375s Selecting previously unselected package cpp. 375s Preparing to unpack .../013-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 375s Unpacking cpp (4:13.2.0-7ubuntu1) ... 375s Selecting previously unselected package libcc1-0:arm64. 375s Preparing to unpack .../014-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libgomp1:arm64. 375s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libitm1:arm64. 375s Preparing to unpack .../016-libitm1_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libatomic1:arm64. 375s Preparing to unpack .../017-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libasan8:arm64. 375s Preparing to unpack .../018-libasan8_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package liblsan0:arm64. 375s Preparing to unpack .../019-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libtsan2:arm64. 375s Preparing to unpack .../020-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libubsan1:arm64. 375s Preparing to unpack .../021-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libhwasan0:arm64. 375s Preparing to unpack .../022-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 375s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 375s Selecting previously unselected package libgcc-13-dev:arm64. 376s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 376s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 376s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 376s Preparing to unpack .../024-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 376s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 376s Selecting previously unselected package gcc-13. 376s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 376s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 376s Selecting previously unselected package gcc-aarch64-linux-gnu. 376s Preparing to unpack .../026-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 376s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 376s Selecting previously unselected package gcc. 376s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 376s Unpacking gcc (4:13.2.0-7ubuntu1) ... 376s Selecting previously unselected package libstdc++-13-dev:arm64. 376s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 376s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 376s Selecting previously unselected package g++-13-aarch64-linux-gnu. 376s Preparing to unpack .../029-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 376s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 377s Selecting previously unselected package g++-13. 377s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_arm64.deb ... 377s Unpacking g++-13 (13.2.0-17ubuntu2) ... 377s Selecting previously unselected package g++-aarch64-linux-gnu. 377s Preparing to unpack .../031-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 377s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 377s Selecting previously unselected package g++. 377s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 377s Unpacking g++ (4:13.2.0-7ubuntu1) ... 377s Selecting previously unselected package build-essential. 377s Preparing to unpack .../033-build-essential_12.10ubuntu1_arm64.deb ... 377s Unpacking build-essential (12.10ubuntu1) ... 377s Selecting previously unselected package dctrl-tools. 377s Preparing to unpack .../034-dctrl-tools_2.24-3build2_arm64.deb ... 377s Unpacking dctrl-tools (2.24-3build2) ... 377s Selecting previously unselected package fonts-dejavu-mono. 377s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ... 377s Unpacking fonts-dejavu-mono (2.37-8) ... 377s Selecting previously unselected package fonts-dejavu-core. 377s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ... 377s Unpacking fonts-dejavu-core (2.37-8) ... 377s Selecting previously unselected package fontconfig-config. 377s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 378s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 378s Selecting previously unselected package libfontconfig1:arm64. 378s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 378s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 378s Selecting previously unselected package fontconfig. 378s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 378s Unpacking fontconfig (2.15.0-1ubuntu1) ... 378s Selecting previously unselected package fonts-glyphicons-halflings. 378s Preparing to unpack .../040-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 378s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 378s Selecting previously unselected package fonts-mathjax. 