0s autopkgtest [12:35:10]: starting date and time: 2026-02-10 12:35:10+0000 0s autopkgtest [12:35:10]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [12:35:10]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dqwqb5sl/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-survey --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- lxd -r lxd-armhf-10.145.243.254 lxd-armhf-10.145.243.254:autopkgtest/ubuntu/resolute/armhf 21s autopkgtest [12:35:31]: testbed dpkg architecture: armhf 23s autopkgtest [12:35:33]: testbed apt version: 3.1.15 27s autopkgtest [12:35:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [12:35:38]: testbed release detected to be: None 36s autopkgtest [12:35:46]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 38s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 38s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 38s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 39s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 39s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [179 kB] 39s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.9 kB] 39s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [259 kB] 39s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1495 kB] 39s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [8156 B] 39s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1404 kB] 39s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 40s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1386 kB] 40s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.9 MB] 44s Fetched 43.2 MB in 6s (7631 kB/s) 45s Reading package lists... 51s autopkgtest [12:36:01]: upgrading testbed (apt dist-upgrade and autopurge) 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s libbrotli1 ubuntu-minimal ubuntu-standard 54s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 345 kB of archives. 54s After this operation, 0 B of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-minimal armhf 1.565 [13.3 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-standard armhf 1.565 [13.3 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.2.0-3 [318 kB] 55s Fetched 345 kB in 0s (748 kB/s) 55s (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 ... 68678 files and directories currently installed.) 55s Preparing to unpack .../ubuntu-minimal_1.565_armhf.deb ... 55s Unpacking ubuntu-minimal (1.565) over (1.564) ... 55s Preparing to unpack .../ubuntu-standard_1.565_armhf.deb ... 55s Unpacking ubuntu-standard (1.565) over (1.564) ... 55s Preparing to unpack .../libbrotli1_1.2.0-3_armhf.deb ... 55s Unpacking libbrotli1:armhf (1.2.0-3) over (1.1.0-2build6) ... 55s Setting up ubuntu-minimal (1.565) ... 55s Setting up libbrotli1:armhf (1.2.0-3) ... 55s Setting up ubuntu-standard (1.565) ... 55s Processing triggers for libc-bin (2.42-2ubuntu4) ... 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 59s Solving dependencies... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s autopkgtest [12:36:12]: rebooting testbed after setup commands that affected boot 102s autopkgtest [12:36:52]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 127s autopkgtest [12:37:17]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 137s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (dsc) [2340 B] 137s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (tar) [2341 kB] 137s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (diff) [4580 B] 137s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC 137s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 137s gpgv: issuer "plessy@debian.org" 137s gpgv: Can't check signature: No public key 137s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found 138s autopkgtest [12:37:28]: testing package r-cran-survey version 4.4-2-2 140s autopkgtest [12:37:30]: build not needed 158s autopkgtest [12:37:48]: test run-unit-test: preparing testbed 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Solving dependencies... 162s The following NEW packages will be installed: 162s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 162s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 162s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 162s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 162s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 162s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 162s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 162s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 162s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 162s r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 162s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 162s r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools 162s r-cran-colorspace r-cran-conquer r-cran-cowplot r-cran-cpp11 r-cran-curl 162s r-cran-data.table r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest 162s r-cran-doby r-cran-dplyr r-cran-e1071 r-cran-evaluate r-cran-fansi 162s r-cran-farver r-cran-fastmap r-cran-foreach r-cran-forecast r-cran-foreign 162s r-cran-formula r-cran-fracdiff r-cran-future r-cran-future.apply 162s r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower 162s r-cran-gtable r-cran-hardhat r-cran-hexbin r-cran-highr r-cran-ipred 162s r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kernsmooth 162s r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle 162s r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate 162s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels 162s r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark 162s r-cran-minqa r-cran-mitools r-cran-modelmetrics r-cran-modelr r-cran-nlme 162s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pbkrtest 162s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr 162s r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr 162s r-cran-quadprog r-cran-quantmod r-cran-quantreg r-cran-r.cache 162s r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6 162s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 162s r-cran-rcppeigen r-cran-rdpack r-cran-recipes r-cran-reformulas 162s r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-rsqlite r-cran-sandwich 162s r-cran-scales r-cran-shape r-cran-sparsem r-cran-sparsevctrs r-cran-squarem 162s r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival 162s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange 162s r-cran-timedate r-cran-tseries r-cran-ttr r-cran-tzdb r-cran-urca 162s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun 162s r-cran-xts r-cran-yaml r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip 162s 0 upgraded, 197 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 168 MB of archives. 162s After this operation, 322 MB of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 162s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 162s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 163s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 163s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 163s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 163s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 163s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 163s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 163s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 163s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 163s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 163s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 163s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 163s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 163s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 163s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 16-20260208-1ubuntu1 [335 kB] 163s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 16-20260208-1ubuntu1 [134 kB] 163s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 163s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 163s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 163s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 163s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 163s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu12 [2142 B] 163s Get:25 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 163s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 163s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 163s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 163s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 164s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 164s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 164s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 164s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 164s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 164s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 164s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 164s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 164s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 164s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 164s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 164s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 164s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 164s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 164s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 164s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 164s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 164s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 164s Get:48 http://ftpmaster.internal/ubuntu resolute/universe armhf node-normalize.css all 8.0.1-5.1 [10.4 kB] 164s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 164s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 164s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 164s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 166s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-abind all 1.4-8-1build1 [67.0 kB] 166s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cardata all 3.0.6-1 [1687 kB] 166s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-formula all 1.2-5-1 [158 kB] 166s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 166s Get:57 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-lattice armhf 0.22-9-1 [1399 kB] 166s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 166s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 166s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mgcv armhf 1.9-4-1 [3515 kB] 166s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 166s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-boot all 1.3-32-1 [636 kB] 166s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 166s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 166s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 166s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-minqa armhf 1.2.8-1 [108 kB] 166s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf libnlopt0 armhf 2.7.1-7ubuntu1 [155 kB] 166s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nloptr armhf 2.2.1-2 [250 kB] 166s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rbibutils armhf 2.3-1 [943 kB] 166s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rdpack all 2.6.3-1 [636 kB] 166s Get:71 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-reformulas all 0.4.4-1 [151 kB] 166s Get:72 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 167s Get:73 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 167s Get:74 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-statmod armhf 1.5.0-1 [294 kB] 167s Get:75 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lme4 armhf 1.1-38-1 [4178 kB] 167s Get:76 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 167s Get:77 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 167s Get:78 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 167s Get:79 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 167s Get:80 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 167s Get:81 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 167s Get:82 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 167s Get:83 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 167s Get:84 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 167s Get:85 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 167s Get:86 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fansi armhf 1.0.6-2 [620 kB] 167s Get:87 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 167s Get:88 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 167s Get:89 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 167s Get:90 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 167s Get:91 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 167s Get:92 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 167s Get:93 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringi armhf 1.8.4-1build2 [884 kB] 167s Get:94 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 167s Get:95 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 167s Get:96 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 167s Get:97 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 167s Get:98 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 167s Get:99 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 167s Get:100 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 167s Get:101 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 167s Get:102 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 167s Get:103 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 167s Get:104 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 168s Get:105 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 168s Get:106 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 168s Get:107 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 168s Get:108 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-deriv all 4.2.0-1 [154 kB] 168s Get:109 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 168s Get:110 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fracdiff armhf 1.5-3-1 [105 kB] 168s Get:111 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-zoo armhf 1.8-15-1 [1025 kB] 168s Get:112 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lmtest armhf 0.9.40-1build1 [400 kB] 168s Get:113 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-timedate armhf 4052.112-1 [1299 kB] 168s Get:114 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quadprog armhf 1.5-8-1build2 [29.8 kB] 168s Get:115 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xts armhf 0.14.1-1 [1181 kB] 168s Get:116 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-curl armhf 7.0.0+dfsg-1 [200 kB] 168s Get:117 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ttr armhf 0.24.4-1 [509 kB] 168s Get:118 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-jsonlite armhf 1.9.1+dfsg-1 [440 kB] 168s Get:119 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quantmod all 0.4.28-1 [1037 kB] 168s Get:120 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tseries armhf 0.10-59-3 [379 kB] 168s Get:121 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-urca armhf 1.3-4-1build1 [1050 kB] 168s Get:122 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpparmadillo armhf 15.2.3-1-1 [915 kB] 168s Get:123 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-forecast armhf 8.23.0-1 [1563 kB] 168s Get:124 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-modelr all 0.1.11-1 [195 kB] 168s Get:125 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-microbenchmark armhf 1.5.0-1 [67.8 kB] 168s Get:126 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-doby all 4.7.1-3 [4741 kB] 169s Get:127 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-evaluate all 1.0.5-1 [117 kB] 169s Get:128 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xfun armhf 0.55+dfsg-1 [589 kB] 169s Get:129 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 169s Get:130 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 169s Get:131 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 169s Get:132 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-knitr all 1.51+dfsg-1 [847 kB] 169s Get:133 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pbkrtest all 0.5.5-1 [217 kB] 169s Get:134 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-sparsem armhf 1.84-2-1 [807 kB] 169s Get:135 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrixmodels all 0.5-4-1 [351 kB] 169s Get:136 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-survival armhf 3.8-6-1 [8253 kB] 169s Get:137 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrixstats armhf 1.5.0-1 [495 kB] 169s Get:138 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-class armhf 7.3-23-1 [88.8 kB] 169s Get:139 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-proxy armhf 0.4-27-1 [180 kB] 169s Get:140 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-e1071 armhf 1.7-17-1 [570 kB] 169s Get:141 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-codetools all 0.2-20-1build1 [91.1 kB] 169s Get:142 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-iterators all 1.0.14-1build1 [336 kB] 169s Get:143 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-foreach all 1.5.2-1build1 [124 kB] 169s Get:144 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 169s Get:145 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-modelmetrics armhf 1.2.2.2-1build2 [152 kB] 169s Get:146 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-plyr armhf 1.8.9-1 [832 kB] 169s Get:147 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-proc armhf 1.18.5-1 [961 kB] 169s Get:148 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tzdb armhf 0.5.0-1 [530 kB] 169s Get:149 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-clock armhf 0.7.2-1 [1858 kB] 169s Get:150 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gower armhf 1.0.2-1 [208 kB] 169s Get:151 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-sparsevctrs armhf 0.2.0-2 [168 kB] 169s Get:152 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-hardhat all 1.4.2+dfsg-1 [596 kB] 169s Get:153 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rpart armhf 4.1.24-1build1 [661 kB] 169s Get:154 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-shape all 1.4.6.1-1 [749 kB] 169s Get:155 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-diagram all 1.6.5-2 [656 kB] 169s Get:156 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-kernsmooth armhf 2.23-26-1build1 [91.4 kB] 169s Get:157 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-digest armhf 0.6.39-1 [211 kB] 169s Get:158 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-globals all 0.19.0-1 [160 kB] 169s Get:159 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 169s Get:160 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-parallelly armhf 1.42.0-1 [540 kB] 169s Get:161 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-future all 1.34.0+dfsg-1 [646 kB] 169s Get:162 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 169s Get:163 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-progressr all 0.15.1-1 [353 kB] 169s Get:164 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-squarem all 2021.1-1build1 [180 kB] 169s Get:165 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lava all 1.8.2+dfsg-1 [2210 kB] 170s Get:166 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-prodlim armhf 2024.06.25-1 [413 kB] 170s Get:167 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ipred armhf 0.9-15-1 [385 kB] 170s Get:168 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-timechange armhf 0.3.0-2 [184 kB] 170s Get:169 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lubridate armhf 1.9.4+dfsg-1 [1008 kB] 170s Get:170 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 170s Get:171 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-reshape2 armhf 1.4.4-2build2 [119 kB] 170s Get:172 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-caret armhf 7.0-1+dfsg-1 [3460 kB] 170s Get:173 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-conquer armhf 1.3.3-1 [460 kB] 170s Get:174 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quantreg armhf 6.1-1 [1428 kB] 170s Get:175 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-car all 3.1-5-1 [1526 kB] 170s Get:176 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-sandwich all 3.1-1-1build1 [1483 kB] 170s Get:177 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-aer all 1.2-15-1 [2607 kB] 170s Get:178 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-bit armhf 4.6.0+dfsg-1 [447 kB] 170s Get:179 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-bit64 armhf 4.6.0-1-4 [489 kB] 170s Get:180 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-blob all 1.3.0-1 [54.1 kB] 170s Get:181 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fastmap armhf 1.2.0-1 [69.8 kB] 170s Get:182 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cachem armhf 1.1.0-1 [73.8 kB] 170s Get:183 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dbi all 1.2.3-1build1 [855 kB] 170s Get:184 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-foreign armhf 0.8.91-1 [240 kB] 170s Get:185 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-hexbin armhf 1.28.5-1 [1580 kB] 170s Get:186 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-memoise all 2.0.1-1build1 [54.5 kB] 170s Get:187 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mitools all 2.4-2build2 [266 kB] 170s Get:188 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-plogr all 0.2.0-3build2 [15.8 kB] 170s Get:189 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 170s Get:190 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r.oo all 1.27.1-1 [978 kB] 170s Get:191 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r.utils all 2.13.0-1 [1423 kB] 170s Get:192 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r.cache all 0.17.0-1 [117 kB] 170s Get:193 http://ftpmaster.internal/ubuntu resolute/main armhf tcl8.6 armhf 8.6.17+dfsg-1build1 [14.6 kB] 170s Get:194 http://ftpmaster.internal/ubuntu resolute/main armhf tcl armhf 8.6.16build1 [4200 B] 170s Get:195 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r.rsp all 0.46.0+ds-1 [1412 kB] 171s Get:196 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rsqlite armhf 2.3.9-1 [1157 kB] 171s Get:197 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-survey armhf 4.4-2-2 [3448 kB] 172s Preconfiguring packages ... 172s Fetched 168 MB in 9s (18.7 MB/s) 172s Selecting previously unselected package libfreetype6:armhf. 172s (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 ... 68678 files and directories currently installed.) 172s Preparing to unpack .../000-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 172s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 172s Selecting previously unselected package fonts-dejavu-mono. 172s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8build1_all.deb ... 172s Unpacking fonts-dejavu-mono (2.37-8build1) ... 172s Selecting previously unselected package fonts-dejavu-core. 172s Preparing to unpack .../002-fonts-dejavu-core_2.37-8build1_all.deb ... 172s Unpacking fonts-dejavu-core (2.37-8build1) ... 172s Selecting previously unselected package fontconfig-config. 172s Preparing to unpack .../003-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 173s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 173s Selecting previously unselected package libfontconfig1:armhf. 173s Preparing to unpack .../004-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 173s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 173s Selecting previously unselected package fontconfig. 173s Preparing to unpack .../005-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 173s Unpacking fontconfig (2.17.1-3ubuntu1) ... 173s Selecting previously unselected package fonts-glyphicons-halflings. 173s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 173s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 173s Selecting previously unselected package fonts-mathjax. 173s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 173s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 173s Selecting previously unselected package libblas3:armhf. 173s Preparing to unpack .../008-libblas3_3.12.1-7ubuntu1_armhf.deb ... 173s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 173s Selecting previously unselected package libpixman-1-0:armhf. 173s Preparing to unpack .../009-libpixman-1-0_0.46.4-1_armhf.deb ... 173s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 173s Selecting previously unselected package libxcb-render0:armhf. 173s Preparing to unpack .../010-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 173s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 173s Selecting previously unselected package libxcb-shm0:armhf. 173s Preparing to unpack .../011-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 173s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 173s Selecting previously unselected package libxrender1:armhf. 173s Preparing to unpack .../012-libxrender1_1%3a0.9.12-1_armhf.deb ... 173s Unpacking libxrender1:armhf (1:0.9.12-1) ... 174s Selecting previously unselected package libcairo2:armhf. 174s Preparing to unpack .../013-libcairo2_1.18.4-3_armhf.deb ... 174s Unpacking libcairo2:armhf (1.18.4-3) ... 174s Selecting previously unselected package libdatrie1:armhf. 174s Preparing to unpack .../014-libdatrie1_0.2.14-1_armhf.deb ... 174s Unpacking libdatrie1:armhf (0.2.14-1) ... 174s Selecting previously unselected package libdeflate0:armhf. 174s Preparing to unpack .../015-libdeflate0_1.23-2build1_armhf.deb ... 174s Unpacking libdeflate0:armhf (1.23-2build1) ... 174s Selecting previously unselected package libgfortran5:armhf. 174s Preparing to unpack .../016-libgfortran5_16-20260208-1ubuntu1_armhf.deb ... 174s Unpacking libgfortran5:armhf (16-20260208-1ubuntu1) ... 174s Selecting previously unselected package libgomp1:armhf. 174s Preparing to unpack .../017-libgomp1_16-20260208-1ubuntu1_armhf.deb ... 174s Unpacking libgomp1:armhf (16-20260208-1ubuntu1) ... 174s Selecting previously unselected package libgraphite2-3:armhf. 174s Preparing to unpack .../018-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 174s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 174s Selecting previously unselected package libharfbuzz0b:armhf. 174s Preparing to unpack .../019-libharfbuzz0b_12.3.2-1_armhf.deb ... 174s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 174s Selecting previously unselected package x11-common. 174s Preparing to unpack .../020-x11-common_1%3a7.7+24ubuntu1_all.deb ... 174s Unpacking x11-common (1:7.7+24ubuntu1) ... 174s Selecting previously unselected package libice6:armhf. 174s Preparing to unpack .../021-libice6_2%3a1.1.1-1build1_armhf.deb ... 174s Unpacking libice6:armhf (2:1.1.1-1build1) ... 174s Selecting previously unselected package libjpeg-turbo8:armhf. 174s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 174s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 174s Selecting previously unselected package libjpeg8:armhf. 174s Preparing to unpack .../023-libjpeg8_8c-2ubuntu12_armhf.deb ... 174s Unpacking libjpeg8:armhf (8c-2ubuntu12) ... 174s Selecting previously unselected package libjs-bootstrap. 174s Preparing to unpack .../024-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 174s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 174s Selecting previously unselected package libjs-highlight.js. 174s Preparing to unpack .../025-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 174s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 174s Selecting previously unselected package libjs-jquery. 174s Preparing to unpack .../026-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 174s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 174s Selecting previously unselected package libjs-jquery-datatables. 174s Preparing to unpack .../027-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 174s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 175s Selecting previously unselected package liblapack3:armhf. 175s Preparing to unpack .../028-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 175s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 175s Selecting previously unselected package liblerc4:armhf. 175s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 175s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 175s Selecting previously unselected package libthai-data. 175s Preparing to unpack .../030-libthai-data_0.1.30-1_all.deb ... 175s Unpacking libthai-data (0.1.30-1) ... 175s Selecting previously unselected package libthai0:armhf. 175s Preparing to unpack .../031-libthai0_0.1.30-1_armhf.deb ... 175s Unpacking libthai0:armhf (0.1.30-1) ... 175s Selecting previously unselected package libpango-1.0-0:armhf. 175s Preparing to unpack .../032-libpango-1.0-0_1.57.0-1_armhf.deb ... 175s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 175s Selecting previously unselected package libpangoft2-1.0-0:armhf. 175s Preparing to unpack .../033-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 175s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 175s Selecting previously unselected package libpangocairo-1.0-0:armhf. 175s Preparing to unpack .../034-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 175s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 175s Selecting previously unselected package libpaper2:armhf. 175s Preparing to unpack .../035-libpaper2_2.2.5-0.3build1_armhf.deb ... 175s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 175s Selecting previously unselected package libpaper-utils. 175s Preparing to unpack .../036-libpaper-utils_2.2.5-0.3build1_armhf.deb ... 175s Unpacking libpaper-utils (2.2.5-0.3build1) ... 175s Selecting previously unselected package libsharpyuv0:armhf. 175s Preparing to unpack .../037-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 175s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 175s Selecting previously unselected package libsm6:armhf. 175s Preparing to unpack .../038-libsm6_2%3a1.2.6-1build1_armhf.deb ... 175s Unpacking libsm6:armhf (2:1.2.6-1build1) ... 175s Selecting previously unselected package libtcl8.6:armhf. 175s Preparing to unpack .../039-libtcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 175s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 175s Selecting previously unselected package libjbig0:armhf. 175s Preparing to unpack .../040-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 175s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 175s Selecting previously unselected package libwebp7:armhf. 175s Preparing to unpack .../041-libwebp7_1.5.0-0.1build1_armhf.deb ... 175s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 175s Selecting previously unselected package libtiff6:armhf. 175s Preparing to unpack .../042-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 175s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 175s Selecting previously unselected package libxft2:armhf. 175s Preparing to unpack .../043-libxft2_2.3.6-1build2_armhf.deb ... 175s Unpacking libxft2:armhf (2.3.6-1build2) ... 175s Selecting previously unselected package libxss1:armhf. 176s Preparing to unpack .../044-libxss1_1%3a1.2.3-1build4_armhf.deb ... 176s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 176s Selecting previously unselected package libtk8.6:armhf. 176s Preparing to unpack .../045-libtk8.6_8.6.17-1_armhf.deb ... 176s Unpacking libtk8.6:armhf (8.6.17-1) ... 176s Selecting previously unselected package libxt6t64:armhf. 176s Preparing to unpack .../046-libxt6t64_1%3a1.2.1-1.3_armhf.deb ... 176s Unpacking libxt6t64:armhf (1:1.2.1-1.3) ... 176s Selecting previously unselected package node-normalize.css. 176s Preparing to unpack .../047-node-normalize.css_8.0.1-5.1_all.deb ... 176s Unpacking node-normalize.css (8.0.1-5.1) ... 176s Selecting previously unselected package zip. 176s Preparing to unpack .../048-zip_3.0-15ubuntu3_armhf.deb ... 176s Unpacking zip (3.0-15ubuntu3) ... 176s Selecting previously unselected package unzip. 176s Preparing to unpack .../049-unzip_6.0-29ubuntu1_armhf.deb ... 176s Unpacking unzip (6.0-29ubuntu1) ... 176s Selecting previously unselected package xdg-utils. 176s Preparing to unpack .../050-xdg-utils_1.2.1-2ubuntu2_all.deb ... 176s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 176s Selecting previously unselected package r-base-core. 176s Preparing to unpack .../051-r-base-core_4.5.2-1ubuntu2_armhf.deb ... 176s Unpacking r-base-core (4.5.2-1ubuntu2) ... 176s Selecting previously unselected package r-cran-abind. 176s Preparing to unpack .../052-r-cran-abind_1.4-8-1build1_all.deb ... 176s Unpacking r-cran-abind (1.4-8-1build1) ... 176s Selecting previously unselected package r-cran-cardata. 176s Preparing to unpack .../053-r-cran-cardata_3.0.6-1_all.deb ... 176s Unpacking r-cran-cardata (3.0.6-1) ... 176s Selecting previously unselected package r-cran-formula. 176s Preparing to unpack .../054-r-cran-formula_1.2-5-1_all.deb ... 176s Unpacking r-cran-formula (1.2-5-1) ... 176s Selecting previously unselected package r-cran-mass. 176s Preparing to unpack .../055-r-cran-mass_7.3-65-1_armhf.deb ... 176s Unpacking r-cran-mass (7.3-65-1) ... 176s Selecting previously unselected package r-cran-lattice. 176s Preparing to unpack .../056-r-cran-lattice_0.22-9-1_armhf.deb ... 176s Unpacking r-cran-lattice (0.22-9-1) ... 176s Selecting previously unselected package r-cran-nlme. 176s Preparing to unpack .../057-r-cran-nlme_3.1.168-1_armhf.deb ... 176s Unpacking r-cran-nlme (3.1.168-1) ... 177s Selecting previously unselected package r-cran-matrix. 177s Preparing to unpack .../058-r-cran-matrix_1.7-4-1_armhf.deb ... 177s Unpacking r-cran-matrix (1.7-4-1) ... 177s Selecting previously unselected package r-cran-mgcv. 177s Preparing to unpack .../059-r-cran-mgcv_1.9-4-1_armhf.deb ... 177s Unpacking r-cran-mgcv (1.9-4-1) ... 177s Selecting previously unselected package r-cran-nnet. 177s Preparing to unpack .../060-r-cran-nnet_7.3-20-1_armhf.deb ... 177s Unpacking r-cran-nnet (7.3-20-1) ... 177s Selecting previously unselected package r-cran-boot. 177s Preparing to unpack .../061-r-cran-boot_1.3-32-1_all.deb ... 177s Unpacking r-cran-boot (1.3-32-1) ... 177s Selecting previously unselected package r-cran-littler. 177s Preparing to unpack .../062-r-cran-littler_0.3.22-1_armhf.deb ... 177s Unpacking r-cran-littler (0.3.22-1) ... 177s Selecting previously unselected package r-cran-pkgkitten. 177s Preparing to unpack .../063-r-cran-pkgkitten_0.2.4-1_all.deb ... 177s Unpacking r-cran-pkgkitten (0.2.4-1) ... 177s Selecting previously unselected package r-cran-rcpp. 177s Preparing to unpack .../064-r-cran-rcpp_1.1.0-1_armhf.deb ... 177s Unpacking r-cran-rcpp (1.1.0-1) ... 177s Selecting previously unselected package r-cran-minqa. 177s Preparing to unpack .../065-r-cran-minqa_1.2.8-1_armhf.deb ... 177s Unpacking r-cran-minqa (1.2.8-1) ... 177s Selecting previously unselected package libnlopt0:armhf. 177s Preparing to unpack .../066-libnlopt0_2.7.1-7ubuntu1_armhf.deb ... 177s Unpacking libnlopt0:armhf (2.7.1-7ubuntu1) ... 177s Selecting previously unselected package r-cran-nloptr. 177s Preparing to unpack .../067-r-cran-nloptr_2.2.1-2_armhf.deb ... 177s Unpacking r-cran-nloptr (2.2.1-2) ... 177s Selecting previously unselected package r-cran-rbibutils. 177s Preparing to unpack .../068-r-cran-rbibutils_2.3-1_armhf.deb ... 177s Unpacking r-cran-rbibutils (2.3-1) ... 177s Selecting previously unselected package r-cran-rdpack. 177s Preparing to unpack .../069-r-cran-rdpack_2.6.3-1_all.deb ... 177s Unpacking r-cran-rdpack (2.6.3-1) ... 177s Selecting previously unselected package r-cran-reformulas. 177s Preparing to unpack .../070-r-cran-reformulas_0.4.4-1_all.deb ... 177s Unpacking r-cran-reformulas (0.4.4-1) ... 177s Selecting previously unselected package r-cran-rlang. 177s Preparing to unpack .../071-r-cran-rlang_1.1.5-3_armhf.deb ... 177s Unpacking r-cran-rlang (1.1.5-3) ... 177s Selecting previously unselected package r-cran-rcppeigen. 177s Preparing to unpack .../072-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 177s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 177s Selecting previously unselected package r-cran-statmod. 178s Preparing to unpack .../073-r-cran-statmod_1.5.0-1_armhf.deb ... 178s Unpacking r-cran-statmod (1.5.0-1) ... 178s Selecting previously unselected package r-cran-lme4. 178s Preparing to unpack .../074-r-cran-lme4_1.1-38-1_armhf.deb ... 178s Unpacking r-cran-lme4 (1.1-38-1) ... 178s Selecting previously unselected package r-cran-backports. 178s Preparing to unpack .../075-r-cran-backports_1.5.0-2_armhf.deb ... 178s Unpacking r-cran-backports (1.5.0-2) ... 178s Selecting previously unselected package r-cran-cli. 178s Preparing to unpack .../076-r-cran-cli_3.6.4-1_armhf.deb ... 178s Unpacking r-cran-cli (3.6.4-1) ... 178s Selecting previously unselected package r-cran-generics. 178s Preparing to unpack .../077-r-cran-generics_0.1.4-1_all.deb ... 178s Unpacking r-cran-generics (0.1.4-1) ... 178s Selecting previously unselected package r-cran-glue. 178s Preparing to unpack .../078-r-cran-glue_1.8.0-1_armhf.deb ... 178s Unpacking r-cran-glue (1.8.0-1) ... 178s Selecting previously unselected package r-cran-lifecycle. 178s Preparing to unpack .../079-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 178s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 178s Selecting previously unselected package r-cran-magrittr. 178s Preparing to unpack .../080-r-cran-magrittr_2.0.3-1_armhf.deb ... 178s Unpacking r-cran-magrittr (2.0.3-1) ... 178s Selecting previously unselected package r-cran-utf8. 178s Preparing to unpack .../081-r-cran-utf8_1.2.4-1_armhf.deb ... 178s Unpacking r-cran-utf8 (1.2.4-1) ... 178s Selecting previously unselected package r-cran-vctrs. 178s Preparing to unpack .../082-r-cran-vctrs_0.6.5-1_armhf.deb ... 178s Unpacking r-cran-vctrs (0.6.5-1) ... 178s Selecting previously unselected package r-cran-pillar. 