0s autopkgtest [23:11:04]: starting date and time: 2026-02-09 23:11:04+0000 0s autopkgtest [23:11:04]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:11:04]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dyzfuoqx/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-13.secgroup --name adt-resolute-arm64-r-cran-survey-20260209-231104-juju-7f2275-prod-proposed-migration-environment-15-12b8b94f-6312-4b22-b4e8-be2eb4190e1f --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-r-cran-survey-20260209-231104-juju-7f2275-prod-proposed-migration-environment-15-12b8b94f-6312-4b22-b4e8-be2eb4190e1f from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 105s autopkgtest [23:12:49]: testbed dpkg architecture: arm64 105s autopkgtest [23:12:49]: testbed apt version: 3.1.15 106s autopkgtest [23:12:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 106s autopkgtest [23:12:50]: testbed release detected to be: None 107s autopkgtest [23:12:51]: updating testbed package index (apt update) 107s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 107s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 107s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 107s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 109s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 109s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 109s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 109s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 109s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 111s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 112s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 112s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 113s Fetched 3862 kB in 5s (801 kB/s) 114s Reading package lists... 114s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 114s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 115s Reading package lists... 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Calculating upgrade... 116s The following packages will be upgraded: 116s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 116s libip6tc2 libxtables12 wget 116s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 2534 kB of archives. 116s After this operation, 18.4 kB of additional disk space will be used. 116s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 116s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 116s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 116s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 116s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 118s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 118s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 118s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 118s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 118s dpkg-preconfigure: unable to re-open stdin: No such file or directory 118s Fetched 2534 kB in 2s (1623 kB/s) 118s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 136597 files and directories currently installed.) 118s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 118s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 118s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 118s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 119s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 119s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 119s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 119s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 119s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 119s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 119s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 119s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 119s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 119s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 119s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 119s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 119s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 119s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 119s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 119s Setting up wget (1.25.0-2ubuntu4) ... 119s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 119s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 119s Setting up dracut-install (109-11ubuntu1) ... 119s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 119s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 119s Setting up iptables (1.8.11-2ubuntu3) ... 119s Setting up iproute2 (6.18.0-1ubuntu1) ... 120s Processing triggers for man-db (2.13.1-1build1) ... 121s Processing triggers for install-info (7.2-5) ... 122s Processing triggers for libc-bin (2.42-2ubuntu4) ... 122s autopkgtest [23:13:05]: upgrading testbed (apt dist-upgrade and autopurge) 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Solving dependencies... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s autopkgtest [23:13:09]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 125s autopkgtest [23:13:09]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 129s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (dsc) [2340 B] 129s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (tar) [2341 kB] 129s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (diff) [4580 B] 129s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC 129s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 129s gpgv: issuer "plessy@debian.org" 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found 130s autopkgtest [23:13:14]: testing package r-cran-survey version 4.4-2-2 130s autopkgtest [23:13:14]: build not needed 133s autopkgtest [23:13:17]: test run-unit-test: preparing testbed 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Solving dependencies... 134s The following NEW packages will be installed: 134s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 134s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 134s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 134s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 134s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 134s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 134s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 134s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 134s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 134s r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 134s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 134s r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools 134s r-cran-colorspace r-cran-conquer r-cran-cowplot r-cran-cpp11 r-cran-curl 134s r-cran-data.table r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest 134s r-cran-doby r-cran-dplyr r-cran-e1071 r-cran-evaluate r-cran-fansi 134s r-cran-farver r-cran-fastmap r-cran-foreach r-cran-forecast r-cran-foreign 134s r-cran-formula r-cran-fracdiff r-cran-future r-cran-future.apply 134s r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower 134s r-cran-gtable r-cran-hardhat r-cran-hexbin r-cran-highr r-cran-ipred 134s r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kernsmooth 134s r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle 134s r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate 134s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels 134s r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark 134s r-cran-minqa r-cran-mitools r-cran-modelmetrics r-cran-modelr r-cran-nlme 134s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pbkrtest 134s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr 134s r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr 134s r-cran-quadprog r-cran-quantmod r-cran-quantreg r-cran-r.cache 134s r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6 134s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 134s r-cran-rcppeigen r-cran-rdpack r-cran-recipes r-cran-reformulas 134s r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-rsqlite r-cran-sandwich 134s r-cran-scales r-cran-shape r-cran-sparsem r-cran-sparsevctrs r-cran-squarem 134s r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival 134s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange 134s r-cran-timedate r-cran-tseries r-cran-ttr r-cran-tzdb r-cran-urca 134s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun 134s r-cran-xts r-cran-yaml r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip 134s 0 upgraded, 196 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 169 MB of archives. 