378s Preparing to unpack .../041-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 378s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 378s Selecting previously unselected package libgfortran5:arm64. 378s Preparing to unpack .../042-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 378s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 378s Selecting previously unselected package libgfortran-13-dev:arm64. 378s Preparing to unpack .../043-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 378s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 378s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 378s Preparing to unpack .../044-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 378s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 378s Selecting previously unselected package gfortran-13. 378s Preparing to unpack .../045-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 378s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 378s Selecting previously unselected package gfortran-aarch64-linux-gnu. 378s Preparing to unpack .../046-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 378s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 378s Selecting previously unselected package gfortran. 378s Preparing to unpack .../047-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 378s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 378s Selecting previously unselected package icu-devtools. 378s Preparing to unpack .../048-icu-devtools_74.2-1ubuntu1_arm64.deb ... 378s Unpacking icu-devtools (74.2-1ubuntu1) ... 378s Selecting previously unselected package libblas3:arm64. 378s Preparing to unpack .../049-libblas3_3.12.0-3_arm64.deb ... 378s Unpacking libblas3:arm64 (3.12.0-3) ... 378s Selecting previously unselected package libblas-dev:arm64. 378s Preparing to unpack .../050-libblas-dev_3.12.0-3_arm64.deb ... 378s Unpacking libblas-dev:arm64 (3.12.0-3) ... 378s Selecting previously unselected package libbz2-dev:arm64. 379s Preparing to unpack .../051-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 379s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 379s Selecting previously unselected package libpixman-1-0:arm64. 379s Preparing to unpack .../052-libpixman-1-0_0.42.2-1_arm64.deb ... 379s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 379s Selecting previously unselected package libxcb-render0:arm64. 379s Preparing to unpack .../053-libxcb-render0_1.15-1_arm64.deb ... 379s Unpacking libxcb-render0:arm64 (1.15-1) ... 379s Selecting previously unselected package libxcb-shm0:arm64. 379s Preparing to unpack .../054-libxcb-shm0_1.15-1_arm64.deb ... 379s Unpacking libxcb-shm0:arm64 (1.15-1) ... 379s Selecting previously unselected package libxrender1:arm64. 379s Preparing to unpack .../055-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 379s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 379s Selecting previously unselected package libcairo2:arm64. 379s Preparing to unpack .../056-libcairo2_1.18.0-1_arm64.deb ... 379s Unpacking libcairo2:arm64 (1.18.0-1) ... 379s Selecting previously unselected package libdatrie1:arm64. 379s Preparing to unpack .../057-libdatrie1_0.2.13-3_arm64.deb ... 379s Unpacking libdatrie1:arm64 (0.2.13-3) ... 379s Selecting previously unselected package libdeflate0:arm64. 379s Preparing to unpack .../058-libdeflate0_1.19-1_arm64.deb ... 379s Unpacking libdeflate0:arm64 (1.19-1) ... 379s Selecting previously unselected package libgraphite2-3:arm64. 379s Preparing to unpack .../059-libgraphite2-3_1.3.14-2_arm64.deb ... 379s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 379s Selecting previously unselected package libharfbuzz0b:arm64. 379s Preparing to unpack .../060-libharfbuzz0b_8.3.0-2_arm64.deb ... 379s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 379s Selecting previously unselected package x11-common. 379s Preparing to unpack .../061-x11-common_1%3a7.7+23ubuntu2_all.deb ... 379s Unpacking x11-common (1:7.7+23ubuntu2) ... 379s Selecting previously unselected package libice6:arm64. 379s Preparing to unpack .../062-libice6_2%3a1.0.10-1build2_arm64.deb ... 379s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 379s Selecting previously unselected package libicu-dev:arm64. 379s Preparing to unpack .../063-libicu-dev_74.2-1ubuntu1_arm64.deb ... 