178s Preparing to unpack .../083-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 178s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 178s Selecting previously unselected package r-cran-r6. 178s Preparing to unpack .../084-r-cran-r6_2.6.1-1_all.deb ... 178s Unpacking r-cran-r6 (2.6.1-1) ... 178s Selecting previously unselected package r-cran-fansi. 178s Preparing to unpack .../085-r-cran-fansi_1.0.6-2_armhf.deb ... 178s Unpacking r-cran-fansi (1.0.6-2) ... 178s Selecting previously unselected package r-cran-pkgconfig. 178s Preparing to unpack .../086-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 178s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 178s Selecting previously unselected package r-cran-tibble. 179s Preparing to unpack .../087-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 179s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 179s Selecting previously unselected package r-cran-withr. 179s Preparing to unpack .../088-r-cran-withr_3.0.2+dfsg-1_all.deb ... 179s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 179s Selecting previously unselected package r-cran-tidyselect. 179s Preparing to unpack .../089-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 179s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 179s Selecting previously unselected package r-cran-dplyr. 179s Preparing to unpack .../090-r-cran-dplyr_1.1.4-4_armhf.deb ... 179s Unpacking r-cran-dplyr (1.1.4-4) ... 179s Selecting previously unselected package r-cran-purrr. 179s Preparing to unpack .../091-r-cran-purrr_1.0.4-1_armhf.deb ... 179s Unpacking r-cran-purrr (1.0.4-1) ... 179s Selecting previously unselected package r-cran-stringi. 179s Preparing to unpack .../092-r-cran-stringi_1.8.4-1build2_armhf.deb ... 179s Unpacking r-cran-stringi (1.8.4-1build2) ... 179s Selecting previously unselected package r-cran-stringr. 179s Preparing to unpack .../093-r-cran-stringr_1.5.1-1_all.deb ... 179s Unpacking r-cran-stringr (1.5.1-1) ... 179s Selecting previously unselected package r-cran-cpp11. 179s Preparing to unpack .../094-r-cran-cpp11_0.5.3-1_all.deb ... 179s Unpacking r-cran-cpp11 (0.5.3-1) ... 179s Selecting previously unselected package r-cran-tidyr. 179s Preparing to unpack .../095-r-cran-tidyr_1.3.1-1_armhf.deb ... 179s Unpacking r-cran-tidyr (1.3.1-1) ... 179s Selecting previously unselected package r-cran-broom. 179s Preparing to unpack .../096-r-cran-broom_1.0.12+dfsg-1_all.deb ... 179s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 179s Selecting previously unselected package r-cran-numderiv. 179s Preparing to unpack .../097-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 179s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 179s Selecting previously unselected package r-cran-gtable. 179s Preparing to unpack .../098-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 179s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 179s Selecting previously unselected package r-cran-isoband. 179s Preparing to unpack .../099-r-cran-isoband_0.2.7-1_armhf.deb ... 179s Unpacking r-cran-isoband (0.2.7-1) ... 179s Selecting previously unselected package r-cran-farver. 179s Preparing to unpack .../100-r-cran-farver_2.1.2-1_armhf.deb ... 179s Unpacking r-cran-farver (2.1.2-1) ... 180s Selecting previously unselected package r-cran-labeling. 180s Preparing to unpack .../101-r-cran-labeling_0.4.3-1_all.deb ... 180s Unpacking r-cran-labeling (0.4.3-1) ... 180s Selecting previously unselected package r-cran-rcolorbrewer. 180s Preparing to unpack .../102-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 180s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 180s Selecting previously unselected package r-cran-viridislite. 180s Preparing to unpack .../103-r-cran-viridislite_0.4.3-1_all.deb ... 180s Unpacking r-cran-viridislite (0.4.3-1) ... 180s Selecting previously unselected package r-cran-scales. 180s Preparing to unpack .../104-r-cran-scales_1.4.0-1_all.deb ... 180s Unpacking r-cran-scales (1.4.0-1) ... 180s Selecting previously unselected package r-cran-ggplot2. 180s Preparing to unpack .../105-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 180s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 180s Selecting previously unselected package r-cran-cowplot. 180s Preparing to unpack .../106-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 180s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 180s Selecting previously unselected package r-cran-deriv. 180s Preparing to unpack .../107-r-cran-deriv_4.2.0-1_all.deb ... 180s Unpacking r-cran-deriv (4.2.0-1) ... 180s Selecting previously unselected package r-cran-colorspace. 180s Preparing to unpack .../108-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 180s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 180s Selecting previously unselected package r-cran-fracdiff. 180s Preparing to unpack .../109-r-cran-fracdiff_1.5-3-1_armhf.deb ... 180s Unpacking r-cran-fracdiff (1.5-3-1) ... 180s Selecting previously unselected package r-cran-zoo. 180s Preparing to unpack .../110-r-cran-zoo_1.8-15-1_armhf.deb ... 180s Unpacking r-cran-zoo (1.8-15-1) ... 180s Selecting previously unselected package r-cran-lmtest. 180s Preparing to unpack .../111-r-cran-lmtest_0.9.40-1build1_armhf.deb ... 180s Unpacking r-cran-lmtest (0.9.40-1build1) ... 180s Selecting previously unselected package r-cran-timedate. 180s Preparing to unpack .../112-r-cran-timedate_4052.112-1_armhf.deb ... 180s Unpacking r-cran-timedate (4052.112-1) ... 180s Selecting previously unselected package r-cran-quadprog. 180s Preparing to unpack .../113-r-cran-quadprog_1.5-8-1build2_armhf.deb ... 180s Unpacking r-cran-quadprog (1.5-8-1build2) ... 180s Selecting previously unselected package r-cran-xts. 180s Preparing to unpack .../114-r-cran-xts_0.14.1-1_armhf.deb ... 180s Unpacking r-cran-xts (0.14.1-1) ... 180s Selecting previously unselected package r-cran-curl. 180s Preparing to unpack .../115-r-cran-curl_7.0.0+dfsg-1_armhf.deb ... 180s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 180s Selecting previously unselected package r-cran-ttr. 180s Preparing to unpack .../116-r-cran-ttr_0.24.4-1_armhf.deb ... 180s Unpacking r-cran-ttr (0.24.4-1) ... 180s Selecting previously unselected package r-cran-jsonlite. 181s Preparing to unpack .../117-r-cran-jsonlite_1.9.1+dfsg-1_armhf.deb ... 181s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 181s Selecting previously unselected package r-cran-quantmod. 181s Preparing to unpack .../118-r-cran-quantmod_0.4.28-1_all.deb ... 181s Unpacking r-cran-quantmod (0.4.28-1) ... 181s Selecting previously unselected package r-cran-tseries. 181s Preparing to unpack .../119-r-cran-tseries_0.10-59-3_armhf.deb ... 181s Unpacking r-cran-tseries (0.10-59-3) ... 181s Selecting previously unselected package r-cran-urca. 181s Preparing to unpack .../120-r-cran-urca_1.3-4-1build1_armhf.deb ... 181s Unpacking r-cran-urca (1.3-4-1build1) ... 181s Selecting previously unselected package r-cran-rcpparmadillo. 181s Preparing to unpack .../121-r-cran-rcpparmadillo_15.2.3-1-1_armhf.deb ... 181s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 181s Selecting previously unselected package r-cran-forecast. 181s Preparing to unpack .../122-r-cran-forecast_8.23.0-1_armhf.deb ... 181s Unpacking r-cran-forecast (8.23.0-1) ... 181s Selecting previously unselected package r-cran-modelr. 181s Preparing to unpack .../123-r-cran-modelr_0.1.11-1_all.deb ... 181s Unpacking r-cran-modelr (0.1.11-1) ... 181s Selecting previously unselected package r-cran-microbenchmark. 181s Preparing to unpack .../124-r-cran-microbenchmark_1.5.0-1_armhf.deb ... 181s Unpacking r-cran-microbenchmark (1.5.0-1) ... 181s Selecting previously unselected package r-cran-doby. 181s Preparing to unpack .../125-r-cran-doby_4.7.1-3_all.deb ... 181s Unpacking r-cran-doby (4.7.1-3) ... 181s Selecting previously unselected package r-cran-evaluate. 181s Preparing to unpack .../126-r-cran-evaluate_1.0.5-1_all.deb ... 181s Unpacking r-cran-evaluate (1.0.5-1) ... 181s Selecting previously unselected package r-cran-xfun. 181s Preparing to unpack .../127-r-cran-xfun_0.55+dfsg-1_armhf.deb ... 181s Unpacking r-cran-xfun (0.55+dfsg-1) ... 181s Selecting previously unselected package r-cran-highr. 181s Preparing to unpack .../128-r-cran-highr_0.11+dfsg-1_all.deb ... 181s Unpacking r-cran-highr (0.11+dfsg-1) ... 182s Selecting previously unselected package r-cran-yaml. 182s Preparing to unpack .../129-r-cran-yaml_2.3.10-1_armhf.deb ... 182s Unpacking r-cran-yaml (2.3.10-1) ... 182s Selecting previously unselected package libjs-mathjax. 182s Preparing to unpack .../130-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 182s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 182s Selecting previously unselected package r-cran-knitr. 182s Preparing to unpack .../131-r-cran-knitr_1.51+dfsg-1_all.deb ... 182s Unpacking r-cran-knitr (1.51+dfsg-1) ... 182s Selecting previously unselected package r-cran-pbkrtest. 182s Preparing to unpack .../132-r-cran-pbkrtest_0.5.5-1_all.deb ... 182s Unpacking r-cran-pbkrtest (0.5.5-1) ... 182s Selecting previously unselected package r-cran-sparsem. 183s Preparing to unpack .../133-r-cran-sparsem_1.84-2-1_armhf.deb ... 183s Unpacking r-cran-sparsem (1.84-2-1) ... 183s Selecting previously unselected package r-cran-matrixmodels. 183s Preparing to unpack .../134-r-cran-matrixmodels_0.5-4-1_all.deb ... 183s Unpacking r-cran-matrixmodels (0.5-4-1) ... 183s Selecting previously unselected package r-cran-survival. 183s Preparing to unpack .../135-r-cran-survival_3.8-6-1_armhf.deb ... 183s Unpacking r-cran-survival (3.8-6-1) ... 183s Selecting previously unselected package r-cran-matrixstats. 183s Preparing to unpack .../136-r-cran-matrixstats_1.5.0-1_armhf.deb ... 183s Unpacking r-cran-matrixstats (1.5.0-1) ... 183s Selecting previously unselected package r-cran-class. 183s Preparing to unpack .../137-r-cran-class_7.3-23-1_armhf.deb ... 183s Unpacking r-cran-class (7.3-23-1) ... 183s Selecting previously unselected package r-cran-proxy. 183s Preparing to unpack .../138-r-cran-proxy_0.4-27-1_armhf.deb ... 183s Unpacking r-cran-proxy (0.4-27-1) ... 183s Selecting previously unselected package r-cran-e1071. 183s Preparing to unpack .../139-r-cran-e1071_1.7-17-1_armhf.deb ... 183s Unpacking r-cran-e1071 (1.7-17-1) ... 183s Selecting previously unselected package r-cran-codetools. 183s Preparing to unpack .../140-r-cran-codetools_0.2-20-1build1_all.deb ... 183s Unpacking r-cran-codetools (0.2-20-1build1) ... 183s Selecting previously unselected package r-cran-iterators. 183s Preparing to unpack .../141-r-cran-iterators_1.0.14-1build1_all.deb ... 183s Unpacking r-cran-iterators (1.0.14-1build1) ... 183s Selecting previously unselected package r-cran-foreach. 183s Preparing to unpack .../142-r-cran-foreach_1.5.2-1build1_all.deb ... 183s Unpacking r-cran-foreach (1.5.2-1build1) ... 183s Selecting previously unselected package r-cran-data.table. 183s Preparing to unpack .../143-r-cran-data.table_1.17.0+dfsg-1_armhf.deb ... 183s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 183s Selecting previously unselected package r-cran-modelmetrics. 183s Preparing to unpack .../144-r-cran-modelmetrics_1.2.2.2-1build2_armhf.deb ... 183s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ... 183s Selecting previously unselected package r-cran-plyr. 183s Preparing to unpack .../145-r-cran-plyr_1.8.9-1_armhf.deb ... 183s Unpacking r-cran-plyr (1.8.9-1) ... 183s Selecting previously unselected package r-cran-proc. 184s Preparing to unpack .../146-r-cran-proc_1.18.5-1_armhf.deb ... 184s Unpacking r-cran-proc (1.18.5-1) ... 184s Selecting previously unselected package r-cran-tzdb. 184s Preparing to unpack .../147-r-cran-tzdb_0.5.0-1_armhf.deb ... 184s Unpacking r-cran-tzdb (0.5.0-1) ... 184s Selecting previously unselected package r-cran-clock. 184s Preparing to unpack .../148-r-cran-clock_0.7.2-1_armhf.deb ... 184s Unpacking r-cran-clock (0.7.2-1) ... 184s Selecting previously unselected package r-cran-gower. 184s Preparing to unpack .../149-r-cran-gower_1.0.2-1_armhf.deb ... 184s Unpacking r-cran-gower (1.0.2-1) ... 184s Selecting previously unselected package r-cran-sparsevctrs. 184s Preparing to unpack .../150-r-cran-sparsevctrs_0.2.0-2_armhf.deb ... 184s Unpacking r-cran-sparsevctrs (0.2.0-2) ... 184s Selecting previously unselected package r-cran-hardhat. 184s Preparing to unpack .../151-r-cran-hardhat_1.4.2+dfsg-1_all.deb ... 184s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ... 184s Selecting previously unselected package r-cran-rpart. 184s Preparing to unpack .../152-r-cran-rpart_4.1.24-1build1_armhf.deb ... 184s Unpacking r-cran-rpart (4.1.24-1build1) ... 184s Selecting previously unselected package r-cran-shape. 184s Preparing to unpack .../153-r-cran-shape_1.4.6.1-1_all.deb ... 184s Unpacking r-cran-shape (1.4.6.1-1) ... 184s Selecting previously unselected package r-cran-diagram. 184s Preparing to unpack .../154-r-cran-diagram_1.6.5-2_all.deb ... 184s Unpacking r-cran-diagram (1.6.5-2) ... 184s Selecting previously unselected package r-cran-kernsmooth. 184s Preparing to unpack .../155-r-cran-kernsmooth_2.23-26-1build1_armhf.deb ... 184s Unpacking r-cran-kernsmooth (2.23-26-1build1) ... 184s Selecting previously unselected package r-cran-digest. 184s Preparing to unpack .../156-r-cran-digest_0.6.39-1_armhf.deb ... 184s Unpacking r-cran-digest (0.6.39-1) ... 184s Selecting previously unselected package r-cran-globals. 184s Preparing to unpack .../157-r-cran-globals_0.19.0-1_all.deb ... 184s Unpacking r-cran-globals (0.19.0-1) ... 184s Selecting previously unselected package r-cran-listenv. 184s Preparing to unpack .../158-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 184s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 184s Selecting previously unselected package r-cran-parallelly. 184s Preparing to unpack .../159-r-cran-parallelly_1.42.0-1_armhf.deb ... 184s Unpacking r-cran-parallelly (1.42.0-1) ... 184s Selecting previously unselected package r-cran-future. 184s Preparing to unpack .../160-r-cran-future_1.34.0+dfsg-1_all.deb ... 184s Unpacking r-cran-future (1.34.0+dfsg-1) ... 184s Selecting previously unselected package r-cran-future.apply. 184s Preparing to unpack .../161-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 184s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 185s Selecting previously unselected package r-cran-progressr. 185s Preparing to unpack .../162-r-cran-progressr_0.15.1-1_all.deb ... 185s Unpacking r-cran-progressr (0.15.1-1) ... 185s Selecting previously unselected package r-cran-squarem. 185s Preparing to unpack .../163-r-cran-squarem_2021.1-1build1_all.deb ... 185s Unpacking r-cran-squarem (2021.1-1build1) ... 185s Selecting previously unselected package r-cran-lava. 185s Preparing to unpack .../164-r-cran-lava_1.8.2+dfsg-1_all.deb ... 185s Unpacking r-cran-lava (1.8.2+dfsg-1) ... 185s Selecting previously unselected package r-cran-prodlim. 185s Preparing to unpack .../165-r-cran-prodlim_2024.06.25-1_armhf.deb ... 185s Unpacking r-cran-prodlim (2024.06.25-1) ... 185s Selecting previously unselected package r-cran-ipred. 185s Preparing to unpack .../166-r-cran-ipred_0.9-15-1_armhf.deb ... 185s Unpacking r-cran-ipred (0.9-15-1) ... 185s Selecting previously unselected package r-cran-timechange. 185s Preparing to unpack .../167-r-cran-timechange_0.3.0-2_armhf.deb ... 185s Unpacking r-cran-timechange (0.3.0-2) ... 185s Selecting previously unselected package r-cran-lubridate. 185s Preparing to unpack .../168-r-cran-lubridate_1.9.4+dfsg-1_armhf.deb ... 185s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 185s Selecting previously unselected package r-cran-recipes. 185s Preparing to unpack .../169-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 185s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 185s Selecting previously unselected package r-cran-reshape2. 185s Preparing to unpack .../170-r-cran-reshape2_1.4.4-2build2_armhf.deb ... 185s Unpacking r-cran-reshape2 (1.4.4-2build2) ... 185s Selecting previously unselected package r-cran-caret. 185s Preparing to unpack .../171-r-cran-caret_7.0-1+dfsg-1_armhf.deb ... 185s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 185s Selecting previously unselected package r-cran-conquer. 185s Preparing to unpack .../172-r-cran-conquer_1.3.3-1_armhf.deb ... 185s Unpacking r-cran-conquer (1.3.3-1) ... 185s Selecting previously unselected package r-cran-quantreg. 185s Preparing to unpack .../173-r-cran-quantreg_6.1-1_armhf.deb ... 185s Unpacking r-cran-quantreg (6.1-1) ... 185s Selecting previously unselected package r-cran-car. 185s Preparing to unpack .../174-r-cran-car_3.1-5-1_all.deb ... 185s Unpacking r-cran-car (3.1-5-1) ... 185s Selecting previously unselected package r-cran-sandwich. 185s Preparing to unpack .../175-r-cran-sandwich_3.1-1-1build1_all.deb ... 185s Unpacking r-cran-sandwich (3.1-1-1build1) ... 185s Selecting previously unselected package r-cran-aer. 185s Preparing to unpack .../176-r-cran-aer_1.2-15-1_all.deb ... 185s Unpacking r-cran-aer (1.2-15-1) ... 185s Selecting previously unselected package r-cran-bit. 185s Preparing to unpack .../177-r-cran-bit_4.6.0+dfsg-1_armhf.deb ... 185s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 186s Selecting previously unselected package r-cran-bit64. 186s Preparing to unpack .../178-r-cran-bit64_4.6.0-1-4_armhf.deb ... 186s Unpacking r-cran-bit64 (4.6.0-1-4) ... 186s Selecting previously unselected package r-cran-blob. 186s Preparing to unpack .../179-r-cran-blob_1.3.0-1_all.deb ... 186s Unpacking r-cran-blob (1.3.0-1) ... 186s Selecting previously unselected package r-cran-fastmap. 186s Preparing to unpack .../180-r-cran-fastmap_1.2.0-1_armhf.deb ... 186s Unpacking r-cran-fastmap (1.2.0-1) ... 186s Selecting previously unselected package r-cran-cachem. 186s Preparing to unpack .../181-r-cran-cachem_1.1.0-1_armhf.deb ... 186s Unpacking r-cran-cachem (1.1.0-1) ... 186s Selecting previously unselected package r-cran-dbi. 186s Preparing to unpack .../182-r-cran-dbi_1.2.3-1build1_all.deb ... 186s Unpacking r-cran-dbi (1.2.3-1build1) ... 186s Selecting previously unselected package r-cran-foreign. 186s Preparing to unpack .../183-r-cran-foreign_0.8.91-1_armhf.deb ... 186s Unpacking r-cran-foreign (0.8.91-1) ... 186s Selecting previously unselected package r-cran-hexbin. 186s Preparing to unpack .../184-r-cran-hexbin_1.28.5-1_armhf.deb ... 186s Unpacking r-cran-hexbin (1.28.5-1) ... 186s Selecting previously unselected package r-cran-memoise. 186s Preparing to unpack .../185-r-cran-memoise_2.0.1-1build1_all.deb ... 186s Unpacking r-cran-memoise (2.0.1-1build1) ... 186s Selecting previously unselected package r-cran-mitools. 186s Preparing to unpack .../186-r-cran-mitools_2.4-2build2_all.deb ... 186s Unpacking r-cran-mitools (2.4-2build2) ... 186s Selecting previously unselected package r-cran-plogr. 186s Preparing to unpack .../187-r-cran-plogr_0.2.0-3build2_all.deb ... 186s Unpacking r-cran-plogr (0.2.0-3build2) ... 186s Selecting previously unselected package r-cran-r.methodss3. 186s Preparing to unpack .../188-r-cran-r.methodss3_1.8.2-1_all.deb ... 186s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 186s Selecting previously unselected package r-cran-r.oo. 186s Preparing to unpack .../189-r-cran-r.oo_1.27.1-1_all.deb ... 186s Unpacking r-cran-r.oo (1.27.1-1) ... 186s Selecting previously unselected package r-cran-r.utils. 186s Preparing to unpack .../190-r-cran-r.utils_2.13.0-1_all.deb ... 186s Unpacking r-cran-r.utils (2.13.0-1) ... 186s Selecting previously unselected package r-cran-r.cache. 186s Preparing to unpack .../191-r-cran-r.cache_0.17.0-1_all.deb ... 186s Unpacking r-cran-r.cache (0.17.0-1) ... 186s Selecting previously unselected package tcl8.6. 186s Preparing to unpack .../192-tcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 186s Unpacking tcl8.6 (8.6.17+dfsg-1build1) ... 186s Selecting previously unselected package tcl. 186s Preparing to unpack .../193-tcl_8.6.16build1_armhf.deb ... 186s Unpacking tcl (8.6.16build1) ... 186s Selecting previously unselected package r-cran-r.rsp. 186s Preparing to unpack .../194-r-cran-r.rsp_0.46.0+ds-1_all.deb ... 186s Unpacking r-cran-r.rsp (0.46.0+ds-1) ... 186s Selecting previously unselected package r-cran-rsqlite. 187s Preparing to unpack .../195-r-cran-rsqlite_2.3.9-1_armhf.deb ... 187s Unpacking r-cran-rsqlite (2.3.9-1) ... 187s Selecting previously unselected package r-cran-survey. 187s Preparing to unpack .../196-r-cran-survey_4.4-2-2_armhf.deb ... 187s Unpacking r-cran-survey (4.4-2-2) ... 187s Setting up libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 187s Setting up libpixman-1-0:armhf (0.46.4-1) ... 187s Setting up libsharpyuv0:armhf (1.5.0-0.1build1) ... 187s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 187s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 187s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 187s Setting up libxrender1:armhf (1:0.9.12-1) ... 187s Setting up libdatrie1:armhf (0.2.14-1) ... 187s Setting up libxcb-render0:armhf (1.17.0-2ubuntu1) ... 187s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 187s Setting up unzip (6.0-29ubuntu1) ... 187s Setting up x11-common (1:7.7+24ubuntu1) ... 187s Setting up libdeflate0:armhf (1.23-2build1) 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... 190s Setting up r-cran-class (7.3-23-1) ... 190s Setting up r-cran-modelmetrics (1.2.2.2-1build2) ... 190s Setting up r-cran-matrixmodels (0.5-4-1) ... 190s Setting up r-cran-sparsevctrs (0.2.0-2) ... 190s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 190s Setting up r-cran-clock (0.7.2-1) ... 190s Setting up r-cran-sandwich (3.1-1-1build1) ... 190s Setting up r-cran-proc (1.18.5-1) ... 190s Setting up r-cran-survival (3.8-6-1) ... 190s Setting up r-cran-xts (0.14.1-1) ... 190s Setting up r-cran-survey (4.4-2-2) ... 190s Setting up r-cran-r.oo (1.27.1-1) ... 190s Setting up r-cran-rdpack (2.6.3-1) ... 190s Setting up r-cran-future (1.34.0+dfsg-1) ... 190s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 190s Setting up r-cran-reshape2 (1.4.4-2build2) ... 190s Setting up r-cran-future.apply (1.11.3+dfsg-1) ... 190s Setting up r-cran-timechange (0.3.0-2) ... 190s Setting up r-cran-memoise (2.0.1-1build1) ... 190s Setting up r-cran-lava (1.8.2+dfsg-1) ... 190s Setting up r-cran-purrr 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Setting up r-cran-broom (1.0.12+dfsg-1) ... 190s Setting up r-cran-conquer (1.3.3-1) ... 190s Setting up r-cran-r.rsp (0.46.0+ds-1) ... 190s Setting up r-cran-forecast (8.23.0-1) ... 190s Setting up r-cran-quantreg (6.1-1) ... 190s Setting up r-cran-modelr (0.1.11-1) ... 190s Setting up r-cran-doby (4.7.1-3) ... 190s Setting up r-cran-pbkrtest (0.5.5-1) ... 190s Setting up r-cran-car (3.1-5-1) ... 190s Setting up r-cran-aer (1.2-15-1) ... 190s Processing triggers for libc-bin (2.42-2ubuntu4) ... 190s Processing triggers for man-db (2.13.1-1build1) ... 192s Processing triggers for install-info (7.2-5) ... 199s autopkgtest [12:38:29]: test run-unit-test: [----------------------- 201s BEGIN TEST 3stage2phase.R 202s 202s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 202s Copyright (C) 2025 The R Foundation for Statistical Computing 202s Platform: arm-unknown-linux-gnueabihf (32-bit) 202s 202s R is free software and comes with ABSOLUTELY NO WARRANTY. 202s You are welcome to redistribute it under certain conditions. 202s Type 'license()' or 'licence()' for distribution details. 202s 202s R is a collaborative project with many contributors. 202s Type 'contributors()' for more information and 202s 'citation()' on how to cite R or R packages in publications. 202s 202s Type 'demo()' for some demos, 'help()' for on-line help, or 202s 'help.start()' for an HTML browser interface to help. 202s Type 'q()' to quit R. 202s 202s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 202s > ## motivated by dietary biomarker substudy in HCHS 202s > 202s > library(survey) 202s Loading required package: grid 202s Loading required package: Matrix 203s Loading required package: survival 203s > 203s > load("simdata1.RData") 203s 203s Attaching package: 'survey' 203s 203s > 203s > twophase.full = twophase(id=list(~block+house+ind,~1), 203s + strata=list(~strat,NULL), 203s + probs=list(~P.block+P.house+P.ind,NULL), 203s + subset=~phase2, 203s + data=simdata1,method='full') 203s The following object is masked from 'package:graphics': 203s 203s dotchart 203s 203s > 203s > twophase.approx = twophase(id=list(~block+house+ind,~1), 203s + strata=list(~strat,NULL), 203s + probs=list(~P.block+P.house+P.ind,NULL), 203s + subset=~phase2, 203s + data=simdata1,method='approx') 203s > 203s > twophase.rep = twophase(id=list(~block,~1), 203s + strata=list(~strat,NULL), 203s + probs=list(~I(P.block*P.house*P.ind),NULL), 203s + subset=~phase2, 203s + data=simdata1,method='full') 204s > 204s > 204s > twophase.repapprox = twophase(id=list(~block,~1), 204s + strata=list(~strat,NULL), 204s + probs=list(~I(P.block*P.house*P.ind),NULL), 204s + subset=~phase2, 204s + data=simdata1,method='approx') 204s > 204s > 204s > svymean(~age, twophase.full) 204s mean SE 204s age 41.116 0.8114 204s > svymean(~age, twophase.approx) 204s mean SE 204s age 41.116 0.6693 204s > svymean(~age, twophase.rep) 204s mean SE 204s age 41.116 0.784 204s > svymean(~age, twophase.repapprox) 204s mean SE 204s age 41.116 0.6592 204s > 204s BEGIN TEST DBIcheck.R 204s 204s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 204s Copyright (C) 2025 The R Foundation for Statistical Computing 204s Platform: arm-unknown-linux-gnueabihf (32-bit) 204s 204s R is free software and comes with ABSOLUTELY NO WARRANTY. 204s You are welcome to redistribute it under certain conditions. 204s Type 'license()' or 'licence()' for distribution details. 204s 204s R is a collaborative project with many contributors. 204s Type 'contributors()' for more information and 204s 'citation()' on how to cite R or R packages in publications. 204s 204s Type 'demo()' for some demos, 'help()' for on-line help, or 204s 'help.start()' for an HTML browser interface to help. 204s Type 'q()' to quit R. 204s 204s > 204s > library(survey) 204s Loading required package: grid 204s Loading required package: Matrix 205s Loading required package: survival 205s 205s Attaching package: 'survey' 205s 205s > library(RSQLite) 205s The following object is masked from 'package:graphics': 205s 205s dotchart 205s 206s > 206s > data(api) 206s > apiclus1$api_stu<-apiclus1$api.stu 206s > apiclus1$comp_imp<-apiclus1$comp.imp 206s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 206s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 206s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 206s > 206s > m<-svymean(~api00+stype,dclus1) 206s > m.db<-svymean(~api00+stype, dbclus1) 206s > all.equal(coef(m),coef(m.db)) 206s [1] TRUE 206s > all.equal(vcov(m), vcov(m.db)) 206s [1] TRUE 206s > 206s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 206s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 206s > all.equal(coef(r), coef(r.db)) 206s [1] TRUE 206s > all.equal(SE(r), SE(r.db)) 206s [1] TRUE 206s > 206s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 206s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 206s > all.equal(coef(b), coef(b.db)) 206s [1] TRUE 206s > all.equal(SE(b), SE(b.db)) 206s [1] TRUE 206s > all.equal(deff(b), deff(b.db)) 206s [1] TRUE 206s > 206s > l<-svyglm(api00~api99+mobility, design=dclus1) 206s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 206s > all.equal(coef(l),coef(l.db)) 206s [1] TRUE 206s > all.equal(vcov(l), vcov(l.db)) 206s [1] TRUE 206s > 206s > dclus1<-update(dclus1, apidiff=api00-api99) 206s > dclus1<-update(dclus1, apipct= apidiff/api99) 206s > dbclus1<-update(dbclus1, apidiff=api00-api99) 206s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 206s > 206s > u<-svymean(~api00+apidiff+apipct, dclus1) 206s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 206s > all.equal(u, u.db) 206s [1] TRUE 206s > 206s > all.equal(nrow(dclus1),nrow(dbclus1)) 206s [1] TRUE 206s > all.equal(nrow(subset(dclus1,stype=="E")), 206s + nrow(subset(dbclus1,stype=="E"))) 206s [1] "Mean relative difference: 0.2708333" 206s > 206s > ## replicate weights 206s > rclus1<-as.svrepdesign(dclus1) 206s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 206s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 206s > m<-svymean(~api00+api99,rclus1) 206s > m.db<-svymean(~api00+api99,db_rclus1) 206s > all.equal(m,m.db) 206s [1] TRUE 206s > 206s > summary(db_rclus1) 206s DB-backed replicate weight design 206s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 206s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 206s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 206s Unstratified cluster jacknife (JK1) with 15 replicates. 206s Variables: 206s [1] "row_names" "cds" "stype" "name" "sname" 206s [6] "snum" "dname" "dnum" "cname" "cnum" 206s [11] "flag" "pcttest" "api00" "api99" "target" 206s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 206s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 206s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 206s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 206s [36] "emer" "enroll" "api_stu" "fpc" "pw" 206s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 206s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 206s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 206s [56] "wt15" 206s > 206s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 206s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 206s > all.equal(s,s.db) 206s [1] TRUE 206s > 206s BEGIN TEST anova-svycoxph.R 206s 206s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 206s Copyright (C) 2025 The R Foundation for Statistical Computing 206s Platform: arm-unknown-linux-gnueabihf (32-bit) 206s 206s R is free software and comes with ABSOLUTELY NO WARRANTY. 206s You are welcome to redistribute it under certain conditions. 206s Type 'license()' or 'licence()' for distribution details. 206s 206s R is a collaborative project with many contributors. 206s Type 'contributors()' for more information and 206s 'citation()' on how to cite R or R packages in publications. 206s 206s Type 'demo()' for some demos, 'help()' for on-line help, or 206s 'help.start()' for an HTML browser interface to help. 206s Type 'q()' to quit R. 206s 206s > 206s > library(survey) 206s Loading required package: grid 206s Loading required package: Matrix 207s Loading required package: survival 207s > example(svycoxph, ask=FALSE) 207s 207s Attaching package: 'survey' 207s 207s The following object is masked from 'package:graphics': 207s 207s dotchart 207s 207s 207s svycxp> ## Somewhat unrealistic example of nonresponse bias. 207s svycxp> data(pbc, package="survival") 207s 207s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 207s 207s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 207s 207s svycxp> pbc$randprob<-fitted(biasmodel) 207s 207s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 207s 207s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 207s 207s svycxp> rpbc<-as.svrepdesign(dpbc) 207s 207s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 207s Call: 207s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 207s albumin, design = dpbc) 207s 207s coef exp(coef) se(coef) robust se z p 207s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 207s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 207s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 207s 207s Likelihood ratio test= on 3 df, p= 207s n= 312, number of events= 144 207s 207s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 207s Call: 207s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 207s protime + albumin, design = rpbc) 207s 207s coef exp(coef) se(coef) z p 207s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 207s protime 0.24487 1.27745 0.09373 2.612 0.00899 207s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 207s 207s Likelihood ratio test=NA on 3 df, p=NA 207s n= 312, number of events= 144 207s 207s svycxp> s<-predict(model,se=TRUE, type="curve", 207s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 208s 208s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 208s 208s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 208s 208s svycxp> quantile(s[[1]], ci=TRUE) 208s 0.75 0.5 0.25 208s 1435 2503 3574 208s attr(,"ci") 208s 0.025 0.975 208s 0.75 1217 1786 208s 0.5 2256 3170 208s 0.25 3222 Inf 208s 208s svycxp> confint(s[[2]], parm=365*(1:5)) 208s 0.025 0.975 208s 365 0.8375139 0.9453781 208s 730 0.7382750 0.8999016 208s 1095 0.4784105 0.7478460 208s 1460 0.3192009 0.6206764 208s 1825 0.2149475 0.5292978 208s > m<-update(model, .~.+I(protime^2)) 208s > a<-anova(m,model) 208s > b<-anova(m, model,force=TRUE) 208s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 208s > 208s BEGIN TEST api.R 208s 208s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 208s Copyright (C) 2025 The R Foundation for Statistical Computing 208s Platform: arm-unknown-linux-gnueabihf (32-bit) 208s 208s R is free software and comes with ABSOLUTELY NO WARRANTY. 208s You are welcome to redistribute it under certain conditions. 208s Type 'license()' or 'licence()' for distribution details. 208s 208s R is a collaborative project with many contributors. 208s Type 'contributors()' for more information and 208s 'citation()' on how to cite R or R packages in publications. 208s 208s Type 'demo()' for some demos, 'help()' for on-line help, or 208s 'help.start()' for an HTML browser interface to help. 208s Type 'q()' to quit R. 208s 208s > library(survey) 208s Loading required package: grid 208s Loading required package: Matrix 209s Loading required package: survival 209s 209s Attaching package: 'survey' 209s 209s The following object is masked from 'package:graphics': 209s 209s dotchart 209s 209s > options(survey.replicates.mse=TRUE) 209s > example(api) 209s 209s api> library(survey) 209s 209s api> data(api) 209s 209s api> mean(apipop$api00) 209s [1] 664.7126 209s 209s api> sum(apipop$enroll, na.rm=TRUE) 209s [1] 3811472 209s 209s api> #stratified sample 209s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 209s 209s api> summary(dstrat) 209s Stratified Independent Sampling design 209s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 209s Probabilities: 209s Min. 1st Qu. Median Mean 3rd Qu. Max. 209s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 209s Stratum Sizes: 209s E H M 209s obs 100 50 50 209s design.PSU 100 50 50 209s actual.PSU 100 50 50 209s Population stratum sizes (PSUs): 209s E H M 209s 4421 755 1018 209s Data variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "pw" "fpc" 209s 209s api> svymean(~api00, dstrat) 209s mean SE 209s api00 662.29 9.4089 209s 209s api> svytotal(~enroll, dstrat, na.rm=TRUE) 209s total SE 209s enroll 3687178 114642 209s 209s api> # one-stage cluster sample 209s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 209s 209s api> summary(dclus1) 209s 1 - level Cluster Sampling design 209s With (15) clusters. 209s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 209s Probabilities: 209s Min. 1st Qu. Median Mean 3rd Qu. Max. 209s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 209s Population size (PSUs): 757 209s Data variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "fpc" "pw" 209s 209s api> svymean(~api00, dclus1) 209s mean SE 209s api00 644.17 23.542 209s 209s api> svytotal(~enroll, dclus1, na.rm=TRUE) 209s total SE 209s enroll 3404940 932235 209s 209s api> # two-stage cluster sample 209s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 209s 209s api> summary(dclus2) 209s 2 - level Cluster Sampling design 209s With (40, 126) clusters. 209s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 209s Probabilities: 209s Min. 1st Qu. Median Mean 3rd Qu. Max. 209s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 209s Population size (PSUs): 757 209s Data variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "pw" "fpc1" "fpc2" 209s 209s api> svymean(~api00, dclus2) 209s mean SE 209s api00 670.81 30.099 209s 209s api> svytotal(~enroll, dclus2, na.rm=TRUE) 209s total SE 209s enroll 2639273 799638 209s 209s api> # two-stage `with replacement' 209s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 209s 209s api> summary(dclus2wr) 209s 2 - level Cluster Sampling design (with replacement) 209s With (40, 126) clusters. 209s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 209s Probabilities: 209s Min. 1st Qu. Median Mean 3rd Qu. Max. 209s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 209s Data variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "pw" "fpc1" "fpc2" 209s 209s api> svymean(~api00, dclus2wr) 209s mean SE 209s api00 670.81 30.712 209s 209s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 209s total SE 209s enroll 2639273 820261 209s 209s api> # convert to replicate weights 209s api> rclus1<-as.svrepdesign(dclus1) 209s 209s api> summary(rclus1) 209s Call: as.svrepdesign.default(dclus1) 209s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 209s Variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "fpc" "pw" 209s 209s api> svymean(~api00, rclus1) 209s mean SE 209s api00 644.17 26.335 209s 209s api> svytotal(~enroll, rclus1, na.rm=TRUE) 209s total SE 209s enroll 3404940 932235 209s 209s api> # post-stratify on school type 209s api> pop.types<-xtabs(~stype, data=apipop) 209s 209s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 209s 209s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 209s 209s api> summary(dclus1p) 209s 1 - level Cluster Sampling design 209s With (15) clusters. 