0s autopkgtest [15:45:19]: starting date and time: 2025-03-15 15:45:19+0000 0s autopkgtest [15:45:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:45:19]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yws4b9fp/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-survey --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.58 lxd-armhf-10.145.243.58:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [15:45:40]: testbed dpkg architecture: armhf 23s autopkgtest [15:45:42]: testbed apt version: 2.9.33 26s autopkgtest [15:45:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [15:45:47]: testbed release detected to be: None 36s autopkgtest [15:45:55]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 65s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 66s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 67s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 68s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 68s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 68s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 86s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 88s Fetched 41.0 MB in 49s (832 kB/s) 89s Reading package lists... 95s autopkgtest [15:46:54]: upgrading testbed (apt dist-upgrade and autopurge) 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 98s Starting 2 pkgProblemResolver with broken count: 0 98s Done 99s Entering ResolveByKeep 99s 99s Calculating upgrade... 100s The following packages will be upgraded: 100s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 100s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 8683 kB of archives. 100s After this operation, 23.6 kB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 109s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 110s Preconfiguring packages ... 110s Fetched 8683 kB in 10s (867 kB/s) 110s (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 ... 64655 files and directories currently installed.) 110s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 110s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Setting up libc6:armhf (2.41-1ubuntu2) ... 111s (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 ... 64655 files and directories currently installed.) 111s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 111s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Setting up libc-bin (2.41-1ubuntu2) ... 111s (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 ... 64655 files and directories currently installed.) 111s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 111s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 111s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 111s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 111s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 111s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 112s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 112s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 112s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 112s Setting up sos (4.9.0-5) ... 112s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 112s Setting up locales (2.41-1ubuntu2) ... 113s Generating locales (this might take a while)... 115s en_US.UTF-8... done 115s Generation complete. 115s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 115s Setting up strace (6.13+ds-1ubuntu1) ... 115s Processing triggers for man-db (2.13.0-1) ... 116s Processing triggers for systemd (257.3-1ubuntu3) ... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s Solving dependencies... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [15:47:25]: rebooting testbed after setup commands that affected boot 167s autopkgtest [15:48:06]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 192s autopkgtest [15:48:31]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 204s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (dsc) [2340 B] 204s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (tar) [2341 kB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (diff) [4580 B] 205s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC 205s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 205s gpgv: issuer "plessy@debian.org" 205s gpgv: Can't check signature: No public key 205s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found 205s autopkgtest [15:48:44]: testing package r-cran-survey version 4.4-2-2 207s autopkgtest [15:48:46]: build not needed 212s autopkgtest [15:48:51]: test run-unit-test: preparing testbed 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 215s Starting pkgProblemResolver with broken count: 0 215s Starting 2 pkgProblemResolver with broken count: 0 215s Done 216s The following NEW packages will be installed: 216s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 216s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 216s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 216s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 216s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 216s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 216s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 216s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 216s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler node-normalize.css 216s r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 216s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 216s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 216s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 216s r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 216s r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby 216s r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi 216s r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign 216s r-cran-formula r-cran-future r-cran-future.apply r-cran-generics 216s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable 216s r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms 216s r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr 216s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 216s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 216s r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats 216s r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools 216s r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr 216s r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly 216s r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 216s r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress 216s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.cache 216s r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6 216s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 216s r-cran-rcppeigen r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes 216s r-cran-reformulas r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang 216s r-cran-rpart r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape 216s r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr 216s r-cran-survey r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 216s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 216s r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun 216s r-cran-yaml r-cran-zip r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip 216s 0 upgraded, 206 newly installed, 0 to remove and 0 not upgraded. 216s Need to get 166 MB of archives. 216s After this operation, 322 MB of additional disk space will be used. 216s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 217s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 217s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 218s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 218s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 218s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 218s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 218s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 221s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 221s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 221s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 221s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 221s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 221s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 222s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 222s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 222s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 222s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 223s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 223s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 223s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 223s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 223s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 223s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 223s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 223s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 224s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 224s Get:28 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 225s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 227s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 227s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 227s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 227s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 228s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 228s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 228s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 228s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 228s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 228s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 228s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 229s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 229s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 229s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 229s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 229s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 229s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 230s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 230s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 230s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 230s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 230s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 268s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-littler armhf 0.3.20-2 [90.9 kB] 269s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf littler all 0.3.20-2 [2554 B] 269s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf node-normalize.css all 8.0.1-5 [10.8 kB] 269s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-abind all 1.4-8-1 [66.9 kB] 269s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cardata all 3.0.5-1 [1819 kB] 271s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-formula all 1.2-5-1 [158 kB] 271s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mass armhf 7.3-64-1 [1105 kB] 273s Get:59 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 275s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nlme armhf 3.1.167-1 [2306 kB] 277s Get:61 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 282s Get:62 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 286s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 286s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-boot all 1.3-31-1 [635 kB] 287s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 287s Get:66 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcpp armhf 1.0.14-1 [1976 kB] 289s Get:67 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-minqa armhf 1.2.8-1 [108 kB] 290s Get:68 http://ftpmaster.internal/ubuntu plucky/universe armhf libnlopt0 armhf 2.7.1-6ubuntu3 [154 kB] 290s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nloptr armhf 2.1.1-1 [250 kB] 290s Get:70 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rbibutils armhf 2.3-1 [943 kB] 291s Get:71 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 292s Get:72 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-reformulas all 0.4.0-1 [91.5 kB] 293s Get:73 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 294s Get:74 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-statmod armhf 1.5.0-1 [294 kB] 295s Get:75 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lme4 armhf 1.1-36-1 [4108 kB] 300s Get:76 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 300s Get:77 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 302s Get:78 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-generics all 0.1.3-1 [81.3 kB] 302s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 302s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rlang armhf 1.1.5-1 [1701 kB] 305s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 305s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 305s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 305s Get:84 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 307s Get:85 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 308s Get:86 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 308s Get:87 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-fansi armhf 1.0.5-1 [611 kB] 308s Get:88 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 309s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 309s Get:90 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 309s Get:91 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 310s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 312s Get:93 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 312s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-stringi armhf 1.8.4-1build1 [887 kB] 314s Get:95 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 314s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cpp11 all 0.5.2-1 [233 kB] 315s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 316s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 318s Get:99 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-numderiv all 2016.8-1.1-3 [115 kB] 318s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 319s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 320s Get:102 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 322s Get:103 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 322s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 324s Get:105 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-munsell all 0.5.1-1 [213 kB] 324s Get:106 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 324s Get:107 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-viridislite all 0.4.2-2 [1088 kB] 326s Get:108 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-scales all 1.3.0-1 [603 kB] 327s Get:109 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 330s Get:110 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 331s Get:111 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-deriv all 4.1.6-1 [151 kB] 331s Get:112 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-modelr all 0.1.11-1 [195 kB] 332s Get:113 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-microbenchmark armhf 1.5.0-1 [67.8 kB] 332s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-doby all 4.6.25-1 [4772 kB] 337s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-evaluate all 1.0.3-1 [114 kB] 338s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-xfun armhf 0.51+dfsg-1 [573 kB] 338s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 338s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 339s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 345s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-knitr all 1.49+dfsg-1 [859 kB] 346s Get:121 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pbkrtest all 0.5.3-1 [178 kB] 347s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-sparsem armhf 1.84-2-1 [807 kB] 348s Get:123 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrixmodels all 0.5-3-1 [361 kB] 348s Get:124 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 357s Get:125 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrixstats armhf 1.5.0-1 [495 kB] 358s Get:126 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcpparmadillo armhf 14.2.3-1-1 [842 kB] 359s Get:127 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-class armhf 7.3-23-1 [88.8 kB] 359s Get:128 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-proxy armhf 0.4-27-1 [180 kB] 359s Get:129 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-e1071 armhf 1.7-16-1 [557 kB] 360s Get:130 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-codetools all 0.2-20-1 [90.5 kB] 360s Get:131 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-iterators all 1.0.14-1 [336 kB] 361s Get:132 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-foreach all 1.5.2-1 [124 kB] 361s Get:133 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 363s Get:134 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-modelmetrics armhf 1.2.2.2-1build1 [120 kB] 363s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-plyr armhf 1.8.9-1 [832 kB] 364s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-proc armhf 1.18.5-1 [961 kB] 366s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tzdb armhf 0.4.0-2 [512 kB] 366s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-clock armhf 0.7.2-1 [1858 kB] 368s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-gower armhf 1.0.2-1 [208 kB] 368s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-hardhat all 1.4.0+dfsg-1 [565 kB] 369s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 370s Get:142 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-shape all 1.4.6.1-1 [749 kB] 371s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-diagram all 1.6.5-2 [656 kB] 372s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-kernsmooth armhf 2.23-26-1 [91.6 kB] 372s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-digest armhf 0.6.37-1 [207 kB] 372s Get:146 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-globals all 0.16.3-1 [120 kB] 372s Get:147 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 372s Get:148 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-parallelly armhf 1.42.0-1 [540 kB] 373s Get:149 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-future all 1.34.0+dfsg-1 [646 kB] 374s Get:150 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 374s Get:151 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-progressr all 0.15.1-1 [353 kB] 375s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-squarem all 2021.1-1 [179 kB] 375s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lava all 1.8.1+dfsg-1 [2191 kB] 378s Get:154 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-prodlim armhf 2024.06.25-1 [413 kB] 378s Get:155 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ipred armhf 0.9-15-1 [385 kB] 379s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-timechange armhf 0.3.0-1 [182 kB] 379s Get:157 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lubridate armhf 1.9.4+dfsg-1 [1008 kB] 380s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-timedate armhf 4041.110-1 [1209 kB] 382s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 384s Get:160 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-reshape2 armhf 1.4.4-2build1 [110 kB] 384s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-caret armhf 7.0-1+dfsg-1 [3460 kB] 388s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-conquer armhf 1.3.3-1 [460 kB] 389s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-quantreg armhf 6.00-1 [1427 kB] 390s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-foreign armhf 0.8.88-1 [240 kB] 390s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ellipsis armhf 0.3.2-2 [35.0 kB] 391s Get:166 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-forcats all 1.0.0-1 [369 kB] 391s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-hms all 1.1.3-1 [96.5 kB] 391s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-clipr all 0.8.0-1 [53.5 kB] 391s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-crayon all 1.5.3-1 [165 kB] 392s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-bit armhf 4.6.0+dfsg-1 [447 kB] 392s Get:171 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-bit64 armhf 4.6.0-1-1ubuntu2 [491 kB] 393s Get:172 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-prettyunits all 1.2.0-1 [162 kB] 393s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-progress all 1.2.3-1 [91.9 kB] 393s Get:174 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-vroom armhf 1.6.5-1 [822 kB] 394s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-readr armhf 2.1.5-1 [752 kB] 395s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-haven armhf 2.5.4-1 [327 kB] 396s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-curl armhf 6.2.1+dfsg-1ubuntu1 [194 kB] 396s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rematch all 2.0.0-1 [18.3 kB] 396s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cellranger all 1.1.0-3 [102 kB] 396s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-readxl armhf 1.4.4-1 [336 kB] 397s Get:181 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-writexl armhf 1.5.1-1 [144 kB] 397s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 397s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.oo all 1.27.0-1 [979 kB] 398s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.utils all 2.13.0-1 [1423 kB] 400s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-zip armhf 2.3.2-1 [137 kB] 400s Get:186 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-openxlsx armhf 4.2.8-1 [2024 kB] 402s Get:187 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rio all 1.2.3-1 [546 kB] 403s Get:188 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-car all 3.1-3-1 [1525 kB] 405s Get:189 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-zoo armhf 1.8-13-1 [996 kB] 407s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lmtest armhf 0.9.40-1 [396 kB] 407s Get:191 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-sandwich all 3.1-1-1 [1483 kB] 409s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-aer all 1.2-14-1 [2597 kB] 412s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-blob all 1.2.4-1 [49.8 kB] 412s Get:194 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-fastmap armhf 1.2.0-1 [69.8 kB] 412s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cachem armhf 1.1.0-1 [73.8 kB] 412s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-dbi all 1.2.3-1 [853 kB] 413s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-hexbin armhf 1.28.5-1 [1580 kB] 415s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-memoise all 2.0.1-1 [53.9 kB] 416s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mitools all 2.4-2build1 [265 kB] 416s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-plogr all 0.2.0-3build1 [15.1 kB] 416s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.cache all 0.16.0-1 [113 kB] 416s Get:202 http://ftpmaster.internal/ubuntu plucky/main armhf tcl8.6 armhf 8.6.16+dfsg-1 [14.6 kB] 416s Get:203 http://ftpmaster.internal/ubuntu plucky/main armhf tcl armhf 8.6.14build1 [4124 B] 416s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.rsp all 0.46.0+ds-1 [1412 kB] 418s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rsqlite armhf 2.3.9-1 [1157 kB] 419s Get:206 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-survey armhf 4.4-2-2 [3448 kB] 424s Preconfiguring packages ... 424s Fetched 166 MB in 3min 27s (802 kB/s) 424s Selecting previously unselected package libfreetype6:armhf. 424s (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 ... 64655 files and directories currently installed.) 424s Preparing to unpack .../000-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 424s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 424s Selecting previously unselected package fonts-dejavu-mono. 424s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ... 424s Unpacking fonts-dejavu-mono (2.37-8) ... 424s Selecting previously unselected package fonts-dejavu-core. 424s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ... 424s Unpacking fonts-dejavu-core (2.37-8) ... 424s Selecting previously unselected package fontconfig-config. 424s Preparing to unpack .../003-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 424s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 424s Selecting previously unselected package libfontconfig1:armhf. 424s Preparing to unpack .../004-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 424s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 425s Selecting previously unselected package fontconfig. 425s Preparing to unpack .../005-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 425s Unpacking fontconfig (2.15.0-2ubuntu1) ... 425s Selecting previously unselected package fonts-glyphicons-halflings. 425s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 425s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 425s Selecting previously unselected package fonts-mathjax. 425s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 425s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 426s Selecting previously unselected package libblas3:armhf. 426s Preparing to unpack .../008-libblas3_3.12.1-2_armhf.deb ... 426s Unpacking libblas3:armhf (3.12.1-2) ... 426s Selecting previously unselected package libpixman-1-0:armhf. 426s Preparing to unpack .../009-libpixman-1-0_0.44.0-3_armhf.deb ... 426s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 426s Selecting previously unselected package libxcb-render0:armhf. 426s Preparing to unpack .../010-libxcb-render0_1.17.0-2_armhf.deb ... 426s Unpacking libxcb-render0:armhf (1.17.0-2) ... 426s Selecting previously unselected package libxcb-shm0:armhf. 426s Preparing to unpack .../011-libxcb-shm0_1.17.0-2_armhf.deb ... 426s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 426s Selecting previously unselected package libxrender1:armhf. 426s Preparing to unpack .../012-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 426s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 426s Selecting previously unselected package libcairo2:armhf. 426s Preparing to unpack .../013-libcairo2_1.18.2-2_armhf.deb ... 426s Unpacking libcairo2:armhf (1.18.2-2) ... 426s Selecting previously unselected package libdatrie1:armhf. 426s Preparing to unpack .../014-libdatrie1_0.2.13-3build1_armhf.deb ... 426s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 426s Selecting previously unselected package libdeflate0:armhf. 426s Preparing to unpack .../015-libdeflate0_1.23-1_armhf.deb ... 426s Unpacking libdeflate0:armhf (1.23-1) ... 426s Selecting previously unselected package libgfortran5:armhf. 426s Preparing to unpack .../016-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 426s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 426s Selecting previously unselected package libgomp1:armhf. 426s Preparing to unpack .../017-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 426s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 426s Selecting previously unselected package libgraphite2-3:armhf. 426s Preparing to unpack .../018-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 426s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 426s Selecting previously unselected package libharfbuzz0b:armhf. 426s Preparing to unpack .../019-libharfbuzz0b_10.2.0-1_armhf.deb ... 426s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 426s Selecting previously unselected package x11-common. 426s Preparing to unpack .../020-x11-common_1%3a7.7+23ubuntu3_all.deb ... 426s Unpacking x11-common (1:7.7+23ubuntu3) ... 426s Selecting previously unselected package libice6:armhf. 426s Preparing to unpack .../021-libice6_2%3a1.1.1-1_armhf.deb ... 426s Unpacking libice6:armhf (2:1.1.1-1) ... 426s Selecting previously unselected package libjpeg-turbo8:armhf. 426s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 426s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 426s Selecting previously unselected package libjpeg8:armhf. 426s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 426s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 426s Selecting previously unselected package libjs-bootstrap. 426s Preparing to unpack .../024-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 426s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 426s Selecting previously unselected package libjs-highlight.js. 426s Preparing to unpack .../025-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 426s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 426s Selecting previously unselected package libjs-jquery. 426s Preparing to unpack .../026-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 426s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 426s Selecting previously unselected package libjs-jquery-datatables. 426s Preparing to unpack .../027-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 426s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 426s Selecting previously unselected package liblapack3:armhf. 426s Preparing to unpack .../028-liblapack3_3.12.1-2_armhf.deb ... 426s Unpacking liblapack3:armhf (3.12.1-2) ... 426s Selecting previously unselected package liblerc4:armhf. 426s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 426s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 426s Selecting previously unselected package libthai-data. 426s Preparing to unpack .../030-libthai-data_0.1.29-2build1_all.deb ... 426s Unpacking libthai-data (0.1.29-2build1) ... 426s Selecting previously unselected package libthai0:armhf. 426s Preparing to unpack .../031-libthai0_0.1.29-2build1_armhf.deb ... 426s Unpacking libthai0:armhf (0.1.29-2build1) ... 426s Selecting previously unselected package libpango-1.0-0:armhf. 426s Preparing to unpack .../032-libpango-1.0-0_1.56.2-1_armhf.deb ... 426s Unpacking libpango-1.0-0:armhf (1.56.2-1) ... 426s Selecting previously unselected package libpangoft2-1.0-0:armhf. 426s Preparing to unpack .../033-libpangoft2-1.0-0_1.56.2-1_armhf.deb ... 426s Unpacking libpangoft2-1.0-0:armhf (1.56.2-1) ... 426s Selecting previously unselected package libpangocairo-1.0-0:armhf. 426s Preparing to unpack .../034-libpangocairo-1.0-0_1.56.2-1_armhf.deb ... 426s Unpacking libpangocairo-1.0-0:armhf (1.56.2-1) ... 426s Selecting previously unselected package libpaper2:armhf. 426s Preparing to unpack .../035-libpaper2_2.2.5-0.3_armhf.deb ... 426s Unpacking libpaper2:armhf (2.2.5-0.3) ... 426s Selecting previously unselected package libpaper-utils. 426s Preparing to unpack .../036-libpaper-utils_2.2.5-0.3_armhf.deb ... 426s Unpacking libpaper-utils (2.2.5-0.3) ... 426s Selecting previously unselected package libsharpyuv0:armhf. 426s Preparing to unpack .../037-libsharpyuv0_1.5.0-0.1_armhf.deb ... 426s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 426s Selecting previously unselected package libsm6:armhf. 426s Preparing to unpack .../038-libsm6_2%3a1.2.4-1_armhf.deb ... 426s Unpacking libsm6:armhf (2:1.2.4-1) ... 426s Selecting previously unselected package libtcl8.6:armhf. 426s Preparing to unpack .../039-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 426s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 426s Selecting previously unselected package libjbig0:armhf. 426s Preparing to unpack .../040-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 426s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 426s Selecting previously unselected package libwebp7:armhf. 426s Preparing to unpack .../041-libwebp7_1.5.0-0.1_armhf.deb ... 426s Unpacking libwebp7:armhf (1.5.0-0.1) ... 426s Selecting previously unselected package libtiff6:armhf. 426s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 426s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 426s Selecting previously unselected package libxft2:armhf. 426s Preparing to unpack .../043-libxft2_2.3.6-1build1_armhf.deb ... 426s Unpacking libxft2:armhf (2.3.6-1build1) ... 426s Selecting previously unselected package libxss1:armhf. 426s Preparing to unpack .../044-libxss1_1%3a1.2.3-1build3_armhf.deb ... 426s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 426s Selecting previously unselected package libtk8.6:armhf. 426s Preparing to unpack .../045-libtk8.6_8.6.16-1_armhf.deb ... 426s Unpacking libtk8.6:armhf (8.6.16-1) ... 426s Selecting previously unselected package libxt6t64:armhf. 426s Preparing to unpack .../046-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 426s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 426s Selecting previously unselected package zip. 426s Preparing to unpack .../047-zip_3.0-14ubuntu2_armhf.deb ... 426s Unpacking zip (3.0-14ubuntu2) ... 426s Selecting previously unselected package unzip. 426s Preparing to unpack .../048-unzip_6.0-28ubuntu6_armhf.deb ... 426s Unpacking unzip (6.0-28ubuntu6) ... 426s Selecting previously unselected package xdg-utils. 426s Preparing to unpack .../049-xdg-utils_1.2.1-2ubuntu1_all.deb ... 426s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 426s Selecting previously unselected package r-base-core. 426s Preparing to unpack .../050-r-base-core_4.4.3-1_armhf.deb ... 426s Unpacking r-base-core (4.4.3-1) ... 427s Selecting previously unselected package r-cran-littler. 427s Preparing to unpack .../051-r-cran-littler_0.3.20-2_armhf.deb ... 427s Unpacking r-cran-littler (0.3.20-2) ... 427s Selecting previously unselected package littler. 427s Preparing to unpack .../052-littler_0.3.20-2_all.deb ... 427s Unpacking littler (0.3.20-2) ... 427s Selecting previously unselected package node-normalize.css. 427s Preparing to unpack .../053-node-normalize.css_8.0.1-5_all.deb ... 427s Unpacking node-normalize.css (8.0.1-5) ... 427s Selecting previously unselected package r-cran-abind. 427s Preparing to unpack .../054-r-cran-abind_1.4-8-1_all.deb ... 427s Unpacking r-cran-abind (1.4-8-1) ... 427s Selecting previously unselected package r-cran-cardata. 427s Preparing to unpack .../055-r-cran-cardata_3.0.5-1_all.deb ... 427s Unpacking r-cran-cardata (3.0.5-1) ... 427s Selecting previously unselected package r-cran-formula. 427s Preparing to unpack .../056-r-cran-formula_1.2-5-1_all.deb ... 427s Unpacking r-cran-formula (1.2-5-1) ... 427s Selecting previously unselected package r-cran-mass. 427s Preparing to unpack .../057-r-cran-mass_7.3-64-1_armhf.deb ... 427s Unpacking r-cran-mass (7.3-64-1) ... 427s Selecting previously unselected package r-cran-lattice. 427s Preparing to unpack .../058-r-cran-lattice_0.22-6-1_armhf.deb ... 427s Unpacking r-cran-lattice (0.22-6-1) ... 427s Selecting previously unselected package r-cran-nlme. 427s Preparing to unpack .../059-r-cran-nlme_3.1.167-1_armhf.deb ... 427s Unpacking r-cran-nlme (3.1.167-1) ... 427s Selecting previously unselected package r-cran-matrix. 427s Preparing to unpack .../060-r-cran-matrix_1.7-3-1_armhf.deb ... 427s Unpacking r-cran-matrix (1.7-3-1) ... 427s Selecting previously unselected package r-cran-mgcv. 427s Preparing to unpack .../061-r-cran-mgcv_1.9-1-1_armhf.deb ... 427s Unpacking r-cran-mgcv (1.9-1-1) ... 427s Selecting previously unselected package r-cran-nnet. 427s Preparing to unpack .../062-r-cran-nnet_7.3-20-1_armhf.deb ... 427s Unpacking r-cran-nnet (7.3-20-1) ... 427s Selecting previously unselected package r-cran-boot. 427s Preparing to unpack .../063-r-cran-boot_1.3-31-1_all.deb ... 427s Unpacking r-cran-boot (1.3-31-1) ... 427s Selecting previously unselected package r-cran-pkgkitten. 427s Preparing to unpack .../064-r-cran-pkgkitten_0.2.4-1_all.deb ... 427s Unpacking r-cran-pkgkitten (0.2.4-1) ... 427s Selecting previously unselected package r-cran-rcpp. 427s Preparing to unpack .../065-r-cran-rcpp_1.0.14-1_armhf.deb ... 427s Unpacking r-cran-rcpp (1.0.14-1) ... 427s Selecting previously unselected package r-cran-minqa. 427s Preparing to unpack .../066-r-cran-minqa_1.2.8-1_armhf.deb ... 427s Unpacking r-cran-minqa (1.2.8-1) ... 427s Selecting previously unselected package libnlopt0:armhf. 427s Preparing to unpack .../067-libnlopt0_2.7.1-6ubuntu3_armhf.deb ... 427s Unpacking libnlopt0:armhf (2.7.1-6ubuntu3) ... 427s Selecting previously unselected package r-cran-nloptr. 427s Preparing to unpack .../068-r-cran-nloptr_2.1.1-1_armhf.deb ... 427s Unpacking r-cran-nloptr (2.1.1-1) ... 428s Selecting previously unselected package r-cran-rbibutils. 428s Preparing to unpack .../069-r-cran-rbibutils_2.3-1_armhf.deb ... 428s Unpacking r-cran-rbibutils (2.3-1) ... 428s Selecting previously unselected package r-cran-rdpack. 428s Preparing to unpack .../070-r-cran-rdpack_2.6.2-1syncable1_all.deb ... 428s Unpacking r-cran-rdpack (2.6.2-1syncable1) ... 428s Selecting previously unselected package r-cran-reformulas. 