379s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 379s Selecting previously unselected package libjpeg-turbo8:arm64. 379s Preparing to unpack .../064-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 379s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 379s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 379s Preparing to unpack .../065-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 379s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 379s Selecting previously unselected package libjpeg8:arm64. 379s Preparing to unpack .../066-libjpeg8_8c-2ubuntu11_arm64.deb ... 379s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 379s Selecting previously unselected package libjpeg8-dev:arm64. 380s Preparing to unpack .../067-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 380s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 380s Selecting previously unselected package libjpeg-dev:arm64. 380s Preparing to unpack .../068-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 380s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 380s Selecting previously unselected package libjs-bootstrap. 380s Preparing to unpack .../069-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 380s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 380s Selecting previously unselected package libjs-highlight.js. 380s Preparing to unpack .../070-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 380s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 380s Selecting previously unselected package libjs-jquery. 380s Preparing to unpack .../071-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 380s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 380s Selecting previously unselected package libjs-jquery-datatables. 380s Preparing to unpack .../072-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 380s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 380s Selecting previously unselected package liblapack3:arm64. 380s Preparing to unpack .../073-liblapack3_3.12.0-3_arm64.deb ... 380s Unpacking liblapack3:arm64 (3.12.0-3) ... 380s Selecting previously unselected package liblapack-dev:arm64. 380s Preparing to unpack .../074-liblapack-dev_3.12.0-3_arm64.deb ... 380s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 380s Selecting previously unselected package liblerc4:arm64. 380s Preparing to unpack .../075-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 380s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 380s Selecting previously unselected package libncurses-dev:arm64. 380s Preparing to unpack .../076-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 380s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 380s Selecting previously unselected package libthai-data. 380s Preparing to unpack .../077-libthai-data_0.1.29-2_all.deb ... 380s Unpacking libthai-data (0.1.29-2) ... 380s Selecting previously unselected package libthai0:arm64. 380s Preparing to unpack .../078-libthai0_0.1.29-2_arm64.deb ... 380s Unpacking libthai0:arm64 (0.1.29-2) ... 380s Selecting previously unselected package libpango-1.0-0:arm64. 380s Preparing to unpack .../079-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 380s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 380s Selecting previously unselected package libpangoft2-1.0-0:arm64. 380s Preparing to unpack .../080-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 380s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 380s Selecting previously unselected package libpangocairo-1.0-0:arm64. 380s Preparing to unpack .../081-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 380s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 380s Selecting previously unselected package libpaper1:arm64. 380s Preparing to unpack .../082-libpaper1_1.1.29_arm64.deb ... 380s Unpacking libpaper1:arm64 (1.1.29) ... 380s Selecting previously unselected package libpaper-utils. 381s Preparing to unpack .../083-libpaper-utils_1.1.29_arm64.deb ... 381s Unpacking libpaper-utils (1.1.29) ... 381s Selecting previously unselected package libpcre2-16-0:arm64. 381s Preparing to unpack .../084-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 381s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 381s Selecting previously unselected package libpcre2-32-0:arm64. 381s Preparing to unpack .../085-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 381s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 381s Selecting previously unselected package libpcre2-posix3:arm64. 