209s dclus1p<-postStratify(dclus1, ~stype, pop.types) 209s Probabilities: 209s Min. 1st Qu. Median Mean 3rd Qu. Max. 209s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 209s Population size (PSUs): 757 209s Data variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "fpc" "pw" 209s 209s api> summary(rclus1p) 209s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 209s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 209s Variables: 209s [1] "cds" "stype" "name" "sname" "snum" "dname" 209s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 209s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 209s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 209s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 209s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 209s [37] "api.stu" "fpc" "pw" 209s 209s api> svymean(~api00, dclus1p) 209s mean SE 209s api00 642.31 23.92 209s 209s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 209s total SE 209s enroll 3680893 406293 209s 209s api> svymean(~api00, rclus1p) 209s mean SE 209s api00 642.31 26.936 209s 209s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 209s total SE 209s enroll 3680893 473434 209s > 209s > options(survey.replicates.mse=FALSE) 209s > example(api) 209s 209s api> library(survey) 209s 209s api> data(api) 210s 210s api> mean(apipop$api00) 210s [1] 664.7126 210s 210s api> sum(apipop$enroll, na.rm=TRUE) 210s [1] 3811472 210s 210s api> #stratified sample 210s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 210s 210s api> summary(dstrat) 210s Stratified Independent Sampling design 210s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 210s Probabilities: 210s Min. 1st Qu. Median Mean 3rd Qu. Max. 210s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 210s Stratum Sizes: 210s E H M 210s obs 100 50 50 210s design.PSU 100 50 50 210s actual.PSU 100 50 50 210s Population stratum sizes (PSUs): 210s E H M 210s 4421 755 1018 210s Data variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "pw" "fpc" 210s 210s api> svymean(~api00, dstrat) 210s mean SE 210s api00 662.29 9.4089 210s 210s api> svytotal(~enroll, dstrat, na.rm=TRUE) 210s total SE 210s enroll 3687178 114642 210s 210s api> # one-stage cluster sample 210s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 210s 210s api> summary(dclus1) 210s 1 - level Cluster Sampling design 210s With (15) clusters. 210s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 210s Probabilities: 210s Min. 1st Qu. Median Mean 3rd Qu. Max. 210s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 210s Population size (PSUs): 757 210s Data variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "fpc" "pw" 210s 210s api> svymean(~api00, dclus1) 210s mean SE 210s api00 644.17 23.542 210s 210s api> svytotal(~enroll, dclus1, na.rm=TRUE) 210s total SE 210s enroll 3404940 932235 210s 210s api> # two-stage cluster sample 210s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 210s 210s api> summary(dclus2) 210s 2 - level Cluster Sampling design 210s With (40, 126) clusters. 210s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 210s Probabilities: 210s Min. 1st Qu. Median Mean 3rd Qu. Max. 210s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 210s Population size (PSUs): 757 210s Data variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "pw" "fpc1" "fpc2" 210s 210s api> svymean(~api00, dclus2) 210s mean SE 210s api00 670.81 30.099 210s 210s api> svytotal(~enroll, dclus2, na.rm=TRUE) 210s total SE 210s enroll 2639273 799638 210s 210s api> # two-stage `with replacement' 210s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 210s 210s api> summary(dclus2wr) 210s 2 - level Cluster Sampling design (with replacement) 210s With (40, 126) clusters. 210s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 210s Probabilities: 210s Min. 1st Qu. Median Mean 3rd Qu. Max. 210s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 210s Data variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "pw" "fpc1" "fpc2" 210s 210s api> svymean(~api00, dclus2wr) 210s mean SE 210s api00 670.81 30.712 210s 210s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 210s total SE 210s enroll 2639273 820261 210s 210s api> # convert to replicate weights 210s api> rclus1<-as.svrepdesign(dclus1) 210s 210s api> summary(rclus1) 210s Call: as.svrepdesign.default(dclus1) 210s Unstratified cluster jacknife (JK1) with 15 replicates. 210s Variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "fpc" "pw" 210s 210s api> svymean(~api00, rclus1) 210s mean SE 210s api00 644.17 26.329 210s 210s api> svytotal(~enroll, rclus1, na.rm=TRUE) 210s total SE 210s enroll 3404940 932235 210s 210s api> # post-stratify on school type 210s api> pop.types<-xtabs(~stype, data=apipop) 210s 210s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 210s 210s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 210s 210s api> summary(dclus1p) 210s 1 - level Cluster Sampling design 210s With (15) clusters. 210s dclus1p<-postStratify(dclus1, ~stype, pop.types) 210s Probabilities: 210s Min. 1st Qu. Median Mean 3rd Qu. Max. 210s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 210s Population size (PSUs): 757 210s Data variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "fpc" "pw" 210s 210s api> summary(rclus1p) 210s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 210s Unstratified cluster jacknife (JK1) with 15 replicates. 210s Variables: 210s [1] "cds" "stype" "name" "sname" "snum" "dname" 210s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 210s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 210s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 210s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 210s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 210s [37] "api.stu" "fpc" "pw" 210s 210s api> svymean(~api00, dclus1p) 210s mean SE 210s api00 642.31 23.92 210s 210s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 210s total SE 210s enroll 3680893 406293 210s 210s api> svymean(~api00, rclus1p) 210s mean SE 210s api00 642.31 26.934 210s 210s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 210s total SE 210s enroll 3680893 473431 210s > 210s BEGIN TEST badcal.R 210s 210s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 210s Copyright (C) 2025 The R Foundation for Statistical Computing 210s Platform: arm-unknown-linux-gnueabihf (32-bit) 210s 210s R is free software and comes with ABSOLUTELY NO WARRANTY. 210s You are welcome to redistribute it under certain conditions. 210s Type 'license()' or 'licence()' for distribution details. 210s 210s R is a collaborative project with many contributors. 210s Type 'contributors()' for more information and 210s 'citation()' on how to cite R or R packages in publications. 210s 210s Type 'demo()' for some demos, 'help()' for on-line help, or 210s 'help.start()' for an HTML browser interface to help. 210s Type 'q()' to quit R. 210s 210s > ## 210s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 210s > ## 210s > library(survey) 210s Loading required package: grid 210s Loading required package: Matrix 211s Loading required package: survival 211s 211s Attaching package: 'survey' 211s 211s The following object is masked from 'package:graphics': 211s 211s dotchart 211s 211s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 211s > des <- svydesign(ids=~1, weights=~w, data=data) 211s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 211s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 211s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 211s > 211s BEGIN TEST brewer_cpp.R 211s 211s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 211s Copyright (C) 2025 The R Foundation for Statistical Computing 211s Platform: arm-unknown-linux-gnueabihf (32-bit) 211s 211s R is free software and comes with ABSOLUTELY NO WARRANTY. 211s You are welcome to redistribute it under certain conditions. 211s Type 'license()' or 'licence()' for distribution details. 211s 211s R is a collaborative project with many contributors. 211s Type 'contributors()' for more information and 211s 'citation()' on how to cite R or R packages in publications. 211s 211s Type 'demo()' for some demos, 'help()' for on-line help, or 211s 'help.start()' for an HTML browser interface to help. 211s Type 'q()' to quit R. 211s 211s > ## pps="brewer" can't use rcpp 211s > ## this checks that it doesn't 211s > library(survey) 211s Loading required package: grid 211s Loading required package: Matrix 212s Loading required package: survival 213s 213s Attaching package: 'survey' 213s 213s The following object is masked from 'package:graphics': 213s 213s dotchart 213s 213s > data(election) 213s > 213s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 213s > options(survey.use_rcpp=TRUE) 213s > a<-svytotal(~Bush+Kerry+Nader, dpps_br) 213s > options(survey.use_rcpp=FALSE) 213s > b<-svytotal(~Bush+Kerry+Nader, dpps_br) 213s > 213s > stopifnot(identical(a,b)) 213s > 213s BEGIN TEST bycovmat.R 213s 213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 213s Copyright (C) 2025 The R Foundation for Statistical Computing 213s Platform: arm-unknown-linux-gnueabihf (32-bit) 213s 213s R is free software and comes with ABSOLUTELY NO WARRANTY. 213s You are welcome to redistribute it under certain conditions. 213s Type 'license()' or 'licence()' for distribution details. 213s 213s R is a collaborative project with many contributors. 213s Type 'contributors()' for more information and 213s 'citation()' on how to cite R or R packages in publications. 213s 213s Type 'demo()' for some demos, 'help()' for on-line help, or 213s 'help.start()' for an HTML browser interface to help. 213s Type 'q()' to quit R. 213s 213s > 213s > library(survey) 213s Loading required package: grid 213s Loading required package: Matrix 214s Loading required package: survival 214s 214s Attaching package: 'survey' 214s 214s The following object is masked from 'package:graphics': 214s 214s dotchart 214s 214s > data(api) 214s > options(survey.replicates.mse=TRUE) 214s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 214s > rclus1<-as.svrepdesign(dclus1) 214s > 214s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 214s + covmat=TRUE,drop.empty.groups=FALSE) 214s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 214s + covmat=TRUE,drop.empty.groups=TRUE) 214s > 214s > stopifnot(all.equal( 214s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 214s + )) 214s > stopifnot(all.equal( 214s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 214s + )) 214s > 214s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 214s > all <- svytotal(~ell+mobility+meals, dclus1) 214s > 214s > stopifnot(all(abs(vcov(svycontrast(all, 214s + list(quote(ell/mobility), 214s + quote(mobility/mobility), 214s + quote(ell/meals),quote(mobility/meals)))) 214s + -vcov(rat))<1e-10)) 214s > 214s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 214s > 214s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 214s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 214s > 214s > con<-svycontrast(all, 214s + list(quote(ell/mobility), 214s + quote(mobility/mobility), 214s + quote(ell/meals),quote(mobility/meals))) 214s > 214s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 214s > 214s > options(survey.replicates.mse=FALSE) 214s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 214s > rclus1<-as.svrepdesign(dclus1) 214s > 214s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 214s + covmat=TRUE,drop.empty.groups=FALSE) 214s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 214s + covmat=TRUE,drop.empty.groups=TRUE) 214s > 214s > stopifnot(all.equal( 214s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 214s + )) 214s > stopifnot(all.equal( 214s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 214s + )) 214s > 214s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 214s > all <- svytotal(~ell+mobility+meals, dclus1) 214s > 214s > stopifnot(all(abs(vcov(svycontrast(all, 214s + list(quote(ell/mobility), 214s + quote(mobility/mobility), 214s + quote(ell/meals),quote(mobility/meals)))) 214s + -vcov(rat))<1e-10)) 214s > 214s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 214s > 214s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 214s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 214s > 214s > con<-svycontrast(all, 214s + list(quote(ell/mobility), 214s + quote(mobility/mobility), 214s + quote(ell/meals),quote(mobility/meals))) 214s > 214s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 214s > 214s > 214s > 214s BEGIN TEST caleg.R 214s 214s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 214s Copyright (C) 2025 The R Foundation for Statistical Computing 214s Platform: arm-unknown-linux-gnueabihf (32-bit) 214s 214s R is free software and comes with ABSOLUTELY NO WARRANTY. 214s You are welcome to redistribute it under certain conditions. 214s Type 'license()' or 'licence()' for distribution details. 214s 214s R is a collaborative project with many contributors. 214s Type 'contributors()' for more information and 214s 'citation()' on how to cite R or R packages in publications. 214s 214s Type 'demo()' for some demos, 'help()' for on-line help, or 214s 'help.start()' for an HTML browser interface to help. 214s Type 'q()' to quit R. 214s 214s > ## 214s > ## Calibration examples 214s > ## 214s > 214s > 214s > ## Example of calibration to first-stage clusters 214s > library(survey) 214s Loading required package: grid 215s Loading required package: Matrix 216s Loading required package: survival 216s 216s Attaching package: 'survey' 216s 216s The following object is masked from 'package:graphics': 216s 216s dotchart 216s 216s > data(api) 216s > 216s > clusters<-table(apiclus2$dnum) 216s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 216s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 216s > 216s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 216s > 216s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 216s > 216s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 216s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 216s > 216s > names(pop)<-names(clusters) 216s > 216s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 216s > 216s > svymean(~api99, dclus2) 216s mean SE 216s api99 642.14 31.434 216s > svymean(~api99, dclus2g) 216s mean SE 216s api99 654.49 29.82 216s > 216s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 216s dnum api99 se 216s 83 83 694.3333 0.0000 216s 132 132 505.0000 0.0000 216s 152 152 574.0000 0.0000 216s 173 173 894.7500 0.0000 216s 198 198 533.7500 0.0000 216s 200 200 589.8000 6.8335 216s 228 228 477.0000 0.0000 216s 295 295 646.4000 0.0000 216s 302 302 903.5000 0.0000 216s 403 403 852.4000 0.0000 216s 452 452 533.0000 0.0000 216s 480 480 614.2000 0.0000 216s 523 523 580.5000 0.0000 216s 534 534 564.6000 0.0000 216s 549 549 896.2000 0.0000 216s 552 552 730.0000 0.0000 216s 570 570 518.4000 7.5478 216s 575 575 800.8000 4.2513 216s 596 596 785.6000 2.4155 216s 620 620 591.6000 10.5869 216s 638 638 560.2000 4.0954 216s 674 674 760.0000 0.0000 216s 679 679 610.2500 0.0000 216s 687 687 718.6667 0.0000 216s 701 701 651.5000 0.0000 216s 711 711 690.5000 0.0000 216s 731 731 702.0000 2.1744 216s 768 768 562.5000 0.0000 216s 781 781 854.4000 0.7456 216s > 216s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 217s dnum api99 se 217s 83 83 694.3333 0 217s 132 132 505.0000 0 217s 152 152 574.0000 0 217s 173 173 894.7500 0 217s 198 198 533.7500 0 217s 200 200 567.5455 0 217s 228 228 477.0000 0 217s 295 295 646.4000 0 217s 302 302 903.5000 0 217s 403 403 852.4000 0 217s 452 452 533.0000 0 217s 480 480 614.2000 0 217s 523 523 580.5000 0 217s 534 534 564.6000 0 217s 549 549 896.2000 0 217s 552 552 730.0000 0 217s 570 570 548.9444 0 217s 575 575 824.5357 0 217s 596 596 787.5714 0 217s 620 620 609.3750 0 217s 638 638 585.6429 0 217s 674 674 760.0000 0 217s 679 679 610.2500 0 217s 687 687 718.6667 0 217s 701 701 651.5000 0 217s 711 711 690.5000 0 217s 731 731 700.6667 0 217s 768 768 562.5000 0 217s 781 781 851.0000 0 217s > 217s > ## Averaging to first stage 217s > 217s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 217s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 217s > 217s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 217s > 217s > svytotal(~enroll,dclus1g) 217s total SE 217s enroll 3811472 0 217s > svytotal(~api.stu,dclus1g) 217s total SE 217s api.stu 3242857 38967 217s > 217s > #variation within clusters should be zero 217s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 217s [1] TRUE 217s > 217s > ##bounded weights 217s > dclus1g<-calibrate(dclus1, ~enroll, pop) 217s > range(weights(dclus1g)/weights(dclus1)) 217s [1] 0.7906782 1.7891164 217s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 217s > range(weights(dclus1gb)/weights(dclus1)) 217s [1] 0.7198751 1.5000000 217s > 217s > ## Ratio estimators 217s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 217s > svytotal(~api.stu,dstrat) 217s total SE 217s api.stu 3086009 99477 217s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 217s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 217s > predict(common, total=total.enroll) 217s $total 217s enroll 217s api.stu 3190038 217s 217s $se 217s enroll 217s api.stu 29565.98 217s 217s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 217s > svytotal(~api.stu, dstratg) 217s total SE 217s api.stu 3190038 29566 217s > 217s > ## postStratify vs calibrate in stratified sample (Ben French) 217s > set.seed(17) 217s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 217s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 217s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 217s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 217s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 217s > postStratify(des,~w,popw)->dps 217s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 217s > 217s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 217s [1] TRUE 217s > 217s > ## missing data in calibrated design 217s > dps$variables$z[1]<-NA 217s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 217s 217s Call: 217s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 217s 217s Survey design: 217s postStratify(des, ~w, popw) 217s 217s Coefficients: 217s Estimate Std. Error t value Pr(>|t|) 217s (Intercept) -0.1203 0.3380 -0.356 0.722 217s z 6.2118 0.6451 9.630 <2e-16 *** 217s x 2.2602 0.2514 8.992 <2e-16 *** 217s --- 217s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 217s 217s (Dispersion parameter for quasibinomial family taken to be 1.919987) 217s 217s Number of Fisher Scoring iterations: 9 217s 217s > 217s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 217s > # should match the ratio estmate above 217s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 217s > svytotal(~api.stu, dstratgh) 217s total SE 217s api.stu 3190038 29566 217s > 217s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 217s > bnds <- list( 217s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 217s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 217s > lapply(bnds, head) 217s $lower 217s [1] 1 1 -Inf -Inf -Inf -Inf 217s 217s $upper 217s [1] 1 1 Inf Inf Inf Inf 217s 217s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 217s > svytotal(~api.stu, dstratg1) 217s total SE 217s api.stu 3190133 29561 217s > head(weights(dstrat)) 217s 1 2 3 4 5 6 217s 44.21 44.21 44.21 44.21 44.21 44.21 217s > head(weights(dstratg1)) 217s 1 2 3 4 5 6 217s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 217s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 217s [1] TRUE 217s > 217s > ## individual boundary constraints as constant values (Daniel Oehm) 217s > bnds <- list( 217s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 217s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 217s > lapply(bnds, head) 217s $lower 217s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 217s 217s $upper 217s [1] 44.21 44.21 Inf Inf Inf Inf 217s 217s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 217s > svytotal(~api.stu, dstratg2) 217s total SE 217s api.stu 3190133 29561 217s > head(weights(dstrat)) 217s 1 2 3 4 5 6 217s 44.21 44.21 44.21 44.21 44.21 44.21 217s > head(weights(dstratg2)) 217s 1 2 3 4 5 6 217s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 217s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 217s [1] TRUE 217s > 217s > # sparse matrix support (Daniel Oehm) 217s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 217s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 217s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 217s > svymean(~api00, dclus1g) 217s mean SE 217s api00 642.31 23.92 217s > svytotal(~enroll, dclus1g) 217s total SE 217s enroll 3680893 406293 217s > 217s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 217s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 217s > svymean(~api00, dclus1g) 217s mean SE 217s api00 642.31 23.92 217s > svytotal(~enroll, dclus1g) 217s total SE 217s enroll 3680893 406293 217s > 217s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 217s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 217s > svymean(~api00, dclus1g) 217s mean SE 217s api00 642.31 23.92 217s > svytotal(~enroll, dclus1g) 217s total SE 217s enroll 3680893 406293 217s > 217s BEGIN TEST check.R 217s 217s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 217s Copyright (C) 2025 The R Foundation for Statistical Computing 217s Platform: arm-unknown-linux-gnueabihf (32-bit) 217s 217s R is free software and comes with ABSOLUTELY NO WARRANTY. 217s You are welcome to redistribute it under certain conditions. 217s Type 'license()' or 'licence()' for distribution details. 217s 217s R is a collaborative project with many contributors. 217s Type 'contributors()' for more information and 217s 'citation()' on how to cite R or R packages in publications. 217s 217s Type 'demo()' for some demos, 'help()' for on-line help, or 217s 'help.start()' for an HTML browser interface to help. 217s Type 'q()' to quit R. 217s 217s > library(survey) 217s Loading required package: grid 217s Loading required package: Matrix 218s Loading required package: survival 219s 219s Attaching package: 'survey' 219s 219s > data(fpc) 219s The following object is masked from 'package:graphics': 219s 219s dotchart 219s 219s > ## test various possibilities for svydesign 219s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 219s variables = ~x, data = fpc, nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7413 219s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 219s data = fpc, nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7413 219s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 219s > a 219s Stratified Warning message: 219s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 219s No weights or probabilities supplied, assuming equal probability 219s Warning message: 219s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 219s No weights or probabilities supplied, assuming equal probability 219s Warning message: 219s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 219s No weights or probabilities supplied, assuming equal probability 219s Independent Sampling design (with replacement) 219s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 219s data = fpc, nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 44.2 6.237 219s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 219s nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.525 0.7796 219s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 219s data = fpc, nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7413 219s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 219s nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.525 0.7796 219s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 219s > a 219s 1 - level Cluster Sampling design (with replacement) 219s With (5) clusters. 219s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.525 0.838 219s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 219s > a 219s 1 - level Cluster Sampling design (with replacement) 219s With (5) clusters. 219s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 219s nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7938 219s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 219s > a 219s 2 - level Cluster Sampling design (with replacement) 219s With (2, 8) clusters. 219s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 219s data = fpc) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.5465 219s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 219s Warning message: 219s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 219s No weights or probabilities supplied, assuming equal probability 219s > a 219s 2 - level Cluster Sampling design (with replacement) 219s With (2, 8) clusters. 219s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 219s > svymean(~x,a) 219s mean SE 219s x 5.525 0.5188 219s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 219s variables = fpc[, "x", drop = FALSE], nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7413 219s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 219s > a 219s Stratified Independent Sampling design (with replacement) 219s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 219s variables = fpc[, 4:6], nest = TRUE) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7413 219s > 219s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 219s > a 219s 1 - level Cluster Sampling design 219s With (5) clusters. 219s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 219s 4:6], fpc = rep(27, 8)) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.7165 219s > 219s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 219s > a 219s Stratified Independent Sampling design 219s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 219s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 219s > svymean(~x,a) 219s mean SE 219s x 5.4481 0.616 219s > 219s BEGIN TEST confintrep.R 219s 219s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 219s Copyright (C) 2025 The R Foundation for Statistical Computing 219s Platform: arm-unknown-linux-gnueabihf (32-bit) 219s 219s R is free software and comes with ABSOLUTELY NO WARRANTY. 219s You are welcome to redistribute it under certain conditions. 219s Type 'license()' or 'licence()' for distribution details. 219s 219s R is a collaborative project with many contributors. 219s Type 'contributors()' for more information and 219s 'citation()' on how to cite R or R packages in publications. 219s 219s Type 'demo()' for some demos, 'help()' for on-line help, or 219s 'help.start()' for an HTML browser interface to help. 219s Type 'q()' to quit R. 219s 219s > library(survey) 219s Loading required package: grid 219s Loading required package: Matrix 220s Loading required package: survival 220s 220s Attaching package: 'survey' 220s 220s The following object is masked from 'package:graphics': 220s 220s dotchart 220s 220s > data(api) 220s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 220s > rclus2<-as.svrepdesign(dclus2) 220s Warning message: 220s In as.svrepdesign.default(dclus2) : 220s Finite population corrections after first stage have been dropped 220s > 220s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial) 220s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint") 220s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial) 220s > if(anyNA(confint(mrep))) stop("NA in confint") 220s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint") 220s > 220s BEGIN TEST contrast-replicates.R 220s 220s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 220s Copyright (C) 2025 The R Foundation for Statistical Computing 220s Platform: arm-unknown-linux-gnueabihf (32-bit) 220s 220s R is free software and comes with ABSOLUTELY NO WARRANTY. 220s You are welcome to redistribute it under certain conditions. 220s Type 'license()' or 'licence()' for distribution details. 220s 220s R is a collaborative project with many contributors. 220s Type 'contributors()' for more information and 220s 'citation()' on how to cite R or R packages in publications. 220s 220s Type 'demo()' for some demos, 'help()' for on-line help, or 220s 'help.start()' for an HTML browser interface to help. 220s Type 'q()' to quit R. 220s 220s > ## test use of replicates in svyby, svycontrast 220s > library(survey) 220s Loading required package: grid 220s Loading required package: Matrix 221s Loading required package: survival 222s 222s Attaching package: 'survey' 222s 222s The following object is masked from 'package:graphics': 222s 222s dotchart 222s 222s > 222s > data(api) 222s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 222s > rclus1<-as.svrepdesign(dclus1) 222s > 222s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 222s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 222s > vcov(c_without) 222s contrast 222s contrast 0.06862947 222s > 222s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 222s > 222s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 222s > 222s > v_with<- vcov(rclus1, c_with$replicates) 222s > 222s > r<- attr(meanlogs_with, "replicates") 222s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 222s > 222s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 222s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 222s > 222s BEGIN TEST coxph-termtest.R 222s 222s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 222s Copyright (C) 2025 The R Foundation for Statistical Computing 222s Platform: arm-unknown-linux-gnueabihf (32-bit) 222s 222s R is free software and comes with ABSOLUTELY NO WARRANTY. 222s You are welcome to redistribute it under certain conditions. 222s Type 'license()' or 'licence()' for distribution details. 222s 222s R is a collaborative project with many contributors. 222s Type 'contributors()' for more information and 222s 'citation()' on how to cite R or R packages in publications. 222s 222s Type 'demo()' for some demos, 'help()' for on-line help, or 222s 'help.start()' for an HTML browser interface to help. 222s Type 'q()' to quit R. 222s 222s > library(survey) 222s Loading required package: grid 222s Loading required package: Matrix 223s Loading required package: survival 223s 223s Attaching package: 'survey' 223s 223s The following object is masked from 'package:graphics': 223s 223s dotchart 223s 223s > library(survival) 223s > set.seed(2021-6-25) 223s > test1 <- list(time=c(4,3,1,1,2,2,3), 223s + status=c(1,1,1,0,1,1,0), 223s + x1=as.factor(rbinom(7, 2, 0.5)), 223s + x=c(0,2,1,1,1,0,0)) 223s > # Fit a stratified model 223s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 223s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 223s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 223s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 223s > 223s > data(pbc, package="survival") 223s > 223s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 223s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 223s > pbc$randprob<-fitted(biasmodel) 223s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 223s > 223s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 223s > library(splines) 223s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 223s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 223s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 223s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 223s > 223s BEGIN TEST deff.R 223s 223s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 223s Copyright (C) 2025 The R Foundation for Statistical Computing 223s Platform: arm-unknown-linux-gnueabihf (32-bit) 223s 223s R is free software and comes with ABSOLUTELY NO WARRANTY. 223s You are welcome to redistribute it under certain conditions. 223s Type 'license()' or 'licence()' for distribution details. 223s 223s R is a collaborative project with many contributors. 223s Type 'contributors()' for more information and 223s 'citation()' on how to cite R or R packages in publications. 223s 223s Type 'demo()' for some demos, 'help()' for on-line help, or 223s 'help.start()' for an HTML browser interface to help. 223s Type 'q()' to quit R. 223s 224s > ## from Takahiro Tsuchiya 224s > library(survey) 224s Loading required package: grid 224s Loading required package: Matrix 225s Loading required package: survival 225s > kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 225s + 1 1 15 100 20 225s + 2 2 143 100 200 225s + 3 3 21 100 11 225s + 4 4 51 100 25 225s + 5 5 337 100 550 225s + 6 6 50 100 30 225s + 7 7 274 100 250 225s + 8 8 145 100 100 225s + 9 9 15 100 10 225s + 10 10 86 100 55 225s + ",open="r"),header=TRUE) 225s > close(tmp) 225s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 225s 225s Attaching package: 'survey' 225s 225s The following object is masked from 'package:graphics': 225s 225s dotchart 225s 225s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 225s mean SE DEff 225s uriage 113.700 35.626 1.0101 225s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 225s uriage 225s uriage 1.010101 225s > 225s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 225s total SE DEff 225s uriage 113700 35626 1.0101 225s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 225s uriage 225s uriage 1.010101 225s > 225s > 225s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 225s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 225s mean SE DEff 225s uriage 243.914 48.752 1.9741 225s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 225s uriage 225s uriage 1.974067 225s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 225s total SE DEff 225s uriage 305136 184965 18.157 225s > (N.hat <- sum(weights(des.pps))) 225s [1] 1251 225s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 225s uriage 225s uriage 18.15669 225s > 225s BEGIN TEST defftest.R 225s 225s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 225s Copyright (C) 2025 The R Foundation for Statistical Computing 225s Platform: arm-unknown-linux-gnueabihf (32-bit) 225s 225s R is free software and comes with ABSOLUTELY NO WARRANTY. 225s You are welcome to redistribute it under certain conditions. 225s Type 'license()' or 'licence()' for distribution details. 225s 225s R is a collaborative project with many contributors. 225s Type 'contributors()' for more information and 225s 'citation()' on how to cite R or R packages in publications. 225s 225s Type 'demo()' for some demos, 'help()' for on-line help, or 225s 'help.start()' for an HTML browser interface to help. 225s Type 'q()' to quit R. 225s 225s > library(survey) 225s Loading required package: grid 225s Loading required package: Matrix 226s Loading required package: survival 226s 226s Attaching package: 'survey' 226s 226s The following object is masked from 'package:graphics': 226s 226s dotchart 226s 226s > 226s > data(api) 226s > 226s > ## one-stage cluster sample 226s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 226s > 226s > # svyglm model 226s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 226s > 226s > #deffs returned from svyglm model - implausibly high 226s > deff(mod) 226s (Intercept) enroll api.stu 226s 1.919945 2.500983 2.686102 226s > #> (Intercept) enroll api.stu 226s > #> 351.3500 457.6799 491.5567 226s > 226s > # run mod with same data and glm() 226s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 226s > 226s > # manually calculate deffs 226s > 226s > clust_se <- summary(mod)$coefficients[,2] 226s > srs_se <- summary(srs_mod)$coefficients[,2] 226s > 226s > deffs <- clust_se^2 / srs_se^2 226s > stopifnot(all.equal(deffs, deff(mod))) 226s > 226s > 226s BEGIN TEST degf-svrepdesign.R 227s 227s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 227s Copyright (C) 2025 The R Foundation for Statistical Computing 227s Platform: arm-unknown-linux-gnueabihf (32-bit) 227s 227s R is free software and comes with ABSOLUTELY NO WARRANTY. 227s You are welcome to redistribute it under certain conditions. 227s Type 'license()' or 'licence()' for distribution details. 227s 227s R is a collaborative project with many contributors. 227s Type 'contributors()' for more information and 227s 'citation()' on how to cite R or R packages in publications. 227s 227s Type 'demo()' for some demos, 'help()' for on-line help, or 227s 'help.start()' for an HTML browser interface to help. 227s Type 'q()' to quit R. 227s 227s > library(survey) 227s Loading required package: grid 227s Loading required package: Matrix 228s Loading required package: survival 228s 228s Attaching package: 'survey' 228s 228s The following object is masked from 'package:graphics': 228s 228s dotchart 228s 228s > data(scd) 228s > 228s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1), 228s + c(0,1,0,1,1,0)) 228s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights) 228s > 228s > stopifnot(degf(scdrep)==3) 228s > 228s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4) 228s > stopifnot(degf(scdrep)==4) 228s > 228s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2) 228s > stopifnot(degf(scdrep)==2) 228s > 228s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 228s + warning=function(w) w) 228s Warning message: 228s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) : 228s No sampling weights provided: equal probability assumed 228s Warning message: 228s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 228s No sampling weights provided: equal probability assumed 228s Warning message: 228s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 228s No sampling weights provided: equal probability assumed 228s > 228s > stopifnot(inherits(msg,"warning")) 228s > 228s > 228s > 228s > 228s BEGIN TEST domain.R 228s 228s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 228s Copyright (C) 2025 The R Foundation for Statistical Computing 228s Platform: arm-unknown-linux-gnueabihf (32-bit) 228s 228s R is free software and comes with ABSOLUTELY NO WARRANTY. 228s You are welcome to redistribute it under certain conditions. 228s Type 'license()' or 'licence()' for distribution details. 228s 228s R is a collaborative project with many contributors. 228s Type 'contributors()' for more information and 228s 'citation()' on how to cite R or R packages in publications. 228s 228s Type 'demo()' for some demos, 'help()' for on-line help, or 228s 'help.start()' for an HTML browser interface to help. 228s Type 'q()' to quit R. 228s 228s > ## 228s > ## Domain means can be written as ratio estimators or as regression coefficients 228s > ## 228s > ## This code checks that subsetting the design object gives the same results as 228s > ## these approaches. 