428s Preparing to unpack .../071-r-cran-reformulas_0.4.0-1_all.deb ... 428s Unpacking r-cran-reformulas (0.4.0-1) ... 428s Selecting previously unselected package r-cran-rcppeigen. 428s Preparing to unpack .../072-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 428s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 428s Selecting previously unselected package r-cran-statmod. 428s Preparing to unpack .../073-r-cran-statmod_1.5.0-1_armhf.deb ... 428s Unpacking r-cran-statmod (1.5.0-1) ... 428s Selecting previously unselected package r-cran-lme4. 428s Preparing to unpack .../074-r-cran-lme4_1.1-36-1_armhf.deb ... 428s Unpacking r-cran-lme4 (1.1-36-1) ... 428s Selecting previously unselected package r-cran-backports. 428s Preparing to unpack .../075-r-cran-backports_1.5.0-2_armhf.deb ... 428s Unpacking r-cran-backports (1.5.0-2) ... 428s Selecting previously unselected package r-cran-cli. 428s Preparing to unpack .../076-r-cran-cli_3.6.4-1_armhf.deb ... 428s Unpacking r-cran-cli (3.6.4-1) ... 428s Selecting previously unselected package r-cran-generics. 428s Preparing to unpack .../077-r-cran-generics_0.1.3-1_all.deb ... 428s Unpacking r-cran-generics (0.1.3-1) ... 428s Selecting previously unselected package r-cran-glue. 428s Preparing to unpack .../078-r-cran-glue_1.8.0-1_armhf.deb ... 428s Unpacking r-cran-glue (1.8.0-1) ... 428s Selecting previously unselected package r-cran-rlang. 428s Preparing to unpack .../079-r-cran-rlang_1.1.5-1_armhf.deb ... 428s Unpacking r-cran-rlang (1.1.5-1) ... 428s Selecting previously unselected package r-cran-lifecycle. 428s Preparing to unpack .../080-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 428s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 428s Selecting previously unselected package r-cran-magrittr. 428s Preparing to unpack .../081-r-cran-magrittr_2.0.3-1_armhf.deb ... 428s Unpacking r-cran-magrittr (2.0.3-1) ... 428s Selecting previously unselected package r-cran-utf8. 428s Preparing to unpack .../082-r-cran-utf8_1.2.4-1_armhf.deb ... 428s Unpacking r-cran-utf8 (1.2.4-1) ... 428s Selecting previously unselected package r-cran-vctrs. 428s Preparing to unpack .../083-r-cran-vctrs_0.6.5-1_armhf.deb ... 428s Unpacking r-cran-vctrs (0.6.5-1) ... 428s Selecting previously unselected package r-cran-pillar. 428s Preparing to unpack .../084-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 428s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 428s Selecting previously unselected package r-cran-r6. 428s Preparing to unpack .../085-r-cran-r6_2.6.1-1_all.deb ... 428s Unpacking r-cran-r6 (2.6.1-1) ... 428s Selecting previously unselected package r-cran-fansi. 428s Preparing to unpack .../086-r-cran-fansi_1.0.5-1_armhf.deb ... 428s Unpacking r-cran-fansi (1.0.5-1) ... 428s Selecting previously unselected package r-cran-pkgconfig. 429s Preparing to unpack .../087-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 429s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 429s Selecting previously unselected package r-cran-tibble. 429s Preparing to unpack .../088-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 429s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 429s Selecting previously unselected package r-cran-withr. 429s Preparing to unpack .../089-r-cran-withr_3.0.2+dfsg-1_all.deb ... 429s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 429s Selecting previously unselected package r-cran-tidyselect. 429s Preparing to unpack .../090-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 429s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 429s Selecting previously unselected package r-cran-dplyr. 429s Preparing to unpack .../091-r-cran-dplyr_1.1.4-4_armhf.deb ... 429s Unpacking r-cran-dplyr (1.1.4-4) ... 429s Selecting previously unselected package r-cran-purrr. 429s Preparing to unpack .../092-r-cran-purrr_1.0.4-1_armhf.deb ... 429s Unpacking r-cran-purrr (1.0.4-1) ... 429s Selecting previously unselected package r-cran-stringi. 429s Preparing to unpack .../093-r-cran-stringi_1.8.4-1build1_armhf.deb ... 429s Unpacking r-cran-stringi (1.8.4-1build1) ... 429s Selecting previously unselected package r-cran-stringr. 429s Preparing to unpack .../094-r-cran-stringr_1.5.1-1_all.deb ... 429s Unpacking r-cran-stringr (1.5.1-1) ... 429s Selecting previously unselected package r-cran-cpp11. 429s Preparing to unpack .../095-r-cran-cpp11_0.5.2-1_all.deb ... 429s Unpacking r-cran-cpp11 (0.5.2-1) ... 429s Selecting previously unselected package r-cran-tidyr. 429s Preparing to unpack .../096-r-cran-tidyr_1.3.1-1_armhf.deb ... 429s Unpacking r-cran-tidyr (1.3.1-1) ... 429s Selecting previously unselected package r-cran-broom. 429s Preparing to unpack .../097-r-cran-broom_1.0.7+dfsg-1_all.deb ... 429s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 429s Selecting previously unselected package r-cran-numderiv. 429s Preparing to unpack .../098-r-cran-numderiv_2016.8-1.1-3_all.deb ... 429s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 429s Selecting previously unselected package r-cran-gtable. 429s Preparing to unpack .../099-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 429s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 429s Selecting previously unselected package r-cran-isoband. 429s Preparing to unpack .../100-r-cran-isoband_0.2.7-1_armhf.deb ... 429s Unpacking r-cran-isoband (0.2.7-1) ... 429s Selecting previously unselected package r-cran-farver. 429s Preparing to unpack .../101-r-cran-farver_2.1.2-1_armhf.deb ... 429s Unpacking r-cran-farver (2.1.2-1) ... 429s Selecting previously unselected package r-cran-labeling. 429s Preparing to unpack .../102-r-cran-labeling_0.4.3-1_all.deb ... 429s Unpacking r-cran-labeling (0.4.3-1) ... 429s Selecting previously unselected package r-cran-colorspace. 429s Preparing to unpack .../103-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 429s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 429s Selecting previously unselected package r-cran-munsell. 429s Preparing to unpack .../104-r-cran-munsell_0.5.1-1_all.deb ... 429s Unpacking r-cran-munsell (0.5.1-1) ... 429s Selecting previously unselected package r-cran-rcolorbrewer. 429s Preparing to unpack .../105-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 429s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 429s Selecting previously unselected package r-cran-viridislite. 429s Preparing to unpack .../106-r-cran-viridislite_0.4.2-2_all.deb ... 429s Unpacking r-cran-viridislite (0.4.2-2) ... 429s Selecting previously unselected package r-cran-scales. 430s Preparing to unpack .../107-r-cran-scales_1.3.0-1_all.deb ... 430s Unpacking r-cran-scales (1.3.0-1) ... 430s Selecting previously unselected package r-cran-ggplot2. 430s Preparing to unpack .../108-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 430s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 430s Selecting previously unselected package r-cran-cowplot. 430s Preparing to unpack .../109-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 430s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 430s Selecting previously unselected package r-cran-deriv. 430s Preparing to unpack .../110-r-cran-deriv_4.1.6-1_all.deb ... 430s Unpacking r-cran-deriv (4.1.6-1) ... 430s Selecting previously unselected package r-cran-modelr. 430s Preparing to unpack .../111-r-cran-modelr_0.1.11-1_all.deb ... 430s Unpacking r-cran-modelr (0.1.11-1) ... 430s Selecting previously unselected package r-cran-microbenchmark. 430s Preparing to unpack .../112-r-cran-microbenchmark_1.5.0-1_armhf.deb ... 430s Unpacking r-cran-microbenchmark (1.5.0-1) ... 430s Selecting previously unselected package r-cran-doby. 430s Preparing to unpack .../113-r-cran-doby_4.6.25-1_all.deb ... 430s Unpacking r-cran-doby (4.6.25-1) ... 430s Selecting previously unselected package r-cran-evaluate. 430s Preparing to unpack .../114-r-cran-evaluate_1.0.3-1_all.deb ... 430s Unpacking r-cran-evaluate (1.0.3-1) ... 430s Selecting previously unselected package r-cran-xfun. 430s Preparing to unpack .../115-r-cran-xfun_0.51+dfsg-1_armhf.deb ... 430s Unpacking r-cran-xfun (0.51+dfsg-1) ... 430s Selecting previously unselected package r-cran-highr. 430s Preparing to unpack .../116-r-cran-highr_0.11+dfsg-1_all.deb ... 430s Unpacking r-cran-highr (0.11+dfsg-1) ... 430s Selecting previously unselected package r-cran-yaml. 430s Preparing to unpack .../117-r-cran-yaml_2.3.10-1_armhf.deb ... 430s Unpacking r-cran-yaml (2.3.10-1) ... 430s Selecting previously unselected package libjs-mathjax. 430s Preparing to unpack .../118-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 430s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 431s Selecting previously unselected package r-cran-knitr. 431s Preparing to unpack .../119-r-cran-knitr_1.49+dfsg-1_all.deb ... 431s Unpacking r-cran-knitr (1.49+dfsg-1) ... 431s Selecting previously unselected package r-cran-pbkrtest. 431s Preparing to unpack .../120-r-cran-pbkrtest_0.5.3-1_all.deb ... 431s Unpacking r-cran-pbkrtest (0.5.3-1) ... 431s Selecting previously unselected package r-cran-sparsem. 431s Preparing to unpack .../121-r-cran-sparsem_1.84-2-1_armhf.deb ... 431s Unpacking r-cran-sparsem (1.84-2-1) ... 431s Selecting previously unselected package r-cran-matrixmodels. 431s Preparing to unpack .../122-r-cran-matrixmodels_0.5-3-1_all.deb ... 431s Unpacking r-cran-matrixmodels (0.5-3-1) ... 431s Selecting previously unselected package r-cran-survival. 431s Preparing to unpack .../123-r-cran-survival_3.8-3-1_armhf.deb ... 431s Unpacking r-cran-survival (3.8-3-1) ... 431s Selecting previously unselected package r-cran-matrixstats. 431s Preparing to unpack .../124-r-cran-matrixstats_1.5.0-1_armhf.deb ... 431s Unpacking r-cran-matrixstats (1.5.0-1) ... 431s Selecting previously unselected package r-cran-rcpparmadillo. 431s Preparing to unpack .../125-r-cran-rcpparmadillo_14.2.3-1-1_armhf.deb ... 431s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 431s Selecting previously unselected package r-cran-class. 431s Preparing to unpack .../126-r-cran-class_7.3-23-1_armhf.deb ... 431s Unpacking r-cran-class (7.3-23-1) ... 431s Selecting previously unselected package r-cran-proxy. 431s Preparing to unpack .../127-r-cran-proxy_0.4-27-1_armhf.deb ... 431s Unpacking r-cran-proxy (0.4-27-1) ... 431s Selecting previously unselected package r-cran-e1071. 431s Preparing to unpack .../128-r-cran-e1071_1.7-16-1_armhf.deb ... 431s Unpacking r-cran-e1071 (1.7-16-1) ... 431s Selecting previously unselected package r-cran-codetools. 431s Preparing to unpack .../129-r-cran-codetools_0.2-20-1_all.deb ... 431s Unpacking r-cran-codetools (0.2-20-1) ... 432s Selecting previously unselected package r-cran-iterators. 432s Preparing to unpack .../130-r-cran-iterators_1.0.14-1_all.deb ... 432s Unpacking r-cran-iterators (1.0.14-1) ... 432s Selecting previously unselected package r-cran-foreach. 432s Preparing to unpack .../131-r-cran-foreach_1.5.2-1_all.deb ... 432s Unpacking r-cran-foreach (1.5.2-1) ... 432s Selecting previously unselected package r-cran-data.table. 432s Preparing to unpack .../132-r-cran-data.table_1.17.0+dfsg-1_armhf.deb ... 432s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 432s Selecting previously unselected package r-cran-modelmetrics. 432s Preparing to unpack .../133-r-cran-modelmetrics_1.2.2.2-1build1_armhf.deb ... 432s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 432s Selecting previously unselected package r-cran-plyr. 432s Preparing to unpack .../134-r-cran-plyr_1.8.9-1_armhf.deb ... 432s Unpacking r-cran-plyr (1.8.9-1) ... 432s Selecting previously unselected package r-cran-proc. 432s Preparing to unpack .../135-r-cran-proc_1.18.5-1_armhf.deb ... 432s Unpacking r-cran-proc (1.18.5-1) ... 432s Selecting previously unselected package r-cran-tzdb. 432s Preparing to unpack .../136-r-cran-tzdb_0.4.0-2_armhf.deb ... 432s Unpacking r-cran-tzdb (0.4.0-2) ... 432s Selecting previously unselected package r-cran-clock. 432s Preparing to unpack .../137-r-cran-clock_0.7.2-1_armhf.deb ... 432s Unpacking r-cran-clock (0.7.2-1) ... 432s Selecting previously unselected package r-cran-gower. 432s Preparing to unpack .../138-r-cran-gower_1.0.2-1_armhf.deb ... 432s Unpacking r-cran-gower (1.0.2-1) ... 432s Selecting previously unselected package r-cran-hardhat. 432s Preparing to unpack .../139-r-cran-hardhat_1.4.0+dfsg-1_all.deb ... 432s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ... 432s Selecting previously unselected package r-cran-rpart. 432s Preparing to unpack .../140-r-cran-rpart_4.1.24-1_armhf.deb ... 432s Unpacking r-cran-rpart (4.1.24-1) ... 432s Selecting previously unselected package r-cran-shape. 432s Preparing to unpack .../141-r-cran-shape_1.4.6.1-1_all.deb ... 432s Unpacking r-cran-shape (1.4.6.1-1) ... 432s Selecting previously unselected package r-cran-diagram. 432s Preparing to unpack .../142-r-cran-diagram_1.6.5-2_all.deb ... 432s Unpacking r-cran-diagram (1.6.5-2) ... 432s Selecting previously unselected package r-cran-kernsmooth. 432s Preparing to unpack .../143-r-cran-kernsmooth_2.23-26-1_armhf.deb ... 432s Unpacking r-cran-kernsmooth (2.23-26-1) ... 432s Selecting previously unselected package r-cran-digest. 432s Preparing to unpack .../144-r-cran-digest_0.6.37-1_armhf.deb ... 432s Unpacking r-cran-digest (0.6.37-1) ... 432s Selecting previously unselected package r-cran-globals. 432s Preparing to unpack .../145-r-cran-globals_0.16.3-1_all.deb ... 432s Unpacking r-cran-globals (0.16.3-1) ... 432s Selecting previously unselected package r-cran-listenv. 432s Preparing to unpack .../146-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 432s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 432s Selecting previously unselected package r-cran-parallelly. 432s Preparing to unpack .../147-r-cran-parallelly_1.42.0-1_armhf.deb ... 432s Unpacking r-cran-parallelly (1.42.0-1) ... 432s Selecting previously unselected package r-cran-future. 432s Preparing to unpack .../148-r-cran-future_1.34.0+dfsg-1_all.deb ... 432s Unpacking r-cran-future (1.34.0+dfsg-1) ... 432s Selecting previously unselected package r-cran-future.apply. 432s Preparing to unpack .../149-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 432s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 432s Selecting previously unselected package r-cran-progressr. 432s Preparing to unpack .../150-r-cran-progressr_0.15.1-1_all.deb ... 432s Unpacking r-cran-progressr (0.15.1-1) ... 433s Selecting previously unselected package r-cran-squarem. 433s Preparing to unpack .../151-r-cran-squarem_2021.1-1_all.deb ... 433s Unpacking r-cran-squarem (2021.1-1) ... 433s Selecting previously unselected package r-cran-lava. 433s Preparing to unpack .../152-r-cran-lava_1.8.1+dfsg-1_all.deb ... 433s Unpacking r-cran-lava (1.8.1+dfsg-1) ... 433s Selecting previously unselected package r-cran-prodlim. 433s Preparing to unpack .../153-r-cran-prodlim_2024.06.25-1_armhf.deb ... 433s Unpacking r-cran-prodlim (2024.06.25-1) ... 433s Selecting previously unselected package r-cran-ipred. 433s Preparing to unpack .../154-r-cran-ipred_0.9-15-1_armhf.deb ... 433s Unpacking r-cran-ipred (0.9-15-1) ... 433s Selecting previously unselected package r-cran-timechange. 433s Preparing to unpack .../155-r-cran-timechange_0.3.0-1_armhf.deb ... 433s Unpacking r-cran-timechange (0.3.0-1) ... 433s Selecting previously unselected package r-cran-lubridate. 433s Preparing to unpack .../156-r-cran-lubridate_1.9.4+dfsg-1_armhf.deb ... 433s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 433s Selecting previously unselected package r-cran-timedate. 433s Preparing to unpack .../157-r-cran-timedate_4041.110-1_armhf.deb ... 433s Unpacking r-cran-timedate (4041.110-1) ... 433s Selecting previously unselected package r-cran-recipes. 433s Preparing to unpack .../158-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 433s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 433s Selecting previously unselected package r-cran-reshape2. 433s Preparing to unpack .../159-r-cran-reshape2_1.4.4-2build1_armhf.deb ... 433s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 433s Selecting previously unselected package r-cran-caret. 433s Preparing to unpack .../160-r-cran-caret_7.0-1+dfsg-1_armhf.deb ... 433s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 433s Selecting previously unselected package r-cran-conquer. 433s Preparing to unpack .../161-r-cran-conquer_1.3.3-1_armhf.deb ... 433s Unpacking r-cran-conquer (1.3.3-1) ... 433s Selecting previously unselected package r-cran-quantreg. 433s Preparing to unpack .../162-r-cran-quantreg_6.00-1_armhf.deb ... 433s Unpacking r-cran-quantreg (6.00-1) ... 433s Selecting previously unselected package r-cran-foreign. 433s Preparing to unpack .../163-r-cran-foreign_0.8.88-1_armhf.deb ... 433s Unpacking r-cran-foreign (0.8.88-1) ... 433s Selecting previously unselected package r-cran-ellipsis. 433s Preparing to unpack .../164-r-cran-ellipsis_0.3.2-2_armhf.deb ... 433s Unpacking r-cran-ellipsis (0.3.2-2) ... 433s Selecting previously unselected package r-cran-forcats. 433s Preparing to unpack .../165-r-cran-forcats_1.0.0-1_all.deb ... 433s Unpacking r-cran-forcats (1.0.0-1) ... 433s Selecting previously unselected package r-cran-hms. 433s Preparing to unpack .../166-r-cran-hms_1.1.3-1_all.deb ... 433s Unpacking r-cran-hms (1.1.3-1) ... 433s Selecting previously unselected package r-cran-clipr. 433s Preparing to unpack .../167-r-cran-clipr_0.8.0-1_all.deb ... 433s Unpacking r-cran-clipr (0.8.0-1) ... 433s Selecting previously unselected package r-cran-crayon. 433s Preparing to unpack .../168-r-cran-crayon_1.5.3-1_all.deb ... 433s Unpacking r-cran-crayon (1.5.3-1) ... 433s Selecting previously unselected package r-cran-bit. 433s Preparing to unpack .../169-r-cran-bit_4.6.0+dfsg-1_armhf.deb ... 433s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 433s Selecting previously unselected package r-cran-bit64. 433s Preparing to unpack .../170-r-cran-bit64_4.6.0-1-1ubuntu2_armhf.deb ... 433s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ... 433s Selecting previously unselected package r-cran-prettyunits. 434s Preparing to unpack .../171-r-cran-prettyunits_1.2.0-1_all.deb ... 434s Unpacking r-cran-prettyunits (1.2.0-1) ... 434s Selecting previously unselected package r-cran-progress. 434s Preparing to unpack .../172-r-cran-progress_1.2.3-1_all.deb ... 434s Unpacking r-cran-progress (1.2.3-1) ... 434s Selecting previously unselected package r-cran-vroom. 434s Preparing to unpack .../173-r-cran-vroom_1.6.5-1_armhf.deb ... 434s Unpacking r-cran-vroom (1.6.5-1) ... 434s Selecting previously unselected package r-cran-readr. 434s Preparing to unpack .../174-r-cran-readr_2.1.5-1_armhf.deb ... 434s Unpacking r-cran-readr (2.1.5-1) ... 434s Selecting previously unselected package r-cran-haven. 434s Preparing to unpack .../175-r-cran-haven_2.5.4-1_armhf.deb ... 434s Unpacking r-cran-haven (2.5.4-1) ... 434s Selecting previously unselected package r-cran-curl. 434s Preparing to unpack .../176-r-cran-curl_6.2.1+dfsg-1ubuntu1_armhf.deb ... 434s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 434s Selecting previously unselected package r-cran-rematch. 434s Preparing to unpack .../177-r-cran-rematch_2.0.0-1_all.deb ... 434s Unpacking r-cran-rematch (2.0.0-1) ... 434s Selecting previously unselected package r-cran-cellranger. 434s Preparing to unpack .../178-r-cran-cellranger_1.1.0-3_all.deb ... 434s Unpacking r-cran-cellranger (1.1.0-3) ... 434s Selecting previously unselected package r-cran-readxl. 434s Preparing to unpack .../179-r-cran-readxl_1.4.4-1_armhf.deb ... 434s Unpacking r-cran-readxl (1.4.4-1) ... 434s Selecting previously unselected package r-cran-writexl. 434s Preparing to unpack .../180-r-cran-writexl_1.5.1-1_armhf.deb ... 434s Unpacking r-cran-writexl (1.5.1-1) ... 434s Selecting previously unselected package r-cran-r.methodss3. 434s Preparing to unpack .../181-r-cran-r.methodss3_1.8.2-1_all.deb ... 434s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 434s Selecting previously unselected package r-cran-r.oo. 434s Preparing to unpack .../182-r-cran-r.oo_1.27.0-1_all.deb ... 434s Unpacking r-cran-r.oo (1.27.0-1) ... 434s Selecting previously unselected package r-cran-r.utils. 434s Preparing to unpack .../183-r-cran-r.utils_2.13.0-1_all.deb ... 434s Unpacking r-cran-r.utils (2.13.0-1) ... 434s Selecting previously unselected package r-cran-zip. 434s Preparing to unpack .../184-r-cran-zip_2.3.2-1_armhf.deb ... 434s Unpacking r-cran-zip (2.3.2-1) ... 434s Selecting previously unselected package r-cran-openxlsx. 434s Preparing to unpack .../185-r-cran-openxlsx_4.2.8-1_armhf.deb ... 434s Unpacking r-cran-openxlsx (4.2.8-1) ... 434s Selecting previously unselected package r-cran-rio. 434s Preparing to unpack .../186-r-cran-rio_1.2.3-1_all.deb ... 434s Unpacking r-cran-rio (1.2.3-1) ... 434s Selecting previously unselected package r-cran-car. 434s Preparing to unpack .../187-r-cran-car_3.1-3-1_all.deb ... 434s Unpacking r-cran-car (3.1-3-1) ... 434s Selecting previously unselected package r-cran-zoo. 434s Preparing to unpack .../188-r-cran-zoo_1.8-13-1_armhf.deb ... 434s Unpacking r-cran-zoo (1.8-13-1) ... 434s Selecting previously unselected package r-cran-lmtest. 434s Preparing to unpack .../189-r-cran-lmtest_0.9.40-1_armhf.deb ... 434s Unpacking r-cran-lmtest (0.9.40-1) ... 434s Selecting previously unselected package r-cran-sandwich. 434s Preparing to unpack .../190-r-cran-sandwich_3.1-1-1_all.deb ... 434s Unpacking r-cran-sandwich (3.1-1-1) ... 434s Selecting previously unselected package r-cran-aer. 434s Preparing to unpack .../191-r-cran-aer_1.2-14-1_all.deb ... 434s Unpacking r-cran-aer (1.2-14-1) ... 435s Selecting previously unselected package r-cran-blob. 435s Preparing to unpack .../192-r-cran-blob_1.2.4-1_all.deb ... 435s Unpacking r-cran-blob (1.2.4-1) ... 435s Selecting previously unselected package r-cran-fastmap. 435s Preparing to unpack .../193-r-cran-fastmap_1.2.0-1_armhf.deb ... 435s Unpacking r-cran-fastmap (1.2.0-1) ... 435s Selecting previously unselected package r-cran-cachem. 435s Preparing to unpack .../194-r-cran-cachem_1.1.0-1_armhf.deb ... 435s Unpacking r-cran-cachem (1.1.0-1) ... 435s Selecting previously unselected package r-cran-dbi. 435s Preparing to unpack .../195-r-cran-dbi_1.2.3-1_all.deb ... 435s Unpacking r-cran-dbi (1.2.3-1) ... 435s Selecting previously unselected package r-cran-hexbin. 435s Preparing to unpack .../196-r-cran-hexbin_1.28.5-1_armhf.deb ... 435s Unpacking r-cran-hexbin (1.28.5-1) ... 435s Selecting previously unselected package r-cran-memoise. 435s Preparing to unpack .../197-r-cran-memoise_2.0.1-1_all.deb ... 435s Unpacking r-cran-memoise (2.0.1-1) ... 435s Selecting previously unselected package r-cran-mitools. 435s Preparing to unpack .../198-r-cran-mitools_2.4-2build1_all.deb ... 435s Unpacking r-cran-mitools (2.4-2build1) ... 435s Selecting previously unselected package r-cran-plogr. 435s Preparing to unpack .../199-r-cran-plogr_0.2.0-3build1_all.deb ... 435s Unpacking r-cran-plogr (0.2.0-3build1) ... 435s Selecting previously unselected package r-cran-r.cache. 435s Preparing to unpack .../200-r-cran-r.cache_0.16.0-1_all.deb ... 435s Unpacking r-cran-r.cache (0.16.0-1) ... 435s Selecting previously unselected package tcl8.6. 435s Preparing to unpack .../201-tcl8.6_8.6.16+dfsg-1_armhf.deb ... 435s Unpacking tcl8.6 (8.6.16+dfsg-1) ... 435s Selecting previously unselected package tcl. 435s Preparing to unpack .../202-tcl_8.6.14build1_armhf.deb ... 435s Unpacking tcl (8.6.14build1) ... 435s Selecting previously unselected package r-cran-r.rsp. 435s Preparing to unpack .../203-r-cran-r.rsp_0.46.0+ds-1_all.deb ... 435s Unpacking r-cran-r.rsp (0.46.0+ds-1) ... 435s Selecting previously unselected package r-cran-rsqlite. 435s Preparing to unpack .../204-r-cran-rsqlite_2.3.9-1_armhf.deb ... 435s Unpacking r-cran-rsqlite (2.3.9-1) ... 435s Selecting previously unselected package r-cran-survey. 435s Preparing to unpack .../205-r-cran-survey_4.4-2-2_armhf.deb ... 435s Unpacking r-cran-survey (4.4-2-2) ... 435s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 435s Setting up libpixman-1-0:armhf (0.44.0-3) ... 435s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 435s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 435s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 435s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 435s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 435s Setting up libdatrie1:armhf (0.2.13-3build1) ... 435s Setting up libxcb-render0:armhf (1.17.0-2) ... 435s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 435s Setting up unzip (6.0-28ubuntu6) ... 435s Setting up x11-common (1:7.7+23ubuntu3) ... 436s Setting up libdeflate0:armhf (1.23-1) ... 436s Setting up libnlopt0:armhf (2.7.1-6ubuntu3) ... 436s Setting up libxcb-shm0:armhf (1.17.0-2) ... 436s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 436s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 436s Setting up zip (3.0-14ubuntu2) ... 436s Setting up libblas3:armhf (3.12.1-2) ... 436s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 436s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 436s Setting up fonts-dejavu-mono (2.37-8) ... 436s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 436s Setting up fonts-dejavu-core (2.37-8) ... 436s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 436s Setting up 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for libc-bin (2.41-1ubuntu2) ... 439s Processing triggers for man-db (2.13.0-1) ... 439s Processing triggers for install-info (7.1.1-1) ... 447s autopkgtest [15:52:46]: test run-unit-test: [----------------------- 449s BEGIN TEST 3stage2phase.R 449s 449s R version 4.4.3 (2025-02-28) -- "Trophy Case" 449s Copyright (C) 2025 The R Foundation for Statistical Computing 449s Platform: arm-unknown-linux-gnueabihf (32-bit) 449s 449s R is free software and comes with ABSOLUTELY NO WARRANTY. 449s You are welcome to redistribute it under certain conditions. 449s Type 'license()' or 'licence()' for distribution details. 449s 449s R is a collaborative project with many contributors. 449s Type 'contributors()' for more information and 449s 'citation()' on how to cite R or R packages in publications. 449s 449s Type 'demo()' for some demos, 'help()' for on-line help, or 449s 'help.start()' for an HTML browser interface to help. 449s Type 'q()' to quit R. 449s 449s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 449s > ## motivated by dietary biomarker substudy in HCHS 449s > 449s > library(survey) 449s Loading required package: grid 449s Loading required package: Matrix 450s Loading required package: survival 450s 450s Attaching package: 'survey' 450s 450s The following object is masked from 'package:graphics': 450s 450s dotchart 450s 450s > 450s > load("simdata1.RData") 450s > 450s > twophase.full = twophase(id=list(~block+house+ind,~1), 450s + strata=list(~strat,NULL), 450s + probs=list(~P.block+P.house+P.ind,NULL), 450s + subset=~phase2, 450s + data=simdata1,method='full') 451s > 451s > twophase.approx = twophase(id=list(~block+house+ind,~1), 451s + strata=list(~strat,NULL), 451s + probs=list(~P.block+P.house+P.ind,NULL), 451s + subset=~phase2, 451s + data=simdata1,method='approx') 451s > 451s > twophase.rep = twophase(id=list(~block,~1), 451s + strata=list(~strat,NULL), 451s + probs=list(~I(P.block*P.house*P.ind),NULL), 451s + subset=~phase2, 451s + data=simdata1,method='full') 451s > 451s > 451s > twophase.repapprox = twophase(id=list(~block,~1), 451s + strata=list(~strat,NULL), 451s + probs=list(~I(P.block*P.house*P.ind),NULL), 451s + subset=~phase2, 451s + data=simdata1,method='approx') 451s > 451s > 451s > svymean(~age, twophase.full) 451s mean SE 451s age 41.116 0.8114 451s > svymean(~age, twophase.approx) 451s mean SE 451s age 41.116 0.6693 451s > svymean(~age, twophase.rep) 451s mean SE 451s age 41.116 0.784 451s > svymean(~age, twophase.repapprox) 451s mean SE 451s age 41.116 0.6592 451s > 451s BEGIN TEST DBIcheck.R 451s 451s R version 4.4.3 (2025-02-28) -- "Trophy Case" 451s Copyright (C) 2025 The R Foundation for Statistical Computing 451s Platform: arm-unknown-linux-gnueabihf (32-bit) 451s 451s R is free software and comes with ABSOLUTELY NO WARRANTY. 451s You are welcome to redistribute it under certain conditions. 451s Type 'license()' or 'licence()' for distribution details. 451s 451s R is a collaborative project with many contributors. 451s Type 'contributors()' for more information and 451s 'citation()' on how to cite R or R packages in publications. 451s 451s Type 'demo()' for some demos, 'help()' for on-line help, or 451s 'help.start()' for an HTML browser interface to help. 451s Type 'q()' to quit R. 451s 451s > 451s > library(survey) 451s Loading required package: grid 451s Loading required package: Matrix 452s Loading required package: survival 452s 452s Attaching package: 'survey' 452s 452s > library(RSQLite) 452s The following object is masked from 'package:graphics': 452s 452s dotchart 452s 453s > 453s > data(api) 453s > apiclus1$api_stu<-apiclus1$api.stu 453s > apiclus1$comp_imp<-apiclus1$comp.imp 453s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 453s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 453s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 453s > 453s > m<-svymean(~api00+stype,dclus1) 453s > m.db<-svymean(~api00+stype, dbclus1) 453s > all.equal(coef(m),coef(m.db)) 453s [1] TRUE 453s > all.equal(vcov(m), vcov(m.db)) 453s [1] TRUE 453s > 453s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 453s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 453s > all.equal(coef(r), coef(r.db)) 453s [1] TRUE 453s > all.equal(SE(r), SE(r.db)) 453s [1] TRUE 453s > 453s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 453s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 453s > all.equal(coef(b), coef(b.db)) 453s [1] TRUE 453s > all.equal(SE(b), SE(b.db)) 453s [1] TRUE 453s > all.equal(deff(b), deff(b.db)) 453s [1] TRUE 453s > 453s > l<-svyglm(api00~api99+mobility, design=dclus1) 453s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 453s > all.equal(coef(l),coef(l.db)) 453s [1] TRUE 453s > all.equal(vcov(l), vcov(l.db)) 453s [1] TRUE 453s > 453s > dclus1<-update(dclus1, apidiff=api00-api99) 453s > dclus1<-update(dclus1, apipct= apidiff/api99) 453s > dbclus1<-update(dbclus1, apidiff=api00-api99) 453s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 453s > 453s > u<-svymean(~api00+apidiff+apipct, dclus1) 453s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 453s > all.equal(u, u.db) 453s [1] TRUE 453s > 453s > all.equal(nrow(dclus1),nrow(dbclus1)) 453s [1] TRUE 453s > all.equal(nrow(subset(dclus1,stype=="E")), 453s + nrow(subset(dbclus1,stype=="E"))) 453s [1] "Mean relative difference: 0.2708333" 453s > 453s > ## replicate weights 453s > rclus1<-as.svrepdesign(dclus1) 453s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 453s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 453s > m<-svymean(~api00+api99,rclus1) 453s > m.db<-svymean(~api00+api99,db_rclus1) 453s > all.equal(m,m.db) 453s [1] TRUE 453s > 453s > summary(db_rclus1) 453s DB-backed replicate weight design 453s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 453s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 453s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 453s Unstratified cluster jacknife (JK1) with 15 replicates. 453s Variables: 453s [1] "row_names" "cds" "stype" "name" "sname" 453s [6] "snum" "dname" "dnum" "cname" "cnum" 453s [11] "flag" "pcttest" "api00" "api99" "target" 453s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 453s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 453s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 453s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 453s [36] "emer" "enroll" "api_stu" "fpc" "pw" 453s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 453s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 453s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 453s [56] "wt15" 453s > 453s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 453s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 453s > all.equal(s,s.db) 453s [1] TRUE 453s > 453s BEGIN TEST anova-svycoxph.R 453s 453s R version 4.4.3 (2025-02-28) -- "Trophy Case" 453s Copyright (C) 2025 The R Foundation for Statistical Computing 453s Platform: arm-unknown-linux-gnueabihf (32-bit) 453s 453s R is free software and comes with ABSOLUTELY NO WARRANTY. 453s You are welcome to redistribute it under certain conditions. 453s Type 'license()' or 'licence()' for distribution details. 453s 453s R is a collaborative project with many contributors. 453s Type 'contributors()' for more information and 453s 'citation()' on how to cite R or R packages in publications. 453s 453s Type 'demo()' for some demos, 'help()' for on-line help, or 453s 'help.start()' for an HTML browser interface to help. 453s Type 'q()' to quit R. 453s 453s > 453s > library(survey) 453s Loading required package: grid 453s Loading required package: Matrix 454s Loading required package: survival 455s 455s Attaching package: 'survey' 455s 455s The following object is masked from 'package:graphics': 455s 455s dotchart 455s 455s > example(svycoxph, ask=FALSE) 455s 455s svycxp> ## Somewhat unrealistic example of nonresponse bias. 455s svycxp> data(pbc, package="survival") 455s 455s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 455s 455s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 455s 455s svycxp> pbc$randprob<-fitted(biasmodel) 455s 455s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 455s 455s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 455s 455s svycxp> rpbc<-as.svrepdesign(dpbc) 455s 455s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 455s Call: 455s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 455s albumin, design = dpbc) 455s 455s coef exp(coef) se(coef) robust se z p 455s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 455s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 455s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 455s 455s Likelihood ratio test= on 3 df, p= 455s n= 312, number of events= 144 455s 455s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 455s Call: 455s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 455s protime + albumin, design = rpbc) 455s 455s coef exp(coef) se(coef) z p 455s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 455s protime 0.24487 1.27745 0.09373 2.612 0.00899 455s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 455s 455s Likelihood ratio test=NA on 3 df, p=NA 455s n= 312, number of events= 144 455s 455s svycxp> s<-predict(model,se=TRUE, type="curve", 455s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 455s 455s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 455s 455s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 455s 455s svycxp> quantile(s[[1]], ci=TRUE) 455s 0.75 0.5 0.25 455s 1435 2503 3574 455s attr(,"ci") 455s 0.025 0.975 455s 0.75 1217 1786 455s 0.5 2256 3170 455s 0.25 3222 Inf 455s 455s svycxp> confint(s[[2]], parm=365*(1:5)) 455s 0.025 0.975 455s 365 0.8375139 0.9453781 455s 730 0.7382750 0.8999016 455s 1095 0.4784105 0.7478460 455s 1460 0.3192009 0.6206764 455s 1825 0.2149475 0.5292978 455s > m<-update(model, .~.+I(protime^2)) 455s > a<-anova(m,model) 455s > b<-anova(m, model,force=TRUE) 455s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 455s > 455s BEGIN TEST api.R 455s 455s R version 4.4.3 (2025-02-28) -- "Trophy Case" 455s Copyright (C) 2025 The R Foundation for Statistical Computing 455s Platform: arm-unknown-linux-gnueabihf (32-bit) 455s 455s R is free software and comes with ABSOLUTELY NO WARRANTY. 455s You are welcome to redistribute it under certain conditions. 455s Type 'license()' or 'licence()' for distribution details. 455s 455s R is a collaborative project with many contributors. 455s Type 'contributors()' for more information and 455s 'citation()' on how to cite R or R packages in publications. 