381s Preparing to unpack .../086-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 381s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 381s Selecting previously unselected package libpcre2-dev:arm64. 381s Preparing to unpack .../087-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 381s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 381s Selecting previously unselected package libpkgconf3:arm64. 381s Preparing to unpack .../088-libpkgconf3_1.8.1-2_arm64.deb ... 381s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 381s Selecting previously unselected package zlib1g-dev:arm64. 381s Preparing to unpack .../089-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 381s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 381s Selecting previously unselected package libpng-dev:arm64. 381s Preparing to unpack .../090-libpng-dev_1.6.43-3_arm64.deb ... 381s Unpacking libpng-dev:arm64 (1.6.43-3) ... 381s Selecting previously unselected package libreadline-dev:arm64. 381s Preparing to unpack .../091-libreadline-dev_8.2-3.1_arm64.deb ... 381s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 381s Selecting previously unselected package libsharpyuv0:arm64. 381s Preparing to unpack .../092-libsharpyuv0_1.3.2-0.4_arm64.deb ... 381s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 381s Selecting previously unselected package libsm6:arm64. 381s Preparing to unpack .../093-libsm6_2%3a1.2.3-1build2_arm64.deb ... 381s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 381s Selecting previously unselected package libtcl8.6:arm64. 381s Preparing to unpack .../094-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 381s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 381s Selecting previously unselected package libjbig0:arm64. 381s Preparing to unpack .../095-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 381s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 381s Selecting previously unselected package libwebp7:arm64. 381s Preparing to unpack .../096-libwebp7_1.3.2-0.4_arm64.deb ... 381s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 381s Selecting previously unselected package libtiff6:arm64. 381s Preparing to unpack .../097-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 381s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 381s Selecting previously unselected package libxft2:arm64. 381s Preparing to unpack .../098-libxft2_2.3.6-1_arm64.deb ... 381s Unpacking libxft2:arm64 (2.3.6-1) ... 381s Selecting previously unselected package libxss1:arm64. 381s Preparing to unpack .../099-libxss1_1%3a1.2.3-1build2_arm64.deb ... 381s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 381s Selecting previously unselected package libtk8.6:arm64. 381s Preparing to unpack .../100-libtk8.6_8.6.13-2_arm64.deb ... 381s Unpacking libtk8.6:arm64 (8.6.13-2) ... 381s Selecting previously unselected package libxt6t64:arm64. 381s Preparing to unpack .../101-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 381s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 381s Selecting previously unselected package zip. 381s Preparing to unpack .../102-zip_3.0-13_arm64.deb ... 381s Unpacking zip (3.0-13) ... 381s Selecting previously unselected package unzip. 382s Preparing to unpack .../103-unzip_6.0-28ubuntu3_arm64.deb ... 382s Unpacking unzip (6.0-28ubuntu3) ... 382s Selecting previously unselected package xdg-utils. 382s Preparing to unpack .../104-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 382s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 382s Selecting previously unselected package r-base-core. 382s Preparing to unpack .../105-r-base-core_4.3.3-2build1_arm64.deb ... 382s Unpacking r-base-core (4.3.3-2build1) ... 382s Selecting previously unselected package r-cran-littler. 382s Preparing to unpack .../106-r-cran-littler_0.3.19-1_arm64.deb ... 382s Unpacking r-cran-littler (0.3.19-1) ... 382s Selecting previously unselected package littler. 382s Preparing to unpack .../107-littler_0.3.19-1_all.deb ... 382s Unpacking littler (0.3.19-1) ... 382s Selecting previously unselected package node-normalize.css. 382s Preparing to unpack .../108-node-normalize.css_8.0.1-5_all.deb ... 382s Unpacking node-normalize.css (8.0.1-5) ... 382s Selecting previously unselected package pkgconf-bin. 382s Preparing to unpack .../109-pkgconf-bin_1.8.1-2_arm64.deb ... 382s Unpacking pkgconf-bin (1.8.1-2) ... 382s Selecting previously unselected package pkgconf:arm64. 