228s > ## 228s > 228s > 228s > library(survey) 228s Loading required package: grid 228s Loading required package: Matrix 229s Loading required package: survival 229s 229s Attaching package: 'survey' 229s 229s The following object is masked from 'package:graphics': 229s 229s dotchart 229s 229s > data(fpc) 229s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 229s > dsub<-subset(dfpc,x>4) 229s > (m1<-svymean(~x,design=dsub)) 229s mean SE 229s x 6.195 0.7555 229s > 229s > ## These should give the same domain estimates and standard errors 229s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 229s I(x > 4) x se 229s FALSE FALSE 3.314286 0.3117042 229s TRUE TRUE 6.195000 0.7555129 229s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 229s > summary(m3) 229s 229s Call: 229s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 229s 229s Survey design: 229s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 229s nest = TRUE) 229s 229s Coefficients: 229s Estimate Std. Error t value Pr(>|t|) 229s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 229s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 229s --- 229s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 229s 229s (Dispersion parameter for gaussian family taken to be 2.557379) 229s 229s Number of Fisher Scoring iterations: 2 229s 229s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 229s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 229s dfpc) 229s Ratios= 229s as.numeric(x > 4) 229s I(x * (x > 4)) 6.195 229s SEs= 229s as.numeric(x > 4) 229s I(x * (x > 4)) 0.7555129 229s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 229s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 229s > 229s > ## with strata 229s > data(api) 229s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 229s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 229s > m2<-svyglm(enroll~comp.imp-1, dstrat) 229s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 229s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 229s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 229s > 229s > ## with calibration 229s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 229s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 229s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 229s 1 - level Cluster Sampling design 229s With (15) clusters. 229s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 229s > 229s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 229s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 229s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 229s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 229s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 229s > 229s > ## with raking 229s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 229s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 229s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 230s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 230s > m2<-svyglm(api00~comp.imp-1, dclus1r) 230s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 230s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 230s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 230s > 230s > 230s > 230s > ## 230s > ## based on bug report from Takahiro Tsuchiya for version 3.4 230s > ## 230s > rei<-read.table(tmp<-textConnection( 230s + " id N n.a h n.ah n.h sub y 230s + 1 1 300 20 1 12 5 TRUE 1 230s + 2 2 300 20 1 12 5 TRUE 2 230s + 3 3 300 20 1 12 5 TRUE 3 230s + 4 4 300 20 1 12 5 TRUE 4 230s + 5 5 300 20 1 12 5 TRUE 5 230s + 6 6 300 20 1 12 5 FALSE NA 230s + 7 7 300 20 1 12 5 FALSE NA 230s + 8 8 300 20 1 12 5 FALSE NA 230s + 9 9 300 20 1 12 5 FALSE NA 230s + 10 10 300 20 1 12 5 FALSE NA 230s + 11 11 300 20 1 12 5 FALSE NA 230s + 12 12 300 20 1 12 5 FALSE NA 230s + 13 13 300 20 2 8 3 TRUE 6 230s + 14 14 300 20 2 8 3 TRUE 7 230s + 15 15 300 20 2 8 3 TRUE 8 230s + 16 16 300 20 2 8 3 FALSE NA 230s + 17 17 300 20 2 8 3 FALSE NA 230s + 18 18 300 20 2 8 3 FALSE NA 230s + 19 19 300 20 2 8 3 FALSE NA 230s + 20 20 300 20 2 8 3 FALSE NA 230s + "), header=TRUE) 230s > close(tmp) 230s > 230s > 230s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 230s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 230s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 230s > 230s > rei$y<-rei$y*(rei$y>3) 230s > ## based on Sarndal et al (9.4.14) 230s > rei$w.ah <- rei$n.ah / rei$n.a 230s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 230s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 230s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 230s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 230s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 230s > 230s > a.rei$f.h<-with(a.rei, n.h/n.ah) 230s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 230s > 230s > a.rei$f<-with(a.rei, n.a/N) 230s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 230s > 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))) 230s > 230s > V 230s [1] 70761.47 230s > Vphase1 230s [1] 44325.47 230s > Vphase2 230s [1] 26436 230s > vcov(tot2) 230s [,1] 230s [1,] 70761.47 230s attr(,"phases") 230s attr(,"phases")$phase1 230s [,1] 230s [1,] 44325.47 230s 230s attr(,"phases")$phase2 230s [,1] 230s [1,] 26436 230s 230s > 230s > ## comparing to regression 230s > reg<-svyglm(y~I(y<4), design=des.rei2) 230s > mn<-svymean(~y, subset(des.rei2,y>3)) 230s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 230s [1] TRUE 230s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 230s [1] TRUE 230s > vcov(mn) 230s [,1] 230s [1,] 0.3292258 230s attr(,"phases") 230s attr(,"phases")$phase1 230s [,1] 230s [1,] 0.1599264 230s 230s attr(,"phases")$phase2 230s [,1] 230s [1,] 0.1692994 230s 230s > vcov(reg) 230s (Intercept) I(y < 4)TRUE 230s (Intercept) 0.3292258 -0.3292258 230s I(y < 4)TRUE -0.3292258 0.5901907 230s attr(,"phases") 230s attr(,"phases")$phase1 230s (Intercept) I(y < 4)TRUE 230s (Intercept) 0.1599264 -0.1599264 230s I(y < 4)TRUE -0.1599264 0.2588542 230s 230s attr(,"phases")$phase2 230s (Intercept) I(y < 4)TRUE 230s (Intercept) 0.1692994 -0.1692994 230s I(y < 4)TRUE -0.1692994 0.3313365 230s 230s > 230s > 230s BEGIN TEST fpc.R 230s 230s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 230s Copyright (C) 2025 The R Foundation for Statistical Computing 230s Platform: arm-unknown-linux-gnueabihf (32-bit) 230s 230s R is free software and comes with ABSOLUTELY NO WARRANTY. 230s You are welcome to redistribute it under certain conditions. 230s Type 'license()' or 'licence()' for distribution details. 230s 230s R is a collaborative project with many contributors. 230s Type 'contributors()' for more information and 230s 'citation()' on how to cite R or R packages in publications. 230s 230s Type 'demo()' for some demos, 'help()' for on-line help, or 230s 'help.start()' for an HTML browser interface to help. 230s Type 'q()' to quit R. 230s 230s > library(survey) 230s Loading required package: grid 230s Loading required package: Matrix 231s Loading required package: survival 231s 231s Attaching package: 'survey' 231s 231s The following object is masked from 'package:graphics': 231s 231s dotchart 231s 231s > ## check many permutations of fpc specification 231s > example(fpc) 231s 231s fpc> data(fpc) 231s 231s fpc> fpc 231s stratid psuid weight nh Nh x 231s 1 1 1 3 5 15 2.8 231s 2 1 2 3 5 15 4.1 231s 3 1 3 3 5 15 6.8 231s 4 1 4 3 5 15 6.8 231s 5 1 5 3 5 15 9.2 231s 6 2 1 4 3 12 3.7 231s 7 2 2 4 3 12 6.6 231s 8 2 3 4 3 12 4.2 231s 231s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 231s fpc+ data=fpc, nest=TRUE) 231s 231s fpc> withoutfpc 231s Stratified Independent Sampling design (with replacement) 231s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 231s data=fpc, nest=TRUE) 231s 231s fpc> svymean(~x, withoutfpc) 231s mean SE 231s x 5.4481 0.7413 231s 231s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 231s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 231s 231s fpc> withfpc 231s Stratified Independent Sampling design 231s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 231s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 231s 231s fpc> svymean(~x, withfpc) 231s mean SE 231s x 5.4481 0.616 231s 231s fpc> ## Other equivalent forms 231s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 231s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 231s 231s fpc> svymean(~x, withfpc) 231s mean SE 231s x 5.4481 0.616 231s 231s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 231s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 231s 231s fpc> svymean(~x, withfpc) 231s mean SE 231s x 5.4481 0.616 231s 231s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 231s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 231s 231s fpc> svymean(~x, withfpc) 231s mean SE 231s x 5.4481 0.616 231s 231s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 231s fpc+ variables=~x,data=fpc,nest=TRUE) 231s 231s fpc> svymean(~x, withfpc) 231s mean SE 231s x 5.4481 0.616 231s 231s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 231s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 231s 231s fpc> svymean(~x, withfpc) 231s mean SE 231s x 5.4481 0.616 231s > 231s > 231s BEGIN TEST glm-scoping.R 231s 231s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 231s Copyright (C) 2025 The R Foundation for Statistical Computing 231s Platform: arm-unknown-linux-gnueabihf (32-bit) 231s 231s R is free software and comes with ABSOLUTELY NO WARRANTY. 231s You are welcome to redistribute it under certain conditions. 231s Type 'license()' or 'licence()' for distribution details. 231s 231s R is a collaborative project with many contributors. 231s Type 'contributors()' for more information and 231s 'citation()' on how to cite R or R packages in publications. 231s 231s Type 'demo()' for some demos, 'help()' for on-line help, or 231s 'help.start()' for an HTML browser interface to help. 231s Type 'q()' to quit R. 231s 231s > ## bug report from Thomas Leeper, fixed in version 3.32-3 231s > 231s > library("survey") 231s Loading required package: grid 231s Loading required package: Matrix 232s Loading required package: survival 233s > data(api) 233s 233s Attaching package: 'survey' 233s 233s The following object is masked from 'package:graphics': 233s 233s dotchart 233s 233s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 233s > 233s > # pass `family` directly (WORKS!) 233s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 233s Stratified Independent Sampling design 233s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 233s fpc = ~fpc) 233s 233s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 233s family = gaussian()) 233s 233s Coefficients: 233s (Intercept) ell meals mobility 233s 820.8873 -0.4806 -3.1415 0.2257 233s 233s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 233s Null Deviance: 3023000 233s Residual Deviance: 1029000 AIC: 2308 233s > 233s > # passing `family` via ... (WORKS!) 233s > myfun1 <- function(formula, design, ...) { 233s + svyglm(formula, design = design, ...) 233s + } 233s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 233s Stratified Independent Sampling design 233s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 233s fpc = ~fpc) 233s 233s Call: svyglm(formula = formula, design = design, family = ..1) 233s 233s Coefficients: 233s (Intercept) ell meals mobility 233s 820.8873 -0.4806 -3.1415 0.2257 233s 233s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 233s Null Deviance: 3023000 233s Residual Deviance: 1029000 AIC: 2308 233s > 233s > # passing `family` via default argument (DOES NOT WORK!) 233s > myfun2 <- function(formula, design, family = gaussian()) { 233s + svyglm(formula, design = design, family = family) 233s + } 233s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 233s Stratified Independent Sampling design 233s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 233s fpc = ~fpc) 233s 233s Call: svyglm(formula = formula, design = design, family = family) 233s 233s Coefficients: 233s (Intercept) ell meals mobility 233s 820.8873 -0.4806 -3.1415 0.2257 233s 233s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 233s Null Deviance: 3023000 233s Residual Deviance: 1029000 AIC: 2308 233s > 233s BEGIN TEST kalton.R 233s 233s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 233s Copyright (C) 2025 The R Foundation for Statistical Computing 233s Platform: arm-unknown-linux-gnueabihf (32-bit) 233s 233s R is free software and comes with ABSOLUTELY NO WARRANTY. 233s You are welcome to redistribute it under certain conditions. 233s Type 'license()' or 'licence()' for distribution details. 233s 233s R is a collaborative project with many contributors. 233s Type 'contributors()' for more information and 233s 'citation()' on how to cite R or R packages in publications. 233s 233s Type 'demo()' for some demos, 'help()' for on-line help, or 233s 'help.start()' for an HTML browser interface to help. 233s Type 'q()' to quit R. 233s 233s > library(survey) 233s Loading required package: grid 233s Loading required package: Matrix 234s Loading required package: survival 234s 234s Attaching package: 'survey' 234s 234s The following object is masked from 'package:graphics': 234s 234s dotchart 234s 234s > 234s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 234s > 234s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 234s > 234s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 234s > 234s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 234s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 234s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 234s > 234s > dkalton<-svydesign(id=~1,data=kaltonsample) 234s Warning message: 234s In svydesign.default(id = ~1, data = kaltonsample) : 234s No weights or probabilities supplied, assuming equal probability 234s > 234s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 234s > 234s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 234s > 234s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 234s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 234s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 234s > 234s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 234s > 234s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 234s > 234s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 234s > 234s > 234s > #table A 234s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 4.00 1.00 1.38 234s 2 1.20 1.07 1.10 234s 3 1.70 1.20 4.00 234s 4 1.83 1.65 1.79 234s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 4.00 1.00 1.37 234s 2 1.20 1.07 1.10 234s 3 1.70 1.20 4.00 234s 4 1.83 1.65 1.79 234s > 234s > #table B 234s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 1.81 1.45 2.02 234s 2 1.08 0.87 1.21 234s 3 2.20 1.76 2.45 234s 4 1.83 1.47 2.04 234s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 1.81 1.45 2.02 234s 2 1.08 0.87 1.21 234s 3 2.20 1.76 2.45 234s 4 1.83 1.47 2.04 234s > 234s > #table C 234s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 1.82 1.50 1.97 234s 2 1.09 0.78 1.24 234s 3 2.19 1.88 2.34 234s 4 1.83 1.52 1.98 234s > 234s > #table D 234s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 1.21 1.17 1.14 234s 2 1.43 1.40 1.36 234s 3 1.66 1.62 1.59 234s 4 1.88 1.85 1.81 234s > 234s > #table G 234s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 1.87 1.46 1.98 234s 2 1.08 0.74 1.27 234s 3 2.17 2.09 2.18 234s 4 1.89 1.49 1.99 234s > 234s > #table G 234s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 234s b 234s a 1 2 3 234s 1 1.81 1.48 1.99 234s 2 1.08 0.75 1.26 234s 3 2.20 2.00 2.20 234s 4 1.83 1.50 2.00 234s > 234s BEGIN TEST logranktest.R 234s 234s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 234s Copyright (C) 2025 The R Foundation for Statistical Computing 234s Platform: arm-unknown-linux-gnueabihf (32-bit) 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 235s Loading required package: grid 235s > ## StackOverflow 63333282 235s > 235s > library(survey) 235s Loading required package: Matrix 236s Loading required package: survival 236s 236s Attaching package: 'survey' 236s 236s The following object is masked from 'package:graphics': 236s 236s dotchart 236s 236s > D = data.frame(unique_id = 1:135, 236s + 236s + weights = rep(1,135), 236s + 236s + 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 , 236s + 236s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 236s + 236s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 236s + 236s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 236s + 236s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 236s + 236s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 236s + 236s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 236s + 236s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 236s + 236s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 236s + 236s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 236s + 236s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 236s + 236s + 2.35699896, 2.94956000, 8.85381736), 236s + 236s + 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, 236s + 236s + 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, 236s + 236s + 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), 236s + 236s + group = c(rep("group1", 40), rep("group2", 95))) 236s > 236s > 236s > 236s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 236s > 236s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 236s > 236s > a<-svylogrank(formula = svykm_formula, design = svy_design) 236s > 236s > ii<-with(D, order(event_time, event_flag)) 236s > 236s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 236s > 236s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 236s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 236s > 236s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 236s > 236s > 236s > stopifnot(all.equal(a[[2]],b[[2]])) 236s > 236s > stopifnot(all.equal(a[[2]],d[[2]])) 236s > 236s > stopifnot(all.equal(a[[2]],f[-1])) 236s > 236s > 236s BEGIN TEST lonely.psu.R 236s 236s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 236s Copyright (C) 2025 The R Foundation for Statistical Computing 236s Platform: arm-unknown-linux-gnueabihf (32-bit) 236s 236s R is free software and comes with ABSOLUTELY NO WARRANTY. 236s You are welcome to redistribute it under certain conditions. 236s Type 'license()' or 'licence()' for distribution details. 236s 236s R is a collaborative project with many contributors. 236s Type 'contributors()' for more information and 236s 'citation()' on how to cite R or R packages in publications. 236s 236s Type 'demo()' for some demos, 'help()' for on-line help, or 236s 'help.start()' for an HTML browser interface to help. 236s Type 'q()' to quit R. 236s 236s > 236s > ## lonely PSUs by design 236s > library(survey) 236s Loading required package: grid 236s Loading required package: Matrix 237s Loading required package: survival 237s 237s Attaching package: 'survey' 237s 237s > data(api) 237s The following object is masked from 'package:graphics': 237s 237s dotchart 237s 237s > ## not certainty PSUs by fpc 237s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 237s > summary(ds) 237s Stratified Independent Sampling design (with replacement) 237s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 237s Probabilities: 237s Min. 1st Qu. Median Mean 3rd Qu. Max. 237s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 237s Stratum Sizes: 237s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 237s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 237s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 237s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 237s Data variables: 237s [1] "cds" "stype" "name" "sname" "snum" "dname" 237s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 237s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 237s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 237s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 237s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 237s [37] "api.stu" "fpc" "pw" 237s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 237s Stratum (413) has only one PSU at stage 1 237s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 237s Stratum413has only one PSU 237s > 237s > options(survey.lonely.psu="fail") 237s > try(svymean(~api00,ds)) 237s > try(svymean(~api00, as.svrepdesign(ds))) 237s > options(survey.lonely.psu="remove") 237s > svymean(~api00,ds) 237s mean SE 237s api00 644.17 5.8058 237s > svymean(~api00, as.svrepdesign(ds)) 237s mean SE 237s api00 644.17 5.8058 237s > options(survey.lonely.psu="certainty") 237s > svymean(~api00,ds) 237s mean SE 237s api00 644.17 5.8058 237s > svymean(~api00, as.svrepdesign(ds)) 237s mean SE 237s api00 644.17 5.8058 237s > options(survey.lonely.psu="adjust") 237s > svymean(~api00,ds) 237s mean SE 237s api00 644.17 5.8281 237s > svymean(~api00, as.svrepdesign(ds)) 237s mean SE 237s api00 644.17 5.8267 237s > options(survey.lonely.psu="average") 237s > svymean(~api00,ds) 237s mean SE 237s api00 644.17 6.0096 237s > svymean(~api00, as.svrepdesign(ds)) 238s mean SE 238s api00 644.17 5.8217 238s > 238s > ## fpc specified 238s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 238s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 238s > summary(ds) 238s Stratified Independent Sampling design 238s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 238s fpc = fpc) 238s Probabilities: 238s Min. 1st Qu. Median Mean 3rd Qu. Max. 238s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 238s Stratum Sizes: 238s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 238s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 238s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 238s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 238s Population stratum sizes (PSUs): 238s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 238s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 238s Data variables: 238s [1] "cds" "stype" "name" "sname" "snum" "dname" 238s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 238s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 238s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 238s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 238s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 238s [37] "api.stu" "fpc" "pw" 238s > 238s > options(survey.lonely.psu="fail") 238s > try(svymean(~api00,ds)) 238s mean SE 238s api00 644.17 5.7344 238s > svymean(~api00, as.svrepdesign(ds)) 238s mean SE 238s api00 644.17 5.7344 238s > options(survey.lonely.psu="remove") 238s > svymean(~api00,ds) 238s mean SE 238s api00 644.17 5.7344 238s > svymean(~api00, as.svrepdesign(ds)) 238s mean SE 238s api00 644.17 5.7344 238s > options(survey.lonely.psu="certainty") 238s > svymean(~api00,ds) 238s mean SE 238s api00 644.17 5.7344 238s > svymean(~api00, as.svrepdesign(ds)) 238s mean SE 238s api00 644.17 5.7344 238s > options(survey.lonely.psu="adjust") 238s > svymean(~api00,ds) 238s mean SE 238s api00 644.17 5.7344 238s > svymean(~api00, as.svrepdesign(ds)) 238s mean SE 238s api00 644.17 5.7344 238s > options(survey.lonely.psu="average") 238s > svymean(~api00,ds) 238s mean SE 238s api00 644.17 5.7344 238s > svymean(~api00, as.svrepdesign(ds)) 238s mean SE 238s api00 644.17 5.7501 238s > 238s > rs<-as.svrepdesign(ds) 238s > svytotal(~api00,rs) 238s total SE 238s api00 3989986 35616 238s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 238s [1] TRUE 238s > 238s > ## lonely PSUs after subsetting 238s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 238s > ds1<-ds[-31,] 238s > summary(ds1) 238s Stratified Independent Sampling design (with replacement) 238s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 238s dnum != 413)) 238s Probabilities: 238s Min. 1st Qu. Median Mean 3rd Qu. Max. 238s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 238s Stratum Sizes: 238s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 238s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 238s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 238s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 238s Data variables: 238s [1] "cds" "stype" "name" "sname" "snum" "dname" 238s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 238s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 238s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 238s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 238s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 238s [37] "api.stu" "fpc" "pw" 238s > 238s > options(survey.lonely.psu="fail") 238s > svymean(~api00,ds1) 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="remove") 238s > svymean(~api00,ds1) 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="certainty") 238s > svymean(~api00,ds1) 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="adjust") 238s > svymean(~api00,ds1) 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="average") 238s > svymean(~api00,ds1) 238s mean SE 238s api00 645.14 5.8909 238s > 238s > ## with adjustment 238s > options(survey.adjust.domain.lonely=TRUE) 238s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 238s > ds1<-ds[-31,] 238s > summary(ds1) 238s Stratified Independent Sampling design (with replacement) 238s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 238s dnum != 413)) 238s Probabilities: 238s Min. 1st Qu. Median Mean 3rd Qu. Max. 238s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 238s Stratum Sizes: 238s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 238s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 238s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 238s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 238s Data variables: 238s [1] "cds" "stype" "name" "sname" "snum" "dname" 238s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 238s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 238s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 238s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 238s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 238s [37] "api.stu" "fpc" "pw" 238s > 238s > options(survey.lonely.psu="fail") 238s > try(svymean(~api00,ds1)) 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="remove") 238s > svymean(~api00,ds1) 238s Warning message: 238s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 238s Stratum (406) has only one PSU at stage 1 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="certainty") 238s > svymean(~api00,ds1) 238s Warning message: 238s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 238s Stratum (406) has only one PSU at stage 1 238s mean SE 238s api00 645.14 5.8909 238s > options(survey.lonely.psu="adjust") 238s > svymean(~api00,ds1) 238s Warning message: 238s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 238s Stratum (406) has only one PSU at stage 1 238s mean SE 238s api00 645.14 5.9119 238s > options(survey.lonely.psu="average") 238s > svymean(~api00,ds1) 238s Warning message: 238s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 238s Stratum (406) has only one PSU at stage 1 238s mean SE 238s api00 645.14 6.0914 238s > 238s > ## checks for `svytotal()` 238s > 238s > df_w_singleton <- data.frame( 238s + Stratum = c(1, 1, 2, 2, 3), 238s + PSU = c(1, 2, 3, 4, 5), 238s + Design_Weight = c(10.5, 10.5, 20, 20, 15), 238s + Sex = c("M", "F", "F", "M", "M"), 238s + Age = c(30.5, 40.5, 35, 52, 44), 238s + Height = c(6.2, 5.0, 5.3, 5.7, 5.5) 238s + ) 238s Warning message: 238s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 238s Stratum (406) has only one PSU at stage 1 238s > 238s > design_w_singleton <- survey::svydesign( 238s + data = df_w_singleton, 238s + ids = ~ PSU, strata = ~ Stratum, 238s + weights = ~ Design_Weight 238s + ) 238s > 238s > options("survey.lonely.psu" = "remove") 238s > 238s > stopifnot(all.equal( 238s + target = 126625, 238s + current = as.numeric( 238s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 238s + ) 238s + )) 238s > 238s > options("survey.lonely.psu" = "certainty") 238s > 238s > stopifnot(all.equal( 238s + target = 126625, 238s + current = as.numeric( 238s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 238s + ) 238s + )) 238s > 238s > options("survey.lonely.psu" = "adjust") 238s > 238s > stopifnot(all.equal( 238s + target = 127579.8, 238s + current = as.numeric( 238s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 238s + ), 238s + scale = 127579.8, tolerance = 0.000001 238s + )) 238s > 238s BEGIN TEST mtcars-var.R 238s 238s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 238s Copyright (C) 2025 The R Foundation for Statistical Computing 238s Platform: arm-unknown-linux-gnueabihf (32-bit) 238s 238s R is free software and comes with ABSOLUTELY NO WARRANTY. 238s You are welcome to redistribute it under certain conditions. 238s Type 'license()' or 'licence()' for distribution details. 238s 238s R is a collaborative project with many contributors. 238s Type 'contributors()' for more information and 238s 'citation()' on how to cite R or R packages in publications. 238s 238s Type 'demo()' for some demos, 'help()' for on-line help, or 238s 'help.start()' for an HTML browser interface to help. 238s Type 'q()' to quit R. 238s 238s > library(survey) 238s Loading required package: grid 238s Loading required package: Matrix 239s Loading required package: survival 239s > 239s > # don't throw an error on domains of size 1, just return NA 239s > input <- mtcars 239s > input$carb <- factor(input$carb) 239s > design <- svydesign(ids = ~0, weights = NULL, data = input) 239s 239s Attaching package: 'survey' 239s 239s The following object is masked from 'package:graphics': 239s 239s dotchart 239s 239s > svyby( 239s + ~mpg, 239s + ~carb, 239s + design, 239s + svyvar 239s + ) 239s carb mpg se 239s 1 1 36.01619 11.2823286 239s 2 2 29.94444 9.0030898 239s 3 3 1.11000 0.4604066 239s 4 4 15.29656 4.3174617 239s 6 6 NA NA 239s 8 8 NA NA 239s > 239s > 239s > ## same n with na.rm=TRUE as subset(, !is.na) 239s > input$mpg[1]<-NA 239s > design <- svydesign(ids = ~0, weights = NULL, data = input) 239s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 239s + svyvar(~mpg, subset(design, !is.na(mpg))))) 239s > 239s BEGIN TEST multistage-rcpp.R 239s 239s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 239s Copyright (C) 2025 The R Foundation for Statistical Computing 239s Platform: arm-unknown-linux-gnueabihf (32-bit) 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > ## temporarily disable while it's being fixed 239s > ## q("no") 239s > 239s > ## 239s > ## Check that multistage() and multistage_rcpp() give same results 239s > ## for different options. 239s > ## 239s > library(survey) 239s Loading required package: grid 239s Loading required package: Matrix 240s Loading required package: survival 241s 241s Attaching package: 'survey' 241s 241s The following object is masked from 'package:graphics': 241s 241s dotchart 241s 241s > 241s > # Check for a simple random sample ---- 241s > 241s > data('api', package = 'survey') 241s > api_srs_design <- svydesign( 241s + data = apisrs, 241s + ids = ~ 1, 241s + weights = ~ 1 241s + ) 241s > 241s > x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob) 241s > 241s > base_r_result <- survey:::multistage(x = x, 241s + clusters = api_srs_design$cluster, 241s + stratas = api_srs_design$strata, 241s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=TRUE, stage = 1, cal = NULL) 241s > 241s > rcpp_result <- survey:::multistage_rcpp(x = x, 241s + clusters = api_srs_design$cluster, 241s + stratas = api_srs_design$strata, 241s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=TRUE, stage = 1, cal = NULL) 241s > 241s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 241s + stop("Differences between `multistage()` and `multistage_rcpp()` for SRS") 241s + } 241s > 241s > # Check for a stratified simple random sample ---- 241s > 241s > apistrat_design <- svydesign( 241s + data = apistrat, 241s + id =~ 1, 241s + strata =~ stype, 241s + weights =~ pw, 241s + fpc =~ fpc 241s + ) 241s > 241s > x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob) 241s > 241s > base_r_result <- survey:::multistage(x = x, 241s + clusters = apistrat_design$cluster, 241s + stratas = apistrat_design$strata, 241s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=TRUE, stage = 1, cal = NULL) 241s > 241s > rcpp_result <- survey:::multistage_rcpp(x = x, 241s + clusters = apistrat_design$cluster, 241s + stratas = apistrat_design$strata, 241s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=TRUE, stage = 1, cal = NULL) 241s > 241s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 241s + stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample") 241s + } 241s > 241s > ##_ Check whether expected true zeroes are actually computed as zeroes ---- 241s > 241s > x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob)) 241s > 241s > base_r_result <- survey:::multistage(x = x, 241s + clusters = apistrat_design$cluster, 241s + stratas = apistrat_design$strata, 241s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=TRUE, stage = 1, cal = NULL) 241s > 241s > rcpp_result <- survey:::multistage_rcpp(x = x, 241s + clusters = apistrat_design$cluster, 241s + stratas = apistrat_design$strata, 241s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=TRUE, stage = 1, cal = NULL) 241s > 241s > if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) { 241s + stop("Computations which should equal zero do not.") 241s + } 241s > 241s > # Create a stratified, multistage design ---- 241s > 241s > data(mu284) 241s > 241s > ## Create three strata, the third of which has only one PSU 241s > mu284_stratified <- rbind( 241s + transform(mu284, stratum = 1, 241s + y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)), 241s + transform(mu284, stratum = 2, 241s + y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)), 241s + transform(mu284[1,], stratum = 3, 241s + y2 = y1 + 2) 241s + ) 241s > 241s > ## Create domain variables which yield a lonely PSU or a lonely SSU 241s > mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19) 241s > mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1) 241s > 241s > ## Create a survey design object with no lonely PSUs 241s > dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3), 241s + strata = ~ stratum, nest = TRUE, 241s + id = ~ id1 + id2, fpc = ~ n1 + n2) 241s > ## Create a survey design with one lonely PSU 241s > dmu284_strat_w_lonely <- svydesign(data = mu284_stratified, 241s + strata = ~ stratum, nest = TRUE, 241s + id = ~ id1 + id2, fpc = ~ n1 + n2) 241s > ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU 241s > dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU) 241s > dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU) 241s > 241s > 241s > # Check same results for different values of 'lonely PSU' options ---- 241s > 241s > lonely_psu_options <- c(certainty = 'certainty', 241s + remove = 'remove', 241s + average = 'average', 241s + adjust = 'adjust') 241s > one_stage_options <- c(TRUE, FALSE) 241s > 241s > design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 241s + 'one.stage' = one_stage_options, 241s + stringsAsFactors = FALSE) 241s > design_lonely_psu_comparisons[['results_match']] <- NA 241s > 241s > ##_ Check for lonely PSUs caused by design ---- 241s > for (i in seq_len(nrow(design_lonely_psu_comparisons))) { 241s + survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i] 241s + one.stage <- design_lonely_psu_comparisons[['one.stage']][i] 241s + options('survey.lonely.psu' = survey.lonely.psu) 241s + 241s + x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob) 241s + 241s + base_r_result <- survey:::multistage(x = x, 241s + clusters = dmu284_strat_w_lonely$cluster, 241s + stratas = dmu284_strat_w_lonely$strata, 241s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=one.stage, stage = 1, cal = NULL) 241s + 241s + rcpp_result <- survey:::multistage_rcpp(x = x, 241s + clusters = dmu284_strat_w_lonely$cluster, 241s + stratas = dmu284_strat_w_lonely$strata, 241s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=one.stage, stage = 1, cal = NULL) 241s + 241s + design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 241s + } 241s > 241s > print(design_lonely_psu_comparisons) 241s survey.lonely.psu one.stage results_match 241s 1 certainty TRUE TRUE 241s 2 remove TRUE TRUE 241s 3 average TRUE TRUE 241s 4 adjust TRUE TRUE 241s 5 certainty FALSE TRUE 241s 6 remove FALSE TRUE 241s 7 average FALSE TRUE 241s 8 adjust FALSE TRUE 241s > if (!all(design_lonely_psu_comparisons$results_match)) { 241s + stop("Results for design lonely PSUs differ between base R and Rcpp implementations.") 241s + } 241s > 241s > ##_ Check for domain lonely PSUs caused by subsetting ---- 241s > 241s > domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 241s + 'survey.adjust.domain.lonely' = c(FALSE, TRUE), 241s + 'one.stage' = one_stage_options, 241s + stringsAsFactors = FALSE) 241s > domain_lonely_psu_comparisons[['results_match']] <- NA 241s > 241s > for (i in seq_len(nrow(domain_lonely_psu_comparisons))) { 241s + 241s + options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i]) 241s + options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i]) 241s + one.stage <- domain_lonely_psu_comparisons[['one.stage']][i] 241s + 241s + 241s + x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob) 241s + suppressWarnings({ 241s + base_r_result <- survey:::multistage(x = x, 241s + clusters = dmu284_strat_domain_lonely_psu$cluster, 241s + stratas = dmu284_strat_domain_lonely_psu$strata, 241s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 241s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=one.stage, stage = 1, cal = NULL) 241s + }) 241s + 241s + rcpp_result <- survey:::multistage_rcpp(x = x, 241s + clusters = dmu284_strat_domain_lonely_psu$cluster, 241s + stratas = dmu284_strat_domain_lonely_psu$strata, 241s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 241s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=one.stage, stage = 1, cal = NULL) 241s + 241s + domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 241s + } 241s Warning messages: 241s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 241s At least one stratum contains only one PSU at stage 1 241s > 241s > print(domain_lonely_psu_comparisons) 241s survey.lonely.psu survey.adjust.domain.lonely one.stage results_match 241s 1 certainty FALSE TRUE TRUE 241s 2 remove FALSE TRUE TRUE 241s 3 average FALSE TRUE TRUE 241s 4 adjust FALSE TRUE TRUE 241s 5 certainty TRUE TRUE TRUE 241s 6 remove TRUE TRUE TRUE 241s 7 average TRUE TRUE TRUE 241s 8 adjust TRUE TRUE TRUE 241s 9 certainty FALSE FALSE TRUE 241s 10 remove FALSE FALSE TRUE 241s 11 average FALSE FALSE TRUE 241s 12 adjust FALSE FALSE TRUE 241s 13 certainty TRUE FALSE TRUE 241s 14 remove TRUE FALSE TRUE 241s 15 average TRUE FALSE TRUE 241s 16 adjust TRUE FALSE TRUE 241s > if (!all(domain_lonely_psu_comparisons$results_match)) { 241s + stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.") 