455s 455s Type 'demo()' for some demos, 'help()' for on-line help, or 455s 'help.start()' for an HTML browser interface to help. 455s Type 'q()' to quit R. 455s 455s > library(survey) 455s Loading required package: grid 455s Loading required package: Matrix 456s Loading required package: survival 457s 457s Attaching package: 'survey' 457s 457s The following object is masked from 'package:graphics': 457s 457s dotchart 457s 457s > options(survey.replicates.mse=TRUE) 457s > example(api) 457s 457s api> library(survey) 457s 457s api> data(api) 457s 457s api> mean(apipop$api00) 457s [1] 664.7126 457s 457s api> sum(apipop$enroll, na.rm=TRUE) 457s [1] 3811472 457s 457s api> #stratified sample 457s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 457s 457s api> summary(dstrat) 457s Stratified Independent Sampling design 457s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 457s Stratum Sizes: 457s E H M 457s obs 100 50 50 457s design.PSU 100 50 50 457s actual.PSU 100 50 50 457s Population stratum sizes (PSUs): 457s E H M 457s 4421 755 1018 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "pw" "fpc" 457s 457s api> svymean(~api00, dstrat) 457s mean SE 457s api00 662.29 9.4089 457s 457s api> svytotal(~enroll, dstrat, na.rm=TRUE) 457s total SE 457s enroll 3687178 114642 457s 457s api> # one-stage cluster sample 457s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 457s 457s api> summary(dclus1) 457s 1 - level Cluster Sampling design 457s With (15) clusters. 457s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 457s Population size (PSUs): 757 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> svymean(~api00, dclus1) 457s mean SE 457s api00 644.17 23.542 457s 457s api> svytotal(~enroll, dclus1, na.rm=TRUE) 457s total SE 457s enroll 3404940 932235 457s 457s api> # two-stage cluster sample 457s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 457s 457s api> summary(dclus2) 457s 2 - level Cluster Sampling design 457s With (40, 126) clusters. 457s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 457s Population size (PSUs): 757 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "pw" "fpc1" "fpc2" 457s 457s api> svymean(~api00, dclus2) 457s mean SE 457s api00 670.81 30.099 457s 457s api> svytotal(~enroll, dclus2, na.rm=TRUE) 457s total SE 457s enroll 2639273 799638 457s 457s api> # two-stage `with replacement' 457s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 457s 457s api> summary(dclus2wr) 457s 2 - level Cluster Sampling design (with replacement) 457s With (40, 126) clusters. 457s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "pw" "fpc1" "fpc2" 457s 457s api> svymean(~api00, dclus2wr) 457s mean SE 457s api00 670.81 30.712 457s 457s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 457s total SE 457s enroll 2639273 820261 457s 457s api> # convert to replicate weights 457s api> rclus1<-as.svrepdesign(dclus1) 457s 457s api> summary(rclus1) 457s Call: as.svrepdesign.default(dclus1) 457s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 457s Variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> svymean(~api00, rclus1) 457s mean SE 457s api00 644.17 26.335 457s 457s api> svytotal(~enroll, rclus1, na.rm=TRUE) 457s total SE 457s enroll 3404940 932235 457s 457s api> # post-stratify on school type 457s api> pop.types<-xtabs(~stype, data=apipop) 457s 457s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 457s 457s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 457s 457s api> summary(dclus1p) 457s 1 - level Cluster Sampling design 457s With (15) clusters. 457s dclus1p<-postStratify(dclus1, ~stype, pop.types) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 457s Population size (PSUs): 757 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> summary(rclus1p) 457s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 457s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 457s Variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> svymean(~api00, dclus1p) 457s mean SE 457s api00 642.31 23.92 457s 457s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 457s total SE 457s enroll 3680893 406293 457s 457s api> svymean(~api00, rclus1p) 457s mean SE 457s api00 642.31 26.936 457s 457s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 457s total SE 457s enroll 3680893 473434 457s > 457s > options(survey.replicates.mse=FALSE) 457s > example(api) 457s 457s api> library(survey) 457s 457s api> data(api) 457s 457s api> mean(apipop$api00) 457s [1] 664.7126 457s 457s api> sum(apipop$enroll, na.rm=TRUE) 457s [1] 3811472 457s 457s api> #stratified sample 457s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 457s 457s api> summary(dstrat) 457s Stratified Independent Sampling design 457s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 457s Stratum Sizes: 457s E H M 457s obs 100 50 50 457s design.PSU 100 50 50 457s actual.PSU 100 50 50 457s Population stratum sizes (PSUs): 457s E H M 457s 4421 755 1018 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "pw" "fpc" 457s 457s api> svymean(~api00, dstrat) 457s mean SE 457s api00 662.29 9.4089 457s 457s api> svytotal(~enroll, dstrat, na.rm=TRUE) 457s total SE 457s enroll 3687178 114642 457s 457s api> # one-stage cluster sample 457s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 457s 457s api> summary(dclus1) 457s 1 - level Cluster Sampling design 457s With (15) clusters. 457s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 457s Population size (PSUs): 757 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> svymean(~api00, dclus1) 457s mean SE 457s api00 644.17 23.542 457s 457s api> svytotal(~enroll, dclus1, na.rm=TRUE) 457s total SE 457s enroll 3404940 932235 457s 457s api> # two-stage cluster sample 457s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 457s 457s api> summary(dclus2) 457s 2 - level Cluster Sampling design 457s With (40, 126) clusters. 457s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 457s Population size (PSUs): 757 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "pw" "fpc1" "fpc2" 457s 457s api> svymean(~api00, dclus2) 457s mean SE 457s api00 670.81 30.099 457s 457s api> svytotal(~enroll, dclus2, na.rm=TRUE) 457s total SE 457s enroll 2639273 799638 457s 457s api> # two-stage `with replacement' 457s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 457s 457s api> summary(dclus2wr) 457s 2 - level Cluster Sampling design (with replacement) 457s With (40, 126) clusters. 457s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "pw" "fpc1" "fpc2" 457s 457s api> svymean(~api00, dclus2wr) 457s mean SE 457s api00 670.81 30.712 457s 457s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 457s total SE 457s enroll 2639273 820261 457s 457s api> # convert to replicate weights 457s api> rclus1<-as.svrepdesign(dclus1) 457s 457s api> summary(rclus1) 457s Call: as.svrepdesign.default(dclus1) 457s Unstratified cluster jacknife (JK1) with 15 replicates. 457s Variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> svymean(~api00, rclus1) 457s mean SE 457s api00 644.17 26.329 457s 457s api> svytotal(~enroll, rclus1, na.rm=TRUE) 457s total SE 457s enroll 3404940 932235 457s 457s api> # post-stratify on school type 457s api> pop.types<-xtabs(~stype, data=apipop) 457s 457s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 457s 457s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 457s 457s api> summary(dclus1p) 457s 1 - level Cluster Sampling design 457s With (15) clusters. 457s dclus1p<-postStratify(dclus1, ~stype, pop.types) 457s Probabilities: 457s Min. 1st Qu. Median Mean 3rd Qu. Max. 457s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 457s Population size (PSUs): 757 457s Data variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> summary(rclus1p) 457s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 457s Unstratified cluster jacknife (JK1) with 15 replicates. 457s Variables: 457s [1] "cds" "stype" "name" "sname" "snum" "dname" 457s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 457s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 457s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 457s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 457s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 457s [37] "api.stu" "fpc" "pw" 457s 457s api> svymean(~api00, dclus1p) 457s mean SE 457s api00 642.31 23.92 457s 457s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 457s total SE 457s enroll 3680893 406293 457s 457s api> svymean(~api00, rclus1p) 457s mean SE 457s api00 642.31 26.934 457s 457s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 457s total SE 457s enroll 3680893 473431 457s > 457s BEGIN TEST badcal.R 457s 457s R version 4.4.3 (2025-02-28) -- "Trophy Case" 457s Copyright (C) 2025 The R Foundation for Statistical Computing 457s Platform: arm-unknown-linux-gnueabihf (32-bit) 457s 457s R is free software and comes with ABSOLUTELY NO WARRANTY. 457s You are welcome to redistribute it under certain conditions. 457s Type 'license()' or 'licence()' for distribution details. 457s 457s R is a collaborative project with many contributors. 457s Type 'contributors()' for more information and 457s 'citation()' on how to cite R or R packages in publications. 457s 457s Type 'demo()' for some demos, 'help()' for on-line help, or 457s 'help.start()' for an HTML browser interface to help. 457s Type 'q()' to quit R. 457s 457s > ## 457s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 457s > ## 457s > library(survey) 457s Loading required package: grid 457s Loading required package: Matrix 458s Loading required package: survival 458s 458s Attaching package: 'survey' 458s 458s The following object is masked from 'package:graphics': 458s 458s dotchart 458s 458s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 458s > des <- svydesign(ids=~1, weights=~w, data=data) 458s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 458s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 458s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 458s > 458s BEGIN TEST brewer_cpp.R 458s 458s R version 4.4.3 (2025-02-28) -- "Trophy Case" 458s Copyright (C) 2025 The R Foundation for Statistical Computing 458s Platform: arm-unknown-linux-gnueabihf (32-bit) 458s 458s R is free software and comes with ABSOLUTELY NO WARRANTY. 458s You are welcome to redistribute it under certain conditions. 458s Type 'license()' or 'licence()' for distribution details. 458s 458s R is a collaborative project with many contributors. 458s Type 'contributors()' for more information and 458s 'citation()' on how to cite R or R packages in publications. 458s 458s Type 'demo()' for some demos, 'help()' for on-line help, or 458s 'help.start()' for an HTML browser interface to help. 458s Type 'q()' to quit R. 458s 458s > ## pps="brewer" can't use rcpp 458s > ## this checks that it doesn't 458s > library(survey) 458s Loading required package: grid 459s Loading required package: Matrix 459s Loading required package: survival 460s 460s Attaching package: 'survey' 460s 460s The following object is masked from 'package:graphics': 460s 460s dotchart 460s 460s > data(election) 460s > 460s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 460s > options(survey.use_rcpp=TRUE) 460s > a<-svytotal(~Bush+Kerry+Nader, dpps_br) 460s > options(survey.use_rcpp=FALSE) 460s > b<-svytotal(~Bush+Kerry+Nader, dpps_br) 460s > 460s > stopifnot(identical(a,b)) 460s > 460s BEGIN TEST bycovmat.R 460s 460s R version 4.4.3 (2025-02-28) -- "Trophy Case" 460s Copyright (C) 2025 The R Foundation for Statistical Computing 460s Platform: arm-unknown-linux-gnueabihf (32-bit) 460s 460s R is free software and comes with ABSOLUTELY NO WARRANTY. 460s You are welcome to redistribute it under certain conditions. 460s Type 'license()' or 'licence()' for distribution details. 460s 460s R is a collaborative project with many contributors. 460s Type 'contributors()' for more information and 460s 'citation()' on how to cite R or R packages in publications. 460s 460s Type 'demo()' for some demos, 'help()' for on-line help, or 460s 'help.start()' for an HTML browser interface to help. 460s Type 'q()' to quit R. 460s 460s > 460s > library(survey) 460s Loading required package: grid 460s Loading required package: Matrix 461s Loading required package: survival 461s 461s Attaching package: 'survey' 461s 461s The following object is masked from 'package:graphics': 461s 461s dotchart 461s 461s > data(api) 461s > options(survey.replicates.mse=TRUE) 461s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 461s > rclus1<-as.svrepdesign(dclus1) 461s > 461s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 461s + covmat=TRUE,drop.empty.groups=FALSE) 461s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 461s + covmat=TRUE,drop.empty.groups=TRUE) 461s > 461s > stopifnot(all.equal( 461s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 461s + )) 461s > stopifnot(all.equal( 461s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 461s + )) 461s > 461s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 461s > all <- svytotal(~ell+mobility+meals, dclus1) 461s > 461s > stopifnot(all(abs(vcov(svycontrast(all, 461s + list(quote(ell/mobility), 461s + quote(mobility/mobility), 461s + quote(ell/meals),quote(mobility/meals)))) 461s + -vcov(rat))<1e-10)) 461s > 461s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 461s > 461s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 461s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 461s > 461s > con<-svycontrast(all, 461s + list(quote(ell/mobility), 461s + quote(mobility/mobility), 461s + quote(ell/meals),quote(mobility/meals))) 461s > 461s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 461s > 461s > options(survey.replicates.mse=FALSE) 461s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 461s > rclus1<-as.svrepdesign(dclus1) 461s > 461s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 461s + covmat=TRUE,drop.empty.groups=FALSE) 461s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 461s + covmat=TRUE,drop.empty.groups=TRUE) 461s > 461s > stopifnot(all.equal( 461s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 461s + )) 461s > stopifnot(all.equal( 461s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 461s + )) 461s > 461s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 461s > all <- svytotal(~ell+mobility+meals, dclus1) 461s > 461s > stopifnot(all(abs(vcov(svycontrast(all, 461s + list(quote(ell/mobility), 461s + quote(mobility/mobility), 461s + quote(ell/meals),quote(mobility/meals)))) 461s + -vcov(rat))<1e-10)) 461s > 461s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 461s > 461s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 461s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 461s > 461s > con<-svycontrast(all, 461s + list(quote(ell/mobility), 461s + quote(mobility/mobility), 461s + quote(ell/meals),quote(mobility/meals))) 461s > 461s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 461s > 461s > 461s > 461s BEGIN TEST caleg.R 461s 461s R version 4.4.3 (2025-02-28) -- "Trophy Case" 461s Copyright (C) 2025 The R Foundation for Statistical Computing 461s Platform: arm-unknown-linux-gnueabihf (32-bit) 461s 461s R is free software and comes with ABSOLUTELY NO WARRANTY. 461s You are welcome to redistribute it under certain conditions. 461s Type 'license()' or 'licence()' for distribution details. 461s 461s R is a collaborative project with many contributors. 461s Type 'contributors()' for more information and 461s 'citation()' on how to cite R or R packages in publications. 461s 461s Type 'demo()' for some demos, 'help()' for on-line help, or 461s 'help.start()' for an HTML browser interface to help. 461s Type 'q()' to quit R. 461s 461s Loading required package: grid 461s > ## 461s > ## Calibration examples 461s > ## 461s > 461s > 461s > ## Example of calibration to first-stage clusters 461s > library(survey) 461s Loading required package: Matrix 462s Loading required package: survival 463s 463s Attaching package: 'survey' 463s 463s > data(api) 463s The following object is masked from 'package:graphics': 463s 463s dotchart 463s 463s > 463s > clusters<-table(apiclus2$dnum) 463s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 463s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 463s > 463s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 463s > 463s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 463s > 463s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 463s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 463s > 463s > names(pop)<-names(clusters) 463s > 463s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 463s > 463s > svymean(~api99, dclus2) 463s mean SE 463s api99 642.14 31.434 463s > svymean(~api99, dclus2g) 463s mean SE 463s api99 654.49 29.82 463s > 463s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 463s dnum api99 se 463s 83 83 694.3333 0.0000 463s 132 132 505.0000 0.0000 463s 152 152 574.0000 0.0000 463s 173 173 894.7500 0.0000 463s 198 198 533.7500 0.0000 463s 200 200 589.8000 6.8335 463s 228 228 477.0000 0.0000 463s 295 295 646.4000 0.0000 463s 302 302 903.5000 0.0000 463s 403 403 852.4000 0.0000 463s 452 452 533.0000 0.0000 463s 480 480 614.2000 0.0000 463s 523 523 580.5000 0.0000 463s 534 534 564.6000 0.0000 463s 549 549 896.2000 0.0000 463s 552 552 730.0000 0.0000 463s 570 570 518.4000 7.5478 463s 575 575 800.8000 4.2513 463s 596 596 785.6000 2.4155 463s 620 620 591.6000 10.5869 463s 638 638 560.2000 4.0954 463s 674 674 760.0000 0.0000 463s 679 679 610.2500 0.0000 463s 687 687 718.6667 0.0000 463s 701 701 651.5000 0.0000 463s 711 711 690.5000 0.0000 463s 731 731 702.0000 2.1744 463s 768 768 562.5000 0.0000 463s 781 781 854.4000 0.7456 463s > 463s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 464s dnum api99 se 464s 83 83 694.3333 0 464s 132 132 505.0000 0 464s 152 152 574.0000 0 464s 173 173 894.7500 0 464s 198 198 533.7500 0 464s 200 200 567.5455 0 464s 228 228 477.0000 0 464s 295 295 646.4000 0 464s 302 302 903.5000 0 464s 403 403 852.4000 0 464s 452 452 533.0000 0 464s 480 480 614.2000 0 464s 523 523 580.5000 0 464s 534 534 564.6000 0 464s 549 549 896.2000 0 464s 552 552 730.0000 0 464s 570 570 548.9444 0 464s 575 575 824.5357 0 464s 596 596 787.5714 0 464s 620 620 609.3750 0 464s 638 638 585.6429 0 464s 674 674 760.0000 0 464s 679 679 610.2500 0 464s 687 687 718.6667 0 464s 701 701 651.5000 0 464s 711 711 690.5000 0 464s 731 731 700.6667 0 464s 768 768 562.5000 0 464s 781 781 851.0000 0 464s > 464s > ## Averaging to first stage 464s > 464s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 464s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 464s > 464s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 464s > 464s > svytotal(~enroll,dclus1g) 464s total SE 464s enroll 3811472 0 464s > svytotal(~api.stu,dclus1g) 464s total SE 464s api.stu 3242857 38967 464s > 464s > #variation within clusters should be zero 464s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 464s [1] TRUE 464s > 464s > ##bounded weights 464s > dclus1g<-calibrate(dclus1, ~enroll, pop) 464s > range(weights(dclus1g)/weights(dclus1)) 464s [1] 0.7906782 1.7891164 464s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 464s > range(weights(dclus1gb)/weights(dclus1)) 464s [1] 0.7198751 1.5000000 464s > 464s > ## Ratio estimators 464s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 464s > svytotal(~api.stu,dstrat) 464s total SE 464s api.stu 3086009 99477 464s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 464s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 464s > predict(common, total=total.enroll) 464s $total 464s enroll 464s api.stu 3190038 464s 464s $se 464s enroll 464s api.stu 29565.98 464s 464s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 464s > svytotal(~api.stu, dstratg) 464s total SE 464s api.stu 3190038 29566 464s > 464s > ## postStratify vs calibrate in stratified sample (Ben French) 464s > set.seed(17) 464s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 464s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 464s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 464s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 464s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 464s > postStratify(des,~w,popw)->dps 464s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 464s > 464s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 464s [1] TRUE 464s > 464s > ## missing data in calibrated design 464s > dps$variables$z[1]<-NA 464s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 464s 464s Call: 464s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 464s 464s Survey design: 464s postStratify(des, ~w, popw) 464s 464s Coefficients: 464s Estimate Std. Error t value Pr(>|t|) 464s (Intercept) -0.1203 0.3380 -0.356 0.722 464s z 6.2118 0.6451 9.630 <2e-16 *** 464s x 2.2602 0.2514 8.992 <2e-16 *** 464s --- 464s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 464s 464s (Dispersion parameter for quasibinomial family taken to be 1.919987) 464s 464s Number of Fisher Scoring iterations: 9 464s 464s > 464s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 464s > # should match the ratio estmate above 464s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 464s > svytotal(~api.stu, dstratgh) 464s total SE 464s api.stu 3190038 29566 464s > 464s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 464s > bnds <- list( 464s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 464s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 464s > lapply(bnds, head) 464s $lower 464s [1] 1 1 -Inf -Inf -Inf -Inf 464s 464s $upper 464s [1] 1 1 Inf Inf Inf Inf 464s 464s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 464s > svytotal(~api.stu, dstratg1) 464s total SE 464s api.stu 3190133 29561 464s > head(weights(dstrat)) 464s 1 2 3 4 5 6 464s 44.21 44.21 44.21 44.21 44.21 44.21 464s > head(weights(dstratg1)) 464s 1 2 3 4 5 6 464s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 464s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 464s [1] TRUE 464s > 464s > ## individual boundary constraints as constant values (Daniel Oehm) 464s > bnds <- list( 464s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 464s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 464s > lapply(bnds, head) 464s $lower 464s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 464s 464s $upper 464s [1] 44.21 44.21 Inf Inf Inf Inf 464s 464s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 464s > svytotal(~api.stu, dstratg2) 464s total SE 464s api.stu 3190133 29561 464s > head(weights(dstrat)) 464s 1 2 3 4 5 6 464s 44.21 44.21 44.21 44.21 44.21 44.21 464s > head(weights(dstratg2)) 464s 1 2 3 4 5 6 464s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 464s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 464s [1] TRUE 464s > 464s > # sparse matrix support (Daniel Oehm) 464s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 464s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 464s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 464s > svymean(~api00, dclus1g) 464s mean SE 464s api00 642.31 23.92 464s > svytotal(~enroll, dclus1g) 464s total SE 464s enroll 3680893 406293 464s > 464s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 464s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 464s > svymean(~api00, dclus1g) 464s mean SE 464s api00 642.31 23.92 464s > svytotal(~enroll, dclus1g) 464s total SE 464s enroll 3680893 406293 464s > 464s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 464s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 464s > svymean(~api00, dclus1g) 464s mean SE 464s api00 642.31 23.92 464s > svytotal(~enroll, dclus1g) 464s total SE 464s enroll 3680893 406293 464s > 464s BEGIN TEST check.R 464s 464s R version 4.4.3 (2025-02-28) -- "Trophy Case" 464s Copyright (C) 2025 The R Foundation for Statistical Computing 464s Platform: arm-unknown-linux-gnueabihf (32-bit) 464s 464s R is free software and comes with ABSOLUTELY NO WARRANTY. 464s You are welcome to redistribute it under certain conditions. 464s Type 'license()' or 'licence()' for distribution details. 464s 464s R is a collaborative project with many contributors. 464s Type 'contributors()' for more information and 464s 'citation()' on how to cite R or R packages in publications. 464s 464s Type 'demo()' for some demos, 'help()' for on-line help, or 464s 'help.start()' for an HTML browser interface to help. 464s Type 'q()' to quit R. 464s 464s > library(survey) 464s Loading required package: grid 464s Loading required package: Matrix 466s Loading required package: survival 466s > data(fpc) 466s 466s Attaching package: 'survey' 466s 466s The following object is masked from 'package:graphics': 466s 466s dotchart 466s 466s Warning message: 466s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 466s No weights or probabilities supplied, assuming equal probability 466s Warning message: 466s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 466s No weights or probabilities supplied, assuming equal probability 466s Warning message: 466s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 466s No weights or probabilities supplied, assuming equal probability 466s Warning message: 466s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 466s No weights or probabilities supplied, assuming equal probability 466s Loading required package: grid 466s > ## test various possibilities for svydesign 466s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 466s variables = ~x, data = fpc, nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7413 466s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 466s data = fpc, nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7413 466s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 466s data = fpc, nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 44.2 6.237 466s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 466s nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.525 0.7796 466s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 466s data = fpc, nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7413 466s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 466s nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.525 0.7796 466s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 466s > a 466s 1 - level Cluster Sampling design (with replacement) 466s With (5) clusters. 466s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.525 0.838 466s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 466s > a 466s 1 - level Cluster Sampling design (with replacement) 466s With (5) clusters. 466s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 466s nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7938 466s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 466s > a 466s 2 - level Cluster Sampling design (with replacement) 466s With (2, 8) clusters. 466s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 466s data = fpc) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.5465 466s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 466s > a 466s 2 - level Cluster Sampling design (with replacement) 466s With (2, 8) clusters. 466s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 466s > svymean(~x,a) 466s mean SE 466s x 5.525 0.5188 466s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 466s variables = fpc[, "x", drop = FALSE], nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7413 466s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 466s > a 466s Stratified Independent Sampling design (with replacement) 466s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 466s variables = fpc[, 4:6], nest = TRUE) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7413 466s > 466s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 466s > a 466s 1 - level Cluster Sampling design 466s With (5) clusters. 466s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 466s 4:6], fpc = rep(27, 8)) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.7165 466s > 466s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 466s > a 466s Stratified Independent Sampling design 466s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 466s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 466s > svymean(~x,a) 466s mean SE 466s x 5.4481 0.616 466s > 466s BEGIN TEST confintrep.R 466s 466s R version 4.4.3 (2025-02-28) -- "Trophy Case" 466s Copyright (C) 2025 The R Foundation for Statistical Computing 466s Platform: arm-unknown-linux-gnueabihf (32-bit) 466s 466s R is free software and comes with ABSOLUTELY NO WARRANTY. 466s You are welcome to redistribute it under certain conditions. 466s Type 'license()' or 'licence()' for distribution details. 466s 466s R is a collaborative project with many contributors. 466s Type 'contributors()' for more information and 466s 'citation()' on how to cite R or R packages in publications. 466s 466s Type 'demo()' for some demos, 'help()' for on-line help, or 466s 'help.start()' for an HTML browser interface to help. 466s Type 'q()' to quit R. 466s 466s > library(survey) 466s Loading required package: Matrix 467s Loading required package: survival 467s 467s Attaching package: 'survey' 467s 467s The following object is masked from 'package:graphics': 467s 467s dotchart 467s 467s > data(api) 467s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 467s > rclus2<-as.svrepdesign(dclus2) 467s Warning message: 467s In as.svrepdesign.default(dclus2) : 467s Finite population corrections after first stage have been dropped 467s > 467s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial) 467s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint") 467s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial) 467s > if(anyNA(confint(mrep))) stop("NA in confint") 467s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint") 467s > 467s BEGIN TEST contrast-replicates.R 467s 467s R version 4.4.3 (2025-02-28) -- "Trophy Case" 467s Copyright (C) 2025 The R Foundation for Statistical Computing 467s Platform: arm-unknown-linux-gnueabihf (32-bit) 467s 467s R is free software and comes with ABSOLUTELY NO WARRANTY. 467s You are welcome to redistribute it under certain conditions. 467s Type 'license()' or 'licence()' for distribution details. 467s 467s R is a collaborative project with many contributors. 467s Type 'contributors()' for more information and 467s 'citation()' on how to cite R or R packages in publications. 467s 467s Type 'demo()' for some demos, 'help()' for on-line help, or 467s 'help.start()' for an HTML browser interface to help. 467s Type 'q()' to quit R. 467s 467s > ## test use of replicates in svyby, svycontrast 467s > library(survey) 467s Loading required package: grid 467s Loading required package: Matrix 468s Loading required package: survival 468s 468s Attaching package: 'survey' 468s 468s The following object is masked from 'package:graphics': 468s 468s dotchart 468s 468s > 468s > data(api) 468s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 468s > rclus1<-as.svrepdesign(dclus1) 468s > 468s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 468s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 468s > vcov(c_without) 468s contrast 468s contrast 0.06862947 468s > 468s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 468s > 468s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 468s > 468s > v_with<- vcov(rclus1, c_with$replicates) 468s > 468s > r<- attr(meanlogs_with, "replicates") 468s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 468s > 468s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 468s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 468s > 468s BEGIN TEST coxph-termtest.R 469s 469s R version 4.4.3 (2025-02-28) -- "Trophy Case" 469s Copyright (C) 2025 The R Foundation for Statistical Computing 469s Platform: arm-unknown-linux-gnueabihf (32-bit) 469s 469s R is free software and comes with ABSOLUTELY NO WARRANTY. 469s You are welcome to redistribute it under certain conditions. 469s Type 'license()' or 'licence()' for distribution details. 469s 469s R is a collaborative project with many contributors. 469s Type 'contributors()' for more information and 469s 'citation()' on how to cite R or R packages in publications. 469s 469s Type 'demo()' for some demos, 'help()' for on-line help, or 469s 'help.start()' for an HTML browser interface to help. 469s Type 'q()' to quit R. 469s 469s > library(survey) 469s Loading required package: grid 469s Loading required package: Matrix 470s Loading required package: survival 470s 470s Attaching package: 'survey' 470s 470s The following object is masked from 'package:graphics': 470s 470s dotchart 470s 470s > library(survival) 470s > set.seed(2021-6-25) 470s > test1 <- list(time=c(4,3,1,1,2,2,3), 470s + status=c(1,1,1,0,1,1,0), 470s + x1=as.factor(rbinom(7, 2, 0.5)), 470s + x=c(0,2,1,1,1,0,0)) 470s > # Fit a stratified model 470s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 470s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 470s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 470s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 470s > 470s > data(pbc, package="survival") 470s > 470s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 470s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 470s > pbc$randprob<-fitted(biasmodel) 470s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 470s > 470s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 470s > library(splines) 470s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 470s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 470s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 470s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 470s > 470s BEGIN TEST deff.R 470s 470s R version 4.4.3 (2025-02-28) -- "Trophy Case" 470s Copyright (C) 2025 The R Foundation for Statistical Computing 470s Platform: arm-unknown-linux-gnueabihf (32-bit) 470s 470s R is free software and comes with ABSOLUTELY NO WARRANTY. 470s You are welcome to redistribute it under certain conditions. 470s Type 'license()' or 'licence()' for distribution details. 470s 470s R is a collaborative project with many contributors. 470s Type 'contributors()' for more information and 470s 'citation()' on how to cite R or R packages in publications. 470s 470s Type 'demo()' for some demos, 'help()' for on-line help, or 470s 'help.start()' for an HTML browser interface to help. 470s Type 'q()' to quit R. 470s 470s Loading required package: grid 470s > ## from Takahiro Tsuchiya 470s > library(survey) 470s Loading required package: Matrix 471s Loading required package: survival 471s 471s Attaching package: 'survey' 471s 471s > kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 471s + 1 1 15 100 20 471s + 2 2 143 100 200 471s + 3 3 21 100 11 471s + 4 4 51 100 25 471s + 5 5 337 100 550 471s + 6 6 50 100 30 471s + 7 7 274 100 250 471s + 8 8 145 100 100 471s + 9 9 15 100 10 471s + 10 10 86 100 55 471s + ",open="r"),header=TRUE) 471s > close(tmp) 471s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 471s The following object is masked from 'package:graphics': 471s 471s dotchart 471s 471s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 471s mean SE DEff 471s uriage 113.700 35.626 1.0101 471s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 471s uriage 471s uriage 1.010101 471s > 471s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 471s total SE DEff 471s uriage 113700 35626 1.0101 471s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 471s uriage 471s uriage 1.010101 471s > 471s > 471s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 471s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 471s mean SE DEff 471s uriage 243.914 48.752 1.9741 471s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 472s uriage 472s uriage 1.974067 472s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 472s total SE DEff 472s uriage 305136 184965 18.157 472s > (N.hat <- sum(weights(des.pps))) 472s [1] 1251 472s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 472s uriage 472s uriage 18.15669 472s > 472s BEGIN TEST defftest.R 472s 472s R version 4.4.3 (2025-02-28) -- "Trophy Case" 472s Copyright (C) 2025 The R Foundation for Statistical Computing 472s Platform: arm-unknown-linux-gnueabihf (32-bit) 472s 472s R is free software and comes with ABSOLUTELY NO WARRANTY. 472s You are welcome to redistribute it under certain conditions. 472s Type 'license()' or 'licence()' for distribution details. 472s 472s R is a collaborative project with many contributors. 472s Type 'contributors()' for more information and 472s 'citation()' on how to cite R or R packages in publications. 472s 472s Type 'demo()' for some demos, 'help()' for on-line help, or 472s 'help.start()' for an HTML browser interface to help. 472s Type 'q()' to quit R. 472s 472s > library(survey) 472s Loading required package: grid 472s Loading required package: Matrix 473s Loading required package: survival 473s 473s Attaching package: 'survey' 473s 473s The following object is masked from 'package:graphics': 473s 473s dotchart 473s 473s > 473s > data(api) 473s > 473s > ## one-stage cluster sample 473s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 473s > 473s > # svyglm model 473s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 473s > 473s > #deffs returned from svyglm model - implausibly high 473s > deff(mod) 473s (Intercept) enroll api.stu 473s 1.919945 2.500983 2.686102 473s > #> (Intercept) enroll api.stu 473s > #> 351.3500 457.6799 491.5567 473s > 473s > # run mod with same data and glm() 473s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 473s > 473s > # manually calculate deffs 473s > 473s > clust_se <- summary(mod)$coefficients[,2] 473s > srs_se <- summary(srs_mod)$coefficients[,2] 473s > 473s > deffs <- clust_se^2 / srs_se^2 473s > stopifnot(all.equal(deffs, deff(mod))) 473s > 473s > 473s BEGIN TEST degf-svrepdesign.R 473s 473s R version 4.4.3 (2025-02-28) -- "Trophy Case" 473s Copyright (C) 2025 The R Foundation for Statistical Computing 473s Platform: arm-unknown-linux-gnueabihf (32-bit) 473s 473s R is free software and comes with ABSOLUTELY NO WARRANTY. 