382s Preparing to unpack .../110-pkgconf_1.8.1-2_arm64.deb ... 382s Unpacking pkgconf:arm64 (1.8.1-2) ... 382s Selecting previously unselected package pkg-config:arm64. 382s Preparing to unpack .../111-pkg-config_1.8.1-2_arm64.deb ... 382s Unpacking pkg-config:arm64 (1.8.1-2) ... 382s Selecting previously unselected package liblzma-dev:arm64. 382s Preparing to unpack .../112-liblzma-dev_5.4.5-0.3_arm64.deb ... 382s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 382s Selecting previously unselected package r-base-dev. 382s Preparing to unpack .../113-r-base-dev_4.3.3-2build1_all.deb ... 382s Unpacking r-base-dev (4.3.3-2build1) ... 382s Selecting previously unselected package pkg-r-autopkgtest. 382s Preparing to unpack .../114-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 382s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 382s Selecting previously unselected package r-cran-backports. 383s Preparing to unpack .../115-r-cran-backports_1.4.1-1_arm64.deb ... 383s Unpacking r-cran-backports (1.4.1-1) ... 383s Selecting previously unselected package r-cran-boot. 383s Preparing to unpack .../116-r-cran-boot_1.3-30-1_all.deb ... 383s Unpacking r-cran-boot (1.3-30-1) ... 383s Selecting previously unselected package r-cran-brio. 383s Preparing to unpack .../117-r-cran-brio_1.1.4-1_arm64.deb ... 383s Unpacking r-cran-brio (1.1.4-1) ... 383s Selecting previously unselected package r-cran-cli. 383s Preparing to unpack .../118-r-cran-cli_3.6.2-1_arm64.deb ... 383s Unpacking r-cran-cli (3.6.2-1) ... 383s Selecting previously unselected package r-cran-generics. 383s Preparing to unpack .../119-r-cran-generics_0.1.3-1_all.deb ... 383s Unpacking r-cran-generics (0.1.3-1) ... 383s Selecting previously unselected package r-cran-glue. 383s Preparing to unpack .../120-r-cran-glue_1.7.0-1_arm64.deb ... 383s Unpacking r-cran-glue (1.7.0-1) ... 383s Selecting previously unselected package r-cran-rlang. 383s Preparing to unpack .../121-r-cran-rlang_1.1.3-1_arm64.deb ... 383s Unpacking r-cran-rlang (1.1.3-1) ... 383s Selecting previously unselected package r-cran-lifecycle. 383s Preparing to unpack .../122-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 383s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 383s Selecting previously unselected package r-cran-magrittr. 383s Preparing to unpack .../123-r-cran-magrittr_2.0.3-1_arm64.deb ... 383s Unpacking r-cran-magrittr (2.0.3-1) ... 383s Selecting previously unselected package r-cran-fansi. 383s Preparing to unpack .../124-r-cran-fansi_1.0.5-1_arm64.deb ... 383s Unpacking r-cran-fansi (1.0.5-1) ... 383s Selecting previously unselected package r-cran-utf8. 383s Preparing to unpack .../125-r-cran-utf8_1.2.4-1_arm64.deb ... 383s Unpacking r-cran-utf8 (1.2.4-1) ... 383s Selecting previously unselected package r-cran-vctrs. 384s Preparing to unpack .../126-r-cran-vctrs_0.6.5-1_arm64.deb ... 384s Unpacking r-cran-vctrs (0.6.5-1) ... 384s Selecting previously unselected package r-cran-pillar. 384s Preparing to unpack .../127-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 384s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 384s Selecting previously unselected package r-cran-r6. 384s Preparing to unpack .../128-r-cran-r6_2.5.1-1_all.deb ... 384s Unpacking r-cran-r6 (2.5.1-1) ... 384s Selecting previously unselected package r-cran-pkgconfig. 384s Preparing to unpack .../129-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 384s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 384s Selecting previously unselected package r-cran-tibble. 384s Preparing to unpack .../130-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 384s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 384s Selecting previously unselected package r-cran-withr. 384s Preparing to unpack .../131-r-cran-withr_2.5.0-1_all.deb ... 384s Unpacking r-cran-withr (2.5.0-1) ... 384s Selecting previously unselected package r-cran-tidyselect. 385s Preparing to unpack .../132-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 385s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 385s Selecting previously unselected package r-cran-dplyr. 385s Preparing to unpack .../133-r-cran-dplyr_1.1.4-1_arm64.deb ... 385s Unpacking r-cran-dplyr (1.1.4-1) ... 385s Selecting previously unselected package r-cran-ellipsis. 385s Preparing to unpack .../134-r-cran-ellipsis_0.3.2-2_arm64.deb ... 385s Unpacking r-cran-ellipsis (0.3.2-2) ... 385s Selecting previously unselected package r-cran-purrr. 