241s + } 241s > 241s > # Checks for edge cases ---- 241s > 241s > ## Zero records ---- 241s > 241s > zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent") 241s > 241s > zero_row_result <- survey:::multistage_rcpp( 241s + x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]), 241s + clusters = zero_row_design$cluster, 241s + stratas = zero_row_design$strata, 241s + nPSUs = zero_row_design$fpc$sampsize, 241s + fpcs = zero_row_design$fpc$popsize, 241s + lonely.psu=getOption("survey.lonely.psu"), 241s + one.stage=one.stage, stage = 1, cal = NULL 241s + ) 241s > 241s > if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) { 241s + stop("`multistage_rcpp()` should return zeros for zero-row inputs.") 241s + } 241s > 241s > 241s BEGIN TEST multistage.R 241s 241s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 241s Copyright (C) 2025 The R Foundation for Statistical Computing 241s Platform: arm-unknown-linux-gnueabihf (32-bit) 241s 241s R is free software and comes with ABSOLUTELY NO WARRANTY. 241s You are welcome to redistribute it under certain conditions. 241s Type 'license()' or 'licence()' for distribution details. 241s 241s R is a collaborative project with many contributors. 241s Type 'contributors()' for more information and 241s 'citation()' on how to cite R or R packages in publications. 241s 241s Type 'demo()' for some demos, 'help()' for on-line help, or 241s 'help.start()' for an HTML browser interface to help. 241s Type 'q()' to quit R. 241s 241s > ## 241s > ## Check that multistage samples still work 241s > ## 241s > library(survey) 241s Loading required package: grid 241s Loading required package: Matrix 242s Loading required package: survival 242s 242s Attaching package: 'survey' 242s 242s The following object is masked from 'package:graphics': 242s 242s dotchart 242s 242s > example(mu284) 242s 242s mu284> data(mu284) 242s 242s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 242s 2 - level Cluster Sampling design 242s With (5, 15) clusters. 242s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 242s 242s mu284> (ytotal<-svytotal(~y1, dmu284)) 242s total SE 242s y1 15080 2274.3 242s 242s mu284> vcov(ytotal) 242s y1 242s y1 5172234 242s > 242s > 243s BEGIN TEST na_action.R 243s 243s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 243s Copyright (C) 2025 The R Foundation for Statistical Computing 243s Platform: arm-unknown-linux-gnueabihf (32-bit) 243s 243s R is free software and comes with ABSOLUTELY NO WARRANTY. 243s You are welcome to redistribute it under certain conditions. 243s Type 'license()' or 'licence()' for distribution details. 243s 243s R is a collaborative project with many contributors. 243s Type 'contributors()' for more information and 243s 'citation()' on how to cite R or R packages in publications. 243s 243s Type 'demo()' for some demos, 'help()' for on-line help, or 243s 'help.start()' for an HTML browser interface to help. 243s Type 'q()' to quit R. 243s 243s > ## from Terry Therneau 243s > library(survey) 243s Loading required package: grid 243s Loading required package: Matrix 244s Loading required package: survival 244s > load("naa.rda") 244s > 244s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 244s 244s Attaching package: 'survey' 244s 244s The following object is masked from 'package:graphics': 244s 244s dotchart 244s 244s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 244s > all.equal(coef(fit1e),coef(fit1o)) 244s [1] TRUE 244s > all.equal(vcov(fit1e),vcov(fit1o)) 244s [1] TRUE 244s > 244s BEGIN TEST newquantile.R 244s 244s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 244s Copyright (C) 2025 The R Foundation for Statistical Computing 244s Platform: arm-unknown-linux-gnueabihf (32-bit) 244s 244s R is free software and comes with ABSOLUTELY NO WARRANTY. 244s You are welcome to redistribute it under certain conditions. 244s Type 'license()' or 'licence()' for distribution details. 244s 244s R is a collaborative project with many contributors. 244s Type 'contributors()' for more information and 244s 'citation()' on how to cite R or R packages in publications. 244s 244s Type 'demo()' for some demos, 'help()' for on-line help, or 244s 'help.start()' for an HTML browser interface to help. 244s Type 'q()' to quit R. 244s 244s > ## quantiles with equal weights 244s > 244s > library(survey) 244s Loading required package: grid 244s Loading required package: Matrix 245s Loading required package: survival 245s 245s Attaching package: 'survey' 245s 245s The following object is masked from 'package:graphics': 245s 245s dotchart 245s 245s > data(api) 246s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 246s > 246s > 246s > for(i in 1:9){ 246s + print(i) 246s + all.equal( 246s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 246s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 246s + ) 246s + 246s + } 246s [1] 1 246s [1] 2 246s [1] 3 246s [1] 4 246s [1] 5 246s [1] 6 246s [1] 7 246s [1] 8 246s [1] 9 246s > 246s BEGIN TEST nwts-cch.R 246s 246s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 246s Copyright (C) 2025 The R Foundation for Statistical Computing 246s Platform: arm-unknown-linux-gnueabihf (32-bit) 246s 246s R is free software and comes with ABSOLUTELY NO WARRANTY. 246s You are welcome to redistribute it under certain conditions. 246s Type 'license()' or 'licence()' for distribution details. 246s 246s R is a collaborative project with many contributors. 246s Type 'contributors()' for more information and 246s 'citation()' on how to cite R or R packages in publications. 246s 246s Type 'demo()' for some demos, 'help()' for on-line help, or 246s 'help.start()' for an HTML browser interface to help. 246s Type 'q()' to quit R. 246s 246s > library(survey) 246s Loading required package: grid 246s Loading required package: Matrix 247s Loading required package: survival 247s > library(survival) 247s > data(nwtco) 247s 247s Attaching package: 'survey' 247s 247s The following object is masked from 'package:graphics': 247s 247s dotchart 247s 247s > 247s > ntwco<-subset(nwtco, !is.na(edrel)) 247s > 247s > load("nwtco-subcohort.rda") 247s > nwtco$subcohort<-subcohort 247s > 247s > d_BorganII <- twophase(id=list(~seqno,~seqno), 247s + strata=list(NULL,~interaction(instit,rel)), 247s + data=nwtco, subset=~I(rel |subcohort)) 248s > 248s > ##Coefficient results same as Splus with code from 248s > ## http://faculty.washington.edu/norm/software.html 248s > ## SE slightly larger due to using sandwich variance. 248s > 248s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 248s Call: 248s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 248s I(age/12), design = d_BorganII) 248s 248s coef exp(coef) se(coef) robust se z p 248s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 248s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 248s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 248s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 248s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 248s 248s Likelihood ratio test= on 5 df, p= 248s n= 1062, number of events= 571 248s > 248s > ## 248s > ## This gives higher standard errors. calibrate() does not recompute the 248s > ## finite population correction if a calibration variable happens to predict 248s > ## sampling perfectly. It probably should. 248s > ## 248s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 248s + strata=list(NULL,~rel), 248s + data=nwtco, subset=~I(rel |subcohort)), 248s + phase=2, formula=~interaction(instit,rel), 248s + epsilon=1e-10) 248s > 248s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 248s Call: 248s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 248s I(age/12), design = d_BorganIIps) 248s 248s coef exp(coef) se(coef) robust se z p 248s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 248s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 248s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 248s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 248s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 248s 248s Likelihood ratio test= on 5 df, p= 248s n= 1062, number of events= 571 248s > 248s BEGIN TEST nwts.R 248s 248s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 248s Copyright (C) 2025 The R Foundation for Statistical Computing 248s Platform: arm-unknown-linux-gnueabihf (32-bit) 248s 248s R is free software and comes with ABSOLUTELY NO WARRANTY. 248s You are welcome to redistribute it under certain conditions. 248s Type 'license()' or 'licence()' for distribution details. 248s 248s R is a collaborative project with many contributors. 248s Type 'contributors()' for more information and 248s 'citation()' on how to cite R or R packages in publications. 248s 248s Type 'demo()' for some demos, 'help()' for on-line help, or 248s 'help.start()' for an HTML browser interface to help. 248s Type 'q()' to quit R. 248s 248s > 248s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 248s > ## data from Norman Breslow's web page. 248s > library(survey) 248s Loading required package: grid 248s Loading required package: Matrix 249s Loading required package: survival 250s 250s Attaching package: 'survey' 250s 250s The following object is masked from 'package:graphics': 250s 250s dotchart 250s 250s > load("nwts.rda") 250s > nwtsnb<-nwts 250s > nwtsnb$case<-nwts$case-nwtsb$case 250s > nwtsnb$control<-nwts$control-nwtsb$control 250s > 250s > a<-rbind(nwtsb,nwtsnb) 250s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 250s > 250s > b<-rbind(a,a) 250s > b$rel<-rep(c(1,0),each=32) 250s > b$n<-ifelse(b$rel,b$case,b$control) 250s > 250s > index<-rep(1:64,b$n) 250s > 250s > nwt.exp<-b[index,c(1:3,6,7)] 250s > nwt.exp$id<-1:4088 250s > 250s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 250s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 250s > 250s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 250s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 250s > 250s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 250s > 250s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 250s 250s Call: 250s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 250s family = quasibinomial) 250s 250s Survey design: 250s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 250s subset = subset, data = data, pps = pps) 250s 250s Coefficients: 250s Estimate Std. Error t value Pr(>|t|) 250s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 250s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 250s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 250s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 250s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 250s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 250s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 250s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 250s --- 250s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 250s 250s (Dispersion parameter for quasibinomial family taken to be 1.000876) 250s 250s Number of Fisher Scoring iterations: 4 250s 250s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 251s 251s Call: 251s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 251s family = quasibinomial) 251s 251s Survey design: 251s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 251s subset = subset, data = data, pps = pps) 251s 251s Coefficients: 251s Estimate Std. Error t value Pr(>|t|) 251s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 251s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 251s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 251s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 251s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 251s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 251s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 251s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 251s --- 251s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 251s 251s (Dispersion parameter for quasibinomial family taken to be 1.000876) 251s 251s Number of Fisher Scoring iterations: 4 251s 251s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 251s 251s Call: 251s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 251s family = quasibinomial) 251s 251s Survey design: 251s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 251s rel)) 251s 251s Coefficients: 251s Estimate Std. Error t value Pr(>|t|) 251s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 251s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 251s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 251s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 251s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 251s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 251s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 251s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 251s --- 251s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 251s 251s (Dispersion parameter for quasibinomial family taken to be 1.000876) 251s 251s Number of Fisher Scoring iterations: 4 251s 251s > 251s > ## check subsets of calibrated designs. 251s > summary(svyglm(rel~factor(stage), 251s + family=quasibinomial,design=subset(dccs8,histol==1))) 251s 251s Call: 251s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 251s histol == 1), family = quasibinomial) 251s 251s Survey design: 251s subset(dccs8, histol == 1) 251s 251s Coefficients: 251s Warning messages: 251s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 251s 2: In summary.glm(g) : 251s observations with zero weight not used for calculating dispersion 251s 3: In summary.glm(glm.object) : 251s observations with zero weight not used for calculating dispersion 251s 4: In `[.twophase2`(design, nas == 0, ) : 251s 1 strata have only one PSU in this subset. 251s 5: In `[.twophase2`(design, nas == 0, ) : 251s 1 strata have only one PSU in this subset. 251s Estimate Std. Error t value Pr(>|t|) 251s (Intercept) -2.7160 0.1083 -25.085 < 2e-16 *** 251s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 251s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 251s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 251s --- 251s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 251s 251s (Dispersion parameter for quasibinomial family taken to be 1.001333) 251s 251s Number of Fisher Scoring iterations: 4 251s 251s > summary(svyglm(rel~factor(stage), 251s + family=quasibinomial,design=subset(gccs8,histol==1))) 251s 251s Call: 251s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 251s histol == 1), family = quasibinomial) 251s 251s Survey design: 251s subset(gccs8, histol == 1) 251s 251s Coefficients: 251s Warning messages: 251s 1: In summary.glm(g) : 251s observations with zero weight not used for calculating dispersion 251s 2: In summary.glm(glm.object) : 251s observations with zero weight not used for calculating dispersion 251s Estimate Std. Error t value Pr(>|t|) 251s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 251s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 251s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 251s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 251s --- 251s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 251s 251s (Dispersion parameter for quasibinomial family taken to be 1.001333) 251s 251s Number of Fisher Scoring iterations: 4 251s 251s > 251s > 251s BEGIN TEST poisson.R 251s 251s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 251s Copyright (C) 2025 The R Foundation for Statistical Computing 251s Platform: arm-unknown-linux-gnueabihf (32-bit) 251s 251s R is free software and comes with ABSOLUTELY NO WARRANTY. 251s You are welcome to redistribute it under certain conditions. 251s Type 'license()' or 'licence()' for distribution details. 251s 251s R is a collaborative project with many contributors. 251s Type 'contributors()' for more information and 251s 'citation()' on how to cite R or R packages in publications. 251s 251s Type 'demo()' for some demos, 'help()' for on-line help, or 251s 'help.start()' for an HTML browser interface to help. 251s Type 'q()' to quit R. 251s 251s > ## check poisson sampling 251s > library(survey) 251s Loading required package: grid 251s Loading required package: Matrix 252s Loading required package: survival 252s 252s Attaching package: 'survey' 252s 252s > data(api) 252s > set.seed(2021-7-15) 252s The following object is masked from 'package:graphics': 252s 252s dotchart 252s 252s > apipop$prob<-apipop$api00/1000 252s > insample<-rbinom(nrow(apipop),1,apipop$prob) 252s > apipois<-apipop[insample,] 252s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 252s > 252s > stopifnot(isTRUE(all.equal( 252s + as.vector(SE(svytotal(~api00,design=des))), 252s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 252s + ))) 252s > 252s > 252s BEGIN TEST pps.R 252s 252s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 252s Copyright (C) 2025 The R Foundation for Statistical Computing 252s Platform: arm-unknown-linux-gnueabihf (32-bit) 252s 252s R is free software and comes with ABSOLUTELY NO WARRANTY. 252s You are welcome to redistribute it under certain conditions. 252s Type 'license()' or 'licence()' for distribution details. 252s 252s R is a collaborative project with many contributors. 252s Type 'contributors()' for more information and 252s 'citation()' on how to cite R or R packages in publications. 252s 252s Type 'demo()' for some demos, 'help()' for on-line help, or 252s 'help.start()' for an HTML browser interface to help. 252s Type 'q()' to quit R. 252s 253s > library(survey) 253s Loading required package: grid 253s Loading required package: Matrix 253s Loading required package: survival 254s 254s Attaching package: 'survey' 254s 254s > data(election) 254s The following object is masked from 'package:graphics': 254s 254s dotchart 254s 254s > 254s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 254s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 254s > svytotal(~Bush+Kerry+Nader, dpps) 254s total SE 254s Bush 64518472 2447629 254s Kerry 51202102 2450787 254s Nader 478530 102420 254s > svytotal(~Bush+Kerry+Nader, dppswr) 254s total SE 254s Bush 64518472 2671455 254s Kerry 51202102 2679433 254s Nader 478530 105303 254s > 254s > ##subsets 254s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 254s total SE 254s Bush 34944285 5399833 254s Kerry 25581714 4028434 254s Nader 478530 102420 254s > 254s > ##multistage: should agree with STRS analysis 254s > data(api) 254s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 254s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 254s > 254s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 254s [1] TRUE 254s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 254s [1] TRUE 254s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 254s [1] TRUE 254s > 254s > ## the new without-replacement methods 254s > data(election) 254s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 254s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 254s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 254s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 254s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 254s > ## Yates-Grundy type 254s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 254s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 254s > 254s > ## The with-replacement approximation 254s > svytotal(~Bush+Kerry+Nader, dpps_ht) 254s total SE 254s Bush 64518472 2604404 254s Kerry 51202102 2523712 254s Nader 478530 102326 254s > svytotal(~Bush+Kerry+Nader, dpps_yg) 254s total SE 254s Bush 64518472 2406526 254s Kerry 51202102 2408091 254s Nader 478530 101664 254s > svytotal(~Bush+Kerry+Nader, dpps_hr) 254s total SE 254s Bush 64518472 2624662 254s Kerry 51202102 2525222 254s Nader 478530 102793 254s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 254s total SE 254s Bush 64518472 2436738 254s Kerry 51202102 2439845 254s Nader 478530 102016 254s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 254s total SE 254s Bush 64518472 2472753 254s Kerry 51202102 2426842 254s Nader 478530 102595 254s > svytotal(~Bush+Kerry+Nader, dpps_br) 254s total SE 254s Bush 64518472 2447629 254s Kerry 51202102 2450787 254s Nader 478530 102420 254s > svytotal(~Bush+Kerry+Nader, dpps_ov) 254s total SE 254s Bush 64518472 2939608 254s Kerry 51202102 1964632 254s Nader 478530 104373 254s > 254s > ## subsets 254s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 254s total SE 254s Bush 34944285 5406348 254s Kerry 25581714 4047741 254s Nader 478530 102326 254s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 254s total SE 254s Bush 34944285 5377659 254s Kerry 25581714 4010908 254s Nader 478530 102016 254s > 254s > ## counts 254s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 254s I(Nader > 0) counts se 254s FALSE FALSE 19 0 254s TRUE TRUE 21 0 254s > 254s BEGIN TEST qrule-swiss.R 254s 254s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 254s Copyright (C) 2025 The R Foundation for Statistical Computing 254s Platform: arm-unknown-linux-gnueabihf (32-bit) 254s 254s R is free software and comes with ABSOLUTELY NO WARRANTY. 254s You are welcome to redistribute it under certain conditions. 254s Type 'license()' or 'licence()' for distribution details. 254s 254s R is a collaborative project with many contributors. 254s Type 'contributors()' for more information and 254s 'citation()' on how to cite R or R packages in publications. 254s 254s Type 'demo()' for some demos, 'help()' for on-line help, or 254s 'help.start()' for an HTML browser interface to help. 254s Type 'q()' to quit R. 254s 254s > library(survey) 254s Loading required package: grid 254s Loading required package: Matrix 255s Loading required package: survival 255s > 255s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1) 255s 255s Attaching package: 'survey' 255s 255s The following object is masked from 'package:graphics': 255s 255s dotchart 255s 255s > 255s > design_no_strat <- svydesign(id = ~id, 255s + probs = ~probs, 255s + data = data_no_strat, 255s + fpc = ~fpc) 255s > 255s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99) 255s > 255s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE, 255s + interval.type = "mean", qrule = "hf1") 255s > 255s > stopifnot(all(diff(res$x[,"quantile"])>=0)) 255s > 255s > 255s > 255s BEGIN TEST quantile.R 256s 256s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 256s Copyright (C) 2025 The R Foundation for Statistical Computing 256s Platform: arm-unknown-linux-gnueabihf (32-bit) 256s 256s R is free software and comes with ABSOLUTELY NO WARRANTY. 256s You are welcome to redistribute it under certain conditions. 256s Type 'license()' or 'licence()' for distribution details. 256s 256s R is a collaborative project with many contributors. 256s Type 'contributors()' for more information and 256s 'citation()' on how to cite R or R packages in publications. 256s 256s Type 'demo()' for some demos, 'help()' for on-line help, or 256s 'help.start()' for an HTML browser interface to help. 256s Type 'q()' to quit R. 256s 256s > library(survey) 256s Loading required package: grid 256s Loading required package: Matrix 257s Loading required package: survival 257s 257s Attaching package: 'survey' 257s 257s The following object is masked from 'package:graphics': 257s 257s dotchart 257s 257s > set.seed(42) 257s > 257s > df<-data.frame(x=exp(rnorm(1000))) 257s > df$y<-round(df$x,1) 257s > ddf<-svydesign(id=~1,data=df) 257s Warning message: 257s In svydesign.default(id = ~1, data = df) : 257s No weights or probabilities supplied, assuming equal probability 257s > rdf<-as.svrepdesign(ddf) 258s > 258s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 258s 0.01 0.1 0.5 0.9 0.99 258s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 258s > 258s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 258s x 258s q0.01 0.01554946 258s q0.1 0.01425828 258s q0.5 0.03428012 258s q0.9 0.16457488 258s q0.99 1.88672412 258s > 258s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 258s 0.01 0.1 0.5 0.9 0.99 258s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 258s > 258s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 258s x 258s q0.01 0.01556240 258s q0.1 0.01420086 258s q0.5 0.03430175 258s q0.9 0.16461019 258s q0.99 1.88818131 258s > 258s > 258s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 258s $quantiles 258s 0.01 0.1 0.5 0.9 0.99 258s y 0.02352941 0.2230769 0.9340909 3.55 9.4 258s 258s $CIs 258s , , y 258s 258s 0.01 0.1 0.5 0.9 0.99 258s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 258s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 258s 258s 258s > 258s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 258s Statistic: 258s y 258s q0.01 0.1 258s q0.1 0.3 258s q0.5 1.0 258s q0.9 3.6 258s q0.99 9.4 258s SE: 258s y 258s q0.01 0.02547977 258s q0.1 0.02547977 258s q0.5 0.02547977 258s q0.9 0.15287859 258s q0.99 1.88302540 258s > 258s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 258s $quantiles 258s 0.01 0.1 0.5 0.9 0.99 258s y 0.02352941 0.2230769 0.9340909 3.55 9.4 258s 258s $CIs 258s , , y 258s 258s 0.01 0.1 0.5 0.9 0.99 258s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 258s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 258s 258s 258s > 258s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 258s Statistic: 258s y 258s q0.01 0.1 258s q0.1 0.3 258s q0.5 1.0 258s q0.9 3.6 258s q0.99 9.4 258s SE: 258s y 258s q0.01 0.02551067 258s q0.1 0.02551067 258s q0.5 0.02551067 258s q0.9 0.15306404 258s q0.99 1.88450896 258s > 258s > 258s > 258s > df<-data.frame(x=exp(rnorm(20))) 258s > df$y<-round(df$x,1) 258s > ddf<-svydesign(id=~1,data=df) 258s > rdf<-as.svrepdesign(ddf) 258s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 258s Warning message: 258s In svydesign.default(id = ~1, data = df) : 258s No weights or probabilities supplied, assuming equal probability 258s 0.01 0.1 0.5 0.9 0.99 258s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 258s > 258s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 258s x 258s q0.01 0.00000000 258s q0.1 0.04598541 258s q0.5 0.25943731 258s q0.9 2.12343073 258s q0.99 1.91998924 258s > 258s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 258s 0.01 0.1 0.5 0.9 0.99 258s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 258s > 258s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 258s x 258s q0.01 0.00000000 258s q0.1 0.04732818 258s q0.5 0.24957966 258s q0.9 2.25211815 258s q0.99 2.04043154 258s > 258s > 258s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 258s $quantiles 258s 0.01 0.1 0.5 0.9 0.99 258s y 0.1 0.15 0.75 2.4 8.68 258s 258s $CIs 258s , , y 258s 258s 0.01 0.1 0.5 0.9 0.99 258s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 258s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 258s 258s 258s > 258s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 258s Statistic: 258s y 258s q0.01 0.10 258s q0.1 0.20 258s q0.5 0.80 258s q0.9 2.40 258s q0.99 8.68 258s SE: 258s y 258s q0.01 0.00000000 258s q0.1 0.02611112 258s q0.5 0.26542051 258s q0.9 2.10908603 258s q0.99 1.91777710 258s > 258s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 258s $quantiles 258s 0.01 0.1 0.5 0.9 0.99 258s y 0.1 0.15 0.75 2.4 8.68 258s 258s $CIs 258s , , y 258s 258s 0.01 0.1 0.5 0.9 0.99 258s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 258s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 258s 258s 258s > 258s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 258s Statistic: 258s y 258s q0.01 0.10 258s q0.1 0.20 258s q0.5 0.80 258s q0.9 2.40 258s q0.99 8.68 258s SE: 258s y 258s q0.01 0.00000000 258s q0.1 0.02551067 258s q0.5 0.25244616 258s q0.9 2.23558589 258s q0.99 2.03881114 258s > 258s BEGIN TEST quantiles-chile.R 258s 258s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 258s Copyright (C) 2025 The R Foundation for Statistical Computing 258s Platform: arm-unknown-linux-gnueabihf (32-bit) 258s 258s R is free software and comes with ABSOLUTELY NO WARRANTY. 258s You are welcome to redistribute it under certain conditions. 258s Type 'license()' or 'licence()' for distribution details. 258s 258s R is a collaborative project with many contributors. 258s Type 'contributors()' for more information and 258s 'citation()' on how to cite R or R packages in publications. 258s 258s Type 'demo()' for some demos, 'help()' for on-line help, or 258s 'help.start()' for an HTML browser interface to help. 258s Type 'q()' to quit R. 258s 258s > library(survey) 258s Loading required package: grid 258s Loading required package: Matrix 259s Loading required package: survival 260s 260s Attaching package: 'survey' 260s 260s The following object is masked from 'package:graphics': 260s 260s dotchart 260s 260s > datos <- readRDS("datos_ejemplo.rds") 260s > 260s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 260s > set.seed(234262762) 260s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 260s > options(survey.lonely.psu="remove") 260s > 260s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 260s > 260s > suppressWarnings({ 260s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 260s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 260s + }) 260s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 260s [1] TRUE 260s > 260s > suppressWarnings({ 260s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 260s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 260s + }) 260s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 260s [1] TRUE 260s > 260s BEGIN TEST rakecheck.R 260s 260s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 260s Copyright (C) 2025 The R Foundation for Statistical Computing 260s Platform: arm-unknown-linux-gnueabihf (32-bit) 260s 260s R is free software and comes with ABSOLUTELY NO WARRANTY. 260s You are welcome to redistribute it under certain conditions. 260s Type 'license()' or 'licence()' for distribution details. 260s 260s R is a collaborative project with many contributors. 260s Type 'contributors()' for more information and 260s 'citation()' on how to cite R or R packages in publications. 260s 260s Type 'demo()' for some demos, 'help()' for on-line help, or 260s 'help.start()' for an HTML browser interface to help. 260s Type 'q()' to quit R. 260s 260s > library(survey) 260s Loading required package: grid 260s Loading required package: Matrix 261s Loading required package: survival 261s 261s Attaching package: 'survey' 261s 261s > 261s > data(api) 261s The following object is masked from 'package:graphics': 261s 261s dotchart 261s 261s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 261s > rclus1 <- as.svrepdesign(dclus1) 261s > 261s > ## population marginal totals for each stratum 261s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 261s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 261s > 261s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 261s > 261s > svymean(~api00, rclus1r) 261s mean SE 261s api00 641.23 26.873 261s > svytotal(~enroll, rclus1r) 261s total SE 261s enroll 3647300 463511 261s > 261s > ff<-~stype+sch.wide 261s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 261s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 261s > 261s > svymean(~api00,rclus1g) 261s mean SE 261s api00 641.23 26.874 261s > svytotal(~enroll,rclus1g) 261s total SE 261s enroll 3647280 463582 261s > 261s > summary(weights(rclus1g)/weights(rclus1r)) 261s V1 V2 V3 V4 V5 V6 261s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 261s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 261s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 261s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 261s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 261s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 261s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 261s V7 V8 V9 V10 V11 261s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 261s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 261s Median :1 Median :1 Median :1 Median :1 Median :1 261s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 261s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 261s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 261s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 261s V12 V13 V14 V15 261s Min. :0.9997 Min. :1 Min. :1 Min. :1 261s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 261s Median :1.0001 Median :1 Median :1 Median :1 261s Mean :1.0000 Mean :1 Mean :1 Mean :1 261s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 261s Max. :1.0002 Max. :1 Max. :1 Max. :1 261s NA's :37 NA's :13 NA's :1 NA's :12 261s > 261s > 261s > ## Do it for a design without replicate weights 261s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 261s > 261s > svymean(~api00, dclus1r) 261s mean SE 261s api00 641.23 23.704 261s > svytotal(~enroll, dclus1r) 261s total SE 261s enroll 3647300 400603 261s > 261s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 261s > 261s > svymean(~api00,dclus1g) 261s mean SE 261s api00 641.23 23.704 261s > svytotal(~enroll,dclus1g) 261s total SE 261s enroll 3647280 400603 261s > 261s > summary(weights(dclus1g)/weights(dclus1r)) 261s Min. 1st Qu. Median Mean 3rd Qu. Max. 261s 1 1 1 1 1 1 261s > 261s > 261s > 261s > ## Example of raking with partial joint distributions 261s > pop.table <- xtabs(~stype+sch.wide,apipop) 261s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 261s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 261s + list(pop.table, pop.imp)) 261s > svymean(~api00, dclus1r2) 261s mean SE 261s api00 642.62 22.732 261s > 261s > ff1 <-~stype*sch.wide+comp.imp 261s > 261s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 261s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 261s > 261s > svymean(~api00, dclus1g2) 261s mean SE 261s api00 642.61 22.731 261s > 261s > summary(weights(dclus1r2)/weights(dclus1g2)) 261s Min. 1st Qu. Median Mean 3rd Qu. Max. 261s 0.999 1.000 1.000 1.000 1.000 1.002 261s > 261s BEGIN TEST raowuboot.R 261s 261s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 261s Copyright (C) 2025 The R Foundation for Statistical Computing 261s Platform: arm-unknown-linux-gnueabihf (32-bit) 261s 261s R is free software and comes with ABSOLUTELY NO WARRANTY. 261s You are welcome to redistribute it under certain conditions. 261s Type 'license()' or 'licence()' for distribution details. 261s 261s R is a collaborative project with many contributors. 261s Type 'contributors()' for more information and 261s 'citation()' on how to cite R or R packages in publications. 261s 261s Type 'demo()' for some demos, 'help()' for on-line help, or 261s 'help.start()' for an HTML browser interface to help. 261s Type 'q()' to quit R. 261s 261s > ## regression test for bug reported by Richard Valliant 261s > library(survey) 262s Loading required package: grid 262s Loading required package: Matrix 262s Loading required package: survival 263s 263s Attaching package: 'survey' 263s 263s > s<-subbootweights(c(1,1),1:2, 50) 263s The following object is masked from 'package:graphics': 263s 263s dotchart 263s 263s > stopifnot(all(s$repweights$weights %in% c(0,2))) 263s > 263s BEGIN TEST regTermTest-missing.R 263s 263s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 263s Copyright (C) 2025 The R Foundation for Statistical Computing 263s Platform: arm-unknown-linux-gnueabihf (32-bit) 263s 263s R is free software and comes with ABSOLUTELY NO WARRANTY. 263s You are welcome to redistribute it under certain conditions. 263s Type 'license()' or 'licence()' for distribution details. 263s 263s R is a collaborative project with many contributors. 263s Type 'contributors()' for more information and 263s 'citation()' on how to cite R or R packages in publications. 263s 263s Type 'demo()' for some demos, 'help()' for on-line help, or 263s 'help.start()' for an HTML browser interface to help. 263s Type 'q()' to quit R. 263s 263s > library(survey) 263s Loading required package: grid 263s Loading required package: Matrix 264s Loading required package: survival 264s 264s Attaching package: 'survey' 264s 264s The following object is masked from 'package:graphics': 264s 264s dotchart 264s 264s > data(nhanes) 264s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 264s > 264s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 264s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 264s > 264s > ta<-regTermTest(a, ~HI_CHOL) 264s > tb<-regTermTest(b, ~HI_CHOL) 264s > 264s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 264s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 264s > 264s BEGIN TEST regpredict.R 264s 264s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 264s Copyright (C) 2025 The R Foundation for Statistical Computing 264s Platform: arm-unknown-linux-gnueabihf (32-bit) 264s 264s R is free software and comes with ABSOLUTELY NO WARRANTY. 264s You are welcome to redistribute it under certain conditions. 264s Type 'license()' or 'licence()' for distribution details. 264s 264s R is a collaborative project with many contributors. 264s Type 'contributors()' for more information and 264s 'citation()' on how to cite R or R packages in publications. 