473s You are welcome to redistribute it under certain conditions. 473s Type 'license()' or 'licence()' for distribution details. 473s 473s R is a collaborative project with many contributors. 473s Type 'contributors()' for more information and 473s 'citation()' on how to cite R or R packages in publications. 473s 473s Type 'demo()' for some demos, 'help()' for on-line help, or 473s 'help.start()' for an HTML browser interface to help. 473s Type 'q()' to quit R. 473s 473s > library(survey) 473s Loading required package: grid 473s Loading required package: Matrix 474s Loading required package: survival 475s 475s Attaching package: 'survey' 475s 475s The following object is masked from 'package:graphics': 475s 475s dotchart 475s 475s > data(scd) 475s > 475s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1), 475s + c(0,1,0,1,1,0)) 475s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights) 475s Warning message: 475s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) : 475s No sampling weights provided: equal probability assumed 475s > 475s > stopifnot(degf(scdrep)==3) 475s > 475s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4) 475s Warning message: 475s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 475s No sampling weights provided: equal probability assumed 475s Warning message: 475s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 475s No sampling weights provided: equal probability assumed 475s > stopifnot(degf(scdrep)==4) 475s > 475s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2) 475s > stopifnot(degf(scdrep)==2) 475s > 475s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 475s + warning=function(w) w) 475s > 475s > stopifnot(inherits(msg,"warning")) 475s > 475s > 475s > 475s > 475s BEGIN TEST domain.R 475s 475s R version 4.4.3 (2025-02-28) -- "Trophy Case" 475s Copyright (C) 2025 The R Foundation for Statistical Computing 475s Platform: arm-unknown-linux-gnueabihf (32-bit) 475s 475s R is free software and comes with ABSOLUTELY NO WARRANTY. 475s You are welcome to redistribute it under certain conditions. 475s Type 'license()' or 'licence()' for distribution details. 475s 475s R is a collaborative project with many contributors. 475s Type 'contributors()' for more information and 475s 'citation()' on how to cite R or R packages in publications. 475s 475s Type 'demo()' for some demos, 'help()' for on-line help, or 475s 'help.start()' for an HTML browser interface to help. 475s Type 'q()' to quit R. 475s 475s > ## 475s > ## Domain means can be written as ratio estimators or as regression coefficients 475s > ## 475s > ## This code checks that subsetting the design object gives the same results as 475s > ## these approaches. 475s > ## 475s > 475s > 475s > library(survey) 475s Loading required package: grid 475s Loading required package: Matrix 476s Loading required package: survival 476s 476s Attaching package: 'survey' 476s 476s > data(fpc) 476s The following object is masked from 'package:graphics': 476s 476s dotchart 476s 476s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 476s > dsub<-subset(dfpc,x>4) 476s > (m1<-svymean(~x,design=dsub)) 476s mean SE 476s x 6.195 0.7555 476s > 476s > ## These should give the same domain estimates and standard errors 476s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 476s I(x > 4) x se 476s FALSE FALSE 3.314286 0.3117042 476s TRUE TRUE 6.195000 0.7555129 476s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 476s > summary(m3) 476s 476s Call: 476s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 476s 476s Survey design: 476s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 476s nest = TRUE) 476s 476s Coefficients: 476s Estimate Std. Error t value Pr(>|t|) 476s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 476s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 476s --- 476s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 476s 476s (Dispersion parameter for gaussian family taken to be 2.557379) 476s 476s Number of Fisher Scoring iterations: 2 476s 476s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 476s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 476s dfpc) 476s Ratios= 476s as.numeric(x > 4) 476s I(x * (x > 4)) 6.195 476s SEs= 476s as.numeric(x > 4) 476s I(x * (x > 4)) 0.7555129 476s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 476s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 476s > 476s > ## with strata 476s > data(api) 476s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 476s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 476s > m2<-svyglm(enroll~comp.imp-1, dstrat) 476s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 476s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 476s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 476s > 476s > ## with calibration 476s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 476s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 476s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 476s 1 - level Cluster Sampling design 476s With (15) clusters. 476s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 476s > 476s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 476s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 476s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 476s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 476s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 476s > 476s > ## with raking 476s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 476s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 476s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 476s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 476s > m2<-svyglm(api00~comp.imp-1, dclus1r) 476s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 476s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 476s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 476s > 476s > 476s > 476s > ## 476s > ## based on bug report from Takahiro Tsuchiya for version 3.4 476s > ## 476s > rei<-read.table(tmp<-textConnection( 476s + " id N n.a h n.ah n.h sub y 476s + 1 1 300 20 1 12 5 TRUE 1 476s + 2 2 300 20 1 12 5 TRUE 2 476s + 3 3 300 20 1 12 5 TRUE 3 476s + 4 4 300 20 1 12 5 TRUE 4 476s + 5 5 300 20 1 12 5 TRUE 5 476s + 6 6 300 20 1 12 5 FALSE NA 476s + 7 7 300 20 1 12 5 FALSE NA 476s + 8 8 300 20 1 12 5 FALSE NA 476s + 9 9 300 20 1 12 5 FALSE NA 476s + 10 10 300 20 1 12 5 FALSE NA 476s + 11 11 300 20 1 12 5 FALSE NA 476s + 12 12 300 20 1 12 5 FALSE NA 476s + 13 13 300 20 2 8 3 TRUE 6 476s + 14 14 300 20 2 8 3 TRUE 7 476s + 15 15 300 20 2 8 3 TRUE 8 476s + 16 16 300 20 2 8 3 FALSE NA 476s + 17 17 300 20 2 8 3 FALSE NA 476s + 18 18 300 20 2 8 3 FALSE NA 476s + 19 19 300 20 2 8 3 FALSE NA 476s + 20 20 300 20 2 8 3 FALSE NA 476s + "), header=TRUE) 476s > close(tmp) 476s > 476s > 476s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 476s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 476s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 476s > 476s > rei$y<-rei$y*(rei$y>3) 476s > ## based on Sarndal et al (9.4.14) 476s > rei$w.ah <- rei$n.ah / rei$n.a 476s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 476s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 476s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 476s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 476s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 476s > 476s > a.rei$f.h<-with(a.rei, n.h/n.ah) 476s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 476s > 476s > a.rei$f<-with(a.rei, n.a/N) 476s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 476s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 476s > 476s > V 476s [1] 70761.47 476s > Vphase1 476s [1] 44325.47 476s > Vphase2 476s [1] 26436 476s > vcov(tot2) 476s [,1] 476s [1,] 70761.47 476s attr(,"phases") 476s attr(,"phases")$phase1 476s [,1] 476s [1,] 44325.47 476s 476s attr(,"phases")$phase2 476s [,1] 476s [1,] 26436 476s 476s > 476s > ## comparing to regression 476s > reg<-svyglm(y~I(y<4), design=des.rei2) 476s > mn<-svymean(~y, subset(des.rei2,y>3)) 476s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 476s [1] TRUE 476s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 476s [1] TRUE 476s > vcov(mn) 476s [,1] 476s [1,] 0.3292258 476s attr(,"phases") 476s attr(,"phases")$phase1 476s [,1] 476s [1,] 0.1599264 476s 476s attr(,"phases")$phase2 476s [,1] 476s [1,] 0.1692994 476s 476s > vcov(reg) 476s (Intercept) I(y < 4)TRUE 476s (Intercept) 0.3292258 -0.3292258 476s I(y < 4)TRUE -0.3292258 0.5901907 476s attr(,"phases") 476s attr(,"phases")$phase1 476s (Intercept) I(y < 4)TRUE 476s (Intercept) 0.1599264 -0.1599264 476s I(y < 4)TRUE -0.1599264 0.2588542 476s 476s attr(,"phases")$phase2 476s (Intercept) I(y < 4)TRUE 476s (Intercept) 0.1692994 -0.1692994 476s I(y < 4)TRUE -0.1692994 0.3313365 476s 476s > 476s > 476s BEGIN TEST fpc.R 476s 476s R version 4.4.3 (2025-02-28) -- "Trophy Case" 476s Copyright (C) 2025 The R Foundation for Statistical Computing 476s Platform: arm-unknown-linux-gnueabihf (32-bit) 476s 476s R is free software and comes with ABSOLUTELY NO WARRANTY. 476s You are welcome to redistribute it under certain conditions. 476s Type 'license()' or 'licence()' for distribution details. 476s 476s R is a collaborative project with many contributors. 476s Type 'contributors()' for more information and 476s 'citation()' on how to cite R or R packages in publications. 476s 476s Type 'demo()' for some demos, 'help()' for on-line help, or 476s 'help.start()' for an HTML browser interface to help. 476s Type 'q()' to quit R. 476s 476s > library(survey) 476s Loading required package: grid 476s Loading required package: Matrix 477s Loading required package: survival 478s 478s Attaching package: 'survey' 478s 478s The following object is masked from 'package:graphics': 478s 478s dotchart 478s 478s > ## check many permutations of fpc specification 478s > example(fpc) 478s 478s fpc> data(fpc) 478s 478s fpc> fpc 478s stratid psuid weight nh Nh x 478s 1 1 1 3 5 15 2.8 478s 2 1 2 3 5 15 4.1 478s 3 1 3 3 5 15 6.8 478s 4 1 4 3 5 15 6.8 478s 5 1 5 3 5 15 9.2 478s 6 2 1 4 3 12 3.7 478s 7 2 2 4 3 12 6.6 478s 8 2 3 4 3 12 4.2 478s 478s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 478s fpc+ data=fpc, nest=TRUE) 478s 478s fpc> withoutfpc 478s Stratified Independent Sampling design (with replacement) 478s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 478s data=fpc, nest=TRUE) 478s 478s fpc> svymean(~x, withoutfpc) 478s mean SE 478s x 5.4481 0.7413 478s 478s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 478s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 478s 478s fpc> withfpc 478s Stratified Independent Sampling design 478s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 478s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 478s 478s fpc> svymean(~x, withfpc) 478s mean SE 478s x 5.4481 0.616 478s 478s fpc> ## Other equivalent forms 478s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 478s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 478s 478s fpc> svymean(~x, withfpc) 478s mean SE 478s x 5.4481 0.616 478s 478s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 478s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 478s 478s fpc> svymean(~x, withfpc) 478s mean SE 478s x 5.4481 0.616 478s 478s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 478s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 478s 478s fpc> svymean(~x, withfpc) 478s mean SE 478s x 5.4481 0.616 478s 478s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 478s fpc+ variables=~x,data=fpc,nest=TRUE) 478s 478s fpc> svymean(~x, withfpc) 478s mean SE 478s x 5.4481 0.616 478s 478s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 478s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 478s 478s fpc> svymean(~x, withfpc) 478s mean SE 478s x 5.4481 0.616 478s > 478s > 478s BEGIN TEST glm-scoping.R 478s 478s R version 4.4.3 (2025-02-28) -- "Trophy Case" 478s Copyright (C) 2025 The R Foundation for Statistical Computing 478s Platform: arm-unknown-linux-gnueabihf (32-bit) 478s 478s R is free software and comes with ABSOLUTELY NO WARRANTY. 478s You are welcome to redistribute it under certain conditions. 478s Type 'license()' or 'licence()' for distribution details. 478s 478s R is a collaborative project with many contributors. 478s Type 'contributors()' for more information and 478s 'citation()' on how to cite R or R packages in publications. 478s 478s Type 'demo()' for some demos, 'help()' for on-line help, or 478s 'help.start()' for an HTML browser interface to help. 478s Type 'q()' to quit R. 478s 478s > ## bug report from Thomas Leeper, fixed in version 3.32-3 478s > 478s > library("survey") 478s Loading required package: grid 478s Loading required package: Matrix 479s Loading required package: survival 479s 479s Attaching package: 'survey' 479s 479s > data(api) 479s The following object is masked from 'package:graphics': 479s 479s dotchart 479s 479s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 479s > 479s > # pass `family` directly (WORKS!) 479s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 479s Stratified Independent Sampling design 479s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 479s fpc = ~fpc) 479s 479s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 479s family = gaussian()) 479s 479s Coefficients: 479s (Intercept) ell meals mobility 479s 820.8873 -0.4806 -3.1415 0.2257 479s 479s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 479s Null Deviance: 3023000 479s Residual Deviance: 1029000 AIC: 2308 479s > 479s > # passing `family` via ... (WORKS!) 479s > myfun1 <- function(formula, design, ...) { 479s + svyglm(formula, design = design, ...) 479s + } 479s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 479s Stratified Independent Sampling design 479s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 479s fpc = ~fpc) 479s 479s Call: svyglm(formula = formula, design = design, family = ..1) 479s 479s Coefficients: 479s (Intercept) ell meals mobility 479s 820.8873 -0.4806 -3.1415 0.2257 479s 479s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 479s Null Deviance: 3023000 479s Residual Deviance: 1029000 AIC: 2308 479s > 479s > # passing `family` via default argument (DOES NOT WORK!) 479s > myfun2 <- function(formula, design, family = gaussian()) { 479s + svyglm(formula, design = design, family = family) 479s + } 479s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 479s Stratified Independent Sampling design 479s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 479s fpc = ~fpc) 479s 479s Call: svyglm(formula = formula, design = design, family = family) 479s 479s Coefficients: 479s (Intercept) ell meals mobility 479s 820.8873 -0.4806 -3.1415 0.2257 479s 479s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 479s Null Deviance: 3023000 479s Residual Deviance: 1029000 AIC: 2308 479s > 479s BEGIN TEST kalton.R 479s 479s R version 4.4.3 (2025-02-28) -- "Trophy Case" 479s Copyright (C) 2025 The R Foundation for Statistical Computing 479s Platform: arm-unknown-linux-gnueabihf (32-bit) 479s 479s R is free software and comes with ABSOLUTELY NO WARRANTY. 479s You are welcome to redistribute it under certain conditions. 479s Type 'license()' or 'licence()' for distribution details. 479s 479s R is a collaborative project with many contributors. 479s Type 'contributors()' for more information and 479s 'citation()' on how to cite R or R packages in publications. 479s 479s Type 'demo()' for some demos, 'help()' for on-line help, or 479s 'help.start()' for an HTML browser interface to help. 479s Type 'q()' to quit R. 479s 479s > library(survey) 479s Loading required package: grid 480s Loading required package: Matrix 481s Loading required package: survival 481s 481s Attaching package: 'survey' 481s 481s The following object is masked from 'package:graphics': 481s 481s dotchart 481s 481s > 481s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 481s > 481s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 481s > 481s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 481s > 481s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 481s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 481s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 481s > 481s > dkalton<-svydesign(id=~1,data=kaltonsample) 481s > 481s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 481s Warning message: 481s In svydesign.default(id = ~1, data = kaltonsample) : 481s No weights or probabilities supplied, assuming equal probability 481s > 481s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 481s > 481s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 481s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 481s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 481s > 481s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 481s > 481s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 481s > 481s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 481s > 481s > 481s > #table A 481s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 4.00 1.00 1.38 481s 2 1.20 1.07 1.10 481s 3 1.70 1.20 4.00 481s 4 1.83 1.65 1.79 481s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 4.00 1.00 1.37 481s 2 1.20 1.07 1.10 481s 3 1.70 1.20 4.00 481s 4 1.83 1.65 1.79 481s > 481s > #table B 481s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 1.81 1.45 2.02 481s 2 1.08 0.87 1.21 481s 3 2.20 1.76 2.45 481s 4 1.83 1.47 2.04 481s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 1.81 1.45 2.02 481s 2 1.08 0.87 1.21 481s 3 2.20 1.76 2.45 481s 4 1.83 1.47 2.04 481s > 481s > #table C 481s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 1.82 1.50 1.97 481s 2 1.09 0.78 1.24 481s 3 2.19 1.88 2.34 481s 4 1.83 1.52 1.98 481s > 481s > #table D 481s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 1.21 1.17 1.14 481s 2 1.43 1.40 1.36 481s 3 1.66 1.62 1.59 481s 4 1.88 1.85 1.81 481s > 481s > #table G 481s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 1.87 1.46 1.98 481s 2 1.08 0.74 1.27 481s 3 2.17 2.09 2.18 481s 4 1.89 1.49 1.99 481s > 481s > #table G 481s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 481s b 481s a 1 2 3 481s 1 1.81 1.48 1.99 481s 2 1.08 0.75 1.26 481s 3 2.20 2.00 2.20 481s 4 1.83 1.50 2.00 481s > 481s BEGIN TEST logranktest.R 481s 481s R version 4.4.3 (2025-02-28) -- "Trophy Case" 481s Copyright (C) 2025 The R Foundation for Statistical Computing 481s Platform: arm-unknown-linux-gnueabihf (32-bit) 481s 481s R is free software and comes with ABSOLUTELY NO WARRANTY. 481s You are welcome to redistribute it under certain conditions. 481s Type 'license()' or 'licence()' for distribution details. 481s 481s R is a collaborative project with many contributors. 481s Type 'contributors()' for more information and 481s 'citation()' on how to cite R or R packages in publications. 481s 481s Type 'demo()' for some demos, 'help()' for on-line help, or 481s 'help.start()' for an HTML browser interface to help. 481s Type 'q()' to quit R. 481s 481s > ## StackOverflow 63333282 481s > 481s > library(survey) 481s Loading required package: grid 481s Loading required package: Matrix 482s Loading required package: survival 482s > D = data.frame(unique_id = 1:135, 482s + 482s + weights = rep(1,135), 482s + 482s + event_time = c(0.53512437, 1.35655869, 2.00414189, 2.37276648, 3.20343526, 0.96618494, 2.57894309, 0.94575080, 1.25347833, 1.44416450, 5.04038200, 7.80587169 , 482s + 482s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 482s + 482s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 482s + 482s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 482s + 482s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 482s + 482s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 482s + 482s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 482s + 482s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 482s + 482s 482s Attaching package: 'survey' 482s 482s The following object is masked from 'package:graphics': 482s 482s dotchart 482s 482s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 482s + 482s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 482s + 482s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 482s + 482s + 2.35699896, 2.94956000, 8.85381736), 482s + 482s + event_flag = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 482s + 482s + 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 482s + 482s + 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0), 482s + 482s + group = c(rep("group1", 40), rep("group2", 95))) 482s > 482s > 482s > 482s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 482s > 482s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 482s > 482s > a<-svylogrank(formula = svykm_formula, design = svy_design) 482s > 482s > ii<-with(D, order(event_time, event_flag)) 482s > 482s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 482s > 482s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 482s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 482s > 482s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 482s > 482s > 482s > stopifnot(all.equal(a[[2]],b[[2]])) 482s > 482s > stopifnot(all.equal(a[[2]],d[[2]])) 482s > 482s > stopifnot(all.equal(a[[2]],f[-1])) 482s > 482s > 482s BEGIN TEST lonely.psu.R 483s 483s R version 4.4.3 (2025-02-28) -- "Trophy Case" 483s Copyright (C) 2025 The R Foundation for Statistical Computing 483s Platform: arm-unknown-linux-gnueabihf (32-bit) 483s 483s R is free software and comes with ABSOLUTELY NO WARRANTY. 483s You are welcome to redistribute it under certain conditions. 483s Type 'license()' or 'licence()' for distribution details. 483s 483s R is a collaborative project with many contributors. 483s Type 'contributors()' for more information and 483s 'citation()' on how to cite R or R packages in publications. 483s 483s Type 'demo()' for some demos, 'help()' for on-line help, or 483s 'help.start()' for an HTML browser interface to help. 483s Type 'q()' to quit R. 483s 483s > 483s > ## lonely PSUs by design 483s > library(survey) 483s Loading required package: grid 483s Loading required package: Matrix 484s Loading required package: survival 484s 484s Attaching package: 'survey' 484s 484s The following object is masked from 'package:graphics': 484s 484s dotchart 484s 484s > data(api) 484s > ## not certainty PSUs by fpc 484s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 484s > summary(ds) 484s Stratified Independent Sampling design (with replacement) 484s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 484s Probabilities: 484s Min. 1st Qu. Median Mean 3rd Qu. Max. 484s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 484s Stratum Sizes: 484s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 484s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 484s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 484s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 484s Data variables: 484s [1] "cds" "stype" "name" "sname" "snum" "dname" 484s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 484s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 484s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 484s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 484s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 484s [37] "api.stu" "fpc" "pw" 484s > 484s > options(survey.lonely.psu="fail") 484s > try(svymean(~api00,ds)) 484s > try(svymean(~api00, as.svrepdesign(ds))) 484s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 484s Stratum (413) has only one PSU at stage 1 484s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 484s Stratum413has only one PSU 484s > options(survey.lonely.psu="remove") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.8058 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.8058 484s > options(survey.lonely.psu="certainty") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.8058 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.8058 484s > options(survey.lonely.psu="adjust") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.8281 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.8267 484s > options(survey.lonely.psu="average") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 6.0096 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.8217 484s > 484s > ## fpc specified 484s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 484s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 484s > summary(ds) 484s Stratified Independent Sampling design 484s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 484s fpc = fpc) 484s Probabilities: 484s Min. 1st Qu. Median Mean 3rd Qu. Max. 484s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 484s Stratum Sizes: 484s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 484s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 484s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 484s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 484s Population stratum sizes (PSUs): 484s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 484s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 484s Data variables: 484s [1] "cds" "stype" "name" "sname" "snum" "dname" 484s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 484s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 484s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 484s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 484s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 484s [37] "api.stu" "fpc" "pw" 484s > 484s > options(survey.lonely.psu="fail") 484s > try(svymean(~api00,ds)) 484s mean SE 484s api00 644.17 5.7344 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.7344 484s > options(survey.lonely.psu="remove") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.7344 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.7344 484s > options(survey.lonely.psu="certainty") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.7344 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.7344 484s > options(survey.lonely.psu="adjust") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.7344 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.7344 484s > options(survey.lonely.psu="average") 484s > svymean(~api00,ds) 484s mean SE 484s api00 644.17 5.7344 484s > svymean(~api00, as.svrepdesign(ds)) 484s mean SE 484s api00 644.17 5.7501 484s > 484s > rs<-as.svrepdesign(ds) 484s > svytotal(~api00,rs) 484s total SE 484s api00 3989986 35616 484s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 484s [1] TRUE 484s > 484s > ## lonely PSUs after subsetting 484s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 484s > ds1<-ds[-31,] 484s > summary(ds1) 484s Stratified Independent Sampling design (with replacement) 484s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 484s dnum != 413)) 484s Probabilities: 484s Min. 1st Qu. Median Mean 3rd Qu. Max. 484s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 484s Stratum Sizes: 484s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 484s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 484s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 484s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 484s Data variables: 484s [1] "cds" "stype" "name" "sname" "snum" "dname" 484s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 484s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 484s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 484s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 484s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 484s [37] "api.stu" "fpc" "pw" 484s > 484s > options(survey.lonely.psu="fail") 484s > svymean(~api00,ds1) 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="remove") 484s > svymean(~api00,ds1) 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="certainty") 484s > svymean(~api00,ds1) 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="adjust") 484s > svymean(~api00,ds1) 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="average") 484s > svymean(~api00,ds1) 484s mean SE 484s api00 645.14 5.8909 484s > 484s > ## with adjustment 484s > options(survey.adjust.domain.lonely=TRUE) 484s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 484s > ds1<-ds[-31,] 484s > summary(ds1) 484s Stratified Independent Sampling design (with replacement) 484s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 484s dnum != 413)) 484s Probabilities: 484s Min. 1st Qu. Median Mean 3rd Qu. Max. 484s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 484s Stratum Sizes: 484s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 484s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 484s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 484s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 484s Data variables: 484s [1] "cds" "stype" "name" "sname" "snum" "dname" 484s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 484s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 484s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 484s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 484s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 484s [37] "api.stu" "fpc" "pw" 484s > 484s > options(survey.lonely.psu="fail") 484s > try(svymean(~api00,ds1)) 484s Warning message: 484s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 484s Stratum (406) has only one PSU at stage 1 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="remove") 484s > svymean(~api00,ds1) 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="certainty") 484s > svymean(~api00,ds1) 484s Warning message: 484s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 484s Stratum (406) has only one PSU at stage 1 484s mean SE 484s api00 645.14 5.8909 484s > options(survey.lonely.psu="adjust") 484s > svymean(~api00,ds1) 484s Warning message: 484s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 484s Stratum (406) has only one PSU at stage 1 484s mean SE 484s api00 645.14 5.9119 484s > options(survey.lonely.psu="average") 484s > svymean(~api00,ds1) 484s Warning message: 484s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 484s Stratum (406) has only one PSU at stage 1 484s mean SE 484s api00 645.14 6.0914 484s > 484s > ## checks for `svytotal()` 484s > 484s > df_w_singleton <- data.frame( 484s + Stratum = c(1, 1, 2, 2, 3), 484s + PSU = c(1, 2, 3, 4, 5), 484s + Design_Weight = c(10.5, 10.5, 20, 20, 15), 484s + Sex = c("M", "F", "F", "M", "M"), 484s + Age = c(30.5, 40.5, 35, 52, 44), 484s + Height = c(6.2, 5.0, 5.3, 5.7, 5.5) 484s + ) 484s > 484s > design_w_singleton <- survey::svydesign( 484s + data = df_w_singleton, 484s + ids = ~ PSU, strata = ~ Stratum, 484s + weights = ~ Design_Weight 484s + ) 484s > 484s > options("survey.lonely.psu" = "remove") 484s > 484s > stopifnot(all.equal( 484s + target = 126625, 484s + current = as.numeric( 484s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 484s + ) 484s + )) 484s Warning message: 484s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 484s Stratum (406) has only one PSU at stage 1 484s > 484s > options("survey.lonely.psu" = "certainty") 484s > 484s > stopifnot(all.equal( 484s + target = 126625, 484s + current = as.numeric( 484s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 484s + ) 484s + )) 484s > 484s > options("survey.lonely.psu" = "adjust") 484s > 484s > stopifnot(all.equal( 484s + target = 127579.8, 484s + current = as.numeric( 484s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 484s + ), 484s + scale = 127579.8, tolerance = 0.000001 484s + )) 484s > 484s BEGIN TEST mtcars-var.R 484s 484s R version 4.4.3 (2025-02-28) -- "Trophy Case" 484s Copyright (C) 2025 The R Foundation for Statistical Computing 484s Platform: arm-unknown-linux-gnueabihf (32-bit) 484s 484s R is free software and comes with ABSOLUTELY NO WARRANTY. 484s You are welcome to redistribute it under certain conditions. 484s Type 'license()' or 'licence()' for distribution details. 484s 484s R is a collaborative project with many contributors. 484s Type 'contributors()' for more information and 484s 'citation()' on how to cite R or R packages in publications. 484s 484s Type 'demo()' for some demos, 'help()' for on-line help, or 484s 'help.start()' for an HTML browser interface to help. 484s Type 'q()' to quit R. 484s 484s > library(survey) 484s Loading required package: grid 484s Loading required package: Matrix 485s Loading required package: survival 486s > 486s > # don't throw an error on domains of size 1, just return NA 486s > input <- mtcars 486s 486s Attaching package: 'survey' 486s 486s > input$carb <- factor(input$carb) 486s > design <- svydesign(ids = ~0, weights = NULL, data = input) 486s > svyby( 486s + ~mpg, 486s + ~carb, 486s + design, 486s + svyvar 486s + ) 486s The following object is masked from 'package:graphics': 486s 486s dotchart 486s 486s carb mpg se 486s 1 1 36.01619 11.2823286 486s 2 2 29.94444 9.0030898 486s 3 3 1.11000 0.4604066 486s 4 4 15.29656 4.3174617 486s 6 6 NA NA 486s 8 8 NA NA 486s > 486s > 486s > ## same n with na.rm=TRUE as subset(, !is.na) 486s > input$mpg[1]<-NA 486s > design <- svydesign(ids = ~0, weights = NULL, data = input) 486s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 486s + svyvar(~mpg, subset(design, !is.na(mpg))))) 486s > 486s BEGIN TEST multistage-rcpp.R 486s 486s R version 4.4.3 (2025-02-28) -- "Trophy Case" 486s Copyright (C) 2025 The R Foundation for Statistical Computing 486s Platform: arm-unknown-linux-gnueabihf (32-bit) 486s 486s R is free software and comes with ABSOLUTELY NO WARRANTY. 486s You are welcome to redistribute it under certain conditions. 486s Type 'license()' or 'licence()' for distribution details. 486s 486s R is a collaborative project with many contributors. 486s Type 'contributors()' for more information and 486s 'citation()' on how to cite R or R packages in publications. 486s 486s Type 'demo()' for some demos, 'help()' for on-line help, or 486s 'help.start()' for an HTML browser interface to help. 486s Type 'q()' to quit R. 486s 486s > ## temporarily disable while it's being fixed 486s > ## q("no") 486s > 486s > ## 486s > ## Check that multistage() and multistage_rcpp() give same results 486s > ## for different options. 