385s Preparing to unpack .../135-r-cran-purrr_1.0.2-1_arm64.deb ... 385s Unpacking r-cran-purrr (1.0.2-1) ... 385s Selecting previously unselected package r-cran-stringi. 385s Preparing to unpack .../136-r-cran-stringi_1.8.3-1_arm64.deb ... 385s Unpacking r-cran-stringi (1.8.3-1) ... 385s Selecting previously unselected package r-cran-stringr. 385s Preparing to unpack .../137-r-cran-stringr_1.5.1-1_all.deb ... 385s Unpacking r-cran-stringr (1.5.1-1) ... 386s Selecting previously unselected package r-cran-cpp11. 386s Preparing to unpack .../138-r-cran-cpp11_0.4.7-1_all.deb ... 386s Unpacking r-cran-cpp11 (0.4.7-1) ... 386s Selecting previously unselected package r-cran-tidyr. 386s Preparing to unpack .../139-r-cran-tidyr_1.3.1-1_arm64.deb ... 386s Unpacking r-cran-tidyr (1.3.1-1) ... 386s Selecting previously unselected package r-cran-broom. 386s Preparing to unpack .../140-r-cran-broom_1.0.5+dfsg-1_all.deb ... 386s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 386s Selecting previously unselected package r-cran-ps. 386s Preparing to unpack .../141-r-cran-ps_1.7.6-1_arm64.deb ... 386s Unpacking r-cran-ps (1.7.6-1) ... 386s Selecting previously unselected package r-cran-processx. 386s Preparing to unpack .../142-r-cran-processx_3.8.3-1_arm64.deb ... 386s Unpacking r-cran-processx (3.8.3-1) ... 386s Selecting previously unselected package r-cran-callr. 386s Preparing to unpack .../143-r-cran-callr_3.7.3-2_all.deb ... 386s Unpacking r-cran-callr (3.7.3-2) ... 386s Selecting previously unselected package r-cran-colorspace. 386s Preparing to unpack .../144-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 386s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 386s Selecting previously unselected package r-cran-crayon. 386s Preparing to unpack .../145-r-cran-crayon_1.5.2-1_all.deb ... 386s Unpacking r-cran-crayon (1.5.2-1) ... 386s Selecting previously unselected package r-cran-desc. 386s Preparing to unpack .../146-r-cran-desc_1.4.3-1_all.deb ... 386s Unpacking r-cran-desc (1.4.3-1) ... 386s Selecting previously unselected package r-cran-diffobj. 386s Preparing to unpack .../147-r-cran-diffobj_0.3.5-1_arm64.deb ... 386s Unpacking r-cran-diffobj (0.3.5-1) ... 386s Selecting previously unselected package r-cran-digest. 386s Preparing to unpack .../148-r-cran-digest_0.6.34-1_arm64.deb ... 386s Unpacking r-cran-digest (0.6.34-1) ... 386s Selecting previously unselected package r-cran-evaluate. 386s Preparing to unpack .../149-r-cran-evaluate_0.23-1_all.deb ... 386s Unpacking r-cran-evaluate (0.23-1) ... 386s Selecting previously unselected package r-cran-farver. 386s Preparing to unpack .../150-r-cran-farver_2.1.1-1_arm64.deb ... 386s Unpacking r-cran-farver (2.1.1-1) ... 386s Selecting previously unselected package r-cran-fs. 386s Preparing to unpack .../151-r-cran-fs_1.6.3+dfsg-1_arm64.deb ... 386s Unpacking r-cran-fs (1.6.3+dfsg-1) ... 386s Selecting previously unselected package r-cran-gtable. 386s Preparing to unpack .../152-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 386s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 386s Selecting previously unselected package r-cran-isoband. 387s Preparing to unpack .../153-r-cran-isoband_0.2.7-1_arm64.deb ... 387s Unpacking r-cran-isoband (0.2.7-1) ... 387s Selecting previously unselected package r-cran-mass. 387s Preparing to unpack .../154-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 387s Unpacking r-cran-mass (7.3-60.0.1-1) ... 387s Selecting previously unselected package r-cran-lattice. 387s Preparing to unpack .../155-r-cran-lattice_0.22-5-1_arm64.deb ... 387s Unpacking r-cran-lattice (0.22-5-1) ... 387s Selecting previously unselected package r-cran-nlme. 387s Preparing to unpack .../156-r-cran-nlme_3.1.164-1_arm64.deb ... 387s Unpacking r-cran-nlme (3.1.164-1) ... 387s Selecting previously unselected package r-cran-matrix. 387s Preparing to unpack .../157-r-cran-matrix_1.6-5-1_arm64.deb ... 387s Unpacking r-cran-matrix (1.6-5-1) ... 387s Selecting previously unselected package r-cran-mgcv. 387s Preparing to unpack .../158-r-cran-mgcv_1.9-1-1_arm64.deb ... 387s Unpacking r-cran-mgcv (1.9-1-1) ... 387s Selecting previously unselected package r-cran-labeling. 387s Preparing to unpack .../159-r-cran-labeling_0.4.3-1_all.deb ... 387s Unpacking r-cran-labeling (0.4.3-1) ... 387s Selecting previously unselected package r-cran-munsell. 387s Preparing to unpack .../160-r-cran-munsell_0.5.0-2build1_all.deb ... 