264s 264s Type 'demo()' for some demos, 'help()' for on-line help, or 264s 'help.start()' for an HTML browser interface to help. 264s Type 'q()' to quit R. 264s 265s > library(survey) 265s Loading required package: grid 265s Loading required package: Matrix 266s Loading required package: survival 266s 266s Attaching package: 'survey' 266s 266s The following object is masked from 'package:graphics': 266s 266s dotchart 266s 266s > data(api) 266s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 266s > 266s > 266s > ## regression estimator of total, three ways 266s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 266s > npop <- sum(!is.na(apipop$enroll)) 266s > 266s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 266s > a <- predict(api.reg, newdata=pop, total=npop) 266s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 266s > 266s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 266s [1] TRUE 266s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 266s [1] TRUE 266s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 266s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 266s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 266s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 266s + } 266s > 266s > ## classical ratio estimator, four ways. 266s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 266s + family=quasi(link="identity", var="mu")) 266s > 266s > a <- predict(api.reg2, newdata=pop, total=npop) 266s > b <- svytotal(~api.stu, 266s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 266s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 266s > 266s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 266s [1] TRUE 266s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 266s [1] TRUE 266s > all.equal(as.vector(coef(a)),as.vector(e$total)) 266s [1] TRUE 266s > all.equal(as.vector(SE(a)), as.vector(e$se)) 266s [1] TRUE 266s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 266s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 266s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 266s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 266s + } 266s > 266s BEGIN TEST rss_scores.R 266s 266s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 266s Copyright (C) 2025 The R Foundation for Statistical Computing 266s Platform: arm-unknown-linux-gnueabihf (32-bit) 266s 266s R is free software and comes with ABSOLUTELY NO WARRANTY. 266s You are welcome to redistribute it under certain conditions. 266s Type 'license()' or 'licence()' for distribution details. 266s 266s R is a collaborative project with many contributors. 266s Type 'contributors()' for more information and 266s 'citation()' on how to cite R or R packages in publications. 266s 266s Type 'demo()' for some demos, 'help()' for on-line help, or 266s 'help.start()' for an HTML browser interface to help. 266s Type 'q()' to quit R. 266s 266s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 266s > library(survey) 266s Loading required package: grid 266s Loading required package: Matrix 267s Loading required package: survival 267s 267s Attaching package: 'survey' 267s 267s The following object is masked from 'package:graphics': 267s 267s dotchart 267s 267s > data(myco) 267s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 267s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 267s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 267s > 267s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 267s > 267s > s<-svyscoretest(m_full, ~Scar) 267s > stopifnot(abs(s[1]-10.73)<0.05) 267s > 267s > t<-svyscoretest(m_full,~Scar,method="individual") 267s > stopifnot(abs(coef(t)- -32.61)<0.1) 267s > stopifnot(abs(vcov(t)-99.1)<0.1) 267s > 267s > 267s BEGIN TEST scoping.R 267s 267s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 267s Copyright (C) 2025 The R Foundation for Statistical Computing 267s Platform: arm-unknown-linux-gnueabihf (32-bit) 267s 267s R is free software and comes with ABSOLUTELY NO WARRANTY. 267s You are welcome to redistribute it under certain conditions. 267s Type 'license()' or 'licence()' for distribution details. 267s 267s R is a collaborative project with many contributors. 267s Type 'contributors()' for more information and 267s 'citation()' on how to cite R or R packages in publications. 267s 267s Type 'demo()' for some demos, 'help()' for on-line help, or 267s 'help.start()' for an HTML browser interface to help. 267s Type 'q()' to quit R. 267s 268s > 268s > ## regression test for testing regression 268s > 268s > library(survey) 268s Loading required package: grid 268s Loading required package: Matrix 269s Loading required package: survival 269s 269s Attaching package: 'survey' 269s 269s The following object is masked from 'package:graphics': 269s 269s dotchart 269s 269s > data(api) 269s > 269s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 269s > 269s > 269s > f<-function(){ 269s + form<-acs.46~stype 269s + svyglm(formula=form, design = dstrat) 269s + } 269s > 269s > g<-function(form){ 269s + svyglm(formula=form, design = dstrat) 269s + } 269s > f() 269s Stratified Independent Sampling design 269s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 269s fpc = ~fpc) 269s 269s Call: svyglm(formula = form, design = dstrat) 269s 269s Coefficients: 269s (Intercept) stypeH stypeM 269s 28.7449 0.7551 0.4022 269s 269s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 269s (66 observations deleted due to missingness) 269s Null Deviance: 1838 269s Residual Deviance: 1835 AIC: 719.8 269s > g(acs.46~stype) 269s Stratified Independent Sampling design 269s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 269s fpc = ~fpc) 269s 269s Call: svyglm(formula = form, design = dstrat) 269s 269s Coefficients: 269s (Intercept) stypeH stypeM 269s 28.7449 0.7551 0.4022 269s 269s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 269s (66 observations deleted due to missingness) 269s Null Deviance: 1838 269s Residual Deviance: 1835 AIC: 719.8 269s > 269s > f<-function(){ 269s + form<-Surv(acs.46)~stype 269s + svycoxph(formula=form, design = dstrat) 269s + } 269s > 269s > g<-function(form){ 269s + svycoxph(formula=form, design = dstrat) 269s + } 269s > 269s > f() 269s Call: 269s svycoxph(formula = form, design = dstrat) 269s 269s coef exp(coef) se(coef) robust se z p 269s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 269s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 269s 269s Likelihood ratio test= on 2 df, p= 269s n= 134, number of events= 134 269s (66 observations deleted due to missingness) 269s > g(Surv(acs.46)~stype) 269s Call: 269s svycoxph(formula = form, design = dstrat) 269s 269s coef exp(coef) se(coef) robust se z p 269s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 269s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 269s 269s Likelihood ratio test= on 2 df, p= 269s n= 134, number of events= 134 269s (66 observations deleted due to missingness) 269s > 269s > ## check coxph for a single predictor 269s > svycoxph(Surv(acs.46)~api00,design=dstrat) 269s Call: 269s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 269s 269s coef exp(coef) se(coef) robust se z p 269s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 269s 269s Likelihood ratio test= on 1 df, p= 269s n= 134, number of events= 134 269s (66 observations deleted due to missingness) 269s > 269s BEGIN TEST survcurve.R 269s 269s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 269s Copyright (C) 2025 The R Foundation for Statistical Computing 269s Platform: arm-unknown-linux-gnueabihf (32-bit) 269s 269s R is free software and comes with ABSOLUTELY NO WARRANTY. 269s You are welcome to redistribute it under certain conditions. 269s Type 'license()' or 'licence()' for distribution details. 269s 269s R is a collaborative project with many contributors. 269s Type 'contributors()' for more information and 269s 'citation()' on how to cite R or R packages in publications. 269s 269s Type 'demo()' for some demos, 'help()' for on-line help, or 269s 'help.start()' for an HTML browser interface to help. 269s Type 'q()' to quit R. 269s 269s > library(survey) 269s Loading required package: grid 269s Loading required package: Matrix 270s Loading required package: survival 270s 270s Attaching package: 'survey' 270s 270s The following object is masked from 'package:graphics': 270s 270s dotchart 270s 270s > library(survival) 270s > 270s > pbc2<-rbind(pbc,pbc) 270s > pbc2$id<-rep(1:418,2) 270s > 270s > dpbc1<-svydesign(id=~1, data=pbc) 270s > dpbc2<-svydesign(id=~id, data=pbc2) 270s > 270s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 270s Warning message: 270s In svydesign.default(id = ~1, data = pbc) : 270s No weights or probabilities supplied, assuming equal probability 270s Warning message: 270s In svydesign.default(id = ~id, data = pbc2) : 270s No weights or probabilities supplied, assuming equal probability 270s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 271s > 271s > (c1<-confint(s1,(1:5)*365)) 271s 0.025 0.975 271s 365 0.6446215 0.8594153 271s 730 0.5410938 0.7766848 271s 1095 0.2683127 0.5103356 271s 1460 0.1444731 0.3722001 271s 1825 0.1009672 0.3204713 271s > (c2<-confint(s2,(1:5)*365)) 271s 0.025 0.975 271s 365 0.6446215 0.8594153 271s 730 0.5410938 0.7766848 271s 1095 0.2683127 0.5103356 271s 1460 0.1444731 0.3722001 271s 1825 0.1009672 0.3204713 271s > all.equal(c1, c2) 271s [1] TRUE 271s > 271s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 271s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 271s > 271s > d<-data.frame(bili=c(5,10)) 271s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 271s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 273s > 273s > (pc1<-confint(p1[[1]],(1:5)*365)) 273s 0.025 0.975 273s 365 0.8410027 0.9266263 273s 730 0.7371114 0.8548312 273s 1095 0.5517779 0.7018583 273s 1460 0.4335073 0.5992819 273s 1825 0.3260899 0.5046241 273s > (pc2<-confint(p2[[1]],(1:5)*365)) 273s 0.025 0.975 273s 365 0.8409490 0.9267054 273s 730 0.7370152 0.8549432 273s 1095 0.5515848 0.7019513 273s 1460 0.4332252 0.5992968 273s 1825 0.3257172 0.5045795 273s > all.equal(pc1, pc2) 273s [1] "Mean relative difference: 0.0002070722" 273s > 273s > (q1<-quantile(p1[[2]])) 273s 0.75 0.5 0.25 273s 489 930 1492 273s > (q2<-quantile(p2[[2]])) 273s 0.75 0.5 0.25 273s 489 930 1492 273s > all.equal(q1,q2) 273s [1] TRUE 273s > 273s BEGIN TEST svyby-strings.R 273s 273s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 273s Copyright (C) 2025 The R Foundation for Statistical Computing 273s Platform: arm-unknown-linux-gnueabihf (32-bit) 273s 273s R is free software and comes with ABSOLUTELY NO WARRANTY. 273s You are welcome to redistribute it under certain conditions. 273s Type 'license()' or 'licence()' for distribution details. 273s 273s R is a collaborative project with many contributors. 273s Type 'contributors()' for more information and 273s 'citation()' on how to cite R or R packages in publications. 273s 273s Type 'demo()' for some demos, 'help()' for on-line help, or 273s 'help.start()' for an HTML browser interface to help. 273s Type 'q()' to quit R. 273s 273s > 273s > ## check that stringsAsFactors fixes the string levels problem 273s > data(api, package = "survey") 273s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 274s > est0 <- 274s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 274s > 274s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 274s > 274s BEGIN TEST svyby_bug.R 274s 274s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 274s Copyright (C) 2025 The R Foundation for Statistical Computing 274s Platform: arm-unknown-linux-gnueabihf (32-bit) 274s 274s R is free software and comes with ABSOLUTELY NO WARRANTY. 274s You are welcome to redistribute it under certain conditions. 274s Type 'license()' or 'licence()' for distribution details. 274s 274s R is a collaborative project with many contributors. 274s Type 'contributors()' for more information and 274s 'citation()' on how to cite R or R packages in publications. 274s 274s Type 'demo()' for some demos, 'help()' for on-line help, or 274s 'help.start()' for an HTML browser interface to help. 274s Type 'q()' to quit R. 274s 275s > library(survey) 275s Loading required package: grid 275s Loading required package: Matrix 276s Loading required package: survival 276s 276s Attaching package: 'survey' 276s 276s The following object is masked from 'package:graphics': 276s 276s dotchart 276s 276s > options(warn=2) 276s > 276s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 276s > data(api) 276s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 276s > svyby(~api99, ~stype, dclus1, svymean ) 276s stype api99 se 276s E E 607.7917 22.81660 276s H H 595.7143 41.76400 276s M M 608.6000 32.56064 276s > 276s > set.seed(123) 276s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 276s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 276s > 276s > # subsetting w/ na.rm = FALSE... 276s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 276s mean SE 276s api99 NA NA 276s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 276s mean SE 276s api99 595.71 41.764 276s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 276s mean SE 276s api99 NA NA 276s > 276s > # ... looks like this: 276s > svyby(~api99, ~stype, dclus1.na , svymean ) 276s stype api99 se 276s E E NA NA 276s H H 595.7143 41.764 276s M M NA NA 276s > 276s > # subsetting w/ na.rm = TRUE... 276s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 276s mean SE 276s api99 606.53 22.901 276s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 276s mean SE 276s api99 595.71 41.764 276s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 276s mean SE 276s api99 613.39 33.224 276s > 276s > # ... looks like this 276s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 276s stype api99 se 276s E E 606.5319 22.90084 276s H H 595.7143 41.76400 276s M M 613.3913 33.22358 276s > 276s > # Without missing values, this works: 276s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 276s stype api99 se 276s E E 607.7917 22.81660 276s H H 595.7143 41.76400 276s M M 608.6000 32.56064 276s > 276s > # ... but this breaks! 276s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 276s stype api99 se 276s E E 606.5319 22.90084 276s H H 595.7143 41.76400 276s M M 613.3913 33.22358 276s > 276s > # ... and i don't think this is the expected behavior 276s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 276s stype api99 se 276s E E NA NA 276s H H 595.7143 41.764 276s M M NA NA 276s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 276s stype api99 se 276s E E 606.5319 22.90084 276s H H 595.7143 41.76400 276s M M 613.3913 33.22358 276s > 276s > 276s > ## Now some more as tests 276s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 276s stype api99 se 276s E E 2894629.0 792809.8 276s H H 282283.9 101492.9 276s M M 477513.4 107555.5 276s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 276s stype api99/api00 se.api99/api00 276s E E 0.9367750 0.006365702 276s H H 0.9630485 0.010520785 276s M M 0.9682246 0.009390982 276s > 276s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 276s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 276s stype (Intercept) se.(Intercept) 276s E E 606.5319 22.90084 276s H H 595.7143 41.76400 276s M M 613.3913 33.22358 276s > 276s BEGIN TEST svyby_se.R 276s 276s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 276s Copyright (C) 2025 The R Foundation for Statistical Computing 276s Platform: arm-unknown-linux-gnueabihf (32-bit) 276s 276s R is free software and comes with ABSOLUTELY NO WARRANTY. 276s You are welcome to redistribute it under certain conditions. 276s Type 'license()' or 'licence()' for distribution details. 276s 276s R is a collaborative project with many contributors. 276s Type 'contributors()' for more information and 276s 'citation()' on how to cite R or R packages in publications. 276s 276s Type 'demo()' for some demos, 'help()' for on-line help, or 276s 'help.start()' for an HTML browser interface to help. 276s Type 'q()' to quit R. 276s 276s Loading required package: grid 276s > library(survey) 276s Loading required package: Matrix 277s Loading required package: survival 277s 277s Attaching package: 'survey' 277s 277s The following object is masked from 'package:graphics': 277s 277s dotchart 277s 277s > data(api) 278s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 278s > 278s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 278s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 278s > 278s > 278s > stopifnot(all.equal(SE(a),SE(b))) 278s > 278s BEGIN TEST svycontrast.R 278s 278s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 278s Copyright (C) 2025 The R Foundation for Statistical Computing 278s Platform: arm-unknown-linux-gnueabihf (32-bit) 278s 278s R is free software and comes with ABSOLUTELY NO WARRANTY. 278s You are welcome to redistribute it under certain conditions. 278s Type 'license()' or 'licence()' for distribution details. 278s 278s R is a collaborative project with many contributors. 278s Type 'contributors()' for more information and 278s 'citation()' on how to cite R or R packages in publications. 278s 278s Type 'demo()' for some demos, 'help()' for on-line help, or 278s 'help.start()' for an HTML browser interface to help. 278s Type 'q()' to quit R. 278s 278s Loading required package: grid 278s > library(survey) 278s Loading required package: Matrix 279s Loading required package: survival 279s 279s Attaching package: 'survey' 279s 279s The following object is masked from 'package:graphics': 279s 279s dotchart 279s 279s > data(api) 279s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 279s > rclus2<-as.svrepdesign(dclus2) 279s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 279s > svycontrast(model, c(ell=1,meals=0)) 279s contrast SE 279s contrast -2.0592 1.6177 279s > a<-svycontrast(model, c(0,1,0,0)) 279s > 279s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 279s > svycontrast(model2, c(ell=1,meals=0)) 279s contrast SE 279s contrast -2.0592 1.6177 279s > a2<-svycontrast(model2, c(0,1,0,0)) 279s > stopifnot(!is.null(a2$replicates)) 279s > 279s BEGIN TEST svyivreg-var.R 279s 279s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 279s Copyright (C) 2025 The R Foundation for Statistical Computing 279s Platform: arm-unknown-linux-gnueabihf (32-bit) 279s 279s R is free software and comes with ABSOLUTELY NO WARRANTY. 279s You are welcome to redistribute it under certain conditions. 279s Type 'license()' or 'licence()' for distribution details. 279s 279s R is a collaborative project with many contributors. 279s Type 'contributors()' for more information and 279s 'citation()' on how to cite R or R packages in publications. 279s 279s Type 'demo()' for some demos, 'help()' for on-line help, or 279s 'help.start()' for an HTML browser interface to help. 279s Type 'q()' to quit R. 279s 279s > 279s > library(survey) 279s Loading required package: grid 279s Loading required package: Matrix 280s Loading required package: survival 281s 281s Attaching package: 'survey' 281s 281s The following object is masked from 'package:graphics': 281s 281s dotchart 281s 281s > data(api) 281s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 281s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 281s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 281s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 281s > 281s BEGIN TEST svyivreg.R 281s 281s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 281s Copyright (C) 2025 The R Foundation for Statistical Computing 281s Platform: arm-unknown-linux-gnueabihf (32-bit) 281s 281s R is free software and comes with ABSOLUTELY NO WARRANTY. 281s You are welcome to redistribute it under certain conditions. 281s Type 'license()' or 'licence()' for distribution details. 281s 281s R is a collaborative project with many contributors. 281s Type 'contributors()' for more information and 281s 'citation()' on how to cite R or R packages in publications. 281s 281s Type 'demo()' for some demos, 'help()' for on-line help, or 281s 'help.start()' for an HTML browser interface to help. 281s Type 'q()' to quit R. 281s 281s > library(survey) 281s Loading required package: grid 281s Loading required package: Matrix 282s Loading required package: survival 282s > library(AER) 282s 282s Attaching package: 'survey' 282s 282s The following object is masked from 'package:graphics': 282s 282s dotchart 282s 282s Loading required package: car 282s Loading required package: carData 282s Loading required package: lmtest 282s Loading required package: zoo 282s 282s Attaching package: 'zoo' 282s 282s The following objects are masked from 'package:base': 282s 282s as.Date, as.Date.numeric 282s 282s Loading required package: sandwich 282s > 282s > load("cigsw.rda") 282s > 282s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 282s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 282s > 282s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 282s [1] TRUE 282s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 282s [1] TRUE 282s > 282s BEGIN TEST svyolr-rake-subset.R 282s 282s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 282s Copyright (C) 2025 The R Foundation for Statistical Computing 282s Platform: arm-unknown-linux-gnueabihf (32-bit) 282s 282s R is free software and comes with ABSOLUTELY NO WARRANTY. 282s You are welcome to redistribute it under certain conditions. 282s Type 'license()' or 'licence()' for distribution details. 282s 282s R is a collaborative project with many contributors. 282s Type 'contributors()' for more information and 282s 'citation()' on how to cite R or R packages in publications. 282s 282s Type 'demo()' for some demos, 'help()' for on-line help, or 282s 'help.start()' for an HTML browser interface to help. 282s Type 'q()' to quit R. 282s 282s > library(survey) 282s Loading required package: grid 283s Loading required package: Matrix 283s Loading required package: survival 284s 284s Attaching package: 'survey' 284s 284s The following object is masked from 'package:graphics': 284s 284s dotchart 284s 284s > data(api) 284s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 284s > 284s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 284s > 284s > ## population marginal totals for each stratum 284s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 284s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 284s > 284s > 284s > ## rake with the population totals 284s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 284s > 284s > # works 284s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 284s > 284s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 284s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 284s > 284s > # fails in 4.1 (should work because NA values are subsetted out) 284s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 284s > 284s BEGIN TEST svyolr.R 284s 284s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 284s Copyright (C) 2025 The R Foundation for Statistical Computing 284s Platform: arm-unknown-linux-gnueabihf (32-bit) 284s 284s R is free software and comes with ABSOLUTELY NO WARRANTY. 284s You are welcome to redistribute it under certain conditions. 284s Type 'license()' or 'licence()' for distribution details. 284s 284s R is a collaborative project with many contributors. 284s Type 'contributors()' for more information and 284s 'citation()' on how to cite R or R packages in publications. 284s 284s Type 'demo()' for some demos, 'help()' for on-line help, or 284s 'help.start()' for an HTML browser interface to help. 284s Type 'q()' to quit R. 284s 284s > library(survey) 284s Loading required package: grid 284s Loading required package: Matrix 285s Loading required package: survival 286s 286s Attaching package: 'survey' 286s 286s The following object is masked from 'package:graphics': 286s 286s dotchart 286s 286s > 286s > ################################################################################ 286s > # Example from svyolr: runs OK 286s > data(api) 286s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 286s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 286s > 286s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 286s > m 286s Call: 286s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 286s 286s Coefficients: 286s avg.ed mobility stypeH stypeM 286s -2.6999217 0.0325042 -1.7574715 -0.6191463 286s 286s Intercepts: 286s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 286s -8.857919 -6.586464 -4.924938 286s > 286s > ## Use regTermTest for testing multiple parameters 286s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 286s > ################################################################################ 286s > 286s > ################################################################################ 286s > # If we wrap everything into a function: error b/c it looks for design variable 286s > # dclus1 in .GlobalEnv 286s > 286s > foo <- function(x){ 286s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 286s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 286s + 286s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 286s + ## Use regTermTest for testing multiple parameters 286s + regTermTest(m, ~avg.ed+stype, method="LRT") 286s + } 286s > 286s > # OK 286s > foo(apiclus1) 286s Working (Rao-Scott+F) LRT for avg.ed stype 286s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 286s Working 2logLR = 0.6580304 p= 0.73257 286s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 286s > 286s > # Clean-up everything but apiclus1 and foo 286s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 286s > 286s > # Error 286s > test2<-foo(apiclus1) 286s > ################################################################################ 286s > all.equal(test,test2) 286s [1] TRUE 286s > 286s > 286s BEGIN TEST toy_example_for_postStratify.R 286s 286s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 286s Copyright (C) 2025 The R Foundation for Statistical Computing 286s Platform: arm-unknown-linux-gnueabihf (32-bit) 286s 286s R is free software and comes with ABSOLUTELY NO WARRANTY. 286s You are welcome to redistribute it under certain conditions. 286s Type 'license()' or 'licence()' for distribution details. 286s 286s R is a collaborative project with many contributors. 286s Type 'contributors()' for more information and 286s 'citation()' on how to cite R or R packages in publications. 286s 286s Type 'demo()' for some demos, 'help()' for on-line help, or 286s 'help.start()' for an HTML browser interface to help. 286s Type 'q()' to quit R. 286s 286s Loading required package: grid 286s > library(survey) 286s Loading required package: Matrix 287s Loading required package: survival 287s 287s Attaching package: 'survey' 287s 287s The following object is masked from 'package:graphics': 287s 287s dotchart 287s 287s > 287s > # Dummy data for testing nonresponse adjustments 287s > toy <- data.frame(id = 1:10, 287s + dummy = 1, 287s + class = c(rep("A", 5), rep("B", 5)), 287s + responded = c(rep(TRUE, 8), FALSE, FALSE), 287s + weight = rep(100, 10)) 287s > 287s > # With jackknife replicate weights 287s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 287s > diag(toy_repweights) <- rep(0, 10) 287s > 287s > # Scramble up which person is in which jackknife group 287s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 287s > 287s > toy_design <- svrepdesign(variables = toy[, 1:4], 287s + weights = toy$weight, 287s + repweights = toy_repweights, 287s + type = "JK1", 287s + scale = 0.9) 287s > 287s > # Get the sum of the weights for the full sample 287s > poptotals <- as.data.frame(svyby(formula = ~dummy, 287s + by = ~class, 287s + design = toy_design, 287s + FUN = survey::svytotal)) 287s > 287s > poptotals$Freq <- poptotals$dummy 287s > poptotals$dummy <- NULL 287s > poptotals$se <- NULL 287s > 287s > # Adjust the weights of the responding sample to match to the full sample 287s > adjusted <- postStratify(design = subset(toy_design, responded), 287s + strata = ~class, 287s + population = poptotals) 287s > 287s > # This works for the weights... 287s > svyby(formula = ~dummy, 287s + by = ~class, 287s + design = adjusted, 287s + FUN = survey::svytotal) 287s class dummy se 287s A A 500 0 287s B B 500 0 287s > 287s > # ...and some, but not all, the replicate weights 287s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 287s > 287s > 287s > 287s BEGIN TEST twophase.R 287s 287s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 287s Copyright (C) 2025 The R Foundation for Statistical Computing 287s Platform: arm-unknown-linux-gnueabihf (32-bit) 287s 287s R is free software and comes with ABSOLUTELY NO WARRANTY. 287s You are welcome to redistribute it under certain conditions. 287s Type 'license()' or 'licence()' for distribution details. 287s 287s R is a collaborative project with many contributors. 287s Type 'contributors()' for more information and 287s 'citation()' on how to cite R or R packages in publications. 287s 287s Type 'demo()' for some demos, 'help()' for on-line help, or 287s 'help.start()' for an HTML browser interface to help. 287s Type 'q()' to quit R. 287s 287s > library(survey) 287s Loading required package: grid 287s Loading required package: Matrix 288s Loading required package: survival 289s 289s Attaching package: 'survey' 289s 289s The following object is masked from 'package:graphics': 289s 289s dotchart 289s 289s > 289s > ## two-phase simple random sampling. 289s > data(pbc, package="survival") 289s > pbc$id<-1:nrow(pbc) 289s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 289s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 289s Two-phase sparse-matrix design: 289s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 289s subset = subset, data = data, pps = pps) 289s Phase 1: 289s Independent Sampling design (with replacement) 289s svydesign(ids = ~id) 289s Phase 2: 289s Independent Sampling design 289s svydesign(ids = ~id, fpc = `*phase1*`) 289s > m<-svymean(~bili, d2pbc) 289s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 289s [1] TRUE 289s > all.equal(as.vector(SE(m)), 289s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 289s + tolerance=0.002) 289s [1] TRUE 289s > 289s > ## two-stage sampling as two-phase 289s > data(mu284) 289s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 289s > mu284.1<-mu284[ii,] 289s > mu284.1$id<-1:nrow(mu284.1) 289s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 289s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 289s > ## first phase cluster sample, second phase stratified within cluster 289s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 289s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 289s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 289s NULL), data = mu284.1, subset = ~sub, method = "approx") 289s Phase 1: 289s 1 - level Cluster Sampling design 289s With (5) clusters. 289s svydesign(ids = ~id1, fpc = ~n1) 289s Phase 2: 289s Stratified Independent Sampling design 289s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 289s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 289s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 289s Two-phase sparse-matrix design: 289s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 289s subset = subset, data = data, pps = pps) 289s Phase 1: 289s 1 - level Cluster Sampling design 289s With (5) clusters. 289s svydesign(ids = ~id1, fpc = ~n1) 289s Phase 2: 289s Stratified Independent Sampling design 289s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 289s > summary(d2mu284) 289s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 289s NULL), data = mu284.1, subset = ~sub, method = "approx") 289s Phase 1: 289s 1 - level Cluster Sampling design 289s With (5) clusters. 289s svydesign(ids = ~id1, fpc = ~n1) 289s Probabilities: 289s Min. 1st Qu. Median Mean 3rd Qu. Max. 289s 0.1 0.1 0.1 0.1 0.1 0.1 289s Population size (PSUs): 50 289s Phase 2: 289s Stratified Independent Sampling design 289s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 289s Probabilities: 289s Min. 1st Qu. Median Mean 3rd Qu. Max. 289s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 289s Stratum Sizes: 289s 19 31 45 47 50 289s obs 3 3 3 3 3 289s design.PSU 3 3 3 3 3 289s actual.PSU 3 3 3 3 3 289s Population stratum sizes (PSUs): 289s 19 31 45 47 50 289s 5 7 8 5 9 289s Data variables: 289s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 289s > t1<-svytotal(~y1, dmu284) 289s > t2<-svytotal(~y1, d2mu284) 289s > t22<-svytotal(~y1,d22mu284) 289s > m1<-svymean(~y1, dmu284) 289s > m2<-svymean(~y1, d2mu284) 289s > m22<-svymean(~y1, d22mu284) 289s > all.equal(coef(t1),coef(t2)) 289s [1] TRUE 289s > all.equal(coef(t1),coef(t22)) 289s [1] TRUE 289s > all.equal(coef(m1),coef(m2)) 289s [1] TRUE 289s > all.equal(coef(m1),coef(m22)) 289s [1] TRUE 289s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 289s [1] TRUE 289s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 289s [1] TRUE 289s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 289s [1] TRUE 289s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 289s [1] TRUE 289s > 289s > ## case-cohort design 289s > ##this example requires R 2.3.1 or later for cch and data. 289s > library("survival") 289s > data(nwtco, package="survival") 289s > ## unstratified, equivalent to Lin & Ying (1993) 289s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 289s + subset=~I(in.subcohort | rel), data=nwtco)) 289s Two-phase sparse-matrix design: 289s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 289s subset = subset, data = data, pps = pps) 289s Phase 1: 289s Independent Sampling design (with replacement) 289s svydesign(ids = ~seqno) 289s Phase 2: 289s Stratified Independent Sampling design 289s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 289s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 289s + design=dcchs) 289s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 289s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 289s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 289s + design=dcchs) 289s > all.equal(coef(cch1),coef(cch1.2)) 289s [1] TRUE 289s > all.equal(SE(cch1),SE(cch1.2)) 289s [1] TRUE 289s > ## Using survival::cch 289s > subcoh <- nwtco$in.subcohort 289s > selccoh <- with(nwtco, rel==1|subcoh==1) 289s > ccoh.data <- nwtco[selccoh,] 289s > ccoh.data$subcohort <- subcoh[selccoh] 289s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 289s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 289s + cohort.size=4028, method="LinYing", robust=TRUE) 289s > 289s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 289s [1] TRUE 289s > ## cch has smaller variances by a factor of 1.0005 because 289s > ## there is a (n/(n-1)) in the survey phase1 varianace 289s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 289s [1] TRUE 289s > 289s > 289s > ## bug report from Takahiro Tsuchiya for version 3.4 289s > ## We used to not match Sarndal exactly, because our old phase-one 289s > ## estimator had a small bias for finite populations 289s > rei<-read.table(tmp<-textConnection( 289s + " id N n.a h n.ah n.h sub y 289s + 1 1 300 20 1 12 5 TRUE 1 289s + 2 2 300 20 1 12 5 TRUE 2 289s + 3 3 300 20 1 12 5 TRUE 3 289s + 4 4 300 20 1 12 5 TRUE 4 289s + 5 5 300 20 1 12 5 TRUE 5 290s + 6 6 300 20 1 12 5 FALSE NA 290s + 7 7 300 20 1 12 5 FALSE NA 290s + 8 8 300 20 1 12 5 FALSE NA 290s + 9 9 300 20 1 12 5 FALSE NA 290s + 10 10 300 20 1 12 5 FALSE NA 290s + 11 11 300 20 1 12 5 FALSE NA 290s + 12 12 300 20 1 12 5 FALSE NA 290s + 13 13 300 20 2 8 3 TRUE 6 290s + 14 14 300 20 2 8 3 TRUE 7 290s + 15 15 300 20 2 8 3 TRUE 8 290s + 16 16 300 20 2 8 3 FALSE NA 290s + 17 17 300 20 2 8 3 FALSE NA 290s + 18 18 300 20 2 8 3 FALSE NA 290s + 19 19 300 20 2 8 3 FALSE NA 290s + 20 20 300 20 2 8 3 FALSE NA 290s + "), header=TRUE) 290s > close(tmp) 290s > 290s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 290s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 290s > tot<- svytotal(~y, des.rei) 290s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 290s + fpc=list(~N,NULL), subset=~sub, data=rei) 290s > tot2<- svytotal(~y, des.rei2) 290s > 290s > ## based on Sarndal et al (9.4.14) 290s > rei$w.ah <- rei$n.ah / rei$n.a 290s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 290s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 290s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 290s > 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)) 290s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 290s > 290s > a.rei$f.h<-with(a.rei, n.h/n.ah) 290s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 290s > 290s > a.rei$f<-with(a.rei, n.a/N) 290s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 290s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 290s > 290s > V 290s [1] 36522.63 290s > Vphase1 290s [1] 24072.63 290s > Vphase2 290s [1] 12450 290s > vcov(tot) 290s y 290s y 35911.05 290s attr(,"phases") 290s attr(,"phases")$phase1 290s [,1] 290s [1,] 23461.05 290s 290s attr(,"phases")$phase2 290s y 290s y 12450 290s 290s > vcov(tot2) 290s [,1] 290s [1,] 36522.63 290s attr(,"phases") 290s attr(,"phases")$phase1 290s [,1] 290s [1,] 24072.63 290s 290s attr(,"phases")$phase2 290s [,1] 290s [1,] 12450 290s 290s > ## phase 2 identical 290s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 290s [1] TRUE 290s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 290s [1] TRUE 290s > ## phase 1 differs by 2.6% for old twophase estimator 290s > Vphase1/attr(vcov(tot),"phases")$phase1 290s [,1] 290s [1,] 1.026068 290s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 290s [1] TRUE 290s > 290s > 290s autopkgtest [12:40:00]: test run-unit-test: -----------------------] 294s run-unit-test PASS 294s autopkgtest [12:40:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 298s autopkgtest [12:40:08]: test pkg-r-autopkgtest: preparing testbed 321s autopkgtest [12:40:30]: testbed dpkg architecture: armhf 322s autopkgtest [12:40:32]: testbed apt version: 3.1.15 326s autopkgtest [12:40:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 328s autopkgtest [12:40:38]: testbed release detected to be: resolute 335s autopkgtest [12:40:45]: updating testbed package index (apt update) 337s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 338s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 338s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 338s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 338s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.9 kB] 338s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [179 kB] 338s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 338s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [259 kB] 338s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1495 kB] 338s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [8156 B] 338s Get:11 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 339s Get:12 http://ftpmaster.internal/ubuntu resolute/main Sources [1404 kB] 339s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1386 kB] 339s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [14.9 MB] 342s Fetched 43.2 MB in 5s (8195 kB/s) 344s Reading package lists... 