486s > ## 486s > library(survey) 486s Loading required package: grid 486s Loading required package: Matrix 487s Loading required package: survival 487s 487s Attaching package: 'survey' 487s 487s > 487s > # Check for a simple random sample ---- 487s > 487s > data('api', package = 'survey') 487s The following object is masked from 'package:graphics': 487s 487s dotchart 487s 487s > api_srs_design <- svydesign( 487s + data = apisrs, 487s + ids = ~ 1, 487s + weights = ~ 1 487s + ) 487s > 487s > x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob) 487s > 487s > base_r_result <- survey:::multistage(x = x, 487s + clusters = api_srs_design$cluster, 487s + stratas = api_srs_design$strata, 487s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=TRUE, stage = 1, cal = NULL) 487s > 487s > rcpp_result <- survey:::multistage_rcpp(x = x, 487s + clusters = api_srs_design$cluster, 487s + stratas = api_srs_design$strata, 487s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=TRUE, stage = 1, cal = NULL) 487s > 487s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 487s + stop("Differences between `multistage()` and `multistage_rcpp()` for SRS") 487s + } 487s > 487s > # Check for a stratified simple random sample ---- 487s > 487s > apistrat_design <- svydesign( 487s + data = apistrat, 487s + id =~ 1, 487s + strata =~ stype, 487s + weights =~ pw, 487s + fpc =~ fpc 487s + ) 487s > 487s > x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob) 487s > 487s > base_r_result <- survey:::multistage(x = x, 487s + clusters = apistrat_design$cluster, 487s + stratas = apistrat_design$strata, 487s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=TRUE, stage = 1, cal = NULL) 487s > 487s > rcpp_result <- survey:::multistage_rcpp(x = x, 487s + clusters = apistrat_design$cluster, 487s + stratas = apistrat_design$strata, 487s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=TRUE, stage = 1, cal = NULL) 487s > 487s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 487s + stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample") 487s + } 487s > 487s > ##_ Check whether expected true zeroes are actually computed as zeroes ---- 487s > 487s > x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob)) 487s > 487s > base_r_result <- survey:::multistage(x = x, 487s + clusters = apistrat_design$cluster, 487s + stratas = apistrat_design$strata, 487s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=TRUE, stage = 1, cal = NULL) 487s > 487s > rcpp_result <- survey:::multistage_rcpp(x = x, 487s + clusters = apistrat_design$cluster, 487s + stratas = apistrat_design$strata, 487s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=TRUE, stage = 1, cal = NULL) 487s > 487s > if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) { 487s + stop("Computations which should equal zero do not.") 487s + } 487s > 487s > # Create a stratified, multistage design ---- 487s > 487s > data(mu284) 487s > 487s > ## Create three strata, the third of which has only one PSU 487s > mu284_stratified <- rbind( 487s + transform(mu284, stratum = 1, 487s + y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)), 487s + transform(mu284, stratum = 2, 487s + y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)), 487s + transform(mu284[1,], stratum = 3, 487s + y2 = y1 + 2) 487s + ) 487s > 487s > ## Create domain variables which yield a lonely PSU or a lonely SSU 487s > mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19) 487s > mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1) 487s > 487s > ## Create a survey design object with no lonely PSUs 487s > dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3), 487s + strata = ~ stratum, nest = TRUE, 487s + id = ~ id1 + id2, fpc = ~ n1 + n2) 487s > ## Create a survey design with one lonely PSU 487s > dmu284_strat_w_lonely <- svydesign(data = mu284_stratified, 487s + strata = ~ stratum, nest = TRUE, 487s + id = ~ id1 + id2, fpc = ~ n1 + n2) 487s > ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU 487s > dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU) 487s > dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU) 487s > 487s > 487s > # Check same results for different values of 'lonely PSU' options ---- 487s > 487s > lonely_psu_options <- c(certainty = 'certainty', 487s + remove = 'remove', 487s + average = 'average', 487s + adjust = 'adjust') 487s > one_stage_options <- c(TRUE, FALSE) 487s > 487s > design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 487s + 'one.stage' = one_stage_options, 487s + stringsAsFactors = FALSE) 487s > design_lonely_psu_comparisons[['results_match']] <- NA 487s > 487s > ##_ Check for lonely PSUs caused by design ---- 487s > for (i in seq_len(nrow(design_lonely_psu_comparisons))) { 487s + survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i] 487s + one.stage <- design_lonely_psu_comparisons[['one.stage']][i] 487s + options('survey.lonely.psu' = survey.lonely.psu) 487s + 487s + x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob) 487s + 487s + base_r_result <- survey:::multistage(x = x, 487s + clusters = dmu284_strat_w_lonely$cluster, 487s + stratas = dmu284_strat_w_lonely$strata, 487s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=one.stage, stage = 1, cal = NULL) 487s + 487s + rcpp_result <- survey:::multistage_rcpp(x = x, 487s + clusters = dmu284_strat_w_lonely$cluster, 487s + stratas = dmu284_strat_w_lonely$strata, 487s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=one.stage, stage = 1, cal = NULL) 487s + 487s + design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 487s + } 487s > 487s > print(design_lonely_psu_comparisons) 487s survey.lonely.psu one.stage results_match 487s 1 certainty TRUE TRUE 487s 2 remove TRUE TRUE 487s 3 average TRUE TRUE 487s 4 adjust TRUE TRUE 487s 5 certainty FALSE TRUE 487s 6 remove FALSE TRUE 487s 7 average FALSE TRUE 487s 8 adjust FALSE TRUE 487s > if (!all(design_lonely_psu_comparisons$results_match)) { 487s + stop("Results for design lonely PSUs differ between base R and Rcpp implementations.") 487s + } 487s > 487s > ##_ Check for domain lonely PSUs caused by subsetting ---- 487s > 487s > domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 487s + 'survey.adjust.domain.lonely' = c(FALSE, TRUE), 487s + 'one.stage' = one_stage_options, 487s + stringsAsFactors = FALSE) 487s > domain_lonely_psu_comparisons[['results_match']] <- NA 487s > 487s > for (i in seq_len(nrow(domain_lonely_psu_comparisons))) { 487s + 487s + options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i]) 487s + options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i]) 487s + one.stage <- domain_lonely_psu_comparisons[['one.stage']][i] 487s + 487s + 487s + x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob) 487s + suppressWarnings({ 487s + base_r_result <- survey:::multistage(x = x, 487s + clusters = dmu284_strat_domain_lonely_psu$cluster, 487s + stratas = dmu284_strat_domain_lonely_psu$strata, 487s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 487s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=one.stage, stage = 1, cal = NULL) 487s + }) 487s + 487s + rcpp_result <- survey:::multistage_rcpp(x = x, 487s + clusters = dmu284_strat_domain_lonely_psu$cluster, 487s + stratas = dmu284_strat_domain_lonely_psu$strata, 487s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 487s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=one.stage, stage = 1, cal = NULL) 487s + 487s + domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 487s + } 487s > 487s > print(domain_lonely_psu_comparisons) 487s survey.lonely.psu survey.adjust.domain.lonely one.stage results_match 487s 1 certainty FALSE TRUE TRUE 487s 2 remove FALSE TRUE TRUE 487s 3 average FALSE TRUE TRUE 487s 4 adjust FALSE TRUE TRUE 487s 5 certainty TRUE TRUE TRUE 487s 6 remove TRUE TRUE TRUE 487s 7 average TRUE TRUE TRUE 487s 8 adjust TRUE TRUE TRUE 487s 9 certainty FALSE FALSE TRUE 487s 10 remove FALSE FALSE TRUE 487s 11 average FALSE FALSE TRUE 487s 12 adjust FALSE FALSE TRUE 487s 13 certainty TRUE FALSE TRUE 487s 14 remove TRUE FALSE TRUE 487s 15 average TRUE FALSE TRUE 487s 16 adjust TRUE FALSE TRUE 487s > if (!all(domain_lonely_psu_comparisons$results_match)) { 487s + stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.") 487s + } 487s > 487s > # Checks for edge cases ---- 487s > 487s > ## Zero records ---- 487s > 487s > zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent") 487s Warning messages: 487s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 487s At least one stratum contains only one PSU at stage 1 487s > 487s > zero_row_result <- survey:::multistage_rcpp( 487s + x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]), 487s + clusters = zero_row_design$cluster, 487s + stratas = zero_row_design$strata, 487s + nPSUs = zero_row_design$fpc$sampsize, 487s + fpcs = zero_row_design$fpc$popsize, 487s + lonely.psu=getOption("survey.lonely.psu"), 487s + one.stage=one.stage, stage = 1, cal = NULL 487s + ) 487s > 487s > if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) { 487s + stop("`multistage_rcpp()` should return zeros for zero-row inputs.") 487s + } 487s > 487s > 487s BEGIN TEST multistage.R 488s 488s R version 4.4.3 (2025-02-28) -- "Trophy Case" 488s Copyright (C) 2025 The R Foundation for Statistical Computing 488s Platform: arm-unknown-linux-gnueabihf (32-bit) 488s 488s R is free software and comes with ABSOLUTELY NO WARRANTY. 488s You are welcome to redistribute it under certain conditions. 488s Type 'license()' or 'licence()' for distribution details. 488s 488s R is a collaborative project with many contributors. 488s Type 'contributors()' for more information and 488s 'citation()' on how to cite R or R packages in publications. 488s 488s Type 'demo()' for some demos, 'help()' for on-line help, or 488s 'help.start()' for an HTML browser interface to help. 488s Type 'q()' to quit R. 488s 488s > ## 488s > ## Check that multistage samples still work 488s > ## 488s > library(survey) 488s Loading required package: grid 488s Loading required package: Matrix 489s Loading required package: survival 489s 489s Attaching package: 'survey' 489s 489s The following object is masked from 'package:graphics': 489s 489s dotchart 489s 489s > example(mu284) 489s 489s mu284> data(mu284) 489s 489s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 489s 2 - level Cluster Sampling design 489s With (5, 15) clusters. 489s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 489s 489s mu284> (ytotal<-svytotal(~y1, dmu284)) 489s total SE 489s y1 15080 2274.3 489s 489s mu284> vcov(ytotal) 489s y1 489s y1 5172234 489s > 489s > 489s BEGIN TEST na_action.R 489s 489s R version 4.4.3 (2025-02-28) -- "Trophy Case" 489s Copyright (C) 2025 The R Foundation for Statistical Computing 489s Platform: arm-unknown-linux-gnueabihf (32-bit) 489s 489s R is free software and comes with ABSOLUTELY NO WARRANTY. 489s You are welcome to redistribute it under certain conditions. 489s Type 'license()' or 'licence()' for distribution details. 489s 489s R is a collaborative project with many contributors. 489s Type 'contributors()' for more information and 489s 'citation()' on how to cite R or R packages in publications. 489s 489s Type 'demo()' for some demos, 'help()' for on-line help, or 489s 'help.start()' for an HTML browser interface to help. 489s Type 'q()' to quit R. 489s 489s > ## from Terry Therneau 489s > library(survey) 489s Loading required package: grid 489s Loading required package: Matrix 490s Loading required package: survival 490s 490s Attaching package: 'survey' 490s 490s The following object is masked from 'package:graphics': 490s 490s dotchart 490s 490s > load("naa.rda") 490s > 490s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 490s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 490s > all.equal(coef(fit1e),coef(fit1o)) 490s [1] TRUE 490s > all.equal(vcov(fit1e),vcov(fit1o)) 490s [1] TRUE 490s > 490s BEGIN TEST newquantile.R 490s 490s R version 4.4.3 (2025-02-28) -- "Trophy Case" 490s Copyright (C) 2025 The R Foundation for Statistical Computing 490s Platform: arm-unknown-linux-gnueabihf (32-bit) 490s 490s R is free software and comes with ABSOLUTELY NO WARRANTY. 490s You are welcome to redistribute it under certain conditions. 490s Type 'license()' or 'licence()' for distribution details. 490s 490s R is a collaborative project with many contributors. 490s Type 'contributors()' for more information and 490s 'citation()' on how to cite R or R packages in publications. 490s 490s Type 'demo()' for some demos, 'help()' for on-line help, or 490s 'help.start()' for an HTML browser interface to help. 490s Type 'q()' to quit R. 490s 491s > ## quantiles with equal weights 491s > 491s > library(survey) 491s Loading required package: grid 491s Loading required package: Matrix 491s Loading required package: survival 492s 492s Attaching package: 'survey' 492s 492s The following object is masked from 'package:graphics': 492s 492s dotchart 492s 492s > data(api) 492s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 492s > 492s > 492s > for(i in 1:9){ 492s + print(i) 492s + all.equal( 492s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 492s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 492s + ) 492s + 492s + } 492s [1] 1 492s [1] 2 492s [1] 3 492s [1] 4 492s [1] 5 492s [1] 6 492s [1] 7 492s [1] 8 492s [1] 9 492s > 492s BEGIN TEST nwts-cch.R 492s 492s R version 4.4.3 (2025-02-28) -- "Trophy Case" 492s Copyright (C) 2025 The R Foundation for Statistical Computing 492s Platform: arm-unknown-linux-gnueabihf (32-bit) 492s 492s R is free software and comes with ABSOLUTELY NO WARRANTY. 492s You are welcome to redistribute it under certain conditions. 492s Type 'license()' or 'licence()' for distribution details. 492s 492s R is a collaborative project with many contributors. 492s Type 'contributors()' for more information and 492s 'citation()' on how to cite R or R packages in publications. 492s 492s Type 'demo()' for some demos, 'help()' for on-line help, or 492s 'help.start()' for an HTML browser interface to help. 492s Type 'q()' to quit R. 492s 492s > library(survey) 492s Loading required package: grid 492s Loading required package: Matrix 493s Loading required package: survival 493s 493s Attaching package: 'survey' 493s 493s The following object is masked from 'package:graphics': 493s 493s dotchart 493s 493s > library(survival) 493s > data(nwtco) 493s > 493s > ntwco<-subset(nwtco, !is.na(edrel)) 493s > 493s > load("nwtco-subcohort.rda") 493s > nwtco$subcohort<-subcohort 493s > 493s > d_BorganII <- twophase(id=list(~seqno,~seqno), 493s + strata=list(NULL,~interaction(instit,rel)), 493s + data=nwtco, subset=~I(rel |subcohort)) 494s > 494s > ##Coefficient results same as Splus with code from 494s > ## http://faculty.washington.edu/norm/software.html 494s > ## SE slightly larger due to using sandwich variance. 494s > 494s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 494s Call: 494s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 494s I(age/12), design = d_BorganII) 494s 494s coef exp(coef) se(coef) robust se z p 494s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 494s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 494s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 494s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 494s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 494s 494s Likelihood ratio test= on 5 df, p= 494s n= 1062, number of events= 571 494s > 494s > ## 494s > ## This gives higher standard errors. calibrate() does not recompute the 494s > ## finite population correction if a calibration variable happens to predict 494s > ## sampling perfectly. It probably should. 494s > ## 494s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 494s + strata=list(NULL,~rel), 494s + data=nwtco, subset=~I(rel |subcohort)), 494s + phase=2, formula=~interaction(instit,rel), 494s + epsilon=1e-10) 494s > 494s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 494s Call: 494s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 494s I(age/12), design = d_BorganIIps) 494s 494s coef exp(coef) se(coef) robust se z p 494s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 494s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 494s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 494s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 494s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 494s 494s Likelihood ratio test= on 5 df, p= 494s n= 1062, number of events= 571 494s > 494s BEGIN TEST nwts.R 494s 494s R version 4.4.3 (2025-02-28) -- "Trophy Case" 494s Copyright (C) 2025 The R Foundation for Statistical Computing 494s Platform: arm-unknown-linux-gnueabihf (32-bit) 494s 494s R is free software and comes with ABSOLUTELY NO WARRANTY. 494s You are welcome to redistribute it under certain conditions. 494s Type 'license()' or 'licence()' for distribution details. 494s 494s R is a collaborative project with many contributors. 494s Type 'contributors()' for more information and 494s 'citation()' on how to cite R or R packages in publications. 494s 494s Type 'demo()' for some demos, 'help()' for on-line help, or 494s 'help.start()' for an HTML browser interface to help. 494s Type 'q()' to quit R. 494s 494s > 494s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 494s > ## data from Norman Breslow's web page. 494s > library(survey) 494s Loading required package: grid 494s Loading required package: Matrix 495s Loading required package: survival 496s 496s Attaching package: 'survey' 496s 496s The following object is masked from 'package:graphics': 496s 496s dotchart 496s 496s > load("nwts.rda") 496s > nwtsnb<-nwts 496s > nwtsnb$case<-nwts$case-nwtsb$case 496s > nwtsnb$control<-nwts$control-nwtsb$control 496s > 496s > a<-rbind(nwtsb,nwtsnb) 496s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 496s > 496s > b<-rbind(a,a) 496s > b$rel<-rep(c(1,0),each=32) 496s > b$n<-ifelse(b$rel,b$case,b$control) 496s > 496s > index<-rep(1:64,b$n) 496s > 496s > nwt.exp<-b[index,c(1:3,6,7)] 496s > nwt.exp$id<-1:4088 496s > 496s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 496s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 496s > 496s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 496s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 497s > 497s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 497s > 497s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 497s 497s Call: 497s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 497s family = quasibinomial) 497s 497s Survey design: 497s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 497s subset = subset, data = data, pps = pps) 497s 497s Coefficients: 497s Estimate Std. Error t value Pr(>|t|) 497s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 497s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 497s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 497s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 497s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 497s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 497s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 497s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 497s --- 497s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 497s 497s (Dispersion parameter for quasibinomial family taken to be 1.000876) 497s 497s Number of Fisher Scoring iterations: 4 497s 497s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 497s 497s Call: 497s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 497s family = quasibinomial) 497s 497s Survey design: 497s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 497s subset = subset, data = data, pps = pps) 497s 497s Coefficients: 497s Estimate Std. Error t value Pr(>|t|) 497s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 497s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 497s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 497s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 497s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 497s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 497s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 497s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 497s --- 497s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 497s 497s (Dispersion parameter for quasibinomial family taken to be 1.000876) 497s 497s Number of Fisher Scoring iterations: 4 497s 497s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 497s 497s Call: 497s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 497s family = quasibinomial) 497s 497s Survey design: 497s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 497s rel)) 497s 497s Coefficients: 497s Estimate Std. Error t value Pr(>|t|) 497s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 497s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 497s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 497s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 497s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 497s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 497s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 497s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 497s --- 497s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 497s 497s (Dispersion parameter for quasibinomial family taken to be 1.000876) 497s 497s Number of Fisher Scoring iterations: 4 497s 497s > 497s > ## check subsets of calibrated designs. 497s > summary(svyglm(rel~factor(stage), 497s + family=quasibinomial,design=subset(dccs8,histol==1))) 497s 497s Call: 497s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 497s histol == 1), family = quasibinomial) 497s 497s Survey design: 497s subset(dccs8, histol == 1) 497s 497s Coefficients: 497s Estimate Std. Error t value Pr(>|t|) 497s (Intercept) -2.7160 0.1083 -25.085 < 2e-16 *** 497s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 497s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 497s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 497s --- 497s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 497s 497s (Dispersion parameter for quasibinomial family taken to be 1.001333) 497s 497s Number of Fisher Scoring iterations: 4 497s 497s Warning messages: 497s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 497s 2: In summary.glm(g) : 497s observations with zero weight not used for calculating dispersion 497s 3: In summary.glm(glm.object) : 497s observations with zero weight not used for calculating dispersion 497s 4: In `[.twophase2`(design, nas == 0, ) : 497s 1 strata have only one PSU in this subset. 497s 5: In `[.twophase2`(design, nas == 0, ) : 497s 1 strata have only one PSU in this subset. 497s > summary(svyglm(rel~factor(stage), 497s + family=quasibinomial,design=subset(gccs8,histol==1))) 497s 497s Call: 497s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 497s histol == 1), family = quasibinomial) 497s 497s Survey design: 497s subset(gccs8, histol == 1) 497s 497s Coefficients: 497s Estimate Std. Error t value Pr(>|t|) 497s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 497s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 497s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 497s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 497s --- 497s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 497s 497s (Dispersion parameter for quasibinomial family taken to be 1.001333) 497s 497s Number of Fisher Scoring iterations: 4 497s 497s > 497s > 497s Warning messages: 497s 1: In summary.glm(g) : 497s observations with zero weight not used for calculating dispersion 497s 2: In summary.glm(glm.object) : 497s observations with zero weight not used for calculating dispersion 497s BEGIN TEST poisson.R 497s 497s R version 4.4.3 (2025-02-28) -- "Trophy Case" 497s Copyright (C) 2025 The R Foundation for Statistical Computing 497s Platform: arm-unknown-linux-gnueabihf (32-bit) 497s 497s R is free software and comes with ABSOLUTELY NO WARRANTY. 497s You are welcome to redistribute it under certain conditions. 497s Type 'license()' or 'licence()' for distribution details. 497s 497s R is a collaborative project with many contributors. 497s Type 'contributors()' for more information and 497s 'citation()' on how to cite R or R packages in publications. 497s 497s Type 'demo()' for some demos, 'help()' for on-line help, or 497s 'help.start()' for an HTML browser interface to help. 497s Type 'q()' to quit R. 497s 497s > ## check poisson sampling 497s > library(survey) 497s Loading required package: grid 497s Loading required package: Matrix 498s Loading required package: survival 498s 498s Attaching package: 'survey' 498s 498s > data(api) 498s The following object is masked from 'package:graphics': 498s 498s dotchart 498s 498s > set.seed(2021-7-15) 498s > apipop$prob<-apipop$api00/1000 498s > insample<-rbinom(nrow(apipop),1,apipop$prob) 498s > apipois<-apipop[insample,] 498s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 498s > 498s > stopifnot(isTRUE(all.equal( 498s + as.vector(SE(svytotal(~api00,design=des))), 498s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 498s + ))) 498s > 498s > 498s BEGIN TEST pps.R 498s 498s R version 4.4.3 (2025-02-28) -- "Trophy Case" 498s Copyright (C) 2025 The R Foundation for Statistical Computing 498s Platform: arm-unknown-linux-gnueabihf (32-bit) 498s 498s R is free software and comes with ABSOLUTELY NO WARRANTY. 498s You are welcome to redistribute it under certain conditions. 498s Type 'license()' or 'licence()' for distribution details. 498s 498s R is a collaborative project with many contributors. 498s Type 'contributors()' for more information and 498s 'citation()' on how to cite R or R packages in publications. 498s 498s Type 'demo()' for some demos, 'help()' for on-line help, or 498s 'help.start()' for an HTML browser interface to help. 498s Type 'q()' to quit R. 498s 499s > library(survey) 499s Loading required package: grid 499s Loading required package: Matrix 499s Loading required package: survival 500s 500s Attaching package: 'survey' 500s 500s The following object is masked from 'package:graphics': 500s 500s dotchart 500s 500s > data(election) 500s > 500s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 500s Loading required package: grid 500s Loading required package: Matrix 500s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 500s > svytotal(~Bush+Kerry+Nader, dpps) 500s total SE 500s Bush 64518472 2447629 500s Kerry 51202102 2450787 500s Nader 478530 102420 500s > svytotal(~Bush+Kerry+Nader, dppswr) 500s total SE 500s Bush 64518472 2671455 500s Kerry 51202102 2679433 500s Nader 478530 105303 500s > 500s > ##subsets 500s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 500s total SE 500s Bush 34944285 5399833 500s Kerry 25581714 4028434 500s Nader 478530 102420 500s > 500s > ##multistage: should agree with STRS analysis 500s > data(api) 500s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 500s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 500s > 500s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 500s [1] TRUE 500s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 500s [1] TRUE 500s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 500s [1] TRUE 500s > 500s > ## the new without-replacement methods 500s > data(election) 500s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 500s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 500s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 500s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 500s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 500s > ## Yates-Grundy type 500s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 500s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 500s > 500s > ## The with-replacement approximation 500s > svytotal(~Bush+Kerry+Nader, dpps_ht) 500s total SE 500s Bush 64518472 2604404 500s Kerry 51202102 2523712 500s Nader 478530 102326 500s > svytotal(~Bush+Kerry+Nader, dpps_yg) 500s total SE 500s Bush 64518472 2406526 500s Kerry 51202102 2408091 500s Nader 478530 101664 500s > svytotal(~Bush+Kerry+Nader, dpps_hr) 500s total SE 500s Bush 64518472 2624662 500s Kerry 51202102 2525222 500s Nader 478530 102793 500s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 500s total SE 500s Bush 64518472 2436738 500s Kerry 51202102 2439845 500s Nader 478530 102016 500s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 500s total SE 500s Bush 64518472 2472753 500s Kerry 51202102 2426842 500s Nader 478530 102595 500s > svytotal(~Bush+Kerry+Nader, dpps_br) 500s total SE 500s Bush 64518472 2447629 500s Kerry 51202102 2450787 500s Nader 478530 102420 500s > svytotal(~Bush+Kerry+Nader, dpps_ov) 500s total SE 500s Bush 64518472 2939608 500s Kerry 51202102 1964632 500s Nader 478530 104373 500s > 500s > ## subsets 500s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 500s total SE 500s Bush 34944285 5406348 500s Kerry 25581714 4047741 500s Nader 478530 102326 500s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 500s total SE 500s Bush 34944285 5377659 500s Kerry 25581714 4010908 500s Nader 478530 102016 500s > 500s > ## counts 500s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 500s I(Nader > 0) counts se 500s FALSE FALSE 19 0 500s TRUE TRUE 21 0 500s > 500s BEGIN TEST qrule-swiss.R 500s 500s R version 4.4.3 (2025-02-28) -- "Trophy Case" 500s Copyright (C) 2025 The R Foundation for Statistical Computing 500s Platform: arm-unknown-linux-gnueabihf (32-bit) 500s 500s R is free software and comes with ABSOLUTELY NO WARRANTY. 500s You are welcome to redistribute it under certain conditions. 500s Type 'license()' or 'licence()' for distribution details. 500s 500s R is a collaborative project with many contributors. 500s Type 'contributors()' for more information and 500s 'citation()' on how to cite R or R packages in publications. 500s 500s Type 'demo()' for some demos, 'help()' for on-line help, or 500s 'help.start()' for an HTML browser interface to help. 500s Type 'q()' to quit R. 500s 500s > library(survey) 501s Loading required package: survival 501s 501s Attaching package: 'survey' 501s 501s The following object is masked from 'package:graphics': 501s 501s dotchart 501s 501s > 501s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1) 501s > 501s > design_no_strat <- svydesign(id = ~id, 501s + probs = ~probs, 501s + data = data_no_strat, 501s + fpc = ~fpc) 501s > 501s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99) 501s > 501s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE, 501s + interval.type = "mean", qrule = "hf1") 501s > 501s > stopifnot(all(diff(res$x[,"quantile"])>=0)) 501s > 501s > 501s > 501s BEGIN TEST quantile.R 502s 502s R version 4.4.3 (2025-02-28) -- "Trophy Case" 502s Copyright (C) 2025 The R Foundation for Statistical Computing 502s Platform: arm-unknown-linux-gnueabihf (32-bit) 502s 502s R is free software and comes with ABSOLUTELY NO WARRANTY. 502s You are welcome to redistribute it under certain conditions. 502s Type 'license()' or 'licence()' for distribution details. 502s 502s R is a collaborative project with many contributors. 502s Type 'contributors()' for more information and 502s 'citation()' on how to cite R or R packages in publications. 502s 502s Type 'demo()' for some demos, 'help()' for on-line help, or 502s 'help.start()' for an HTML browser interface to help. 502s Type 'q()' to quit R. 502s 502s > library(survey) 502s Loading required package: grid 502s Loading required package: Matrix 503s Loading required package: survival 503s 503s Attaching package: 'survey' 503s 503s The following object is masked from 'package:graphics': 503s 503s dotchart 503s 503s > set.seed(42) 503s > 503s > df<-data.frame(x=exp(rnorm(1000))) 503s > df$y<-round(df$x,1) 503s > ddf<-svydesign(id=~1,data=df) 503s Warning message: 503s > rdf<-as.svrepdesign(ddf) 503s In svydesign.default(id = ~1, data = df) : 503s No weights or probabilities supplied, assuming equal probability 503s > 503s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 503s 0.01 0.1 0.5 0.9 0.99 503s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 503s > 503s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 504s x 504s q0.01 0.01554946 504s q0.1 0.01425828 504s q0.5 0.03428012 504s q0.9 0.16457488 504s q0.99 1.88672412 504s > 504s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 504s 0.01 0.1 0.5 0.9 0.99 504s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 504s > 504s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 504s x 504s q0.01 0.01556240 504s q0.1 0.01420086 504s q0.5 0.03430175 504s q0.9 0.16461019 504s q0.99 1.88818131 504s > 504s > 504s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 504s $quantiles 504s 0.01 0.1 0.5 0.9 0.99 504s y 0.02352941 0.2230769 0.9340909 3.55 9.4 504s 504s $CIs 504s , , y 504s 504s 0.01 0.1 0.5 0.9 0.99 504s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 504s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 504s 504s 504s > 504s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 504s Statistic: 504s y 504s q0.01 0.1 504s q0.1 0.3 504s q0.5 1.0 504s q0.9 3.6 504s q0.99 9.4 504s SE: 504s y 504s q0.01 0.02547977 504s q0.1 0.02547977 504s q0.5 0.02547977 504s q0.9 0.15287859 504s q0.99 1.88302540 504s > 504s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 504s $quantiles 504s 0.01 0.1 0.5 0.9 0.99 504s y 0.02352941 0.2230769 0.9340909 3.55 9.4 504s 504s $CIs 504s , , y 504s 504s 0.01 0.1 0.5 0.9 0.99 504s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 504s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 504s 504s 504s > 504s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 504s Statistic: 504s y 504s q0.01 0.1 504s q0.1 0.3 504s q0.5 1.0 504s q0.9 3.6 504s q0.99 9.4 504s SE: 504s y 504s q0.01 0.02551067 504s q0.1 0.02551067 504s q0.5 0.02551067 504s q0.9 0.15306404 504s q0.99 1.88450896 504s > 504s > 504s > 504s > df<-data.frame(x=exp(rnorm(20))) 504s > df$y<-round(df$x,1) 504s > ddf<-svydesign(id=~1,data=df) 504s Warning message: 504s In svydesign.default(id = ~1, data = df) : 504s No weights or probabilities supplied, assuming equal probability 504s > rdf<-as.svrepdesign(ddf) 504s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 504s 0.01 0.1 0.5 0.9 0.99 504s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 504s > 504s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 504s x 504s q0.01 0.00000000 504s q0.1 0.04598541 504s q0.5 0.25943731 504s q0.9 2.12343073 504s q0.99 1.91998924 504s > 504s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 504s 0.01 0.1 0.5 0.9 0.99 504s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 504s > 504s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 504s x 504s q0.01 0.00000000 504s q0.1 0.04732818 504s q0.5 0.24957966 504s q0.9 2.25211815 504s q0.99 2.04043154 504s > 504s > 504s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 504s $quantiles 504s 0.01 0.1 0.5 0.9 0.99 504s y 0.1 0.15 0.75 2.4 8.68 504s 504s $CIs 504s , , y 504s 504s 0.01 0.1 0.5 0.9 0.99 504s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 504s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 504s 504s 504s > 504s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 504s Statistic: 504s y 504s q0.01 0.10 504s q0.1 0.20 504s q0.5 0.80 504s q0.9 2.40 504s q0.99 8.68 504s SE: 504s y 504s q0.01 0.00000000 504s q0.1 0.02611112 504s q0.5 0.26542051 504s q0.9 2.10908603 504s q0.99 1.91777710 504s > 504s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 504s $quantiles 504s 0.01 0.1 0.5 0.9 0.99 504s y 0.1 0.15 0.75 2.4 8.68 504s 504s $CIs 504s , , y 504s 504s 0.01 0.1 0.5 0.9 0.99 504s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 504s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 504s 504s 504s > 504s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 504s Statistic: 504s y 504s q0.01 0.10 504s q0.1 0.20 504s q0.5 0.80 504s q0.9 2.40 504s q0.99 8.68 504s SE: 504s y 504s q0.01 0.00000000 504s q0.1 0.02551067 504s q0.5 0.25244616 504s q0.9 2.23558589 504s q0.99 2.03881114 504s > 504s BEGIN TEST quantiles-chile.R 504s 504s R version 4.4.3 (2025-02-28) -- "Trophy Case" 504s Copyright (C) 2025 The R Foundation for Statistical Computing 504s Platform: arm-unknown-linux-gnueabihf (32-bit) 504s 504s R is free software and comes with ABSOLUTELY NO WARRANTY. 504s You are welcome to redistribute it under certain conditions. 504s Type 'license()' or 'licence()' for distribution details. 504s 504s R is a collaborative project with many contributors. 504s Type 'contributors()' for more information and 504s 'citation()' on how to cite R or R packages in publications. 504s 504s Type 'demo()' for some demos, 'help()' for on-line help, or 504s 'help.start()' for an HTML browser interface to help. 504s Type 'q()' to quit R. 504s 504s > library(survey) 504s Loading required package: grid 504s Loading required package: Matrix 505s Loading required package: survival 505s 505s Attaching package: 'survey' 505s 505s The following object is masked from 'package:graphics': 505s 505s dotchart 505s 505s > datos <- readRDS("datos_ejemplo.rds") 505s > 505s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 505s > set.seed(234262762) 505s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 505s > options(survey.lonely.psu="remove") 505s > 505s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 505s > 505s > suppressWarnings({ 505s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 505s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 505s + }) 505s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 505s [1] TRUE 505s > 505s > suppressWarnings({ 505s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 505s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 505s + }) 505s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 505s [1] TRUE 505s > 505s BEGIN TEST rakecheck.R 505s 505s R version 4.4.3 (2025-02-28) -- "Trophy Case" 505s Copyright (C) 2025 The R Foundation for Statistical Computing 505s Platform: arm-unknown-linux-gnueabihf (32-bit) 505s 505s R is free software and comes with ABSOLUTELY NO WARRANTY. 505s You are welcome to redistribute it under certain conditions. 505s Type 'license()' or 'licence()' for distribution details. 505s 505s R is a collaborative project with many contributors. 505s Type 'contributors()' for more information and 505s 'citation()' on how to cite R or R packages in publications. 