387s Unpacking r-cran-munsell (0.5.0-2build1) ... 387s Selecting previously unselected package r-cran-rcolorbrewer. 387s Preparing to unpack .../161-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 387s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 387s Selecting previously unselected package r-cran-viridislite. 387s Preparing to unpack .../162-r-cran-viridislite_0.4.2-2_all.deb ... 387s Unpacking r-cran-viridislite (0.4.2-2) ... 387s Selecting previously unselected package r-cran-scales. 387s Preparing to unpack .../163-r-cran-scales_1.3.0-1_all.deb ... 387s Unpacking r-cran-scales (1.3.0-1) ... 387s Selecting previously unselected package r-cran-ggplot2. 387s Preparing to unpack .../164-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 387s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 387s Selecting previously unselected package r-cran-xfun. 387s Preparing to unpack .../165-r-cran-xfun_0.41+dfsg-1_arm64.deb ... 387s Unpacking r-cran-xfun (0.41+dfsg-1) ... 387s Selecting previously unselected package r-cran-highr. 387s Preparing to unpack .../166-r-cran-highr_0.10+dfsg-1_all.deb ... 387s Unpacking r-cran-highr (0.10+dfsg-1) ... 387s Selecting previously unselected package r-cran-jsonlite. 387s Preparing to unpack .../167-r-cran-jsonlite_1.8.8+dfsg-1_arm64.deb ... 387s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 387s Selecting previously unselected package r-cran-yaml. 387s Preparing to unpack .../168-r-cran-yaml_2.3.8-1_arm64.deb ... 387s Unpacking r-cran-yaml (2.3.8-1) ... 387s Selecting previously unselected package libjs-mathjax. 387s Preparing to unpack .../169-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 387s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 388s Selecting previously unselected package r-cran-knitr. 388s Preparing to unpack .../170-r-cran-knitr_1.45+dfsg-1_all.deb ... 388s Unpacking r-cran-knitr (1.45+dfsg-1) ... 388s Selecting previously unselected package r-cran-pkgkitten. 389s Preparing to unpack .../171-r-cran-pkgkitten_0.2.3-1_all.deb ... 389s Unpacking r-cran-pkgkitten (0.2.3-1) ... 389s Selecting previously unselected package r-cran-rcpp. 389s Preparing to unpack .../172-r-cran-rcpp_1.0.12-1_arm64.deb ... 389s Unpacking r-cran-rcpp (1.0.12-1) ... 389s Selecting previously unselected package r-cran-minqa. 389s Preparing to unpack .../173-r-cran-minqa_1.2.6-1_arm64.deb ... 389s Unpacking r-cran-minqa (1.2.6-1) ... 389s Selecting previously unselected package libnlopt0:arm64. 389s Preparing to unpack .../174-libnlopt0_2.7.1-5build2_arm64.deb ... 389s Unpacking libnlopt0:arm64 (2.7.1-5build2) ... 389s Selecting previously unselected package r-cran-pkgbuild. 389s Preparing to unpack .../175-r-cran-pkgbuild_1.4.3-1_all.deb ... 389s Unpacking r-cran-pkgbuild (1.4.3-1) ... 389s Selecting previously unselected package r-cran-rprojroot. 389s Preparing to unpack .../176-r-cran-rprojroot_2.0.4-1_all.deb ... 389s Unpacking r-cran-rprojroot (2.0.4-1) ... 389s Selecting previously unselected package r-cran-pkgload. 390s Preparing to unpack .../177-r-cran-pkgload_1.3.4-1_all.deb ... 390s Unpacking r-cran-pkgload (1.3.4-1) ... 390s Selecting previously unselected package r-cran-praise. 390s Preparing to unpack .../178-r-cran-praise_1.0.0-4build1_all.deb ... 390s Unpacking r-cran-praise (1.0.0-4build1) ... 390s Selecting previously unselected package r-cran-rematch2. 390s Preparing to unpack .../179-r-cran-rematch2_2.1.2-2build1_all.deb ... 390s Unpacking r-cran-rematch2 (2.1.2-2build1) ... 390s Selecting previously unselected package r-cran-waldo. 390s Preparing to unpack .../180-r-cran-waldo_0.5.2-1build1_all.deb ... 390s Unpacking r-cran-waldo (0.5.2-1build1) ... 390s Selecting previously unselected package r-cran-testthat. 390s Preparing to unpack .../181-r-cran-testthat_3.2.1-1_arm64.deb ... 390s Unpacking r-cran-testthat (3.2.1-1) ... 390s Selecting previously unselected package r-cran-nloptr. 390s Preparing to unpack .../182-r-cran-nloptr_2.0.3-1_arm64.deb ... 390s Unpacking r-cran-nloptr (2.0.3-1) ... 390s Selecting previously unselected package r-cran-rcppeigen. 390s Preparing to unpack .../183-r-cran-rcppeigen_0.3.3.9.4-1_arm64.deb ... 390s Unpacking r-cran-rcppeigen (0.3.3.9.4-1) ... 390s Selecting previously unselected package r-cran-statmod. 391s Preparing to unpack .../184-r-cran-statmod_1.5.0-1_arm64.deb ... 391s Unpacking r-cran-statmod (1.5.0-1) ... 391s Selecting previously unselected package r-cran-lme4. 