349s autopkgtest [12:40:59]: upgrading testbed (apt dist-upgrade and autopurge) 351s Reading package lists... 351s Building dependency tree... 351s Reading state information... 351s Calculating upgrade... 352s The following packages will be upgraded: 352s libbrotli1 ubuntu-minimal ubuntu-standard 352s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 352s Need to get 345 kB of archives. 352s After this operation, 0 B of additional disk space will be used. 352s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-minimal armhf 1.565 [13.3 kB] 352s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf ubuntu-standard armhf 1.565 [13.3 kB] 352s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.2.0-3 [318 kB] 353s Fetched 345 kB in 1s (571 kB/s) 353s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 68678 files and directories currently installed.) 353s Preparing to unpack .../ubuntu-minimal_1.565_armhf.deb ... 353s Unpacking ubuntu-minimal (1.565) over (1.564) ... 353s Preparing to unpack .../ubuntu-standard_1.565_armhf.deb ... 353s Unpacking ubuntu-standard (1.565) over (1.564) ... 353s Preparing to unpack .../libbrotli1_1.2.0-3_armhf.deb ... 353s Unpacking libbrotli1:armhf (1.2.0-3) over (1.1.0-2build6) ... 353s Setting up ubuntu-minimal (1.565) ... 353s Setting up libbrotli1:armhf (1.2.0-3) ... 353s Setting up ubuntu-standard (1.565) ... 353s Processing triggers for libc-bin (2.42-2ubuntu4) ... 356s Reading package lists... 356s Building dependency tree... 356s Reading state information... 356s Solving dependencies... 357s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 359s autopkgtest [12:41:09]: rebooting testbed after setup commands that affected boot 422s Reading package lists... 423s Building dependency tree... 423s Reading state information... 423s Solving dependencies... 423s The following NEW packages will be installed: 423s build-essential cpp cpp-15 cpp-15-arm-linux-gnueabihf 423s cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config 423s fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax 423s g++ g++-15 g++-15-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-15 423s gcc-15-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gfortran gfortran-15 423s gfortran-15-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf icu-devtools 423s libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 423s libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 423s libfreetype6 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 423s libgraphite2-3 libharfbuzz0b libice6 libicu-dev libisl23 libjbig0 423s libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 423s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 423s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblzma-dev libmpc3 423s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 423s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 423s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 423s libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 libthai-data 423s libthai0 libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7 libxcb-render0 423s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 libzstd-dev linux-libc-dev 423s node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core 423s r-base-dev r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 423s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 423s r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools 423s r-cran-colorspace r-cran-conquer r-cran-cowplot r-cran-cpp11 r-cran-curl 423s r-cran-data.table r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest 423s r-cran-doby r-cran-dplyr r-cran-e1071 r-cran-evaluate r-cran-fansi 423s r-cran-farver r-cran-fastmap r-cran-foreach r-cran-forecast r-cran-foreign 423s r-cran-formula r-cran-fracdiff r-cran-future r-cran-future.apply 423s r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower 423s r-cran-gtable r-cran-hardhat r-cran-hexbin r-cran-highr r-cran-ipred 423s r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kernsmooth 423s r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle 423s r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate 423s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels 423s r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark 423s r-cran-minqa r-cran-mitools r-cran-modelmetrics r-cran-modelr r-cran-nlme 423s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pbkrtest 423s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr 423s r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr 423s r-cran-quadprog r-cran-quantmod r-cran-quantreg r-cran-r6 r-cran-rbibutils 423s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 423s r-cran-rdpack r-cran-recipes r-cran-reformulas r-cran-reshape2 r-cran-rlang 423s r-cran-rpart r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape 423s r-cran-sparsem r-cran-sparsevctrs r-cran-squarem r-cran-statmod 423s r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival r-cran-tibble 423s r-cran-tidyr r-cran-tidyselect r-cran-timechange r-cran-timedate 423s r-cran-tseries r-cran-ttr r-cran-tzdb r-cran-urca r-cran-utf8 r-cran-vctrs 423s r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xts r-cran-yaml 423s r-cran-zoo rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev 424s 0 upgraded, 246 newly installed, 0 to remove and 0 not upgraded. 424s Need to get 247 MB of archives. 424s After this operation, 570 MB of additional disk space will be used. 424s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 424s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.19.0-3.3 [1804 kB] 425s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 425s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 425s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 425s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 426s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 426s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 427s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 427s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 427s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 427s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 16-20260208-1ubuntu1 [40.7 kB] 427s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 16-20260208-1ubuntu1 [134 kB] 427s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 16-20260208-1ubuntu1 [3003 kB] 427s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 16-20260208-1ubuntu1 [1203 kB] 427s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 427s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 428s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 428s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 428s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 428s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 428s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 429s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 429s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 429s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 429s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 429s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf dctrl-tools armhf 2.24-3build4 [95.0 kB] 429s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 429s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 429s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 429s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 429s Get:32 http://ftpmaster.internal/ubuntu resolute/main 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Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran armhf 4:15.2.0-4ubuntu1 [1162 B] 429s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf icu-devtools armhf 78.2-1ubuntu1 [203 kB] 429s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 429s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libblas-dev armhf 3.12.1-7ubuntu1 [141 kB] 429s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-dev armhf 1.0.8-6build2 [31.2 kB] 429s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 429s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 429s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 429s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 429s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 429s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 429s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 429s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate-dev armhf 1.23-2build1 [45.1 kB] 429s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 429s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 429s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 429s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 430s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf libicu-dev armhf 78.2-1ubuntu1 [12.2 MB] 430s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 430s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8-dev armhf 2.1.5-4ubuntu3 [265 kB] 430s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu12 [2142 B] 430s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8-dev armhf 8c-2ubuntu12 [1480 B] 430s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-dev armhf 8c-2ubuntu12 [1480 B] 430s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 430s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 430s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 430s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 430s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 430s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack-dev armhf 3.12.1-7ubuntu1 [2207 kB] 431s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 431s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf libncurses-dev armhf 6.6+20251231-1 [348 kB] 431s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 431s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 431s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 431s Get:75 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 431s Get:76 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 431s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 431s Get:78 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 431s Get:79 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-16-0 armhf 10.46-1 [206 kB] 431s Get:80 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-32-0 armhf 10.46-1 [197 kB] 431s Get:81 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-posix3 armhf 10.46-1 [6286 B] 431s Get:82 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-dev armhf 10.46-1 [744 kB] 431s Get:83 http://ftpmaster.internal/ubuntu resolute/main armhf libpkgconf3 armhf 1.8.1-4build1 [26.6 kB] 431s Get:84 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 431s Get:85 http://ftpmaster.internal/ubuntu resolute/main armhf libpng-dev armhf 1.6.54-1 [252 kB] 431s Get:86 http://ftpmaster.internal/ubuntu resolute/main armhf libreadline-dev armhf 8.3-3 [165 kB] 431s Get:87 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 431s Get:88 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 431s Get:89 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 431s Get:90 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 431s Get:91 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 431s Get:92 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 431s Get:93 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 431s Get:94 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 431s Get:95 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 431s Get:96 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 431s Get:97 http://ftpmaster.internal/ubuntu resolute/main armhf libzstd-dev armhf 1.5.7+dfsg-3 [342 kB] 431s Get:98 http://ftpmaster.internal/ubuntu resolute/universe armhf node-normalize.css all 8.0.1-5.1 [10.4 kB] 431s Get:99 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 431s Get:100 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 431s Get:101 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 431s Get:102 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 434s Get:103 http://ftpmaster.internal/ubuntu resolute/main armhf liblzma-dev armhf 5.8.2-2 [167 kB] 434s Get:104 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf-bin armhf 1.8.1-4build1 [21.4 kB] 434s Get:105 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf armhf 1.8.1-4build1 [16.8 kB] 434s Get:106 http://ftpmaster.internal/ubuntu resolute/main armhf libtirpc-dev armhf 1.3.6+ds-1 [184 kB] 434s Get:107 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-dev all 4.5.2-1ubuntu2 [1880 B] 434s Get:108 http://ftpmaster.internal/ubuntu resolute/universe armhf pkg-r-autopkgtest all 20250812 [6158 B] 434s Get:109 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-abind all 1.4-8-1build1 [67.0 kB] 434s Get:110 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cardata all 3.0.6-1 [1687 kB] 434s Get:111 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-formula all 1.2-5-1 [158 kB] 434s Get:112 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 434s Get:113 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-lattice armhf 0.22-9-1 [1399 kB] 434s Get:114 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 434s Get:115 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 435s Get:116 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mgcv armhf 1.9-4-1 [3515 kB] 435s Get:117 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nnet armhf 7.3-20-1 [111 kB] 435s Get:118 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-boot all 1.3-32-1 [636 kB] 435s Get:119 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 435s Get:120 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 435s Get:121 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 435s Get:122 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-minqa armhf 1.2.8-1 [108 kB] 435s Get:123 http://ftpmaster.internal/ubuntu resolute/universe armhf libnlopt0 armhf 2.7.1-7ubuntu1 [155 kB] 435s Get:124 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nloptr armhf 2.2.1-2 [250 kB] 435s Get:125 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rbibutils armhf 2.3-1 [943 kB] 435s Get:126 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rdpack all 2.6.3-1 [636 kB] 435s Get:127 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-reformulas all 0.4.4-1 [151 kB] 435s Get:128 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 435s Get:129 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 435s Get:130 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-statmod armhf 1.5.0-1 [294 kB] 435s Get:131 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lme4 armhf 1.1-38-1 [4178 kB] 435s Get:132 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-backports armhf 1.5.0-2 [121 kB] 435s Get:133 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 435s Get:134 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 435s Get:135 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 435s Get:136 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 435s Get:137 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 435s Get:138 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-utf8 armhf 1.2.4-1 [136 kB] 435s Get:139 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 435s Get:140 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 435s Get:141 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-r6 all 2.6.1-1 [101 kB] 435s Get:142 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fansi armhf 1.0.6-2 [620 kB] 435s Get:143 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 435s Get:144 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tibble armhf 3.2.1+dfsg-3 [420 kB] 435s Get:145 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-withr all 3.0.2+dfsg-1 [214 kB] 435s Get:146 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyselect armhf 1.2.1+dfsg-1 [222 kB] 435s Get:147 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dplyr armhf 1.1.4-4 [1533 kB] 435s Get:148 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-purrr armhf 1.0.4-1 [550 kB] 435s Get:149 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringi armhf 1.8.4-1build2 [884 kB] 435s Get:150 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-stringr all 1.5.1-1 [290 kB] 435s Get:151 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 435s Get:152 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tidyr armhf 1.3.1-1 [1152 kB] 435s Get:153 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 435s Get:154 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 435s Get:155 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 435s Get:156 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-isoband armhf 0.2.7-1 [1477 kB] 435s Get:157 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-farver armhf 2.1.2-1 [1355 kB] 435s Get:158 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-labeling all 0.4.3-1 [62.1 kB] 435s Get:159 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 435s Get:160 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-viridislite all 0.4.3-1 [1088 kB] 435s Get:161 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-scales all 1.4.0-1 [725 kB] 435s Get:162 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 436s Get:163 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 436s Get:164 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-deriv all 4.2.0-1 [154 kB] 436s Get:165 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-colorspace armhf 2.1-1+dfsg-1 [1561 kB] 436s Get:166 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fracdiff armhf 1.5-3-1 [105 kB] 436s Get:167 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-zoo armhf 1.8-15-1 [1025 kB] 436s Get:168 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lmtest armhf 0.9.40-1build1 [400 kB] 436s Get:169 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-timedate armhf 4052.112-1 [1299 kB] 436s Get:170 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quadprog armhf 1.5-8-1build2 [29.8 kB] 436s Get:171 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xts armhf 0.14.1-1 [1181 kB] 436s Get:172 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-curl armhf 7.0.0+dfsg-1 [200 kB] 436s Get:173 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ttr armhf 0.24.4-1 [509 kB] 436s Get:174 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-jsonlite armhf 1.9.1+dfsg-1 [440 kB] 436s Get:175 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quantmod all 0.4.28-1 [1037 kB] 436s Get:176 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tseries armhf 0.10-59-3 [379 kB] 436s Get:177 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-urca armhf 1.3-4-1build1 [1050 kB] 436s Get:178 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpparmadillo armhf 15.2.3-1-1 [915 kB] 436s Get:179 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-forecast armhf 8.23.0-1 [1563 kB] 436s Get:180 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-modelr all 0.1.11-1 [195 kB] 436s Get:181 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-microbenchmark armhf 1.5.0-1 [67.8 kB] 436s Get:182 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-doby all 4.7.1-3 [4741 kB] 436s Get:183 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-evaluate all 1.0.5-1 [117 kB] 436s Get:184 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xfun armhf 0.55+dfsg-1 [589 kB] 436s Get:185 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 436s Get:186 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 436s Get:187 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 436s Get:188 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-knitr all 1.51+dfsg-1 [847 kB] 436s Get:189 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pbkrtest all 0.5.5-1 [217 kB] 436s Get:190 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-sparsem armhf 1.84-2-1 [807 kB] 436s Get:191 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrixmodels all 0.5-4-1 [351 kB] 436s Get:192 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-survival armhf 3.8-6-1 [8253 kB] 437s Get:193 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrixstats armhf 1.5.0-1 [495 kB] 437s Get:194 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-class armhf 7.3-23-1 [88.8 kB] 437s Get:195 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-proxy armhf 0.4-27-1 [180 kB] 437s Get:196 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-e1071 armhf 1.7-17-1 [570 kB] 437s Get:197 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-codetools all 0.2-20-1build1 [91.1 kB] 437s Get:198 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-iterators all 1.0.14-1build1 [336 kB] 437s Get:199 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-foreach all 1.5.2-1build1 [124 kB] 437s Get:200 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-data.table armhf 1.17.0+dfsg-1 [2111 kB] 437s Get:201 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-modelmetrics armhf 1.2.2.2-1build2 [152 kB] 437s Get:202 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-plyr armhf 1.8.9-1 [832 kB] 437s Get:203 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-proc armhf 1.18.5-1 [961 kB] 437s Get:204 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-tzdb armhf 0.5.0-1 [530 kB] 437s Get:205 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-clock armhf 0.7.2-1 [1858 kB] 437s Get:206 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gower armhf 1.0.2-1 [208 kB] 437s Get:207 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-sparsevctrs armhf 0.2.0-2 [168 kB] 437s Get:208 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-hardhat all 1.4.2+dfsg-1 [596 kB] 437s Get:209 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rpart armhf 4.1.24-1build1 [661 kB] 438s Get:210 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-shape all 1.4.6.1-1 [749 kB] 438s Get:211 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-diagram all 1.6.5-2 [656 kB] 438s Get:212 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-kernsmooth armhf 2.23-26-1build1 [91.4 kB] 438s Get:213 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-digest armhf 0.6.39-1 [211 kB] 438s Get:214 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-globals all 0.19.0-1 [160 kB] 438s Get:215 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 438s Get:216 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-parallelly armhf 1.42.0-1 [540 kB] 438s Get:217 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-future all 1.34.0+dfsg-1 [646 kB] 438s Get:218 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 438s Get:219 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-progressr all 0.15.1-1 [353 kB] 438s Get:220 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-squarem all 2021.1-1build1 [180 kB] 438s Get:221 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lava all 1.8.2+dfsg-1 [2210 kB] 438s Get:222 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-prodlim armhf 2024.06.25-1 [413 kB] 438s Get:223 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ipred armhf 0.9-15-1 [385 kB] 438s Get:224 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-timechange armhf 0.3.0-2 [184 kB] 438s Get:225 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lubridate armhf 1.9.4+dfsg-1 [1008 kB] 438s Get:226 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 438s Get:227 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-reshape2 armhf 1.4.4-2build2 [119 kB] 438s Get:228 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-caret armhf 7.0-1+dfsg-1 [3460 kB] 438s Get:229 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-conquer armhf 1.3.3-1 [460 kB] 438s Get:230 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quantreg armhf 6.1-1 [1428 kB] 438s Get:231 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-car all 3.1-5-1 [1526 kB] 438s Get:232 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-sandwich all 3.1-1-1build1 [1483 kB] 438s Get:233 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-aer all 1.2-15-1 [2607 kB] 438s Get:234 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-bit armhf 4.6.0+dfsg-1 [447 kB] 438s Get:235 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-bit64 armhf 4.6.0-1-4 [489 kB] 438s Get:236 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-blob all 1.3.0-1 [54.1 kB] 438s Get:237 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fastmap armhf 1.2.0-1 [69.8 kB] 438s Get:238 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cachem armhf 1.1.0-1 [73.8 kB] 438s Get:239 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-dbi all 1.2.3-1build1 [855 kB] 439s Get:240 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-foreign armhf 0.8.91-1 [240 kB] 439s Get:241 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-hexbin armhf 1.28.5-1 [1580 kB] 439s Get:242 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-memoise all 2.0.1-1build1 [54.5 kB] 439s Get:243 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mitools all 2.4-2build2 [266 kB] 439s Get:244 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-plogr all 0.2.0-3build2 [15.8 kB] 439s Get:245 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rsqlite armhf 2.3.9-1 [1157 kB] 439s Get:246 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-survey armhf 4.4-2-2 [3448 kB] 440s Preconfiguring packages ... 440s Fetched 247 MB in 15s (16.1 MB/s) 440s Selecting previously unselected package libc-dev-bin. 440s (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 ... 68678 files and directories currently installed.) 440s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_armhf.deb ... 440s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 440s Selecting previously unselected package linux-libc-dev:armhf. 440s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_armhf.deb ... 440s Unpacking linux-libc-dev:armhf (6.19.0-3.3) ... 440s Selecting previously unselected package libcrypt-dev:armhf. 440s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 440s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 440s Selecting previously unselected package rpcsvc-proto. 440s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 440s Unpacking rpcsvc-proto (1.4.3-1build1) ... 440s Selecting previously unselected package libc6-dev:armhf. 440s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_armhf.deb ... 440s Unpacking libc6-dev:armhf (2.42-2ubuntu4) ... 440s Selecting previously unselected package libisl23:armhf. 440s Preparing to unpack .../005-libisl23_0.27-1build1_armhf.deb ... 440s Unpacking libisl23:armhf (0.27-1build1) ... 440s Selecting previously unselected package libmpc3:armhf. 440s Preparing to unpack .../006-libmpc3_1.3.1-2_armhf.deb ... 440s Unpacking libmpc3:armhf (1.3.1-2) ... 440s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 441s Preparing to unpack .../007-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 441s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 441s Selecting previously unselected package cpp-15. 441s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 441s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 441s Selecting previously unselected package cpp-arm-linux-gnueabihf. 441s Preparing to unpack .../009-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 441s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 441s Selecting previously unselected package cpp. 441s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 441s Unpacking cpp (4:15.2.0-4ubuntu1) ... 441s Selecting previously unselected package libcc1-0:armhf. 441s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_armhf.deb ... 441s Unpacking libcc1-0:armhf (16-20260208-1ubuntu1) ... 441s Selecting previously unselected package libgomp1:armhf. 441s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_armhf.deb ... 441s Unpacking libgomp1:armhf (16-20260208-1ubuntu1) ... 441s Selecting previously unselected package libasan8:armhf. 441s Preparing to unpack .../013-libasan8_16-20260208-1ubuntu1_armhf.deb ... 441s Unpacking libasan8:armhf (16-20260208-1ubuntu1) ... 441s Selecting previously unselected package libubsan1:armhf. 441s Preparing to unpack .../014-libubsan1_16-20260208-1ubuntu1_armhf.deb ... 441s Unpacking libubsan1:armhf (16-20260208-1ubuntu1) ... 441s Selecting previously unselected package libgcc-15-dev:armhf. 441s Preparing to unpack .../015-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 441s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 441s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 441s Preparing to unpack .../016-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 441s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 442s Selecting previously unselected package gcc-15. 442s Preparing to unpack .../017-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 442s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 442s Selecting previously unselected package gcc-arm-linux-gnueabihf. 442s Preparing to unpack .../018-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 442s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 442s Selecting previously unselected package gcc. 442s Preparing to unpack .../019-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 442s Unpacking gcc (4:15.2.0-4ubuntu1) ... 442s Selecting previously unselected package libstdc++-15-dev:armhf. 442s Preparing to unpack .../020-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 442s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 442s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 442s Preparing to unpack .../021-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 442s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 442s Selecting previously unselected package g++-15. 442s Preparing to unpack .../022-g++-15_15.2.0-12ubuntu1_armhf.deb ... 442s Unpacking g++-15 (15.2.0-12ubuntu1) ... 442s Selecting previously unselected package g++-arm-linux-gnueabihf. 442s Preparing to unpack .../023-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 442s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 442s Selecting previously unselected package g++. 442s Preparing to unpack .../024-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 442s Unpacking g++ (4:15.2.0-4ubuntu1) ... 442s Selecting previously unselected package build-essential. 442s Preparing to unpack .../025-build-essential_12.12ubuntu2_armhf.deb ... 442s Unpacking build-essential (12.12ubuntu2) ... 442s Selecting previously unselected package dctrl-tools. 442s Preparing to unpack .../026-dctrl-tools_2.24-3build4_armhf.deb ... 442s Unpacking dctrl-tools (2.24-3build4) ... 443s Selecting previously unselected package libfreetype6:armhf. 443s Preparing to unpack .../027-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 443s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 443s Selecting previously unselected package fonts-dejavu-mono. 443s Preparing to unpack .../028-fonts-dejavu-mono_2.37-8build1_all.deb ... 443s Unpacking fonts-dejavu-mono (2.37-8build1) ... 443s Selecting previously unselected package fonts-dejavu-core. 443s Preparing to unpack .../029-fonts-dejavu-core_2.37-8build1_all.deb ... 443s Unpacking fonts-dejavu-core (2.37-8build1) ... 443s Selecting previously unselected package fontconfig-config. 443s Preparing to unpack .../030-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 443s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 443s Selecting previously unselected package libfontconfig1:armhf. 443s Preparing to unpack .../031-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 443s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 443s Selecting previously unselected package fontconfig. 443s Preparing to unpack .../032-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 443s Unpacking fontconfig (2.17.1-3ubuntu1) ... 443s Selecting previously unselected package fonts-glyphicons-halflings. 443s Preparing to unpack .../033-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 443s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 443s Selecting previously unselected package fonts-mathjax. 443s Preparing to unpack .../034-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 443s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 443s Selecting previously unselected package libgfortran5:armhf. 443s Preparing to unpack .../035-libgfortran5_16-20260208-1ubuntu1_armhf.deb ... 443s Unpacking libgfortran5:armhf (16-20260208-1ubuntu1) ... 443s Selecting previously unselected package libgfortran-15-dev:armhf. 443s Preparing to unpack .../036-libgfortran-15-dev_15.2.0-12ubuntu1_armhf.deb ... 443s Unpacking libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 443s Selecting previously unselected package gfortran-15-arm-linux-gnueabihf. 443s Preparing to unpack .../037-gfortran-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 443s Unpacking gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 444s Selecting previously unselected package gfortran-15. 444s Preparing to unpack .../038-gfortran-15_15.2.0-12ubuntu1_armhf.deb ... 444s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 444s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 444s Preparing to unpack .../039-gfortran-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 444s Unpacking gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 444s Selecting previously unselected package gfortran. 444s Preparing to unpack .../040-gfortran_4%3a15.2.0-4ubuntu1_armhf.deb ... 444s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 444s Selecting previously unselected package icu-devtools. 444s Preparing to unpack .../041-icu-devtools_78.2-1ubuntu1_armhf.deb ... 444s Unpacking icu-devtools (78.2-1ubuntu1) ... 444s Selecting previously unselected package libblas3:armhf. 444s Preparing to unpack .../042-libblas3_3.12.1-7ubuntu1_armhf.deb ... 444s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 444s Selecting previously unselected package libblas-dev:armhf. 444s Preparing to unpack .../043-libblas-dev_3.12.1-7ubuntu1_armhf.deb ... 444s Unpacking libblas-dev:armhf (3.12.1-7ubuntu1) ... 444s Selecting previously unselected package libbz2-dev:armhf. 444s Preparing to unpack .../044-libbz2-dev_1.0.8-6build2_armhf.deb ... 444s Unpacking libbz2-dev:armhf (1.0.8-6build2) ... 444s Selecting previously unselected package libpixman-1-0:armhf. 444s Preparing to unpack .../045-libpixman-1-0_0.46.4-1_armhf.deb ... 444s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 444s Selecting previously unselected package libxcb-render0:armhf. 444s Preparing to unpack .../046-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 444s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 444s Selecting previously unselected package libxcb-shm0:armhf. 444s Preparing to unpack .../047-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 444s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 444s Selecting previously unselected package libxrender1:armhf. 444s Preparing to unpack .../048-libxrender1_1%3a0.9.12-1_armhf.deb ... 444s Unpacking libxrender1:armhf (1:0.9.12-1) ... 444s Selecting previously unselected package libcairo2:armhf. 444s Preparing to unpack .../049-libcairo2_1.18.4-3_armhf.deb ... 444s Unpacking libcairo2:armhf (1.18.4-3) ... 444s Selecting previously unselected package libdatrie1:armhf. 444s Preparing to unpack .../050-libdatrie1_0.2.14-1_armhf.deb ... 444s Unpacking libdatrie1:armhf (0.2.14-1) ... 444s Selecting previously unselected package libdeflate0:armhf. 444s Preparing to unpack .../051-libdeflate0_1.23-2build1_armhf.deb ... 444s Unpacking libdeflate0:armhf (1.23-2build1) ... 444s Selecting previously unselected package libdeflate-dev:armhf. 444s Preparing to unpack .../052-libdeflate-dev_1.23-2build1_armhf.deb ... 444s Unpacking libdeflate-dev:armhf (1.23-2build1) ... 444s Selecting previously unselected package libgraphite2-3:armhf. 444s Preparing to unpack .../053-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 444s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 444s Selecting previously unselected package libharfbuzz0b:armhf. 444s Preparing to unpack .../054-libharfbuzz0b_12.3.2-1_armhf.deb ... 444s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 444s Selecting previously unselected package x11-common. 444s Preparing to unpack .../055-x11-common_1%3a7.7+24ubuntu1_all.deb ... 444s Unpacking x11-common (1:7.7+24ubuntu1) ... 444s Selecting previously unselected package libice6:armhf. 444s Preparing to unpack .../056-libice6_2%3a1.1.1-1build1_armhf.deb ... 444s Unpacking libice6:armhf (2:1.1.1-1build1) ... 444s Selecting previously unselected package libicu-dev:armhf. 444s Preparing to unpack .../057-libicu-dev_78.2-1ubuntu1_armhf.deb ... 444s Unpacking libicu-dev:armhf (78.2-1ubuntu1) ... 445s Selecting previously unselected package libjpeg-turbo8:armhf. 445s Preparing to unpack .../058-libjpeg-turbo8_2.1.5-4ubuntu3_armhf.deb ... 445s Unpacking libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 445s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 445s Preparing to unpack .../059-libjpeg-turbo8-dev_2.1.5-4ubuntu3_armhf.deb ... 445s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 445s Selecting previously unselected package libjpeg8:armhf. 445s Preparing to unpack .../060-libjpeg8_8c-2ubuntu12_armhf.deb ... 445s Unpacking libjpeg8:armhf (8c-2ubuntu12) ... 445s Selecting previously unselected package libjpeg8-dev:armhf. 445s Preparing to unpack .../061-libjpeg8-dev_8c-2ubuntu12_armhf.deb ... 