505s 505s Type 'demo()' for some demos, 'help()' for on-line help, or 505s 'help.start()' for an HTML browser interface to help. 505s Type 'q()' to quit R. 505s 505s Loading required package: grid 505s > library(survey) 506s Loading required package: Matrix 506s Loading required package: survival 507s 507s Attaching package: 'survey' 507s 507s The following object is masked from 'package:graphics': 507s 507s dotchart 507s 507s > 507s > data(api) 507s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 507s > rclus1 <- as.svrepdesign(dclus1) 507s > 507s > ## population marginal totals for each stratum 507s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 507s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 507s > 507s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 507s > 507s > svymean(~api00, rclus1r) 507s mean SE 507s api00 641.23 26.873 507s > svytotal(~enroll, rclus1r) 507s total SE 507s enroll 3647300 463511 507s > 507s > ff<-~stype+sch.wide 507s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 507s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 507s > 507s > svymean(~api00,rclus1g) 507s mean SE 507s api00 641.23 26.874 507s > svytotal(~enroll,rclus1g) 507s total SE 507s enroll 3647280 463582 507s > 507s > summary(weights(rclus1g)/weights(rclus1r)) 507s V1 V2 V3 V4 V5 V6 507s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 507s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 507s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 507s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 507s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 507s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 507s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 507s V7 V8 V9 V10 V11 507s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 507s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 507s Median :1 Median :1 Median :1 Median :1 Median :1 507s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 507s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 507s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 507s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 507s V12 V13 V14 V15 507s Min. :0.9997 Min. :1 Min. :1 Min. :1 507s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 507s Median :1.0001 Median :1 Median :1 Median :1 507s Mean :1.0000 Mean :1 Mean :1 Mean :1 507s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 507s Max. :1.0002 Max. :1 Max. :1 Max. :1 507s NA's :37 NA's :13 NA's :1 NA's :12 507s > 507s > 507s > ## Do it for a design without replicate weights 507s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 507s > 507s > svymean(~api00, dclus1r) 507s mean SE 507s api00 641.23 23.704 507s > svytotal(~enroll, dclus1r) 507s total SE 507s enroll 3647300 400603 507s > 507s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 507s > 507s > svymean(~api00,dclus1g) 507s mean SE 507s api00 641.23 23.704 507s > svytotal(~enroll,dclus1g) 507s total SE 507s enroll 3647280 400603 507s > 507s > summary(weights(dclus1g)/weights(dclus1r)) 507s Min. 1st Qu. Median Mean 3rd Qu. Max. 507s 1 1 1 1 1 1 507s > 507s > 507s > 507s > ## Example of raking with partial joint distributions 507s > pop.table <- xtabs(~stype+sch.wide,apipop) 507s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 507s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 507s + list(pop.table, pop.imp)) 507s > svymean(~api00, dclus1r2) 507s mean SE 507s api00 642.62 22.732 507s > 507s > ff1 <-~stype*sch.wide+comp.imp 507s > 507s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 507s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 507s > 507s > svymean(~api00, dclus1g2) 507s mean SE 507s api00 642.61 22.731 507s > 507s > summary(weights(dclus1r2)/weights(dclus1g2)) 507s Min. 1st Qu. Median Mean 3rd Qu. Max. 507s 0.999 1.000 1.000 1.000 1.000 1.002 507s > 507s BEGIN TEST raowuboot.R 507s 507s R version 4.4.3 (2025-02-28) -- "Trophy Case" 507s Copyright (C) 2025 The R Foundation for Statistical Computing 507s Platform: arm-unknown-linux-gnueabihf (32-bit) 507s 507s R is free software and comes with ABSOLUTELY NO WARRANTY. 507s You are welcome to redistribute it under certain conditions. 507s Type 'license()' or 'licence()' for distribution details. 507s 507s R is a collaborative project with many contributors. 507s Type 'contributors()' for more information and 507s 'citation()' on how to cite R or R packages in publications. 507s 507s Type 'demo()' for some demos, 'help()' for on-line help, or 507s 'help.start()' for an HTML browser interface to help. 507s Type 'q()' to quit R. 507s 507s > ## regression test for bug reported by Richard Valliant 507s > library(survey) 507s Loading required package: grid 507s Loading required package: Matrix 508s Loading required package: survival 508s 508s Attaching package: 'survey' 508s 508s The following object is masked from 'package:graphics': 508s 508s dotchart 508s 508s > s<-subbootweights(c(1,1),1:2, 50) 508s > stopifnot(all(s$repweights$weights %in% c(0,2))) 508s > 508s BEGIN TEST regTermTest-missing.R 508s 508s R version 4.4.3 (2025-02-28) -- "Trophy Case" 508s Copyright (C) 2025 The R Foundation for Statistical Computing 508s Platform: arm-unknown-linux-gnueabihf (32-bit) 508s 508s R is free software and comes with ABSOLUTELY NO WARRANTY. 508s You are welcome to redistribute it under certain conditions. 508s Type 'license()' or 'licence()' for distribution details. 508s 508s R is a collaborative project with many contributors. 508s Type 'contributors()' for more information and 508s 'citation()' on how to cite R or R packages in publications. 508s 508s Type 'demo()' for some demos, 'help()' for on-line help, or 508s 'help.start()' for an HTML browser interface to help. 508s Type 'q()' to quit R. 508s 509s > library(survey) 509s Loading required package: grid 509s Loading required package: Matrix 510s Loading required package: survival 510s > data(nhanes) 510s 510s Attaching package: 'survey' 510s 510s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 510s The following object is masked from 'package:graphics': 510s 510s dotchart 510s 510s > 510s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 510s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 510s > 510s > ta<-regTermTest(a, ~HI_CHOL) 510s > tb<-regTermTest(b, ~HI_CHOL) 510s > 510s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 510s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 510s > 510s BEGIN TEST regpredict.R 510s 510s R version 4.4.3 (2025-02-28) -- "Trophy Case" 510s Copyright (C) 2025 The R Foundation for Statistical Computing 510s Platform: arm-unknown-linux-gnueabihf (32-bit) 510s 510s R is free software and comes with ABSOLUTELY NO WARRANTY. 510s You are welcome to redistribute it under certain conditions. 510s Type 'license()' or 'licence()' for distribution details. 510s 510s R is a collaborative project with many contributors. 510s Type 'contributors()' for more information and 510s 'citation()' on how to cite R or R packages in publications. 510s 510s Type 'demo()' for some demos, 'help()' for on-line help, or 510s 'help.start()' for an HTML browser interface to help. 510s Type 'q()' to quit R. 510s 510s > library(survey) 510s Loading required package: grid 510s Loading required package: Matrix 511s Loading required package: survival 511s > data(api) 511s 511s Attaching package: 'survey' 511s 511s The following object is masked from 'package:graphics': 511s 511s dotchart 511s 511s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 511s > 511s > 511s > ## regression estimator of total, three ways 511s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 511s > npop <- sum(!is.na(apipop$enroll)) 511s > 511s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 511s > a <- predict(api.reg, newdata=pop, total=npop) 511s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 511s > 511s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 511s [1] TRUE 511s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 511s [1] TRUE 511s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 511s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 511s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 511s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 511s + } 511s > 511s > ## classical ratio estimator, four ways. 511s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 511s + family=quasi(link="identity", var="mu")) 512s > 512s > a <- predict(api.reg2, newdata=pop, total=npop) 512s > b <- svytotal(~api.stu, 512s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 512s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 512s > 512s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 512s [1] TRUE 512s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 512s [1] TRUE 512s > all.equal(as.vector(coef(a)),as.vector(e$total)) 512s [1] TRUE 512s > all.equal(as.vector(SE(a)), as.vector(e$se)) 512s [1] TRUE 512s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 512s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 512s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 512s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 512s + } 512s > 512s BEGIN TEST rss_scores.R 512s 512s R version 4.4.3 (2025-02-28) -- "Trophy Case" 512s Copyright (C) 2025 The R Foundation for Statistical Computing 512s Platform: arm-unknown-linux-gnueabihf (32-bit) 512s 512s R is free software and comes with ABSOLUTELY NO WARRANTY. 512s You are welcome to redistribute it under certain conditions. 512s Type 'license()' or 'licence()' for distribution details. 512s 512s R is a collaborative project with many contributors. 512s Type 'contributors()' for more information and 512s 'citation()' on how to cite R or R packages in publications. 512s 512s Type 'demo()' for some demos, 'help()' for on-line help, or 512s 'help.start()' for an HTML browser interface to help. 512s Type 'q()' to quit R. 512s 512s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 512s > library(survey) 512s Loading required package: grid 512s Loading required package: Matrix 513s Loading required package: survival 513s 513s Attaching package: 'survey' 513s 513s The following object is masked from 'package:graphics': 513s 513s dotchart 513s 513s > data(myco) 513s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 513s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 513s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 513s > 513s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 513s > 513s > s<-svyscoretest(m_full, ~Scar) 513s > stopifnot(abs(s[1]-10.73)<0.05) 513s > 513s > t<-svyscoretest(m_full,~Scar,method="individual") 513s > stopifnot(abs(coef(t)- -32.61)<0.1) 513s > stopifnot(abs(vcov(t)-99.1)<0.1) 513s > 513s > 513s BEGIN TEST scoping.R 513s 513s R version 4.4.3 (2025-02-28) -- "Trophy Case" 513s Copyright (C) 2025 The R Foundation for Statistical Computing 513s Platform: arm-unknown-linux-gnueabihf (32-bit) 513s 513s R is free software and comes with ABSOLUTELY NO WARRANTY. 513s You are welcome to redistribute it under certain conditions. 513s Type 'license()' or 'licence()' for distribution details. 513s 513s R is a collaborative project with many contributors. 513s Type 'contributors()' for more information and 513s 'citation()' on how to cite R or R packages in publications. 513s 513s Type 'demo()' for some demos, 'help()' for on-line help, or 513s 'help.start()' for an HTML browser interface to help. 513s Type 'q()' to quit R. 513s 513s > 513s > ## regression test for testing regression 513s > 513s > library(survey) 513s Loading required package: grid 513s Loading required package: Matrix 514s Loading required package: survival 514s 514s Attaching package: 'survey' 514s 514s The following object is masked from 'package:graphics': 514s 514s dotchart 514s 514s > data(api) 514s > 514s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 514s > 514s > 514s > f<-function(){ 514s + form<-acs.46~stype 514s + svyglm(formula=form, design = dstrat) 514s + } 514s > 514s > g<-function(form){ 514s + svyglm(formula=form, design = dstrat) 514s + } 514s > f() 514s Stratified Independent Sampling design 514s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 514s fpc = ~fpc) 514s 514s Call: svyglm(formula = form, design = dstrat) 514s 514s Coefficients: 514s (Intercept) stypeH stypeM 514s 28.7449 0.7551 0.4022 514s 514s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 514s (66 observations deleted due to missingness) 514s Null Deviance: 1838 514s Residual Deviance: 1835 AIC: 719.8 514s > g(acs.46~stype) 515s Stratified Independent Sampling design 515s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 515s fpc = ~fpc) 515s 515s Call: svyglm(formula = form, design = dstrat) 515s 515s Coefficients: 515s (Intercept) stypeH stypeM 515s 28.7449 0.7551 0.4022 515s 515s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 515s (66 observations deleted due to missingness) 515s Null Deviance: 1838 515s Residual Deviance: 1835 AIC: 719.8 515s > 515s > f<-function(){ 515s + form<-Surv(acs.46)~stype 515s + svycoxph(formula=form, design = dstrat) 515s + } 515s > 515s > g<-function(form){ 515s + svycoxph(formula=form, design = dstrat) 515s + } 515s > 515s > f() 515s Call: 515s svycoxph(formula = form, design = dstrat) 515s 515s coef exp(coef) se(coef) robust se z p 515s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 515s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 515s 515s Likelihood ratio test= on 2 df, p= 515s n= 134, number of events= 134 515s (66 observations deleted due to missingness) 515s > g(Surv(acs.46)~stype) 515s Call: 515s svycoxph(formula = form, design = dstrat) 515s 515s coef exp(coef) se(coef) robust se z p 515s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 515s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 515s 515s Likelihood ratio test= on 2 df, p= 515s n= 134, number of events= 134 515s (66 observations deleted due to missingness) 515s > 515s > ## check coxph for a single predictor 515s > svycoxph(Surv(acs.46)~api00,design=dstrat) 515s Call: 515s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 515s 515s coef exp(coef) se(coef) robust se z p 515s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 515s 515s Likelihood ratio test= on 1 df, p= 515s n= 134, number of events= 134 515s (66 observations deleted due to missingness) 515s > 515s BEGIN TEST survcurve.R 515s 515s R version 4.4.3 (2025-02-28) -- "Trophy Case" 515s Copyright (C) 2025 The R Foundation for Statistical Computing 515s Platform: arm-unknown-linux-gnueabihf (32-bit) 515s 515s R is free software and comes with ABSOLUTELY NO WARRANTY. 515s You are welcome to redistribute it under certain conditions. 515s Type 'license()' or 'licence()' for distribution details. 515s 515s R is a collaborative project with many contributors. 515s Type 'contributors()' for more information and 515s 'citation()' on how to cite R or R packages in publications. 515s 515s Type 'demo()' for some demos, 'help()' for on-line help, or 515s 'help.start()' for an HTML browser interface to help. 515s Type 'q()' to quit R. 515s 515s > library(survey) 515s Loading required package: grid 515s Loading required package: Matrix 516s Loading required package: survival 516s 516s Attaching package: 'survey' 516s 516s > library(survival) 516s The following object is masked from 'package:graphics': 516s 516s dotchart 516s 516s > 516s > pbc2<-rbind(pbc,pbc) 516s > pbc2$id<-rep(1:418,2) 516s > 516s > dpbc1<-svydesign(id=~1, data=pbc) 516s > dpbc2<-svydesign(id=~id, data=pbc2) 516s Warning message: 516s In svydesign.default(id = ~1, data = pbc) : 516s No weights or probabilities supplied, assuming equal probability 516s > 516s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 516s Warning message: 516s In svydesign.default(id = ~id, data = pbc2) : 516s No weights or probabilities supplied, assuming equal probability 516s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 516s > 516s > (c1<-confint(s1,(1:5)*365)) 516s 0.025 0.975 516s 365 0.6446215 0.8594153 516s 730 0.5410938 0.7766848 516s 1095 0.2683127 0.5103356 516s 1460 0.1444731 0.3722001 516s 1825 0.1009672 0.3204713 516s > (c2<-confint(s2,(1:5)*365)) 516s 0.025 0.975 516s 365 0.6446215 0.8594153 516s 730 0.5410938 0.7766848 516s 1095 0.2683127 0.5103356 516s 1460 0.1444731 0.3722001 516s 1825 0.1009672 0.3204713 516s > all.equal(c1, c2) 516s [1] TRUE 516s > 516s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 516s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 516s > 516s > d<-data.frame(bili=c(5,10)) 516s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 516s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 519s > 519s > (pc1<-confint(p1[[1]],(1:5)*365)) 519s 0.025 0.975 519s 365 0.8410027 0.9266263 519s 730 0.7371114 0.8548312 519s 1095 0.5517779 0.7018583 519s 1460 0.4335073 0.5992819 519s 1825 0.3260899 0.5046241 519s > (pc2<-confint(p2[[1]],(1:5)*365)) 519s 0.025 0.975 519s 365 0.8409490 0.9267054 519s 730 0.7370152 0.8549432 519s 1095 0.5515848 0.7019513 519s 1460 0.4332252 0.5992968 519s 1825 0.3257172 0.5045795 519s > all.equal(pc1, pc2) 519s [1] "Mean relative difference: 0.0002070722" 519s > 519s > (q1<-quantile(p1[[2]])) 519s 0.75 0.5 0.25 519s 489 930 1492 519s > (q2<-quantile(p2[[2]])) 519s 0.75 0.5 0.25 519s 489 930 1492 519s > all.equal(q1,q2) 519s [1] TRUE 519s > 519s BEGIN TEST svyby-strings.R 519s 519s R version 4.4.3 (2025-02-28) -- "Trophy Case" 519s Copyright (C) 2025 The R Foundation for Statistical Computing 519s Platform: arm-unknown-linux-gnueabihf (32-bit) 519s 519s R is free software and comes with ABSOLUTELY NO WARRANTY. 519s You are welcome to redistribute it under certain conditions. 519s Type 'license()' or 'licence()' for distribution details. 519s 519s R is a collaborative project with many contributors. 519s Type 'contributors()' for more information and 519s 'citation()' on how to cite R or R packages in publications. 519s 519s Type 'demo()' for some demos, 'help()' for on-line help, or 519s 'help.start()' for an HTML browser interface to help. 519s Type 'q()' to quit R. 519s 519s > 519s > ## check that stringsAsFactors fixes the string levels problem 519s > data(api, package = "survey") 519s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 520s > est0 <- 520s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 520s > 520s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 520s > 520s BEGIN TEST svyby_bug.R 520s 520s R version 4.4.3 (2025-02-28) -- "Trophy Case" 520s Copyright (C) 2025 The R Foundation for Statistical Computing 520s Platform: arm-unknown-linux-gnueabihf (32-bit) 520s 520s R is free software and comes with ABSOLUTELY NO WARRANTY. 520s You are welcome to redistribute it under certain conditions. 520s Type 'license()' or 'licence()' for distribution details. 520s 520s R is a collaborative project with many contributors. 520s Type 'contributors()' for more information and 520s 'citation()' on how to cite R or R packages in publications. 520s 520s Type 'demo()' for some demos, 'help()' for on-line help, or 520s 'help.start()' for an HTML browser interface to help. 520s Type 'q()' to quit R. 520s 520s > library(survey) 520s Loading required package: grid 520s Loading required package: Matrix 521s Loading required package: survival 521s 521s Attaching package: 'survey' 521s 521s The following object is masked from 'package:graphics': 521s 521s dotchart 521s 521s > options(warn=2) 521s > 521s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 521s > data(api) 522s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 522s > svyby(~api99, ~stype, dclus1, svymean ) 522s stype api99 se 522s E E 607.7917 22.81660 522s H H 595.7143 41.76400 522s M M 608.6000 32.56064 522s > 522s > set.seed(123) 522s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 522s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 522s > 522s > # subsetting w/ na.rm = FALSE... 522s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 522s mean SE 522s api99 NA NA 522s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 522s mean SE 522s api99 595.71 41.764 522s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 522s mean SE 522s api99 NA NA 522s > 522s > # ... looks like this: 522s > svyby(~api99, ~stype, dclus1.na , svymean ) 522s stype api99 se 522s E E NA NA 522s H H 595.7143 41.764 522s M M NA NA 522s > 522s > # subsetting w/ na.rm = TRUE... 522s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 522s mean SE 522s api99 606.53 22.901 522s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 522s mean SE 522s api99 595.71 41.764 522s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 522s mean SE 522s api99 613.39 33.224 522s > 522s > # ... looks like this 522s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 522s stype api99 se 522s E E 606.5319 22.90084 522s H H 595.7143 41.76400 522s M M 613.3913 33.22358 522s > 522s > # Without missing values, this works: 522s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 522s stype api99 se 522s E E 607.7917 22.81660 522s H H 595.7143 41.76400 522s M M 608.6000 32.56064 522s > 522s > # ... but this breaks! 522s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 522s stype api99 se 522s E E 606.5319 22.90084 522s H H 595.7143 41.76400 522s M M 613.3913 33.22358 522s > 522s > # ... and i don't think this is the expected behavior 522s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 522s stype api99 se 522s E E NA NA 522s H H 595.7143 41.764 522s M M NA NA 522s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 522s stype api99 se 522s E E 606.5319 22.90084 522s H H 595.7143 41.76400 522s M M 613.3913 33.22358 522s > 522s > 522s > ## Now some more as tests 522s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 522s stype api99 se 522s E E 2894629.0 792809.8 522s H H 282283.9 101492.9 522s M M 477513.4 107555.5 522s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 522s stype api99/api00 se.api99/api00 522s E E 0.9367750 0.006365702 522s H H 0.9630485 0.010520785 522s M M 0.9682246 0.009390982 522s > 522s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 522s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 522s stype (Intercept) se.(Intercept) 522s E E 606.5319 22.90084 522s H H 595.7143 41.76400 522s M M 613.3913 33.22358 522s > 522s BEGIN TEST svyby_se.R 522s 522s R version 4.4.3 (2025-02-28) -- "Trophy Case" 522s Copyright (C) 2025 The R Foundation for Statistical Computing 522s Platform: arm-unknown-linux-gnueabihf (32-bit) 522s 522s R is free software and comes with ABSOLUTELY NO WARRANTY. 522s You are welcome to redistribute it under certain conditions. 522s Type 'license()' or 'licence()' for distribution details. 522s 522s R is a collaborative project with many contributors. 522s Type 'contributors()' for more information and 522s 'citation()' on how to cite R or R packages in publications. 522s 522s Type 'demo()' for some demos, 'help()' for on-line help, or 522s 'help.start()' for an HTML browser interface to help. 522s Type 'q()' to quit R. 522s 522s > library(survey) 522s Loading required package: grid 522s Loading required package: Matrix 523s Loading required package: survival 523s 523s Attaching package: 'survey' 523s 523s > data(api) 523s The following object is masked from 'package:graphics': 523s 523s dotchart 523s 523s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 523s > 523s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 523s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 523s > 523s > 523s > stopifnot(all.equal(SE(a),SE(b))) 523s > 523s BEGIN TEST svycontrast.R 523s 523s R version 4.4.3 (2025-02-28) -- "Trophy Case" 523s Copyright (C) 2025 The R Foundation for Statistical Computing 523s Platform: arm-unknown-linux-gnueabihf (32-bit) 523s 523s R is free software and comes with ABSOLUTELY NO WARRANTY. 523s You are welcome to redistribute it under certain conditions. 523s Type 'license()' or 'licence()' for distribution details. 523s 523s R is a collaborative project with many contributors. 523s Type 'contributors()' for more information and 523s 'citation()' on how to cite R or R packages in publications. 523s 523s Type 'demo()' for some demos, 'help()' for on-line help, or 523s 'help.start()' for an HTML browser interface to help. 523s Type 'q()' to quit R. 523s 523s > library(survey) 523s Loading required package: grid 523s Loading required package: Matrix 524s Loading required package: survival 525s 525s Attaching package: 'survey' 525s 525s The following object is masked from 'package:graphics': 525s 525s dotchart 525s 525s > data(api) 525s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 525s > rclus2<-as.svrepdesign(dclus2) 525s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 525s > svycontrast(model, c(ell=1,meals=0)) 525s contrast SE 525s contrast -2.0592 1.6177 525s > a<-svycontrast(model, c(0,1,0,0)) 525s > 525s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 525s > svycontrast(model2, c(ell=1,meals=0)) 525s contrast SE 525s contrast -2.0592 1.6177 525s > a2<-svycontrast(model2, c(0,1,0,0)) 525s > stopifnot(!is.null(a2$replicates)) 525s > 525s BEGIN TEST svyivreg-var.R 525s 525s R version 4.4.3 (2025-02-28) -- "Trophy Case" 525s Copyright (C) 2025 The R Foundation for Statistical Computing 525s Platform: arm-unknown-linux-gnueabihf (32-bit) 525s 525s R is free software and comes with ABSOLUTELY NO WARRANTY. 525s You are welcome to redistribute it under certain conditions. 525s Type 'license()' or 'licence()' for distribution details. 525s 525s R is a collaborative project with many contributors. 525s Type 'contributors()' for more information and 525s 'citation()' on how to cite R or R packages in publications. 525s 525s Type 'demo()' for some demos, 'help()' for on-line help, or 525s 'help.start()' for an HTML browser interface to help. 525s Type 'q()' to quit R. 525s 525s > 525s > library(survey) 525s Loading required package: grid 525s Loading required package: Matrix 526s Loading required package: survival 526s 526s Attaching package: 'survey' 526s 526s The following object is masked from 'package:graphics': 526s 526s dotchart 526s 526s > data(api) 526s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 526s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 526s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 526s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 526s > 526s BEGIN TEST svyivreg.R 526s 526s R version 4.4.3 (2025-02-28) -- "Trophy Case" 526s Copyright (C) 2025 The R Foundation for Statistical Computing 526s Platform: arm-unknown-linux-gnueabihf (32-bit) 526s 526s R is free software and comes with ABSOLUTELY NO WARRANTY. 526s You are welcome to redistribute it under certain conditions. 526s Type 'license()' or 'licence()' for distribution details. 526s 526s R is a collaborative project with many contributors. 526s Type 'contributors()' for more information and 526s 'citation()' on how to cite R or R packages in publications. 526s 526s Type 'demo()' for some demos, 'help()' for on-line help, or 526s 'help.start()' for an HTML browser interface to help. 526s Type 'q()' to quit R. 526s 526s > library(survey) 526s Loading required package: grid 527s Loading required package: Matrix 527s Loading required package: survival 528s 528s Attaching package: 'survey' 528s 528s > library(AER) 528s The following object is masked from 'package:graphics': 528s 528s dotchart 528s 528s Loading required package: car 528s Loading required package: carData 528s Loading required package: lmtest 528s Loading required package: zoo 528s 528s Attaching package: 'zoo' 528s 528s The following objects are masked from 'package:base': 528s 528s as.Date, as.Date.numeric 528s 528s Loading required package: sandwich 528s > 528s > load("cigsw.rda") 528s > 528s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 528s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 528s > 528s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 528s [1] TRUE 528s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 528s [1] TRUE 528s > 528s BEGIN TEST svyolr-rake-subset.R 528s 528s R version 4.4.3 (2025-02-28) -- "Trophy Case" 528s Copyright (C) 2025 The R Foundation for Statistical Computing 528s Platform: arm-unknown-linux-gnueabihf (32-bit) 528s 528s R is free software and comes with ABSOLUTELY NO WARRANTY. 528s You are welcome to redistribute it under certain conditions. 528s Type 'license()' or 'licence()' for distribution details. 528s 528s R is a collaborative project with many contributors. 528s Type 'contributors()' for more information and 528s 'citation()' on how to cite R or R packages in publications. 528s 528s Type 'demo()' for some demos, 'help()' for on-line help, or 528s 'help.start()' for an HTML browser interface to help. 528s Type 'q()' to quit R. 528s 528s > library(survey) 528s Loading required package: grid 528s Loading required package: Matrix 529s Loading required package: survival 529s 529s Attaching package: 'survey' 529s 529s The following object is masked from 'package:graphics': 529s 529s dotchart 529s 529s > data(api) 529s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 529s > 529s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 529s > 529s > ## population marginal totals for each stratum 529s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 529s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 529s > 529s > 529s > ## rake with the population totals 529s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 529s > 529s > # works 529s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 529s > 529s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 529s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 529s > 529s > # fails in 4.1 (should work because NA values are subsetted out) 529s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 530s > 530s BEGIN TEST svyolr.R 530s 530s R version 4.4.3 (2025-02-28) -- "Trophy Case" 530s Copyright (C) 2025 The R Foundation for Statistical Computing 530s Platform: arm-unknown-linux-gnueabihf (32-bit) 530s 530s R is free software and comes with ABSOLUTELY NO WARRANTY. 530s You are welcome to redistribute it under certain conditions. 530s Type 'license()' or 'licence()' for distribution details. 530s 530s R is a collaborative project with many contributors. 530s Type 'contributors()' for more information and 530s 'citation()' on how to cite R or R packages in publications. 530s 530s Type 'demo()' for some demos, 'help()' for on-line help, or 530s 'help.start()' for an HTML browser interface to help. 530s Type 'q()' to quit R. 530s 530s > library(survey) 530s Loading required package: grid 530s Loading required package: Matrix 531s Loading required package: survival 531s > 531s > ################################################################################ 531s > # Example from svyolr: runs OK 531s > data(api) 531s 531s Attaching package: 'survey' 531s 531s The following object is masked from 'package:graphics': 531s 531s dotchart 531s 531s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 531s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 531s > 531s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 531s > m 531s Call: 531s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 531s 531s Coefficients: 531s avg.ed mobility stypeH stypeM 531s -2.6999217 0.0325042 -1.7574715 -0.6191463 531s 531s Intercepts: 531s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 531s -8.857919 -6.586464 -4.924938 531s > 531s > ## Use regTermTest for testing multiple parameters 531s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 531s > ################################################################################ 531s > 531s > ################################################################################ 531s > # If we wrap everything into a function: error b/c it looks for design variable 531s > # dclus1 in .GlobalEnv 531s > 531s > foo <- function(x){ 531s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 531s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 531s + 531s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 531s + ## Use regTermTest for testing multiple parameters 531s + regTermTest(m, ~avg.ed+stype, method="LRT") 531s + } 531s > 531s > # OK 531s > foo(apiclus1) 531s Working (Rao-Scott+F) LRT for avg.ed stype 531s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 531s Working 2logLR = 0.6580304 p= 0.73257 531s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 531s > 531s > # Clean-up everything but apiclus1 and foo 531s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 531s > 531s > # Error 531s > test2<-foo(apiclus1) 531s > ################################################################################ 531s > all.equal(test,test2) 531s [1] TRUE 531s > 531s > 531s BEGIN TEST toy_example_for_postStratify.R 531s 531s R version 4.4.3 (2025-02-28) -- "Trophy Case" 531s Copyright (C) 2025 The R Foundation for Statistical Computing 531s Platform: arm-unknown-linux-gnueabihf (32-bit) 531s 531s R is free software and comes with ABSOLUTELY NO WARRANTY. 531s You are welcome to redistribute it under certain conditions. 531s Type 'license()' or 'licence()' for distribution details. 531s 531s R is a collaborative project with many contributors. 531s Type 'contributors()' for more information and 531s 'citation()' on how to cite R or R packages in publications. 531s 531s Type 'demo()' for some demos, 'help()' for on-line help, or 531s 'help.start()' for an HTML browser interface to help. 531s Type 'q()' to quit R. 531s 531s Loading required package: grid 531s > library(survey) 531s Loading required package: Matrix 532s Loading required package: survival 533s 533s Attaching package: 'survey' 533s 533s The following object is masked from 'package:graphics': 533s 533s dotchart 533s 533s > 533s > # Dummy data for testing nonresponse adjustments 533s > toy <- data.frame(id = 1:10, 533s + dummy = 1, 533s + class = c(rep("A", 5), rep("B", 5)), 533s + responded = c(rep(TRUE, 8), FALSE, FALSE), 533s + weight = rep(100, 10)) 533s > 533s > # With jackknife replicate weights 533s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 533s > diag(toy_repweights) <- rep(0, 10) 533s > 533s > # Scramble up which person is in which jackknife group 533s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 533s > 533s > toy_design <- svrepdesign(variables = toy[, 1:4], 533s + weights = toy$weight, 533s + repweights = toy_repweights, 533s + type = "JK1", 533s + scale = 0.9) 533s > 533s > # Get the sum of the weights for the full sample 533s > poptotals <- as.data.frame(svyby(formula = ~dummy, 533s + by = ~class, 533s + design = toy_design, 533s + FUN = survey::svytotal)) 533s > 533s > poptotals$Freq <- poptotals$dummy 533s > poptotals$dummy <- NULL 533s > poptotals$se <- NULL 533s > 533s > # Adjust the weights of the responding sample to match to the full sample 533s > adjusted <- postStratify(design = subset(toy_design, responded), 533s + strata = ~class, 533s + population = poptotals) 533s > 533s > # This works for the weights... 533s > svyby(formula = ~dummy, 533s + by = ~class, 533s + design = adjusted, 533s + FUN = survey::svytotal) 533s class dummy se 533s A A 500 0 533s B B 500 0 533s > 533s > # ...and some, but not all, the replicate weights 533s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 533s > 533s > 533s > 533s BEGIN TEST twophase.R 533s 533s R version 4.4.3 (2025-02-28) -- "Trophy Case" 533s Copyright (C) 2025 The R Foundation for Statistical Computing 533s Platform: arm-unknown-linux-gnueabihf (32-bit) 533s 533s R is free software and comes with ABSOLUTELY NO WARRANTY. 533s You are welcome to redistribute it under certain conditions. 533s Type 'license()' or 'licence()' for distribution details. 533s 533s R is a collaborative project with many contributors. 533s Type 'contributors()' for more information and 533s 'citation()' on how to cite R or R packages in publications. 533s 533s Type 'demo()' for some demos, 'help()' for on-line help, or 533s 'help.start()' for an HTML browser interface to help. 533s Type 'q()' to quit R. 533s 533s > library(survey) 533s Loading required package: grid 533s Loading required package: Matrix 534s Loading required package: survival 534s 534s Attaching package: 'survey' 534s 534s > 534s > ## two-phase simple random sampling. 534s > data(pbc, package="survival") 534s The following object is masked from 'package:graphics': 534s 534s dotchart 534s 534s > pbc$id<-1:nrow(pbc) 534s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 534s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 534s Two-phase sparse-matrix design: 534s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 534s subset = subset, data = data, pps = pps) 534s Phase 1: 534s Independent Sampling design (with replacement) 534s svydesign(ids = ~id) 534s Phase 2: 534s Independent Sampling design 534s svydesign(ids = ~id, fpc = `*phase1*`) 534s > m<-svymean(~bili, d2pbc) 534s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 534s [1] TRUE 534s > all.equal(as.vector(SE(m)), 534s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 534s + tolerance=0.002) 534s [1] TRUE 534s > 534s > ## two-stage sampling as two-phase 534s > data(mu284) 534s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 534s > mu284.1<-mu284[ii,] 534s > mu284.1$id<-1:nrow(mu284.1) 534s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 534s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 534s > ## first phase cluster sample, second phase stratified within cluster 534s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 534s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 534s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 534s NULL), data = mu284.1, subset = ~sub, method = "approx") 534s Phase 1: 534s 1 - level Cluster Sampling design 534s With (5) clusters. 