391s Preparing to unpack .../185-r-cran-lme4_1.1-35.1-4_arm64.deb ... 391s Unpacking r-cran-lme4 (1.1-35.1-4) ... 391s Selecting previously unselected package r-cran-numderiv. 391s Preparing to unpack .../186-r-cran-numderiv_2016.8-1.1-3_all.deb ... 391s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 391s Selecting previously unselected package r-cran-lmertest. 391s Preparing to unpack .../187-r-cran-lmertest_3.1-3-2_all.deb ... 391s Unpacking r-cran-lmertest (3.1-3-2) ... 391s Selecting previously unselected package r-cran-pbkrtest. 391s Preparing to unpack .../188-r-cran-pbkrtest_0.5.2-2_all.deb ... 391s Unpacking r-cran-pbkrtest (0.5.2-2) ... 391s Selecting previously unselected package autopkgtest-satdep. 391s Preparing to unpack .../189-2-autopkgtest-satdep.deb ... 391s Unpacking autopkgtest-satdep (0) ... 391s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 391s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 391s Setting up 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(0.3.3.9.4-1) ... 395s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 395s Setting up r-cran-ellipsis (0.3.2-2) ... 395s Setting up r-cran-minqa (1.2.6-1) ... 395s Setting up r-base-dev (4.3.3-2build1) ... 395s Setting up r-cran-stringr (1.5.1-1) ... 395s Setting up r-cran-callr (3.7.3-2) ... 395s Setting up r-cran-desc (1.4.3-1) ... 395s Setting up r-cran-munsell (0.5.0-2build1) ... 395s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 395s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 395s Setting up r-cran-scales (1.3.0-1) ... 395s Setting up r-cran-purrr (1.0.2-1) ... 395s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 395s Setting up r-cran-pkgbuild (1.4.3-1) ... 395s Setting up r-cran-dplyr (1.1.4-1) ... 395s Setting up r-cran-pkgload (1.3.4-1) ... 395s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 395s Setting up r-cran-rematch2 (2.1.2-2build1) ... 395s Setting up r-cran-waldo (0.5.2-1build1) ... 395s Setting up r-cran-tidyr (1.3.1-1) ... 395s Setting up r-cran-testthat (3.2.1-1) ... 395s Setting up r-cran-broom (1.0.5+dfsg-1) ... 395s Setting up r-cran-nloptr (2.0.3-1) ... 395s Setting up r-cran-lme4 (1.1-35.1-4) ... 395s Setting up r-cran-lmertest (3.1-3-2) ... 395s Setting up r-cran-pbkrtest (0.5.2-2) ... 395s Setting up autopkgtest-satdep (0) ... 395s Processing triggers for man-db (2.12.0-3) ... 396s Processing triggers for install-info (7.1-3) ... 396s Processing triggers for libc-bin (2.39-0ubuntu2) ... 405s (Reading database ... 93307 files and directories currently installed.) 405s Removing autopkgtest-satdep (0) ... 406s autopkgtest [19:09:13]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 406s autopkgtest [19:09:13]: test pkg-r-autopkgtest: [----------------------- 407s Test: Try to load the R library lmerTest 407s 407s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 407s Copyright (C) 2024 The R Foundation for Statistical Computing 407s Platform: aarch64-unknown-linux-gnu (64-bit) 407s 407s R is free software and comes with ABSOLUTELY NO WARRANTY. 407s You are welcome to redistribute it under certain conditions. 407s Type 'license()' or 'licence()' for distribution details. 407s 407s R is a collaborative project with many contributors. 407s Type 'contributors()' for more information and 407s 'citation()' on how to cite R or R packages in publications. 407s 407s Type 'demo()' for some demos, 'help()' for on-line help, or 407s 'help.start()' for an HTML browser interface to help. 407s Type 'q()' to quit R. 407s 407s > library('lmerTest') 407s Loading required package: lme4 407s Loading required package: Matrix 409s > 409s > 409s 409s Attaching package: ‘lmerTest’ 409s 409s The following object is masked from ‘package:lme4’: 409s 409s lmer 409s 409s The following object is masked from ‘package:stats’: 409s 409s step 409s 409s Other tests are currently unsupported! 409s They will be progressively added. 409s autopkgtest [19:09:16]: test pkg-r-autopkgtest: -----------------------] 410s pkg-r-autopkgtest PASS 410s autopkgtest [19:09:17]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 410s autopkgtest [19:09:17]: @@@@@@@@@@@@@@@@@@@@ summary 410s run-unit-test PASS 410s pkg-r-autopkgtest PASS 421s Creating nova instance adt-noble-arm64-r-cran-lmertest-20240316-190227-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)... 421s Creating nova instance adt-noble-arm64-r-cran-lmertest-20240316-190227-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...