445s Unpacking libjpeg8-dev:armhf (8c-2ubuntu12) ... 445s Selecting previously unselected package libjpeg-dev:armhf. 445s Preparing to unpack .../062-libjpeg-dev_8c-2ubuntu12_armhf.deb ... 445s Unpacking libjpeg-dev:armhf (8c-2ubuntu12) ... 445s Selecting previously unselected package libjs-bootstrap. 445s Preparing to unpack .../063-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 445s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 445s Selecting previously unselected package libjs-highlight.js. 445s Preparing to unpack .../064-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 445s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 445s Selecting previously unselected package libjs-jquery. 445s Preparing to unpack .../065-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 445s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 445s Selecting previously unselected package libjs-jquery-datatables. 445s Preparing to unpack .../066-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 445s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 445s Selecting previously unselected package liblapack3:armhf. 445s Preparing to unpack .../067-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 445s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 446s Selecting previously unselected package liblapack-dev:armhf. 446s Preparing to unpack .../068-liblapack-dev_3.12.1-7ubuntu1_armhf.deb ... 446s Unpacking liblapack-dev:armhf (3.12.1-7ubuntu1) ... 446s Selecting previously unselected package liblerc4:armhf. 446s Preparing to unpack .../069-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 446s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 446s Selecting previously unselected package libncurses-dev:armhf. 446s Preparing to unpack .../070-libncurses-dev_6.6+20251231-1_armhf.deb ... 446s Unpacking libncurses-dev:armhf (6.6+20251231-1) ... 446s Selecting previously unselected package libthai-data. 446s Preparing to unpack .../071-libthai-data_0.1.30-1_all.deb ... 446s Unpacking libthai-data (0.1.30-1) ... 446s Selecting previously unselected package libthai0:armhf. 446s Preparing to unpack .../072-libthai0_0.1.30-1_armhf.deb ... 446s Unpacking libthai0:armhf (0.1.30-1) ... 446s Selecting previously unselected package libpango-1.0-0:armhf. 446s Preparing to unpack .../073-libpango-1.0-0_1.57.0-1_armhf.deb ... 446s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 446s Selecting previously unselected package libpangoft2-1.0-0:armhf. 446s Preparing to unpack .../074-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 446s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 446s Selecting previously unselected package libpangocairo-1.0-0:armhf. 446s Preparing to unpack .../075-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 446s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 446s Selecting previously unselected package libpaper2:armhf. 446s Preparing to unpack .../076-libpaper2_2.2.5-0.3build1_armhf.deb ... 446s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 446s Selecting previously unselected package libpaper-utils. 446s Preparing to unpack .../077-libpaper-utils_2.2.5-0.3build1_armhf.deb ... 446s Unpacking libpaper-utils (2.2.5-0.3build1) ... 446s Selecting previously unselected package libpcre2-16-0:armhf. 446s Preparing to unpack .../078-libpcre2-16-0_10.46-1_armhf.deb ... 446s Unpacking libpcre2-16-0:armhf (10.46-1) ... 446s Selecting previously unselected package libpcre2-32-0:armhf. 446s Preparing to unpack .../079-libpcre2-32-0_10.46-1_armhf.deb ... 446s Unpacking libpcre2-32-0:armhf (10.46-1) ... 446s Selecting previously unselected package libpcre2-posix3:armhf. 446s Preparing to unpack .../080-libpcre2-posix3_10.46-1_armhf.deb ... 446s Unpacking libpcre2-posix3:armhf (10.46-1) ... 446s Selecting previously unselected package libpcre2-dev:armhf. 446s Preparing to unpack .../081-libpcre2-dev_10.46-1_armhf.deb ... 446s Unpacking libpcre2-dev:armhf (10.46-1) ... 446s Selecting previously unselected package libpkgconf3:armhf. 446s Preparing to unpack .../082-libpkgconf3_1.8.1-4build1_armhf.deb ... 446s Unpacking libpkgconf3:armhf (1.8.1-4build1) ... 446s Selecting previously unselected package zlib1g-dev:armhf. 446s Preparing to unpack .../083-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_armhf.deb ... 446s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 446s Selecting previously unselected package libpng-dev:armhf. 446s Preparing to unpack .../084-libpng-dev_1.6.54-1_armhf.deb ... 446s Unpacking libpng-dev:armhf (1.6.54-1) ... 446s Selecting previously unselected package libreadline-dev:armhf. 446s Preparing to unpack .../085-libreadline-dev_8.3-3_armhf.deb ... 446s Unpacking libreadline-dev:armhf (8.3-3) ... 446s Selecting previously unselected package libsharpyuv0:armhf. 446s Preparing to unpack .../086-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 446s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 446s Selecting previously unselected package libsm6:armhf. 446s Preparing to unpack .../087-libsm6_2%3a1.2.6-1build1_armhf.deb ... 446s Unpacking libsm6:armhf (2:1.2.6-1build1) ... 446s Selecting previously unselected package libtcl8.6:armhf. 446s Preparing to unpack .../088-libtcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 446s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 447s Selecting previously unselected package libjbig0:armhf. 447s Preparing to unpack .../089-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 447s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 447s Selecting previously unselected package libwebp7:armhf. 447s Preparing to unpack .../090-libwebp7_1.5.0-0.1build1_armhf.deb ... 447s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 447s Selecting previously unselected package libtiff6:armhf. 447s Preparing to unpack .../091-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 447s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 447s Selecting previously unselected package libxft2:armhf. 447s Preparing to unpack .../092-libxft2_2.3.6-1build2_armhf.deb ... 447s Unpacking libxft2:armhf (2.3.6-1build2) ... 447s Selecting previously unselected package libxss1:armhf. 447s Preparing to unpack .../093-libxss1_1%3a1.2.3-1build4_armhf.deb ... 447s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 447s Selecting previously unselected package libtk8.6:armhf. 447s Preparing to unpack .../094-libtk8.6_8.6.17-1_armhf.deb ... 447s Unpacking libtk8.6:armhf (8.6.17-1) ... 447s Selecting previously unselected package libxt6t64:armhf. 447s Preparing to unpack .../095-libxt6t64_1%3a1.2.1-1.3_armhf.deb ... 447s Unpacking libxt6t64:armhf (1:1.2.1-1.3) ... 447s Selecting previously unselected package libzstd-dev:armhf. 447s Preparing to unpack .../096-libzstd-dev_1.5.7+dfsg-3_armhf.deb ... 447s Unpacking libzstd-dev:armhf (1.5.7+dfsg-3) ... 447s Selecting previously unselected package node-normalize.css. 447s Preparing to unpack .../097-node-normalize.css_8.0.1-5.1_all.deb ... 447s Unpacking node-normalize.css (8.0.1-5.1) ... 447s Selecting previously unselected package zip. 447s Preparing to unpack .../098-zip_3.0-15ubuntu3_armhf.deb ... 447s Unpacking zip (3.0-15ubuntu3) ... 447s Selecting previously unselected package unzip. 447s Preparing to unpack .../099-unzip_6.0-29ubuntu1_armhf.deb ... 447s Unpacking unzip (6.0-29ubuntu1) ... 447s Selecting previously unselected package xdg-utils. 447s Preparing to unpack .../100-xdg-utils_1.2.1-2ubuntu2_all.deb ... 447s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 447s Selecting previously unselected package r-base-core. 447s Preparing to unpack .../101-r-base-core_4.5.2-1ubuntu2_armhf.deb ... 447s Unpacking r-base-core (4.5.2-1ubuntu2) ... 448s Selecting previously unselected package liblzma-dev:armhf. 448s Preparing to unpack .../102-liblzma-dev_5.8.2-2_armhf.deb ... 448s Unpacking liblzma-dev:armhf (5.8.2-2) ... 448s Selecting previously unselected package pkgconf-bin. 448s Preparing to unpack .../103-pkgconf-bin_1.8.1-4build1_armhf.deb ... 448s Unpacking pkgconf-bin (1.8.1-4build1) ... 448s Selecting previously unselected package pkgconf:armhf. 448s Preparing to unpack .../104-pkgconf_1.8.1-4build1_armhf.deb ... 448s Unpacking pkgconf:armhf (1.8.1-4build1) ... 448s Selecting previously unselected package libtirpc-dev:armhf. 448s Preparing to unpack .../105-libtirpc-dev_1.3.6+ds-1_armhf.deb ... 448s Unpacking libtirpc-dev:armhf (1.3.6+ds-1) ... 448s Selecting previously unselected package r-base-dev. 448s Preparing to unpack .../106-r-base-dev_4.5.2-1ubuntu2_all.deb ... 448s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 448s Selecting previously unselected package pkg-r-autopkgtest. 448s Preparing to unpack .../107-pkg-r-autopkgtest_20250812_all.deb ... 448s Unpacking pkg-r-autopkgtest (20250812) ... 448s Selecting previously unselected package r-cran-abind. 448s Preparing to unpack .../108-r-cran-abind_1.4-8-1build1_all.deb ... 448s Unpacking r-cran-abind (1.4-8-1build1) ... 448s Selecting previously unselected package r-cran-cardata. 448s Preparing to unpack .../109-r-cran-cardata_3.0.6-1_all.deb ... 448s Unpacking r-cran-cardata (3.0.6-1) ... 448s Selecting previously unselected package r-cran-formula. 448s Preparing to unpack .../110-r-cran-formula_1.2-5-1_all.deb ... 448s Unpacking r-cran-formula (1.2-5-1) ... 448s Selecting previously unselected package r-cran-mass. 448s Preparing to unpack .../111-r-cran-mass_7.3-65-1_armhf.deb ... 448s Unpacking r-cran-mass (7.3-65-1) ... 448s Selecting previously unselected package r-cran-lattice. 448s Preparing to unpack .../112-r-cran-lattice_0.22-9-1_armhf.deb ... 448s Unpacking r-cran-lattice (0.22-9-1) ... 448s Selecting previously unselected package r-cran-nlme. 448s Preparing to unpack .../113-r-cran-nlme_3.1.168-1_armhf.deb ... 448s Unpacking r-cran-nlme (3.1.168-1) ... 448s Selecting previously unselected package r-cran-matrix. 448s Preparing to unpack .../114-r-cran-matrix_1.7-4-1_armhf.deb ... 448s Unpacking r-cran-matrix (1.7-4-1) ... 448s Selecting previously unselected package r-cran-mgcv. 448s Preparing to unpack .../115-r-cran-mgcv_1.9-4-1_armhf.deb ... 448s Unpacking r-cran-mgcv (1.9-4-1) ... 448s Selecting previously unselected package r-cran-nnet. 448s Preparing to unpack .../116-r-cran-nnet_7.3-20-1_armhf.deb ... 448s Unpacking r-cran-nnet (7.3-20-1) ... 448s Selecting previously unselected package r-cran-boot. 448s Preparing to unpack .../117-r-cran-boot_1.3-32-1_all.deb ... 448s Unpacking r-cran-boot (1.3-32-1) ... 449s Selecting previously unselected package r-cran-littler. 449s Preparing to unpack .../118-r-cran-littler_0.3.22-1_armhf.deb ... 449s Unpacking r-cran-littler (0.3.22-1) ... 449s Selecting previously unselected package r-cran-pkgkitten. 449s Preparing to unpack .../119-r-cran-pkgkitten_0.2.4-1_all.deb ... 449s Unpacking r-cran-pkgkitten (0.2.4-1) ... 449s Selecting previously unselected package r-cran-rcpp. 449s Preparing to unpack .../120-r-cran-rcpp_1.1.0-1_armhf.deb ... 449s Unpacking r-cran-rcpp (1.1.0-1) ... 449s Selecting previously unselected package r-cran-minqa. 449s Preparing to unpack .../121-r-cran-minqa_1.2.8-1_armhf.deb ... 449s Unpacking r-cran-minqa (1.2.8-1) ... 449s Selecting previously unselected package libnlopt0:armhf. 449s Preparing to unpack .../122-libnlopt0_2.7.1-7ubuntu1_armhf.deb ... 449s Unpacking libnlopt0:armhf (2.7.1-7ubuntu1) ... 449s Selecting previously unselected package r-cran-nloptr. 449s Preparing to unpack .../123-r-cran-nloptr_2.2.1-2_armhf.deb ... 449s Unpacking r-cran-nloptr (2.2.1-2) ... 449s Selecting previously unselected package r-cran-rbibutils. 449s Preparing to unpack .../124-r-cran-rbibutils_2.3-1_armhf.deb ... 449s Unpacking r-cran-rbibutils (2.3-1) ... 449s Selecting previously unselected package r-cran-rdpack. 449s Preparing to unpack .../125-r-cran-rdpack_2.6.3-1_all.deb ... 449s Unpacking r-cran-rdpack (2.6.3-1) ... 449s Selecting previously unselected package r-cran-reformulas. 449s Preparing to unpack .../126-r-cran-reformulas_0.4.4-1_all.deb ... 449s Unpacking r-cran-reformulas (0.4.4-1) ... 449s Selecting previously unselected package r-cran-rlang. 449s Preparing to unpack .../127-r-cran-rlang_1.1.5-3_armhf.deb ... 449s Unpacking r-cran-rlang (1.1.5-3) ... 449s Selecting previously unselected package r-cran-rcppeigen. 449s Preparing to unpack .../128-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 449s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 449s Selecting previously unselected package r-cran-statmod. 449s Preparing to unpack .../129-r-cran-statmod_1.5.0-1_armhf.deb ... 449s Unpacking r-cran-statmod (1.5.0-1) ... 449s Selecting previously unselected package r-cran-lme4. 449s Preparing to unpack .../130-r-cran-lme4_1.1-38-1_armhf.deb ... 449s Unpacking r-cran-lme4 (1.1-38-1) ... 449s Selecting previously unselected package r-cran-backports. 449s Preparing to unpack .../131-r-cran-backports_1.5.0-2_armhf.deb ... 449s Unpacking r-cran-backports (1.5.0-2) ... 449s Selecting previously unselected package r-cran-cli. 450s Preparing to unpack .../132-r-cran-cli_3.6.4-1_armhf.deb ... 450s Unpacking r-cran-cli (3.6.4-1) ... 450s Selecting previously unselected package r-cran-generics. 450s Preparing to unpack .../133-r-cran-generics_0.1.4-1_all.deb ... 450s Unpacking r-cran-generics (0.1.4-1) ... 450s Selecting previously unselected package r-cran-glue. 450s Preparing to unpack .../134-r-cran-glue_1.8.0-1_armhf.deb ... 450s Unpacking r-cran-glue (1.8.0-1) ... 450s Selecting previously unselected package r-cran-lifecycle. 450s Preparing to unpack .../135-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 450s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 450s Selecting previously unselected package r-cran-magrittr. 450s Preparing to unpack .../136-r-cran-magrittr_2.0.3-1_armhf.deb ... 450s Unpacking r-cran-magrittr (2.0.3-1) ... 450s Selecting previously unselected package r-cran-utf8. 450s Preparing to unpack .../137-r-cran-utf8_1.2.4-1_armhf.deb ... 450s Unpacking r-cran-utf8 (1.2.4-1) ... 450s Selecting previously unselected package r-cran-vctrs. 450s Preparing to unpack .../138-r-cran-vctrs_0.6.5-1_armhf.deb ... 450s Unpacking r-cran-vctrs (0.6.5-1) ... 450s Selecting previously unselected package r-cran-pillar. 450s Preparing to unpack .../139-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 450s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 450s Selecting previously unselected package r-cran-r6. 450s Preparing to unpack .../140-r-cran-r6_2.6.1-1_all.deb ... 450s Unpacking r-cran-r6 (2.6.1-1) ... 450s Selecting previously unselected package r-cran-fansi. 450s Preparing to unpack .../141-r-cran-fansi_1.0.6-2_armhf.deb ... 450s Unpacking r-cran-fansi (1.0.6-2) ... 450s Selecting previously unselected package r-cran-pkgconfig. 450s Preparing to unpack .../142-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 450s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 450s Selecting previously unselected package r-cran-tibble. 450s Preparing to unpack .../143-r-cran-tibble_3.2.1+dfsg-3_armhf.deb ... 450s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 450s Selecting previously unselected package r-cran-withr. 450s Preparing to unpack .../144-r-cran-withr_3.0.2+dfsg-1_all.deb ... 450s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 450s Selecting previously unselected package r-cran-tidyselect. 450s Preparing to unpack .../145-r-cran-tidyselect_1.2.1+dfsg-1_armhf.deb ... 450s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 451s Selecting previously unselected package r-cran-dplyr. 451s Preparing to unpack .../146-r-cran-dplyr_1.1.4-4_armhf.deb ... 451s Unpacking r-cran-dplyr (1.1.4-4) ... 451s Selecting previously unselected package r-cran-purrr. 451s Preparing to unpack .../147-r-cran-purrr_1.0.4-1_armhf.deb ... 451s Unpacking r-cran-purrr (1.0.4-1) ... 451s Selecting previously unselected package r-cran-stringi. 451s Preparing to unpack .../148-r-cran-stringi_1.8.4-1build2_armhf.deb ... 451s Unpacking r-cran-stringi (1.8.4-1build2) ... 451s Selecting previously unselected package r-cran-stringr. 451s Preparing to unpack .../149-r-cran-stringr_1.5.1-1_all.deb ... 451s Unpacking r-cran-stringr (1.5.1-1) ... 451s Selecting previously unselected package r-cran-cpp11. 451s Preparing to unpack .../150-r-cran-cpp11_0.5.3-1_all.deb ... 451s Unpacking r-cran-cpp11 (0.5.3-1) ... 451s Selecting previously unselected package r-cran-tidyr. 451s Preparing to unpack .../151-r-cran-tidyr_1.3.1-1_armhf.deb ... 451s Unpacking r-cran-tidyr (1.3.1-1) ... 451s Selecting previously unselected package r-cran-broom. 451s Preparing to unpack .../152-r-cran-broom_1.0.12+dfsg-1_all.deb ... 451s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 451s Selecting previously unselected package r-cran-numderiv. 451s Preparing to unpack .../153-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 451s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 451s Selecting previously unselected package r-cran-gtable. 451s Preparing to unpack .../154-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 451s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 451s Selecting previously unselected package r-cran-isoband. 451s Preparing to unpack .../155-r-cran-isoband_0.2.7-1_armhf.deb ... 451s Unpacking r-cran-isoband (0.2.7-1) ... 451s Selecting previously unselected package r-cran-farver. 451s Preparing to unpack .../156-r-cran-farver_2.1.2-1_armhf.deb ... 451s Unpacking r-cran-farver (2.1.2-1) ... 451s Selecting previously unselected package r-cran-labeling. 451s Preparing to unpack .../157-r-cran-labeling_0.4.3-1_all.deb ... 451s Unpacking r-cran-labeling (0.4.3-1) ... 451s Selecting previously unselected package r-cran-rcolorbrewer. 451s Preparing to unpack .../158-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 451s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 451s Selecting previously unselected package r-cran-viridislite. 451s Preparing to unpack .../159-r-cran-viridislite_0.4.3-1_all.deb ... 451s Unpacking r-cran-viridislite (0.4.3-1) ... 452s Selecting previously unselected package r-cran-scales. 452s Preparing to unpack .../160-r-cran-scales_1.4.0-1_all.deb ... 452s Unpacking r-cran-scales (1.4.0-1) ... 452s Selecting previously unselected package r-cran-ggplot2. 452s Preparing to unpack .../161-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 452s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 452s Selecting previously unselected package r-cran-cowplot. 452s Preparing to unpack .../162-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 452s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 452s Selecting previously unselected package r-cran-deriv. 452s Preparing to unpack .../163-r-cran-deriv_4.2.0-1_all.deb ... 452s Unpacking r-cran-deriv (4.2.0-1) ... 452s Selecting previously unselected package r-cran-colorspace. 452s Preparing to unpack .../164-r-cran-colorspace_2.1-1+dfsg-1_armhf.deb ... 452s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 452s Selecting previously unselected package r-cran-fracdiff. 452s Preparing to unpack .../165-r-cran-fracdiff_1.5-3-1_armhf.deb ... 452s Unpacking r-cran-fracdiff (1.5-3-1) ... 452s Selecting previously unselected package r-cran-zoo. 452s Preparing to unpack .../166-r-cran-zoo_1.8-15-1_armhf.deb ... 452s Unpacking r-cran-zoo (1.8-15-1) ... 452s Selecting previously unselected package r-cran-lmtest. 452s Preparing to unpack .../167-r-cran-lmtest_0.9.40-1build1_armhf.deb ... 452s Unpacking r-cran-lmtest (0.9.40-1build1) ... 452s Selecting previously unselected package r-cran-timedate. 452s Preparing to unpack .../168-r-cran-timedate_4052.112-1_armhf.deb ... 452s Unpacking r-cran-timedate (4052.112-1) ... 452s Selecting previously unselected package r-cran-quadprog. 452s Preparing to unpack .../169-r-cran-quadprog_1.5-8-1build2_armhf.deb ... 452s Unpacking r-cran-quadprog (1.5-8-1build2) ... 452s Selecting previously unselected package r-cran-xts. 452s Preparing to unpack .../170-r-cran-xts_0.14.1-1_armhf.deb ... 452s Unpacking r-cran-xts (0.14.1-1) ... 452s Selecting previously unselected package r-cran-curl. 452s Preparing to unpack .../171-r-cran-curl_7.0.0+dfsg-1_armhf.deb ... 452s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 452s Selecting previously unselected package r-cran-ttr. 452s Preparing to unpack .../172-r-cran-ttr_0.24.4-1_armhf.deb ... 452s Unpacking r-cran-ttr (0.24.4-1) ... 452s Selecting previously unselected package r-cran-jsonlite. 452s Preparing to unpack .../173-r-cran-jsonlite_1.9.1+dfsg-1_armhf.deb ... 452s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 452s Selecting previously unselected package r-cran-quantmod. 452s Preparing to unpack .../174-r-cran-quantmod_0.4.28-1_all.deb ... 452s Unpacking r-cran-quantmod (0.4.28-1) ... 453s Selecting previously unselected package r-cran-tseries. 453s Preparing to unpack .../175-r-cran-tseries_0.10-59-3_armhf.deb ... 453s Unpacking r-cran-tseries (0.10-59-3) ... 453s Selecting previously unselected package r-cran-urca. 453s Preparing to unpack .../176-r-cran-urca_1.3-4-1build1_armhf.deb ... 453s Unpacking r-cran-urca (1.3-4-1build1) ... 453s Selecting previously unselected package r-cran-rcpparmadillo. 453s Preparing to unpack .../177-r-cran-rcpparmadillo_15.2.3-1-1_armhf.deb ... 453s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 453s Selecting previously unselected package r-cran-forecast. 453s Preparing to unpack .../178-r-cran-forecast_8.23.0-1_armhf.deb ... 453s Unpacking r-cran-forecast (8.23.0-1) ... 453s Selecting previously unselected package r-cran-modelr. 453s Preparing to unpack .../179-r-cran-modelr_0.1.11-1_all.deb ... 453s Unpacking r-cran-modelr (0.1.11-1) ... 453s Selecting previously unselected package r-cran-microbenchmark. 453s Preparing to unpack .../180-r-cran-microbenchmark_1.5.0-1_armhf.deb ... 453s Unpacking r-cran-microbenchmark (1.5.0-1) ... 453s Selecting previously unselected package r-cran-doby. 453s Preparing to unpack .../181-r-cran-doby_4.7.1-3_all.deb ... 453s Unpacking r-cran-doby (4.7.1-3) ... 453s Selecting previously unselected package r-cran-evaluate. 453s Preparing to unpack .../182-r-cran-evaluate_1.0.5-1_all.deb ... 453s Unpacking r-cran-evaluate (1.0.5-1) ... 453s Selecting previously unselected package r-cran-xfun. 453s Preparing to unpack .../183-r-cran-xfun_0.55+dfsg-1_armhf.deb ... 453s Unpacking r-cran-xfun (0.55+dfsg-1) ... 453s Selecting previously unselected package r-cran-highr. 453s Preparing to unpack .../184-r-cran-highr_0.11+dfsg-1_all.deb ... 453s Unpacking r-cran-highr (0.11+dfsg-1) ... 453s Selecting previously unselected package r-cran-yaml. 453s Preparing to unpack .../185-r-cran-yaml_2.3.10-1_armhf.deb ... 453s Unpacking r-cran-yaml (2.3.10-1) ... 453s Selecting previously unselected package libjs-mathjax. 453s Preparing to unpack .../186-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 453s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 454s Selecting previously unselected package r-cran-knitr. 454s Preparing to unpack .../187-r-cran-knitr_1.51+dfsg-1_all.deb ... 454s Unpacking r-cran-knitr (1.51+dfsg-1) ... 454s Selecting previously unselected package r-cran-pbkrtest. 454s Preparing to unpack .../188-r-cran-pbkrtest_0.5.5-1_all.deb ... 454s Unpacking r-cran-pbkrtest (0.5.5-1) ... 454s Selecting previously unselected package r-cran-sparsem. 455s Preparing to unpack .../189-r-cran-sparsem_1.84-2-1_armhf.deb ... 455s Unpacking r-cran-sparsem (1.84-2-1) ... 455s Selecting previously unselected package r-cran-matrixmodels. 455s Preparing to unpack .../190-r-cran-matrixmodels_0.5-4-1_all.deb ... 455s Unpacking r-cran-matrixmodels (0.5-4-1) ... 455s Selecting previously unselected package r-cran-survival. 455s Preparing to unpack .../191-r-cran-survival_3.8-6-1_armhf.deb ... 455s Unpacking r-cran-survival (3.8-6-1) ... 455s Selecting previously unselected package r-cran-matrixstats. 455s Preparing to unpack .../192-r-cran-matrixstats_1.5.0-1_armhf.deb ... 455s Unpacking r-cran-matrixstats (1.5.0-1) ... 455s Selecting previously unselected package r-cran-class. 455s Preparing to unpack .../193-r-cran-class_7.3-23-1_armhf.deb ... 455s Unpacking r-cran-class (7.3-23-1) ... 455s Selecting previously unselected package r-cran-proxy. 455s Preparing to unpack .../194-r-cran-proxy_0.4-27-1_armhf.deb ... 455s Unpacking r-cran-proxy (0.4-27-1) ... 455s Selecting previously unselected package r-cran-e1071. 455s Preparing to unpack .../195-r-cran-e1071_1.7-17-1_armhf.deb ... 455s Unpacking r-cran-e1071 (1.7-17-1) ... 455s Selecting previously unselected package r-cran-codetools. 455s Preparing to unpack .../196-r-cran-codetools_0.2-20-1build1_all.deb ... 455s Unpacking r-cran-codetools (0.2-20-1build1) ... 455s Selecting previously unselected package r-cran-iterators. 455s Preparing to unpack .../197-r-cran-iterators_1.0.14-1build1_all.deb ... 455s Unpacking r-cran-iterators (1.0.14-1build1) ... 455s Selecting previously unselected package r-cran-foreach. 455s Preparing to unpack .../198-r-cran-foreach_1.5.2-1build1_all.deb ... 455s Unpacking r-cran-foreach (1.5.2-1build1) ... 455s Selecting previously unselected package r-cran-data.table. 455s Preparing to unpack .../199-r-cran-data.table_1.17.0+dfsg-1_armhf.deb ... 455s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 455s Selecting previously unselected package r-cran-modelmetrics. 455s Preparing to unpack .../200-r-cran-modelmetrics_1.2.2.2-1build2_armhf.deb ... 455s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ... 455s Selecting previously unselected package r-cran-plyr. 455s Preparing to unpack .../201-r-cran-plyr_1.8.9-1_armhf.deb ... 455s Unpacking r-cran-plyr (1.8.9-1) ... 456s Selecting previously unselected package r-cran-proc. 456s Preparing to unpack .../202-r-cran-proc_1.18.5-1_armhf.deb ... 456s Unpacking r-cran-proc (1.18.5-1) ... 456s Selecting previously unselected package r-cran-tzdb. 456s Preparing to unpack .../203-r-cran-tzdb_0.5.0-1_armhf.deb ... 456s Unpacking r-cran-tzdb (0.5.0-1) ... 456s Selecting previously unselected package r-cran-clock. 456s Preparing to unpack .../204-r-cran-clock_0.7.2-1_armhf.deb ... 456s Unpacking r-cran-clock (0.7.2-1) ... 456s Selecting previously unselected package r-cran-gower. 456s Preparing to unpack .../205-r-cran-gower_1.0.2-1_armhf.deb ... 456s Unpacking r-cran-gower (1.0.2-1) ... 456s Selecting previously unselected package r-cran-sparsevctrs. 456s Preparing to unpack .../206-r-cran-sparsevctrs_0.2.0-2_armhf.deb ... 456s Unpacking r-cran-sparsevctrs (0.2.0-2) ... 456s Selecting previously unselected package r-cran-hardhat. 456s Preparing to unpack .../207-r-cran-hardhat_1.4.2+dfsg-1_all.deb ... 456s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ... 456s Selecting previously unselected package r-cran-rpart. 456s Preparing to unpack .../208-r-cran-rpart_4.1.24-1build1_armhf.deb ... 456s Unpacking r-cran-rpart (4.1.24-1build1) ... 456s Selecting previously unselected package r-cran-shape. 456s Preparing to unpack .../209-r-cran-shape_1.4.6.1-1_all.deb ... 456s Unpacking r-cran-shape (1.4.6.1-1) ... 456s Selecting previously unselected package r-cran-diagram. 456s Preparing to unpack .../210-r-cran-diagram_1.6.5-2_all.deb ... 456s Unpacking r-cran-diagram (1.6.5-2) ... 456s Selecting previously unselected package r-cran-kernsmooth. 456s Preparing to unpack .../211-r-cran-kernsmooth_2.23-26-1build1_armhf.deb ... 456s Unpacking r-cran-kernsmooth (2.23-26-1build1) ... 456s Selecting previously unselected package r-cran-digest. 456s Preparing to unpack .../212-r-cran-digest_0.6.39-1_armhf.deb ... 456s Unpacking r-cran-digest (0.6.39-1) ... 456s Selecting previously unselected package r-cran-globals. 457s Preparing to unpack .../213-r-cran-globals_0.19.0-1_all.deb ... 457s Unpacking r-cran-globals (0.19.0-1) ... 457s Selecting previously unselected package r-cran-listenv. 457s Preparing to unpack .../214-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 457s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 457s Selecting previously unselected package r-cran-parallelly. 457s Preparing to unpack .../215-r-cran-parallelly_1.42.0-1_armhf.deb ... 457s Unpacking r-cran-parallelly (1.42.0-1) ... 457s Selecting previously unselected package r-cran-future. 457s Preparing to unpack .../216-r-cran-future_1.34.0+dfsg-1_all.deb ... 457s Unpacking r-cran-future (1.34.0+dfsg-1) ... 457s Selecting previously unselected package r-cran-future.apply. 457s Preparing to unpack .../217-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 457s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 457s Selecting previously unselected package r-cran-progressr. 457s Preparing to unpack .../218-r-cran-progressr_0.15.1-1_all.deb ... 457s Unpacking r-cran-progressr (0.15.1-1) ... 457s Selecting previously unselected package r-cran-squarem. 457s Preparing to unpack .../219-r-cran-squarem_2021.1-1build1_all.deb ... 457s Unpacking r-cran-squarem (2021.1-1build1) ... 457s Selecting previously unselected package r-cran-lava. 457s Preparing to unpack .../220-r-cran-lava_1.8.2+dfsg-1_all.deb ... 457s Unpacking r-cran-lava (1.8.2+dfsg-1) ... 457s Selecting previously unselected package r-cran-prodlim. 457s Preparing to unpack .../221-r-cran-prodlim_2024.06.25-1_armhf.deb ... 457s Unpacking r-cran-prodlim (2024.06.25-1) ... 457s Selecting previously unselected package r-cran-ipred. 457s Preparing to unpack .../222-r-cran-ipred_0.9-15-1_armhf.deb ... 457s Unpacking r-cran-ipred (0.9-15-1) ... 457s Selecting previously unselected package r-cran-timechange. 458s Preparing to unpack .../223-r-cran-timechange_0.3.0-2_armhf.deb ... 458s Unpacking r-cran-timechange (0.3.0-2) ... 458s Selecting previously unselected package r-cran-lubridate. 458s Preparing to unpack .../224-r-cran-lubridate_1.9.4+dfsg-1_armhf.deb ... 458s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 458s Selecting previously unselected package r-cran-recipes. 458s Preparing to unpack .../225-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 458s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 458s Selecting previously unselected package r-cran-reshape2. 458s Preparing to unpack .../226-r-cran-reshape2_1.4.4-2build2_armhf.deb ... 458s Unpacking r-cran-reshape2 (1.4.4-2build2) ... 458s Selecting previously unselected package r-cran-caret. 458s Preparing to unpack .../227-r-cran-caret_7.0-1+dfsg-1_armhf.deb ... 458s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 458s Selecting previously unselected package r-cran-conquer. 458s Preparing to unpack .../228-r-cran-conquer_1.3.3-1_armhf.deb ... 458s Unpacking r-cran-conquer (1.3.3-1) ... 458s Selecting previously unselected package r-cran-quantreg. 458s Preparing to unpack .../229-r-cran-quantreg_6.1-1_armhf.deb ... 458s Unpacking r-cran-quantreg (6.1-1) ... 458s Selecting previously unselected package r-cran-car. 458s Preparing to unpack .../230-r-cran-car_3.1-5-1_all.deb ... 458s Unpacking r-cran-car (3.1-5-1) ... 458s Selecting previously unselected package r-cran-sandwich. 458s Preparing to unpack .../231-r-cran-sandwich_3.1-1-1build1_all.deb ... 458s Unpacking r-cran-sandwich (3.1-1-1build1) ... 458s Selecting previously unselected package r-cran-aer. 458s Preparing to unpack .../232-r-cran-aer_1.2-15-1_all.deb ... 458s Unpacking r-cran-aer (1.2-15-1) ... 458s Selecting previously unselected package r-cran-bit. 459s Preparing to unpack .../233-r-cran-bit_4.6.0+dfsg-1_armhf.deb ... 459s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 459s Selecting previously unselected package r-cran-bit64. 459s Preparing to unpack .../234-r-cran-bit64_4.6.0-1-4_armhf.deb 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.../240-r-cran-hexbin_1.28.5-1_armhf.deb ... 459s Unpacking r-cran-hexbin (1.28.5-1) ... 459s Selecting previously unselected package r-cran-memoise. 459s Preparing to unpack .../241-r-cran-memoise_2.0.1-1build1_all.deb ... 459s Unpacking r-cran-memoise (2.0.1-1build1) ... 459s Selecting previously unselected package r-cran-mitools. 459s Preparing to unpack .../242-r-cran-mitools_2.4-2build2_all.deb ... 459s Unpacking r-cran-mitools (2.4-2build2) ... 459s Selecting previously unselected package r-cran-plogr. 459s Preparing to unpack .../243-r-cran-plogr_0.2.0-3build2_all.deb ... 459s Unpacking r-cran-plogr (0.2.0-3build2) ... 459s Selecting previously unselected package r-cran-rsqlite. 459s Preparing to unpack .../244-r-cran-rsqlite_2.3.9-1_armhf.deb ... 459s Unpacking r-cran-rsqlite (2.3.9-1) ... 459s Selecting previously unselected package r-cran-survey. 459s Preparing to unpack .../245-r-cran-survey_4.4-2-2_armhf.deb ... 459s Unpacking r-cran-survey (4.4-2-2) ... 459s Setting up libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 459s Setting up libpixman-1-0:armhf (0.46.4-1) ... 459s Setting up libsharpyuv0:armhf (1.5.0-0.1build1) ... 459s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ... 459s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 459s Setting up libzstd-dev:armhf (1.5.7+dfsg-3) ... 459s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ... 459s Setting up libxrender1:armhf (1:0.9.12-1) ... 459s Setting up libdatrie1:armhf (0.2.14-1) ... 459s Setting up libxcb-render0:armhf (1.17.0-2ubuntu1) ... 459s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 459s Setting up unzip (6.0-29ubuntu1) ... 459s Setting up x11-common (1:7.7+24ubuntu1) ... 460s Setting up libdeflate0:armhf (1.23-2build1) ... 460s Setting up linux-libc-dev:armhf (6.19.0-3.3) ... 460s Setting up libnlopt0:armhf (2.7.1-7ubuntu1) ... 460s Setting up libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 460s Setting up libgomp1:armhf (16-20260208-1ubuntu1) ... 460s Setting up libjbig0:armhf (2.1-6.1ubuntu3) ... 460s Setting up libpcre2-16-0:armhf (10.46-1) ... 460s Setting up zip (3.0-15ubuntu3) ... 460s Setting up libpcre2-32-0:armhf (10.46-1) ... 460s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 460s 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 460s Setting up libtirpc-dev:armhf (1.3.6+ds-1) ... 460s Setting up libpkgconf3:armhf (1.8.1-4build1) ... 460s Setting up rpcsvc-proto (1.4.3-1build1) ... 460s Setting up libfreetype6:armhf (2.14.1+dfsg-2) ... 460s Setting up fonts-dejavu-mono (2.37-8build1) ... 460s Setting up libmpc3:armhf (1.3.1-2) ... 460s Setting up libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 460s Setting up icu-devtools (78.2-1ubuntu1) ... 460s Setting up fonts-dejavu-core (2.37-8build1) ... 460s Setting up pkgconf-bin (1.8.1-4build1) ... 460s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 460s Setting up libgfortran5:armhf (16-20260208-1ubuntu1) ... 460s Setting up libwebp7:armhf (1.5.0-0.1build1) ... 460s Setting up liblzma-dev:armhf (5.8.2-2) ... 460s Setting up libubsan1:armhf (16-20260208-1ubuntu1) ... 460s Setting up libpcre2-posix3:armhf (10.46-1) ... 460s Setting up libjs-highlight.js (10.7.3+dfsg-2) ... 460s Setting up libcrypt-dev:armhf (1:4.5.1-1) ... 460s Setting up libasan8:armhf (16-20260208-1ubuntu1) ... 460s Setting up libharfbuzz0b:armhf (12.3.2-1) ... 460s Setting up libthai-data (0.1.30-1) ... 460s Setting up libxss1:armhf (1:1.2.3-1build4) ... 460s Setting up libpaper2:armhf (2.2.5-0.3build1) ... 460s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 460s Setting up libisl23:armhf (0.27-1build1) ... 460s Setting up libc-dev-bin (2.42-2ubuntu4) ... 460s Setting up libdeflate-dev:armhf (1.23-2build1) ... 460s Setting up node-normalize.css (8.0.1-5.1) ... 460s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 460s Setting up xdg-utils (1.2.1-2ubuntu2) ... 460s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 460s Setting up libcc1-0:armhf (16-20260208-1ubuntu1) ... 460s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 460s Setting up libblas-dev:armhf (3.12.1-7ubuntu1) ... 460s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 460s Setting up dctrl-tools (2.24-3build4) ... 460s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 460s Setting up libjpeg8:armhf (8c-2ubuntu12) ... 460s Setting up libice6:armhf (2:1.1.1-1build1) ... 460s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 460s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 460s Setting up libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 460s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 460s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 461s Setting up libpaper-utils (2.2.5-0.3build1) ... 461s Setting up libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 461s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 461s Setting up pkgconf:armhf (1.8.1-4build1) ... 461s Setting up libthai0:armhf (0.1.30-1) ... 461s Setting up liblapack-dev:armhf (3.12.1-7ubuntu1) ... 461s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 461s Setting up cpp-15 (15.2.0-12ubuntu1) ... 461s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 461s Setting up cpp (4:15.2.0-4ubuntu1) ... 461s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 461s Setting up libfontconfig1:armhf (2.17.1-3ubuntu1) ... 461s Setting up libsm6:armhf (2:1.2.6-1build1) ... 461s Setting up libicu-dev:armhf (78.2-1ubuntu1) ... 461s Setting up libbz2-dev:armhf 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triggers for install-info (7.2-5) ... 479s autopkgtest [12:43:09]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 479s autopkgtest [12:43:09]: test pkg-r-autopkgtest: [----------------------- 481s Test: Try to load the R library survey 481s 481s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 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 482s > library('survey') 482s Loading required package: grid 482s Loading required package: Matrix 483s Loading required package: survival 483s 483s Attaching package: ‘survey’ 483s 483s The following object is masked from ‘package:graphics’: 483s 483s dotchart 483s 483s > 483s autopkgtest [12:43:13]: test pkg-r-autopkgtest: -----------------------] 489s pkg-r-autopkgtest PASS 489s autopkgtest [12:43:19]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 493s autopkgtest [12:43:23]: @@@@@@@@@@@@@@@@@@@@ summary 493s run-unit-test PASS 493s pkg-r-autopkgtest PASS