534s svydesign(ids = ~id1, fpc = ~n1) 534s Phase 2: 534s Stratified Independent Sampling design 534s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 534s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 534s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 534s Two-phase sparse-matrix design: 534s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 534s subset = subset, data = data, pps = pps) 534s Phase 1: 534s 1 - level Cluster Sampling design 534s With (5) clusters. 534s svydesign(ids = ~id1, fpc = ~n1) 534s Phase 2: 534s Stratified Independent Sampling design 534s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 534s > summary(d2mu284) 534s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 534s NULL), data = mu284.1, subset = ~sub, method = "approx") 534s Phase 1: 534s 1 - level Cluster Sampling design 534s With (5) clusters. 534s svydesign(ids = ~id1, fpc = ~n1) 534s Probabilities: 534s Min. 1st Qu. Median Mean 3rd Qu. Max. 534s 0.1 0.1 0.1 0.1 0.1 0.1 534s Population size (PSUs): 50 534s Phase 2: 534s Stratified Independent Sampling design 534s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 534s Probabilities: 534s Min. 1st Qu. Median Mean 3rd Qu. Max. 534s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 534s Stratum Sizes: 534s 19 31 45 47 50 534s obs 3 3 3 3 3 534s design.PSU 3 3 3 3 3 534s actual.PSU 3 3 3 3 3 534s Population stratum sizes (PSUs): 534s 19 31 45 47 50 534s 5 7 8 5 9 534s Data variables: 534s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 534s > t1<-svytotal(~y1, dmu284) 534s > t2<-svytotal(~y1, d2mu284) 534s > t22<-svytotal(~y1,d22mu284) 534s > m1<-svymean(~y1, dmu284) 534s > m2<-svymean(~y1, d2mu284) 534s > m22<-svymean(~y1, d22mu284) 534s > all.equal(coef(t1),coef(t2)) 534s [1] TRUE 534s > all.equal(coef(t1),coef(t22)) 534s [1] TRUE 534s > all.equal(coef(m1),coef(m2)) 534s [1] TRUE 534s > all.equal(coef(m1),coef(m22)) 534s [1] TRUE 534s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 534s [1] TRUE 534s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 534s [1] TRUE 534s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 534s [1] TRUE 534s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 534s [1] TRUE 534s > 534s > ## case-cohort design 534s > ##this example requires R 2.3.1 or later for cch and data. 534s > library("survival") 534s > data(nwtco, package="survival") 534s > ## unstratified, equivalent to Lin & Ying (1993) 534s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 534s + subset=~I(in.subcohort | rel), data=nwtco)) 535s Two-phase sparse-matrix design: 535s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 535s subset = subset, data = data, pps = pps) 535s Phase 1: 535s Independent Sampling design (with replacement) 535s svydesign(ids = ~seqno) 535s Phase 2: 535s Stratified Independent Sampling design 535s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 535s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 535s + design=dcchs) 535s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 535s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 535s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 535s + design=dcchs) 535s > all.equal(coef(cch1),coef(cch1.2)) 535s [1] TRUE 535s > all.equal(SE(cch1),SE(cch1.2)) 535s [1] TRUE 535s > ## Using survival::cch 535s > subcoh <- nwtco$in.subcohort 535s > selccoh <- with(nwtco, rel==1|subcoh==1) 535s > ccoh.data <- nwtco[selccoh,] 535s > ccoh.data$subcohort <- subcoh[selccoh] 535s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 535s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 535s + cohort.size=4028, method="LinYing", robust=TRUE) 535s > 535s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 535s [1] TRUE 535s > ## cch has smaller variances by a factor of 1.0005 because 535s > ## there is a (n/(n-1)) in the survey phase1 varianace 535s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 535s [1] TRUE 535s > 535s > 535s > ## bug report from Takahiro Tsuchiya for version 3.4 535s > ## We used to not match Sarndal exactly, because our old phase-one 535s > ## estimator had a small bias for finite populations 535s > rei<-read.table(tmp<-textConnection( 535s + " id N n.a h n.ah n.h sub y 535s + 1 1 300 20 1 12 5 TRUE 1 535s + 2 2 300 20 1 12 5 TRUE 2 535s + 3 3 300 20 1 12 5 TRUE 3 535s + 4 4 300 20 1 12 5 TRUE 4 535s + 5 5 300 20 1 12 5 TRUE 5 535s + 6 6 300 20 1 12 5 FALSE NA 535s + 7 7 300 20 1 12 5 FALSE NA 535s + 8 8 300 20 1 12 5 FALSE NA 535s + 9 9 300 20 1 12 5 FALSE NA 535s + 10 10 300 20 1 12 5 FALSE NA 535s + 11 11 300 20 1 12 5 FALSE NA 535s + 12 12 300 20 1 12 5 FALSE NA 535s + 13 13 300 20 2 8 3 TRUE 6 535s + 14 14 300 20 2 8 3 TRUE 7 535s + 15 15 300 20 2 8 3 TRUE 8 535s + 16 16 300 20 2 8 3 FALSE NA 535s + 17 17 300 20 2 8 3 FALSE NA 535s + 18 18 300 20 2 8 3 FALSE NA 535s + 19 19 300 20 2 8 3 FALSE NA 535s + 20 20 300 20 2 8 3 FALSE NA 535s + "), header=TRUE) 535s > close(tmp) 535s > 535s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 535s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 535s > tot<- svytotal(~y, des.rei) 535s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 535s + fpc=list(~N,NULL), subset=~sub, data=rei) 535s > tot2<- svytotal(~y, des.rei2) 535s > 535s > ## based on Sarndal et al (9.4.14) 535s > rei$w.ah <- rei$n.ah / rei$n.a 535s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 535s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 535s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 535s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 535s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 535s > 535s > a.rei$f.h<-with(a.rei, n.h/n.ah) 535s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 535s > 535s > a.rei$f<-with(a.rei, n.a/N) 535s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 535s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 535s > 535s > V 535s [1] 36522.63 535s > Vphase1 535s [1] 24072.63 535s > Vphase2 535s [1] 12450 535s > vcov(tot) 535s y 535s y 35911.05 535s attr(,"phases") 535s attr(,"phases")$phase1 535s [,1] 535s [1,] 23461.05 535s 535s attr(,"phases")$phase2 535s y 535s y 12450 535s 535s > vcov(tot2) 535s [,1] 535s [1,] 36522.63 535s attr(,"phases") 535s attr(,"phases")$phase1 535s [,1] 535s [1,] 24072.63 535s 535s attr(,"phases")$phase2 535s [,1] 535s [1,] 12450 535s 535s > ## phase 2 identical 535s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 535s [1] TRUE 535s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 535s [1] TRUE 535s > ## phase 1 differs by 2.6% for old twophase estimator 535s > Vphase1/attr(vcov(tot),"phases")$phase1 535s [,1] 535s [1,] 1.026068 535s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 535s [1] TRUE 535s > 535s > 535s autopkgtest [15:54:14]: test run-unit-test: -----------------------] 539s run-unit-test PASS 539s autopkgtest [15:54:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 543s autopkgtest [15:54:22]: test pkg-r-autopkgtest: preparing testbed 566s autopkgtest [15:54:45]: testbed dpkg architecture: armhf 567s autopkgtest [15:54:46]: testbed apt version: 2.9.33 571s autopkgtest [15:54:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 573s autopkgtest [15:54:52]: testbed release detected to be: plucky 581s autopkgtest [15:55:00]: updating testbed package index (apt update) 583s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 583s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 584s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 584s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 584s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 584s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 584s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 585s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 585s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 585s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 585s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 585s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 585s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 585s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 585s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 586s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 587s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 610s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 612s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 612s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 612s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 629s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 631s Fetched 41.0 MB in 48s (852 kB/s) 632s Reading package lists... 638s autopkgtest [15:55:57]: upgrading testbed (apt dist-upgrade and autopurge) 639s Reading package lists... 640s Building dependency tree... 640s Reading state information... 640s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 640s Starting 2 pkgProblemResolver with broken count: 0 640s Done 641s Entering ResolveByKeep 642s 642s Calculating upgrade... 642s The following packages will be upgraded: 642s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 642s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 642s Need to get 8683 kB of archives. 642s After this operation, 23.6 kB of additional disk space will be used. 642s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 646s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 647s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 651s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 652s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 652s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 652s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 653s Preconfiguring packages ... 653s Fetched 8683 kB in 10s (859 kB/s) 653s (Reading database ... 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upgraded. 670s autopkgtest [15:56:29]: rebooting testbed after setup commands that affected boot 735s Reading package lists... 735s Building dependency tree... 735s Reading state information... 736s Starting pkgProblemResolver with broken count: 0 736s Starting 2 pkgProblemResolver with broken count: 0 736s Done 737s The following NEW packages will be installed: 737s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 737s cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config 737s fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax 737s g++ g++-14 g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 737s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gfortran gfortran-14 737s gfortran-14-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf icu-devtools 737s libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 737s libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 737s libfreetype6 libgcc-14-dev libgfortran-14-dev libgfortran5 libgomp1 737s libgraphite2-3 libharfbuzz0b libice6 libicu-dev libisl23 libjbig0 737s libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 737s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 737s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblzma-dev libmpc3 737s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 737s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 737s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 737s libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 libthai-data 737s libthai0 libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7 libxcb-render0 737s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler 737s node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core 737s r-base-dev r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 737s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 737s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 737s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 737s r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 737s r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby 737s r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi 737s r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign 737s r-cran-formula r-cran-future r-cran-future.apply r-cran-generics 737s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable 737s r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms 737s r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr 737s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 737s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 737s r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats 737s r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools 737s r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr 737s r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly 737s r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 737s r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress 737s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg 737s r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rbibutils 737s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 737s r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 737s r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang r-cran-rpart 737s r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape r-cran-sparsem 737s r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey 737s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 737s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 737s r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun 737s r-cran-yaml r-cran-zip r-cran-zoo rpcsvc-proto unzip x11-common xdg-utils 737s zip zlib1g-dev 737s 0 upgraded, 257 newly installed, 0 to remove and 0 not upgraded. 737s Need to get 243 MB of archives. 737s After this operation, 563 MB of additional disk space will be used. 737s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-dev-bin armhf 2.41-1ubuntu2 [23.0 kB] 737s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.14.0-10.10 [1683 kB] 739s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 739s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 739s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6-dev armhf 2.41-1ubuntu2 [1396 kB] 740s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 741s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 741s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9220 kB] 751s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu3 [1030 B] 751s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 751s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 751s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250222-0ubuntu1 [38.9 kB] 751s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 751s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250222-0ubuntu1 [2955 kB] 754s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250222-0ubuntu1 [1191 kB] 756s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu3 [897 kB] 756s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [18.0 MB] 776s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu3 [506 kB] 777s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 777s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 777s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu3 [2573 kB] 779s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [10.5 MB] 790s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu3 [21.8 kB] 790s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 790s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 790s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 790s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 790s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 790s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 792s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 793s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 793s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 793s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 793s Get:34 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 793s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 795s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 795s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran-14-dev armhf 14.2.0-17ubuntu3 [370 kB] 796s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9763 kB] 806s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14 armhf 14.2.0-17ubuntu3 [13.6 kB] 806s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 806s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 806s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 807s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 807s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 807s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 807s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 807s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 807s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 807s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 807s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 808s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 808s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 808s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 808s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 808s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 808s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 808s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 809s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 821s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 821s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 821s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 821s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 821s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 821s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 822s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 822s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 822s Get:67 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 823s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 825s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 827s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 827s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 828s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 828s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 828s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 828s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 828s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 828s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 828s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 828s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 829s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 829s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 829s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 829s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 829s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 830s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libpng-dev armhf 1.6.47-1 [251 kB] 831s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline-dev armhf 8.2-6 [153 kB] 831s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 831s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 831s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 832s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 832s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 832s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 832s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 832s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 832s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 833s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 833s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 833s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 834s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 834s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 866s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-littler armhf 0.3.20-2 [90.9 kB] 866s Get:102 http://ftpmaster.internal/ubuntu plucky/universe armhf littler all 0.3.20-2 [2554 B] 866s Get:103 http://ftpmaster.internal/ubuntu plucky/universe armhf node-normalize.css all 8.0.1-5 [10.8 kB] 866s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.4-1 [166 kB] 866s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 866s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 866s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 866s Get:108 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-dev all 4.4.3-1 [4176 B] 866s Get:109 http://ftpmaster.internal/ubuntu plucky/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 866s Get:110 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-abind all 1.4-8-1 [66.9 kB] 866s Get:111 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cardata all 3.0.5-1 [1819 kB] 868s Get:112 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-formula all 1.2-5-1 [158 kB] 868s Get:113 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mass armhf 7.3-64-1 [1105 kB] 870s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 871s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nlme armhf 3.1.167-1 [2306 kB] 874s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 878s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 882s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 882s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-boot all 1.3-31-1 [635 kB] 883s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 883s Get:121 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcpp armhf 1.0.14-1 [1976 kB] 885s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-minqa armhf 1.2.8-1 [108 kB] 885s Get:123 http://ftpmaster.internal/ubuntu plucky/universe armhf libnlopt0 armhf 2.7.1-6ubuntu3 [154 kB] 886s Get:124 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nloptr armhf 2.1.1-1 [250 kB] 886s Get:125 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rbibutils armhf 2.3-1 [943 kB] 887s Get:126 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 888s Get:127 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-reformulas all 0.4.0-1 [91.5 kB] 888s Get:128 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 889s Get:129 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-statmod armhf 1.5.0-1 [294 kB] 890s Get:130 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lme4 armhf 1.1-36-1 [4108 kB] 895s Get:131 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 895s Get:132 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 897s Get:133 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-generics all 0.1.3-1 [81.3 kB] 897s Get:134 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 897s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rlang armhf 1.1.5-1 [1701 kB] 899s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 899s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 899s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 899s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 901s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 901s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 901s Get:142 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-fansi armhf 1.0.5-1 [611 kB] 902s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 902s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 903s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 903s Get:146 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 903s Get:147 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 905s Get:148 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 906s Get:149 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-stringi armhf 1.8.4-1build1 [887 kB] 907s Get:150 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 907s Get:151 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cpp11 all 0.5.2-1 [233 kB] 907s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 909s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 911s Get:154 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-numderiv all 2016.8-1.1-3 [115 kB] 911s Get:155 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 911s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 913s Get:157 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 915s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 915s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 917s Get:160 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-munsell all 0.5.1-1 [213 kB] 917s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 917s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-viridislite all 0.4.2-2 [1088 kB] 918s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-scales all 1.3.0-1 [603 kB] 919s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 924s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 924s Get:166 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-deriv all 4.1.6-1 [151 kB] 925s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-modelr all 0.1.11-1 [195 kB] 925s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-microbenchmark armhf 1.5.0-1 [67.8 kB] 925s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-doby all 4.6.25-1 [4772 kB] 930s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-evaluate all 1.0.3-1 [114 kB] 930s Get:171 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-xfun armhf 0.51+dfsg-1 [573 kB] 931s Get:172 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 931s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 931s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 938s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-knitr all 1.49+dfsg-1 [859 kB] 939s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-pbkrtest all 0.5.3-1 [178 kB] 939s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-sparsem armhf 1.84-2-1 [807 kB] 940s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrixmodels all 0.5-3-1 [361 kB] 940s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 950s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrixstats armhf 1.5.0-1 [495 kB] 950s Get:181 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rcpparmadillo armhf 14.2.3-1-1 [842 kB] 951s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-class armhf 7.3-23-1 [88.8 kB] 951s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-proxy armhf 0.4-27-1 [180 kB] 952s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-e1071 armhf 1.7-16-1 [557 kB] 952s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-codetools all 0.2-20-1 [90.5 kB] 952s Get:186 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-iterators all 1.0.14-1 [336 kB] 953s Get:187 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-foreach all 1.5.2-1 [124 kB] 953s Get:188 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 956s Get:189 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-modelmetrics armhf 1.2.2.2-1build1 [120 kB] 956s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-plyr armhf 1.8.9-1 [832 kB] 957s Get:191 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-proc armhf 1.18.5-1 [961 kB] 958s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-tzdb armhf 0.4.0-2 [512 kB] 959s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-clock armhf 0.7.2-1 [1858 kB] 961s Get:194 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-gower armhf 1.0.2-1 [208 kB] 961s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-hardhat all 1.4.0+dfsg-1 [565 kB] 962s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 963s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-shape all 1.4.6.1-1 [749 kB] 964s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-diagram all 1.6.5-2 [656 kB] 964s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-kernsmooth armhf 2.23-26-1 [91.6 kB] 964s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-digest armhf 0.6.37-1 [207 kB] 965s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-globals all 0.16.3-1 [120 kB] 965s Get:202 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 965s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-parallelly armhf 1.42.0-1 [540 kB] 966s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-future all 1.34.0+dfsg-1 [646 kB] 967s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 967s Get:206 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-progressr all 0.15.1-1 [353 kB] 968s Get:207 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-squarem all 2021.1-1 [179 kB] 968s Get:208 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lava all 1.8.1+dfsg-1 [2191 kB] 970s Get:209 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-prodlim armhf 2024.06.25-1 [413 kB] 971s Get:210 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ipred armhf 0.9-15-1 [385 kB] 971s Get:211 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-timechange armhf 0.3.0-1 [182 kB] 972s Get:212 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lubridate armhf 1.9.4+dfsg-1 [1008 kB] 973s Get:213 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-timedate armhf 4041.110-1 [1209 kB] 974s Get:214 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 977s Get:215 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-reshape2 armhf 1.4.4-2build1 [110 kB] 977s Get:216 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-caret armhf 7.0-1+dfsg-1 [3460 kB] 980s Get:217 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-conquer armhf 1.3.3-1 [460 kB] 981s Get:218 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-quantreg armhf 6.00-1 [1427 kB] 982s Get:219 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-foreign armhf 0.8.88-1 [240 kB] 983s Get:220 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-ellipsis armhf 0.3.2-2 [35.0 kB] 983s Get:221 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-forcats all 1.0.0-1 [369 kB] 983s Get:222 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-hms all 1.1.3-1 [96.5 kB] 983s Get:223 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-clipr all 0.8.0-1 [53.5 kB] 984s Get:224 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-crayon all 1.5.3-1 [165 kB] 984s Get:225 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-bit armhf 4.6.0+dfsg-1 [447 kB] 984s Get:226 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-bit64 armhf 4.6.0-1-1ubuntu2 [491 kB] 985s Get:227 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-prettyunits all 1.2.0-1 [162 kB] 985s Get:228 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-progress all 1.2.3-1 [91.9 kB] 985s Get:229 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-vroom armhf 1.6.5-1 [822 kB] 986s Get:230 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-readr armhf 2.1.5-1 [752 kB] 987s Get:231 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-haven armhf 2.5.4-1 [327 kB] 987s Get:232 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-curl armhf 6.2.1+dfsg-1ubuntu1 [194 kB] 987s Get:233 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rematch all 2.0.0-1 [18.3 kB] 987s Get:234 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cellranger all 1.1.0-3 [102 kB] 988s Get:235 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-readxl armhf 1.4.4-1 [336 kB] 988s Get:236 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-writexl armhf 1.5.1-1 [144 kB] 988s Get:237 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 988s Get:238 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.oo all 1.27.0-1 [979 kB] 989s Get:239 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-r.utils all 2.13.0-1 [1423 kB] 991s Get:240 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-zip armhf 2.3.2-1 [137 kB] 991s Get:241 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-openxlsx armhf 4.2.8-1 [2024 kB] 993s Get:242 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rio all 1.2.3-1 [546 kB] 994s Get:243 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-car all 3.1-3-1 [1525 kB] 996s Get:244 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-zoo armhf 1.8-13-1 [996 kB] 997s Get:245 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lmtest armhf 0.9.40-1 [396 kB] 998s Get:246 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-sandwich all 3.1-1-1 [1483 kB] 999s Get:247 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-aer all 1.2-14-1 [2597 kB] 1002s Get:248 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-blob all 1.2.4-1 [49.8 kB] 1002s Get:249 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-fastmap armhf 1.2.0-1 [69.8 kB] 1002s Get:250 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cachem armhf 1.1.0-1 [73.8 kB] 1003s Get:251 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-dbi all 1.2.3-1 [853 kB] 1004s Get:252 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-hexbin armhf 1.28.5-1 [1580 kB] 1006s Get:253 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-memoise all 2.0.1-1 [53.9 kB] 1006s Get:254 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mitools all 2.4-2build1 [265 kB] 1006s Get:255 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-plogr all 0.2.0-3build1 [15.1 kB] 1006s Get:256 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-rsqlite armhf 2.3.9-1 [1157 kB] 1008s Get:257 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-survey armhf 4.4-2-2 [3448 kB] 1012s Preconfiguring packages ... 1012s Fetched 243 MB in 4min 35s (884 kB/s) 1012s Selecting previously unselected package libc-dev-bin. 1012s (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 ... 64655 files and directories currently installed.) 1012s Preparing to unpack .../000-libc-dev-bin_2.41-1ubuntu2_armhf.deb ... 1012s Unpacking libc-dev-bin (2.41-1ubuntu2) ... 1012s Selecting previously unselected package linux-libc-dev:armhf. 1012s Preparing to unpack .../001-linux-libc-dev_6.14.0-10.10_armhf.deb ... 1012s Unpacking linux-libc-dev:armhf (6.14.0-10.10) ... 1013s Selecting previously unselected package libcrypt-dev:armhf. 1013s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 1013s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 1013s Selecting previously unselected package rpcsvc-proto. 1013s Preparing to unpack .../003-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 1013s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 1013s Selecting previously unselected package libc6-dev:armhf. 1013s Preparing to unpack .../004-libc6-dev_2.41-1ubuntu2_armhf.deb ... 1013s Unpacking libc6-dev:armhf (2.41-1ubuntu2) ... 1013s Selecting previously unselected package libisl23:armhf. 1013s Preparing to unpack .../005-libisl23_0.27-1_armhf.deb ... 1013s Unpacking libisl23:armhf (0.27-1) ... 1013s Selecting previously unselected package libmpc3:armhf. 1013s Preparing to unpack .../006-libmpc3_1.3.1-1build2_armhf.deb ... 1013s Unpacking libmpc3:armhf (1.3.1-1build2) ... 1013s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 1013s Preparing to unpack .../007-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 1013s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 1013s Selecting previously unselected package cpp-14. 1013s Preparing to unpack .../008-cpp-14_14.2.0-17ubuntu3_armhf.deb ... 1013s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 1013s Selecting previously unselected package cpp-arm-linux-gnueabihf. 1013s Preparing to unpack .../009-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 1013s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 1013s Selecting previously unselected package cpp. 1013s Preparing to unpack .../010-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 1013s Unpacking cpp (4:14.2.0-1ubuntu1) ... 1013s Selecting previously unselected package libcc1-0:armhf. 1013s Preparing to unpack .../011-libcc1-0_15-20250222-0ubuntu1_armhf.deb ... 1013s Unpacking libcc1-0:armhf (15-20250222-0ubuntu1) ... 1013s Selecting previously unselected package libgomp1:armhf. 1013s Preparing to unpack .../012-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 1013s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 1013s Selecting previously unselected package libasan8:armhf. 1013s Preparing to unpack .../013-libasan8_15-20250222-0ubuntu1_armhf.deb ... 