134s After this operation, 337 MB of additional disk space will be used. 134s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 134s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 135s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 135s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 135s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 135s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 135s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 138s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 138s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 138s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 138s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 138s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 138s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 138s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 138s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 138s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 138s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 138s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 138s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 138s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 138s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 138s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 138s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 138s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 138s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 138s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 138s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 138s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 141s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 141s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 141s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 141s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 141s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 141s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 141s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 141s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 141s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 141s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 141s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 143s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 143s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 143s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 143s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 143s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 143s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 144s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 144s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 144s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 144s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 144s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 144s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 182s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-abind all 1.4-8-1build1 [67.0 kB] 182s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cardata all 3.0.6-1 [1687 kB] 184s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 184s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 186s Get:56 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-lattice arm64 0.22-9-1 [1399 kB] 187s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 191s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 195s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-4-1 [3546 kB] 200s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 200s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-boot all 1.3-32-1 [636 kB] 201s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 201s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 201s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 203s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-minqa arm64 1.2.8-1 [112 kB] 203s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnlopt0 arm64 2.7.1-7ubuntu1 [177 kB] 203s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nloptr arm64 2.2.1-2 [250 kB] 203s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rbibutils arm64 2.3-1 [1016 kB] 205s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rdpack all 2.6.3-1 [636 kB] 205s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reformulas all 0.4.4-1 [151 kB] 205s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 208s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcppeigen arm64 0.3.4.0.2-1 [1422 kB] 209s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 209s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lme4 arm64 1.1-38-1 [4177 kB] 214s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 214s Get:76 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 215s Get:77 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 215s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 215s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 215s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 215s Get:81 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 215s Get:82 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 217s Get:83 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 217s Get:84 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 217s Get:85 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 218s Get:86 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 218s Get:87 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 218s Get:88 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 218s Get:89 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 218s Get:90 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 220s Get:91 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 220s Get:92 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build2 [901 kB] 221s Get:93 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 221s Get:94 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 222s Get:95 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 223s Get:96 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 225s Get:97 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 225s Get:98 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 225s Get:99 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 227s Get:100 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 