1013s Unpacking libasan8:armhf (15-20250222-0ubuntu1) ... 1013s Selecting previously unselected package libubsan1:armhf. 1013s Preparing to unpack .../014-libubsan1_15-20250222-0ubuntu1_armhf.deb ... 1013s Unpacking libubsan1:armhf (15-20250222-0ubuntu1) ... 1013s Selecting previously unselected package libgcc-14-dev:armhf. 1013s Preparing to unpack .../015-libgcc-14-dev_14.2.0-17ubuntu3_armhf.deb ... 1013s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 1013s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 1013s Preparing to unpack .../016-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 1013s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 1014s Selecting previously unselected package gcc-14. 1014s Preparing to unpack .../017-gcc-14_14.2.0-17ubuntu3_armhf.deb ... 1014s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 1014s Selecting previously unselected package gcc-arm-linux-gnueabihf. 1014s Preparing to unpack .../018-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 1014s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 1014s Selecting previously unselected package gcc. 1014s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 1014s Unpacking gcc (4:14.2.0-1ubuntu1) ... 1014s Selecting previously unselected package libstdc++-14-dev:armhf. 1014s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-17ubuntu3_armhf.deb ... 1014s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 1014s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 1014s Preparing to unpack .../021-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 1014s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 1014s Selecting previously unselected package g++-14. 1014s Preparing to unpack .../022-g++-14_14.2.0-17ubuntu3_armhf.deb ... 1014s Unpacking g++-14 (14.2.0-17ubuntu3) ... 1014s Selecting previously unselected package g++-arm-linux-gnueabihf. 1014s Preparing to unpack .../023-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 1014s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 1014s Selecting previously unselected package g++. 1015s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 1015s Unpacking g++ (4:14.2.0-1ubuntu1) ... 1015s Selecting previously unselected package build-essential. 1015s Preparing to unpack .../025-build-essential_12.10ubuntu1_armhf.deb ... 1015s Unpacking build-essential (12.10ubuntu1) ... 1015s Selecting previously unselected package dctrl-tools. 1015s Preparing to unpack .../026-dctrl-tools_2.24-3build3_armhf.deb ... 1015s Unpacking dctrl-tools (2.24-3build3) ... 1015s Selecting previously unselected package libfreetype6:armhf. 1015s Preparing to unpack .../027-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 1015s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 1015s Selecting previously unselected package fonts-dejavu-mono. 1015s Preparing to unpack .../028-fonts-dejavu-mono_2.37-8_all.deb ... 1015s Unpacking fonts-dejavu-mono (2.37-8) ... 1015s Selecting previously unselected package fonts-dejavu-core. 1015s Preparing to unpack .../029-fonts-dejavu-core_2.37-8_all.deb ... 1015s Unpacking fonts-dejavu-core (2.37-8) ... 1015s Selecting previously unselected package fontconfig-config. 1015s Preparing to unpack .../030-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 1015s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 1015s Selecting previously unselected package libfontconfig1:armhf. 1015s Preparing to unpack .../031-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 1015s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 1015s Selecting previously unselected package fontconfig. 1015s Preparing to unpack .../032-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 1015s Unpacking fontconfig (2.15.0-2ubuntu1) ... 1015s Selecting previously unselected package fonts-glyphicons-halflings. 1015s Preparing to unpack .../033-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 1015s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 1015s Selecting previously unselected package fonts-mathjax. 1015s Preparing to unpack .../034-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 1015s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 1015s Selecting previously unselected package libgfortran5:armhf. 1015s Preparing to unpack .../035-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 1015s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 1015s Selecting previously unselected package libgfortran-14-dev:armhf. 1015s Preparing to unpack .../036-libgfortran-14-dev_14.2.0-17ubuntu3_armhf.deb ... 1015s Unpacking libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 1015s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 1015s Preparing to unpack .../037-gfortran-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 1015s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 1016s Selecting previously unselected package gfortran-14. 1016s Preparing to unpack .../038-gfortran-14_14.2.0-17ubuntu3_armhf.deb ... 1016s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 1016s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 1016s Preparing to unpack .../039-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 1016s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 1016s Selecting previously unselected package gfortran. 1016s Preparing to unpack .../040-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 1016s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 1016s Selecting previously unselected package icu-devtools. 1016s Preparing to unpack .../041-icu-devtools_76.1-1ubuntu2_armhf.deb ... 1016s Unpacking icu-devtools (76.1-1ubuntu2) ... 1016s Selecting previously unselected package libblas3:armhf. 1016s Preparing to unpack .../042-libblas3_3.12.1-2_armhf.deb ... 1016s Unpacking libblas3:armhf (3.12.1-2) ... 1016s Selecting previously unselected package libblas-dev:armhf. 1016s Preparing to unpack .../043-libblas-dev_3.12.1-2_armhf.deb ... 1016s Unpacking libblas-dev:armhf (3.12.1-2) ... 1016s Selecting previously unselected package libbz2-dev:armhf. 1016s Preparing to unpack .../044-libbz2-dev_1.0.8-6_armhf.deb ... 1016s Unpacking libbz2-dev:armhf (1.0.8-6) ... 1016s Selecting previously unselected package libpixman-1-0:armhf. 1016s Preparing to unpack .../045-libpixman-1-0_0.44.0-3_armhf.deb ... 1016s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 1016s Selecting previously unselected package libxcb-render0:armhf. 1016s Preparing to unpack .../046-libxcb-render0_1.17.0-2_armhf.deb ... 1016s Unpacking libxcb-render0:armhf (1.17.0-2) ... 1016s Selecting previously unselected package libxcb-shm0:armhf. 1016s Preparing to unpack .../047-libxcb-shm0_1.17.0-2_armhf.deb ... 1016s 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previously unselected package libgraphite2-3:armhf. 1017s Preparing to unpack .../053-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 1017s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 1017s Selecting previously unselected package libharfbuzz0b:armhf. 1017s Preparing to unpack .../054-libharfbuzz0b_10.2.0-1_armhf.deb ... 1017s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 1017s Selecting previously unselected package x11-common. 1017s Preparing to unpack .../055-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1017s Unpacking x11-common (1:7.7+23ubuntu3) ... 1017s Selecting previously unselected package libice6:armhf. 1017s Preparing to unpack .../056-libice6_2%3a1.1.1-1_armhf.deb ... 1017s Unpacking libice6:armhf (2:1.1.1-1) ... 1017s Selecting previously unselected package libicu-dev:armhf. 1017s Preparing to unpack .../057-libicu-dev_76.1-1ubuntu2_armhf.deb ... 1017s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 1017s Selecting previously unselected package libjpeg-turbo8:armhf. 1017s 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unpack .../063-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 1018s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 1018s Selecting previously unselected package libjs-highlight.js. 1018s Preparing to unpack .../064-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 1018s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 1018s Selecting previously unselected package libjs-jquery. 1018s Preparing to unpack .../065-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 1018s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1018s Selecting previously unselected package libjs-jquery-datatables. 1018s Preparing to unpack .../066-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 1018s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 1018s Selecting previously unselected package liblapack3:armhf. 1018s Preparing to unpack .../067-liblapack3_3.12.1-2_armhf.deb ... 1018s Unpacking liblapack3:armhf (3.12.1-2) ... 1018s Selecting previously unselected package liblapack-dev:armhf. 1018s Preparing to unpack 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Selecting previously unselected package libpng-dev:armhf. 1019s Preparing to unpack .../084-libpng-dev_1.6.47-1_armhf.deb ... 1019s Unpacking libpng-dev:armhf (1.6.47-1) ... 1019s Selecting previously unselected package libreadline-dev:armhf. 1019s Preparing to unpack .../085-libreadline-dev_8.2-6_armhf.deb ... 1019s Unpacking libreadline-dev:armhf (8.2-6) ... 1019s Selecting previously unselected package libsharpyuv0:armhf. 1019s Preparing to unpack .../086-libsharpyuv0_1.5.0-0.1_armhf.deb ... 1019s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 1019s Selecting previously unselected package libsm6:armhf. 1019s Preparing to unpack .../087-libsm6_2%3a1.2.4-1_armhf.deb ... 1019s Unpacking libsm6:armhf (2:1.2.4-1) ... 1019s Selecting previously unselected package libtcl8.6:armhf. 1019s Preparing to unpack .../088-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 1019s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 1019s Selecting previously unselected package libjbig0:armhf. 1019s Preparing to unpack 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libtk8.6:armhf (8.6.16-1) ... 1019s Selecting previously unselected package libxt6t64:armhf. 1019s Preparing to unpack .../095-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 1019s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 1019s Selecting previously unselected package zip. 1019s Preparing to unpack .../096-zip_3.0-14ubuntu2_armhf.deb ... 1019s Unpacking zip (3.0-14ubuntu2) ... 1019s Selecting previously unselected package unzip. 1019s Preparing to unpack .../097-unzip_6.0-28ubuntu6_armhf.deb ... 1019s Unpacking unzip (6.0-28ubuntu6) ... 1020s Selecting previously unselected package xdg-utils. 1020s Preparing to unpack .../098-xdg-utils_1.2.1-2ubuntu1_all.deb ... 1020s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 1020s Selecting previously unselected package r-base-core. 1020s Preparing to unpack .../099-r-base-core_4.4.3-1_armhf.deb ... 1020s Unpacking r-base-core (4.4.3-1) ... 1020s Selecting previously unselected package r-cran-littler. 1020s Preparing to unpack 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package libtirpc-dev:armhf. 1020s Preparing to unpack .../106-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 1020s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 1020s Selecting previously unselected package r-base-dev. 1020s Preparing to unpack .../107-r-base-dev_4.4.3-1_all.deb ... 1020s Unpacking r-base-dev (4.4.3-1) ... 1020s Selecting previously unselected package pkg-r-autopkgtest. 1020s Preparing to unpack .../108-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 1020s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 1020s Selecting previously unselected package r-cran-abind. 1020s Preparing to unpack .../109-r-cran-abind_1.4-8-1_all.deb ... 1020s Unpacking r-cran-abind (1.4-8-1) ... 1020s Selecting previously unselected package r-cran-cardata. 1020s Preparing to unpack .../110-r-cran-cardata_3.0.5-1_all.deb ... 1020s Unpacking r-cran-cardata (3.0.5-1) ... 1020s Selecting previously unselected package r-cran-formula. 1020s Preparing to unpack .../111-r-cran-formula_1.2-5-1_all.deb ... 1020s Unpacking r-cran-formula (1.2-5-1) ... 1020s Selecting previously unselected package r-cran-mass. 1021s Preparing to unpack .../112-r-cran-mass_7.3-64-1_armhf.deb ... 1021s Unpacking r-cran-mass (7.3-64-1) ... 1021s Selecting previously unselected package r-cran-lattice. 1021s Preparing to unpack .../113-r-cran-lattice_0.22-6-1_armhf.deb ... 1021s Unpacking r-cran-lattice (0.22-6-1) ... 1021s Selecting previously unselected package r-cran-nlme. 1021s Preparing to unpack .../114-r-cran-nlme_3.1.167-1_armhf.deb ... 1021s Unpacking r-cran-nlme (3.1.167-1) ... 1021s Selecting previously unselected package r-cran-matrix. 1021s Preparing to unpack .../115-r-cran-matrix_1.7-3-1_armhf.deb ... 1021s Unpacking r-cran-matrix (1.7-3-1) ... 1021s Selecting previously unselected package r-cran-mgcv. 1021s Preparing to unpack .../116-r-cran-mgcv_1.9-1-1_armhf.deb ... 1021s Unpacking r-cran-mgcv (1.9-1-1) ... 1021s Selecting previously unselected package r-cran-nnet. 1021s Preparing to unpack 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unselected package r-cran-nloptr. 1021s Preparing to unpack .../123-r-cran-nloptr_2.1.1-1_armhf.deb ... 1021s Unpacking r-cran-nloptr (2.1.1-1) ... 1021s Selecting previously unselected package r-cran-rbibutils. 1021s Preparing to unpack .../124-r-cran-rbibutils_2.3-1_armhf.deb ... 1021s Unpacking r-cran-rbibutils (2.3-1) ... 1021s Selecting previously unselected package r-cran-rdpack. 1021s Preparing to unpack .../125-r-cran-rdpack_2.6.2-1syncable1_all.deb ... 1021s Unpacking r-cran-rdpack (2.6.2-1syncable1) ... 1021s Selecting previously unselected package r-cran-reformulas. 1021s Preparing to unpack .../126-r-cran-reformulas_0.4.0-1_all.deb ... 1021s Unpacking r-cran-reformulas (0.4.0-1) ... 1021s Selecting previously unselected package r-cran-rcppeigen. 1022s Preparing to unpack .../127-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 1022s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 1022s Selecting previously unselected package r-cran-statmod. 1022s Preparing to unpack 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package r-cran-rlang. 1024s Preparing to unpack .../134-r-cran-rlang_1.1.5-1_armhf.deb ... 1024s Unpacking r-cran-rlang (1.1.5-1) ... 1024s Selecting previously unselected package r-cran-lifecycle. 1024s Preparing to unpack .../135-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 1024s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 1024s Selecting previously unselected package r-cran-magrittr. 1024s Preparing to unpack .../136-r-cran-magrittr_2.0.3-1_armhf.deb ... 1024s Unpacking r-cran-magrittr (2.0.3-1) ... 1024s Selecting previously unselected package r-cran-utf8. 1024s Preparing to unpack .../137-r-cran-utf8_1.2.4-1_armhf.deb ... 1024s Unpacking r-cran-utf8 (1.2.4-1) ... 1024s Selecting previously unselected package r-cran-vctrs. 1024s Preparing to unpack .../138-r-cran-vctrs_0.6.5-1_armhf.deb ... 1024s Unpacking r-cran-vctrs (0.6.5-1) ... 1024s Selecting previously unselected package r-cran-pillar. 1024s Preparing to unpack .../139-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 1024s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 1024s Selecting previously unselected package r-cran-r6. 1024s Preparing to unpack .../140-r-cran-r6_2.6.1-1_all.deb ... 1024s Unpacking r-cran-r6 (2.6.1-1) ... 1024s Selecting previously unselected package r-cran-fansi. 1024s Preparing to unpack .../141-r-cran-fansi_1.0.5-1_armhf.deb ... 1024s Unpacking r-cran-fansi (1.0.5-1) ... 1024s Selecting previously unselected package r-cran-pkgconfig. 1024s Preparing to unpack .../142-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 1024s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 1024s Selecting previously unselected package r-cran-tibble. 1024s Preparing to unpack .../143-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 1024s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 1024s Selecting previously unselected package r-cran-withr. 1024s Preparing to unpack .../144-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1024s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1024s Selecting previously unselected package r-cran-tidyselect. 1024s Preparing to unpack .../145-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 1024s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 1024s Selecting previously unselected package r-cran-dplyr. 1024s Preparing to unpack .../146-r-cran-dplyr_1.1.4-4_armhf.deb ... 1024s Unpacking r-cran-dplyr (1.1.4-4) ... 1024s Selecting previously unselected package r-cran-purrr. 1024s Preparing to unpack .../147-r-cran-purrr_1.0.4-1_armhf.deb ... 1024s Unpacking r-cran-purrr (1.0.4-1) ... 1024s Selecting previously unselected package r-cran-stringi. 1024s Preparing to unpack .../148-r-cran-stringi_1.8.4-1build1_armhf.deb ... 1024s Unpacking r-cran-stringi (1.8.4-1build1) ... 1024s Selecting previously unselected package r-cran-stringr. 1024s Preparing to unpack .../149-r-cran-stringr_1.5.1-1_all.deb ... 1024s Unpacking r-cran-stringr (1.5.1-1) ... 1024s Selecting previously unselected package r-cran-cpp11. 1024s Preparing to unpack .../150-r-cran-cpp11_0.5.2-1_all.deb ... 1024s Unpacking r-cran-cpp11 (0.5.2-1) ... 1024s Selecting previously unselected package r-cran-tidyr. 1024s Preparing to unpack .../151-r-cran-tidyr_1.3.1-1_armhf.deb ... 1024s Unpacking r-cran-tidyr (1.3.1-1) ... 1024s Selecting previously unselected package r-cran-broom. 1024s Preparing to unpack .../152-r-cran-broom_1.0.7+dfsg-1_all.deb ... 1024s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 1024s Selecting previously unselected package r-cran-numderiv. 1024s Preparing to unpack .../153-r-cran-numderiv_2016.8-1.1-3_all.deb ... 1024s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 1024s Selecting previously unselected package r-cran-gtable. 1024s Preparing to unpack .../154-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1024s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 1024s Selecting previously unselected package r-cran-isoband. 1024s Preparing to unpack .../155-r-cran-isoband_0.2.7-1_armhf.deb ... 1024s Unpacking r-cran-isoband (0.2.7-1) ... 1024s Selecting previously unselected package r-cran-farver. 1024s Preparing to unpack .../156-r-cran-farver_2.1.2-1_armhf.deb ... 1024s Unpacking r-cran-farver (2.1.2-1) ... 1024s Selecting previously unselected package r-cran-labeling. 1024s Preparing to unpack .../157-r-cran-labeling_0.4.3-1_all.deb ... 1024s Unpacking r-cran-labeling (0.4.3-1) ... 1024s Selecting previously unselected package r-cran-colorspace. 1024s Preparing to unpack .../158-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 1024s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 1024s Selecting previously unselected package r-cran-munsell. 1024s Preparing to unpack .../159-r-cran-munsell_0.5.1-1_all.deb ... 1024s Unpacking r-cran-munsell (0.5.1-1) ... 1024s Selecting previously unselected package r-cran-rcolorbrewer. 1024s Preparing to unpack .../160-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 1024s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 1024s Selecting previously unselected package r-cran-viridislite. 1024s Preparing to unpack .../161-r-cran-viridislite_0.4.2-2_all.deb ... 1024s Unpacking r-cran-viridislite (0.4.2-2) ... 1024s Selecting previously unselected package r-cran-scales. 1024s Preparing to unpack .../162-r-cran-scales_1.3.0-1_all.deb ... 1024s Unpacking r-cran-scales (1.3.0-1) ... 1024s Selecting previously unselected package r-cran-ggplot2. 1024s Preparing to unpack .../163-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 1024s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 1024s Selecting previously unselected package r-cran-cowplot. 1024s Preparing to unpack .../164-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 1024s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 1024s Selecting previously unselected package r-cran-deriv. 1024s Preparing to unpack .../165-r-cran-deriv_4.1.6-1_all.deb ... 1024s Unpacking r-cran-deriv (4.1.6-1) ... 1024s Selecting previously unselected package r-cran-modelr. 1024s Preparing to unpack .../166-r-cran-modelr_0.1.11-1_all.deb ... 1024s Unpacking r-cran-modelr (0.1.11-1) ... 1024s Selecting previously unselected package r-cran-microbenchmark. 1024s Preparing to unpack .../167-r-cran-microbenchmark_1.5.0-1_armhf.deb ... 1024s Unpacking r-cran-microbenchmark (1.5.0-1) ... 1024s Selecting previously unselected package r-cran-doby. 1024s Preparing to unpack .../168-r-cran-doby_4.6.25-1_all.deb ... 1024s Unpacking r-cran-doby (4.6.25-1) ... 1024s Selecting previously unselected package r-cran-evaluate. 1024s Preparing to unpack .../169-r-cran-evaluate_1.0.3-1_all.deb ... 1024s Unpacking r-cran-evaluate (1.0.3-1) ... 1024s Selecting previously unselected package r-cran-xfun. 1024s Preparing to unpack .../170-r-cran-xfun_0.51+dfsg-1_armhf.deb ... 1024s Unpacking r-cran-xfun (0.51+dfsg-1) ... 1024s Selecting previously unselected package r-cran-highr. 1024s Preparing to unpack .../171-r-cran-highr_0.11+dfsg-1_all.deb ... 1024s Unpacking r-cran-highr (0.11+dfsg-1) ... 1024s Selecting previously unselected package r-cran-yaml. 1024s Preparing to unpack .../172-r-cran-yaml_2.3.10-1_armhf.deb ... 1024s Unpacking r-cran-yaml (2.3.10-1) ... 1024s Selecting previously unselected package libjs-mathjax. 1024s Preparing to unpack .../173-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 1024s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 1025s Selecting previously unselected package r-cran-knitr. 1025s Preparing to unpack .../174-r-cran-knitr_1.49+dfsg-1_all.deb ... 1025s Unpacking r-cran-knitr (1.49+dfsg-1) ... 1025s Selecting previously unselected package r-cran-pbkrtest. 1025s Preparing to unpack .../175-r-cran-pbkrtest_0.5.3-1_all.deb ... 1025s Unpacking r-cran-pbkrtest (0.5.3-1) ... 1025s Selecting previously unselected package r-cran-sparsem. 1025s Preparing to unpack .../176-r-cran-sparsem_1.84-2-1_armhf.deb ... 1025s Unpacking r-cran-sparsem (1.84-2-1) ... 1025s Selecting previously unselected package r-cran-matrixmodels. 1025s Preparing to unpack .../177-r-cran-matrixmodels_0.5-3-1_all.deb ... 1025s Unpacking r-cran-matrixmodels (0.5-3-1) ... 1025s Selecting previously unselected package r-cran-survival. 1025s Preparing to unpack .../178-r-cran-survival_3.8-3-1_armhf.deb ... 1025s Unpacking r-cran-survival (3.8-3-1) ... 1025s Selecting previously unselected package r-cran-matrixstats. 1025s Preparing to unpack .../179-r-cran-matrixstats_1.5.0-1_armhf.deb ... 1025s Unpacking r-cran-matrixstats (1.5.0-1) ... 1025s Selecting previously unselected package r-cran-rcpparmadillo. 1025s Preparing to unpack .../180-r-cran-rcpparmadillo_14.2.3-1-1_armhf.deb ... 1025s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 1025s Selecting previously unselected package r-cran-class. 1025s Preparing to unpack .../181-r-cran-class_7.3-23-1_armhf.deb ... 1025s Unpacking r-cran-class (7.3-23-1) ... 1025s Selecting previously unselected package r-cran-proxy. 1025s Preparing to unpack .../182-r-cran-proxy_0.4-27-1_armhf.deb ... 1025s Unpacking r-cran-proxy (0.4-27-1) ... 1025s Selecting previously unselected package r-cran-e1071. 1025s Preparing to unpack .../183-r-cran-e1071_1.7-16-1_armhf.deb ... 1025s Unpacking r-cran-e1071 (1.7-16-1) ... 1025s Selecting previously unselected package r-cran-codetools. 1025s Preparing to unpack .../184-r-cran-codetools_0.2-20-1_all.deb ... 1025s Unpacking r-cran-codetools (0.2-20-1) ... 1025s Selecting previously unselected package r-cran-iterators. 1026s Preparing to unpack .../185-r-cran-iterators_1.0.14-1_all.deb ... 1026s Unpacking r-cran-iterators (1.0.14-1) ... 1026s Selecting previously unselected package r-cran-foreach. 1026s Preparing to unpack .../186-r-cran-foreach_1.5.2-1_all.deb ... 1026s Unpacking r-cran-foreach (1.5.2-1) ... 1026s Selecting previously unselected package r-cran-data.table. 1026s Preparing to unpack .../187-r-cran-data.table_1.17.0+dfsg-1_armhf.deb ... 1026s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 1026s Selecting previously unselected package r-cran-modelmetrics. 1026s Preparing to unpack .../188-r-cran-modelmetrics_1.2.2.2-1build1_armhf.deb ... 1026s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 1026s Selecting previously unselected package r-cran-plyr. 1026s Preparing to unpack .../189-r-cran-plyr_1.8.9-1_armhf.deb ... 1026s Unpacking r-cran-plyr (1.8.9-1) ... 1026s Selecting previously unselected package r-cran-proc. 1026s Preparing to unpack .../190-r-cran-proc_1.18.5-1_armhf.deb ... 1026s Unpacking r-cran-proc (1.18.5-1) ... 1026s Selecting previously unselected package r-cran-tzdb. 1026s Preparing to unpack .../191-r-cran-tzdb_0.4.0-2_armhf.deb ... 1026s Unpacking r-cran-tzdb (0.4.0-2) ... 1026s Selecting previously unselected package r-cran-clock. 1026s Preparing to unpack .../192-r-cran-clock_0.7.2-1_armhf.deb ... 1026s Unpacking r-cran-clock (0.7.2-1) ... 1026s Selecting previously unselected package r-cran-gower. 1026s Preparing to unpack .../193-r-cran-gower_1.0.2-1_armhf.deb ... 1026s Unpacking r-cran-gower (1.0.2-1) ... 1026s Selecting previously unselected package r-cran-hardhat. 1026s Preparing to unpack .../194-r-cran-hardhat_1.4.0+dfsg-1_all.deb ... 1026s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ... 1026s Selecting previously unselected package r-cran-rpart. 1026s Preparing to unpack .../195-r-cran-rpart_4.1.24-1_armhf.deb ... 1026s Unpacking r-cran-rpart (4.1.24-1) ... 1026s Selecting previously unselected package r-cran-shape. 1026s Preparing to unpack .../196-r-cran-shape_1.4.6.1-1_all.deb ... 1026s Unpacking r-cran-shape (1.4.6.1-1) ... 1026s Selecting previously unselected package r-cran-diagram. 1026s Preparing to unpack .../197-r-cran-diagram_1.6.5-2_all.deb ... 1026s Unpacking r-cran-diagram (1.6.5-2) ... 1026s Selecting previously unselected package r-cran-kernsmooth. 1026s Preparing to unpack .../198-r-cran-kernsmooth_2.23-26-1_armhf.deb ... 1026s Unpacking r-cran-kernsmooth (2.23-26-1) ... 1026s Selecting previously unselected package r-cran-digest. 1026s Preparing to unpack .../199-r-cran-digest_0.6.37-1_armhf.deb ... 1026s Unpacking r-cran-digest (0.6.37-1) ... 1026s Selecting previously unselected package r-cran-globals. 1026s Preparing to unpack .../200-r-cran-globals_0.16.3-1_all.deb ... 1026s Unpacking r-cran-globals (0.16.3-1) ... 1027s Selecting previously unselected package r-cran-listenv. 1027s Preparing to unpack .../201-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 1027s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 1027s Selecting previously unselected package r-cran-parallelly. 1027s Preparing to unpack .../202-r-cran-parallelly_1.42.0-1_armhf.deb ... 1027s Unpacking r-cran-parallelly (1.42.0-1) ... 1027s Selecting previously unselected package r-cran-future. 1027s Preparing to unpack .../203-r-cran-future_1.34.0+dfsg-1_all.deb ... 1027s Unpacking r-cran-future (1.34.0+dfsg-1) ... 1027s Selecting previously unselected package r-cran-future.apply. 1027s Preparing to unpack .../204-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 1027s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 1027s Selecting previously unselected package r-cran-progressr. 1027s Preparing to unpack .../205-r-cran-progressr_0.15.1-1_all.deb ... 1027s Unpacking r-cran-progressr (0.15.1-1) ... 1027s Selecting previously unselected package r-cran-squarem. 1027s Preparing to unpack .../206-r-cran-squarem_2021.1-1_all.deb ... 1027s Unpacking r-cran-squarem (2021.1-1) ... 1027s Selecting previously unselected package r-cran-lava. 1027s Preparing to unpack .../207-r-cran-lava_1.8.1+dfsg-1_all.deb ... 1027s Unpacking r-cran-lava (1.8.1+dfsg-1) ... 1027s Selecting previously unselected package r-cran-prodlim. 1027s Preparing to unpack .../208-r-cran-prodlim_2024.06.25-1_armhf.deb ... 1027s Unpacking r-cran-prodlim (2024.06.25-1) ... 1027s Selecting previously unselected package r-cran-ipred. 1027s Preparing to unpack .../209-r-cran-ipred_0.9-15-1_armhf.deb ... 1027s Unpacking r-cran-ipred (0.9-15-1) ... 1027s Selecting previously unselected package r-cran-timechange. 1027s Preparing to unpack .../210-r-cran-timechange_0.3.0-1_armhf.deb ... 1027s Unpacking r-cran-timechange (0.3.0-1) ... 1027s Selecting previously unselected package r-cran-lubridate. 1027s Preparing to unpack .../211-r-cran-lubridate_1.9.4+dfsg-1_armhf.deb ... 1027s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 1027s Selecting previously unselected package r-cran-timedate. 1027s Preparing to unpack .../212-r-cran-timedate_4041.110-1_armhf.deb ... 1027s Unpacking r-cran-timedate (4041.110-1) ... 1027s Selecting previously unselected package r-cran-recipes. 1027s Preparing to unpack .../213-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 1027s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 1027s Selecting previously unselected package r-cran-reshape2. 1027s Preparing to unpack .../214-r-cran-reshape2_1.4.4-2build1_armhf.deb ... 1027s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 1027s Selecting previously unselected package r-cran-caret. 1027s Preparing to unpack .../215-r-cran-caret_7.0-1+dfsg-1_armhf.deb ... 1027s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 1027s Selecting previously unselected package r-cran-conquer. 1027s Preparing to unpack .../216-r-cran-conquer_1.3.3-1_armhf.deb ... 1027s Unpacking r-cran-conquer (1.3.3-1) ... 1027s Selecting previously unselected package r-cran-quantreg. 1028s Preparing to unpack .../217-r-cran-quantreg_6.00-1_armhf.deb ... 1028s Unpacking r-cran-quantreg (6.00-1) ... 1028s Selecting previously unselected package r-cran-foreign. 1028s Preparing to unpack .../218-r-cran-foreign_0.8.88-1_armhf.deb ... 1028s Unpacking r-cran-foreign (0.8.88-1) ... 1028s Selecting previously unselected package r-cran-ellipsis. 1028s Preparing to unpack .../219-r-cran-ellipsis_0.3.2-2_armhf.deb ... 1028s Unpacking r-cran-ellipsis (0.3.2-2) ... 1028s Selecting previously unselected package r-cran-forcats. 1028s Preparing to unpack .../220-r-cran-forcats_1.0.0-1_all.deb ... 1028s Unpacking r-cran-forcats (1.0.0-1) ... 1028s Selecting previously unselected package r-cran-hms. 1028s Preparing to unpack .../221-r-cran-hms_1.1.3-1_all.deb ... 1028s Unpacking r-cran-hms (1.1.3-1) ... 1028s Selecting previously unselected package r-cran-clipr. 1028s Preparing to unpack .../222-r-cran-clipr_0.8.0-1_all.deb ... 1028s Unpacking r-cran-clipr (0.8.0-1) ... 1028s Selecting previously unselected package r-cran-crayon. 1028s Preparing to unpack .../223-r-cran-crayon_1.5.3-1_all.deb ... 1028s Unpacking r-cran-crayon (1.5.3-1) ... 1028s Selecting previously unselected package r-cran-bit. 1028s Preparing to unpack .../224-r-cran-bit_4.6.0+dfsg-1_armhf.deb ... 1028s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 1028s Selecting previously unselected package r-cran-bit64. 1028s Preparing to unpack .../225-r-cran-bit64_4.6.0-1-1ubuntu2_armhf.deb ... 1028s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ... 1028s Selecting previously unselected package r-cran-prettyunits. 1028s Preparing to unpack .../226-r-cran-prettyunits_1.2.0-1_all.deb ... 1028s Unpacking r-cran-prettyunits (1.2.0-1) ... 1028s Selecting previously unselected package r-cran-progress. 1028s Preparing to unpack .../227-r-cran-progress_1.2.3-1_all.deb ... 1028s Unpacking r-cran-progress (1.2.3-1) ... 1028s Selecting previously unselected package r-cran-vroom. 1028s Preparing to unpack .../228-r-cran-vroom_1.6.5-1_armhf.deb ... 1028s Unpacking r-cran-vroom (1.6.5-1) ... 1028s Selecting previously unselected package r-cran-readr. 1028s Preparing to unpack .../229-r-cran-readr_2.1.5-1_armhf.deb ... 1028s Unpacking r-cran-readr (2.1.5-1) ... 1028s Selecting previously unselected package r-cran-haven. 1028s Preparing to unpack .../230-r-cran-haven_2.5.4-1_armhf.deb ... 1028s Unpacking r-cran-haven (2.5.4-1) ... 1028s Selecting previously unselected package r-cran-curl. 1028s Preparing to unpack .../231-r-cran-curl_6.2.1+dfsg-1ubuntu1_armhf.deb ... 1028s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 1028s Selecting previously unselected package r-cran-rematch. 1028s Preparing to unpack .../232-r-cran-rematch_2.0.0-1_all.deb ... 1028s Unpacking r-cran-rematch (2.0.0-1) ... 1028s Selecting previously unselected package r-cran-cellranger. 1028s Preparing to unpack .../233-r-cran-cellranger_1.1.0-3_all.deb ... 1028s Unpacking r-cran-cellranger (1.1.0-3) ... 1028s Selecting previously unselected package r-cran-readxl. 1028s Preparing to unpack .../234-r-cran-readxl_1.4.4-1_armhf.deb ... 1028s Unpacking r-cran-readxl (1.4.4-1) ... 1028s Selecting previously unselected package r-cran-writexl. 1028s Preparing to unpack .../235-r-cran-writexl_1.5.1-1_armhf.deb ... 1028s Unpacking r-cran-writexl (1.5.1-1) ... 1028s Selecting previously unselected package r-cran-r.methodss3. 1028s Preparing to unpack .../236-r-cran-r.methodss3_1.8.2-1_all.deb ... 1028s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 1029s Selecting previously unselected package r-cran-r.oo. 1029s Preparing to unpack .../237-r-cran-r.oo_1.27.0-1_all.deb ... 1029s Unpacking r-cran-r.oo (1.27.0-1) ... 1029s Selecting previously unselected package r-cran-r.utils. 1029s Preparing to unpack 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1033s Setting up r-cran-timedate (4041.110-1) ... 1033s Setting up r-cran-highr (0.11+dfsg-1) ... 1033s Setting up r-cran-foreach (1.5.2-1) ... 1033s Setting up r-cran-prettyunits (1.2.0-1) ... 1033s Setting up r-cran-fansi (1.0.5-1) ... 1033s Setting up r-cran-cardata (3.0.5-1) ... 1033s Setting up r-cran-mass (7.3-64-1) ... 1033s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 1033s Setting up r-cran-glue (1.8.0-1) ... 1033s Setting up r-cran-foreign (0.8.88-1) ... 1033s Setting up r-cran-writexl (1.5.1-1) ... 1033s Setting up r-cran-bit (4.6.0+dfsg-1) ... 1033s Setting up r-cran-cli (3.6.4-1) ... 1033s Setting up gfortran (4:14.2.0-1ubuntu1) ... 1033s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1033s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 1033s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 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Setting up r-cran-recipes (1.1.0+dfsg-1) ... 1033s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 1033s Setting up r-cran-readxl (1.4.4-1) ... 1033s Setting up r-cran-haven (2.5.4-1) ... 1033s Setting up r-cran-caret (7.0-1+dfsg-1) ... 1033s Setting up r-cran-broom (1.0.7+dfsg-1) ... 1033s Setting up r-cran-conquer (1.3.3-1) ... 1033s Setting up r-cran-rio (1.2.3-1) ... 1033s Setting up r-cran-quantreg (6.00-1) ... 1033s Setting up r-cran-modelr (0.1.11-1) ... 1033s Setting up r-cran-doby (4.6.25-1) ... 1033s Setting up r-cran-pbkrtest (0.5.3-1) ... 1033s Setting up r-cran-car (3.1-3-1) ... 1033s Setting up r-cran-aer (1.2-14-1) ... 1033s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1033s Processing triggers for man-db (2.13.0-1) ... 1035s Processing triggers for install-info (7.1.1-1) ... 1048s autopkgtest [16:02:47]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1048s autopkgtest [16:02:47]: test pkg-r-autopkgtest: [----------------------- 1050s Test: Try to load the R library survey 1050s 1050s R version 4.4.3 (2025-02-28) -- "Trophy Case" 1050s Copyright (C) 2025 The R Foundation for Statistical Computing 1050s Platform: arm-unknown-linux-gnueabihf (32-bit) 1050s 1050s R is free software and comes with ABSOLUTELY NO WARRANTY. 1050s You are welcome to redistribute it under certain conditions. 1050s Type 'license()' or 'licence()' for distribution details. 1050s 1050s R is a collaborative project with many contributors. 1050s Type 'contributors()' for more information and 1050s 'citation()' on how to cite R or R packages in publications. 1050s 1050s Type 'demo()' for some demos, 'help()' for on-line help, or 1050s 'help.start()' for an HTML browser interface to help. 1050s Type 'q()' to quit R. 1050s 1050s > library('survey') 1050s Loading required package: grid 1050s Loading required package: Matrix 1052s Loading required package: survival 1053s 1053s Attaching package: ‘survey’ 1053s 1053s The following object is masked from ‘package:graphics’: 1053s 1053s dotchart 1053s 1053s > 1053s > 1053s Other tests are currently unsupported! 1053s They will be progressively added. 1053s autopkgtest [16:02:52]: test pkg-r-autopkgtest: -----------------------] 1057s autopkgtest [16:02:56]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1057s pkg-r-autopkgtest PASS 1060s autopkgtest [16:02:59]: @@@@@@@@@@@@@@@@@@@@ summary 1060s run-unit-test PASS 1060s pkg-r-autopkgtest PASS