230s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 230s Get:102 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 230s Get:103 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 231s Get:104 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 232s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 236s Get:106 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 237s Get:107 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-deriv all 4.2.0-1 [154 kB] 237s Get:108 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 239s Get:109 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB] 239s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-zoo arm64 1.8-15-1 [1025 kB] 240s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lmtest arm64 0.9.40-1build1 [400 kB] 240s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timedate arm64 4052.112-1 [1298 kB] 242s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quadprog arm64 1.5-8-1build2 [31.9 kB] 242s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xts arm64 0.14.1-1 [1189 kB] 243s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-curl arm64 7.0.0+dfsg-1 [202 kB] 243s Get:116 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB] 243s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB] 243s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quantmod all 0.4.28-1 [1037 kB] 244s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tseries arm64 0.10-59-3 [381 kB] 244s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-urca arm64 1.3-4-1build1 [1050 kB] 246s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 15.2.3-1-1 [916 kB] 247s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-forecast arm64 8.23.0-1 [1564 kB] 249s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 249s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-microbenchmark arm64 1.5.0-1 [67.5 kB] 249s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-doby all 4.7.1-3 [4741 kB] 255s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.5-1 [117 kB] 255s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.55+dfsg-1 [587 kB] 256s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 256s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 256s Get:130 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 264s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 266s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 266s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sparsem arm64 1.84-2-1 [812 kB] 267s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrixmodels all 0.5-4-1 [351 kB] 268s Get:135 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survival arm64 3.8-6-1 [8270 kB] 280s Get:136 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB] 280s Get:137 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-class arm64 7.3-23-1 [90.5 kB] 280s Get:138 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-proxy arm64 0.4-27-1 [181 kB] 280s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-e1071 arm64 1.7-17-1 [576 kB] 281s Get:140 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-codetools all 0.2-20-1build1 [91.1 kB] 281s Get:141 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-iterators all 1.0.14-1build1 [336 kB] 281s Get:142 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-foreach all 1.5.2-1build1 [124 kB] 281s Get:143 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 283s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelmetrics arm64 1.2.2.2-1build2 [143 kB] 283s Get:145 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 284s Get:146 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-proc arm64 1.18.5-1 [963 kB] 285s Get:147 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tzdb arm64 0.5.0-1 [530 kB] 286s Get:148 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-clock arm64 0.7.2-1 [1829 kB] 289s Get:149 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gower arm64 1.0.2-1 [208 kB] 289s Get:150 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sparsevctrs arm64 0.2.0-2 [169 kB] 289s Get:151 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-hardhat all 1.4.2+dfsg-1 [596 kB] 290s Get:152 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rpart arm64 4.1.24-1build1 [665 kB] 291s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-shape all 1.4.6.1-1 [749 kB] 292s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-diagram all 1.6.5-2 [656 kB] 293s Get:155 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-kernsmooth arm64 2.23-26-1build1 [93.6 kB] 293s Get:156 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-digest arm64 0.6.39-1 [196 kB] 293s Get:157 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-globals all 0.19.0-1 [160 kB] 293s Get:158 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 293s Get:159 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-parallelly arm64 1.42.0-1 [540 kB] 293s Get:160 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 294s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 294s Get:162 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-progressr all 0.15.1-1 [353 kB] 294s Get:163 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-squarem all 2021.1-1build1 [180 kB] 294s Get:164 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lava all 1.8.2+dfsg-1 [2210 kB] 297s Get:165 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-prodlim arm64 2024.06.25-1 [415 kB] 297s Get:166 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ipred arm64 0.9-15-1 [386 kB] 297s Get:167 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timechange arm64 0.3.0-2 [175 kB] 297s Get:168 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lubridate arm64 1.9.4+dfsg-1 [1009 kB] 298s Get:169 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 301s Get:170 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reshape2 arm64 1.4.4-2build2 [118 kB] 301s Get:171 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-caret arm64 7.0-1+dfsg-1 [3461 kB] 306s Get:172 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-conquer arm64 1.3.3-1 [440 kB] 306s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quantreg arm64 6.1-1 [1437 kB] 309s Get:174 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-car all 3.1-5-1 [1526 kB] 311s Get:175 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sandwich all 3.1-1-1build1 [1483 kB] 313s Get:176 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-aer all 1.2-15-1 [2607 kB] 316s Get:177 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit arm64 4.6.0+dfsg-1 [450 kB] 316s Get:178 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit64 arm64 4.6.0-1-4 [495 kB] 316s Get:179 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-blob all 1.3.0-1 [54.1 kB] 316s Get:180 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB] 316s Get:181 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB] 317s Get:182 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbi all 1.2.3-1build1 [855 kB] 318s Get:183 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-foreign arm64 0.8.91-1 [243 kB] 318s Get:184 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-hexbin arm64 1.28.5-1 [1580 kB] 320s Get:185 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-memoise all 2.0.1-1build1 [54.5 kB] 320s Get:186 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mitools all 2.4-2build2 [266 kB] 320s Get:187 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plogr all 0.2.0-3build2 [15.8 kB] 320s Get:188 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 320s Get:189 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.oo all 1.27.1-1 [978 kB] 322s Get:190 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.utils all 2.13.0-1 [1423 kB] 323s Get:191 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.cache all 0.17.0-1 [117 kB] 323s Get:192 http://ftpmaster.internal/ubuntu resolute/main arm64 tcl8.6 arm64 8.6.17+dfsg-1build1 [14.8 kB] 323s Get:193 http://ftpmaster.internal/ubuntu resolute/main arm64 tcl arm64 8.6.16build1 [4200 B] 323s Get:194 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r.rsp all 0.46.0+ds-1 [1412 kB] 325s Get:195 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rsqlite arm64 2.3.9-1 [1247 kB] 327s Get:196 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survey arm64 4.4-2-2 [3448 kB] 333s Preconfiguring packages ... 333s Fetched 169 MB in 3min 18s (851 kB/s) 333s Selecting previously unselected package fonts-dejavu-mono. 333s (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 ... 136600 files and directories currently installed.) 333s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ... 333s Unpacking fonts-dejavu-mono (2.37-8build1) ... 333s Selecting previously unselected package fonts-dejavu-core. 333s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ... 333s Unpacking fonts-dejavu-core (2.37-8build1) ... 333s Selecting previously unselected package fontconfig-config. 333s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 333s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 333s Selecting previously unselected package libfontconfig1:arm64. 333s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 333s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 333s Selecting previously unselected package fontconfig. 333s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 333s Unpacking fontconfig (2.17.1-3ubuntu1) ... 333s Selecting previously unselected package fonts-glyphicons-halflings. 333s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 333s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 333s Selecting previously unselected package fonts-mathjax. 333s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 333s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 333s Selecting previously unselected package libblas3:arm64. 333s Preparing to unpack .../007-libblas3_3.12.1-7ubuntu1_arm64.deb ... 333s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 333s Selecting previously unselected package libpixman-1-0:arm64. 334s Preparing to unpack .../008-libpixman-1-0_0.46.4-1_arm64.deb ... 334s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 334s Selecting previously unselected package libxcb-render0:arm64. 334s Preparing to unpack .../009-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 334s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 334s Selecting previously unselected package libxcb-shm0:arm64. 334s Preparing to unpack .../010-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 334s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 334s Selecting previously unselected package libxrender1:arm64. 334s Preparing to unpack .../011-libxrender1_1%3a0.9.12-1_arm64.deb ... 334s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 334s Selecting previously unselected package libcairo2:arm64. 334s Preparing to unpack .../012-libcairo2_1.18.4-3_arm64.deb ... 334s Unpacking libcairo2:arm64 (1.18.4-3) ... 334s Selecting previously unselected package libdatrie1:arm64. 334s Preparing to unpack .../013-libdatrie1_0.2.14-1_arm64.deb ... 334s Unpacking libdatrie1:arm64 (0.2.14-1) ... 334s Selecting previously unselected package libdeflate0:arm64. 334s Preparing to unpack .../014-libdeflate0_1.23-2build1_arm64.deb ... 334s Unpacking libdeflate0:arm64 (1.23-2build1) ... 334s Selecting previously unselected package libgfortran5:arm64. 334s Preparing to unpack .../015-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 334s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 334s Selecting previously unselected package libgomp1:arm64. 334s Preparing to unpack .../016-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 334s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 334s Selecting previously unselected package libgraphite2-3:arm64. 334s Preparing to unpack .../017-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 334s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 334s Selecting previously unselected package libharfbuzz0b:arm64. 334s Preparing to unpack .../018-libharfbuzz0b_12.3.2-1_arm64.deb ... 334s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 334s Selecting previously unselected package x11-common. 334s Preparing to unpack .../019-x11-common_1%3a7.7+24ubuntu1_all.deb ... 334s Unpacking x11-common (1:7.7+24ubuntu1) ... 334s Selecting previously unselected package libice6:arm64. 334s Preparing to unpack .../020-libice6_2%3a1.1.1-1build1_arm64.deb ... 334s Unpacking libice6:arm64 (2:1.1.1-1build1) ... 334s Selecting previously unselected package libjpeg-turbo8:arm64. 334s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-4ubuntu3_arm64.deb ... 334s Unpacking libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 334s Selecting previously unselected package libjpeg8:arm64. 334s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_arm64.deb ... 334s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 334s Selecting previously unselected package libjs-bootstrap. 334s Preparing to unpack .../023-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 334s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 334s Selecting previously unselected package libjs-highlight.js. 334s Preparing to unpack .../024-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 334s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 334s Selecting previously unselected package libjs-jquery. 334s Preparing to unpack .../025-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 334s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 334s Selecting previously unselected package libjs-jquery-datatables. 334s Preparing to unpack .../026-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 334s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 334s Selecting previously unselected package liblapack3:arm64. 334s Preparing to unpack .../027-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 334s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 334s Selecting previously unselected package liblerc4:arm64. 334s Preparing to unpack .../028-liblerc4_4.0.0+ds-5ubuntu2_arm64.deb ... 334s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu2) ... 334s Selecting previously unselected package libthai-data. 334s Preparing to unpack .../029-libthai-data_0.1.30-1_all.deb ... 334s Unpacking libthai-data (0.1.30-1) ... 334s Selecting previously unselected package libthai0:arm64. 334s Preparing to unpack .../030-libthai0_0.1.30-1_arm64.deb ... 334s Unpacking libthai0:arm64 (0.1.30-1) ... 334s Selecting previously unselected package libpango-1.0-0:arm64. 334s Preparing to unpack .../031-libpango-1.0-0_1.57.0-1_arm64.deb ... 334s Unpacking libpango-1.0-0:arm64 (1.57.0-1) ... 335s Selecting previously unselected package libpangoft2-1.0-0:arm64. 335s Preparing to unpack .../032-libpangoft2-1.0-0_1.57.0-1_arm64.deb ... 335s Unpacking libpangoft2-1.0-0:arm64 (1.57.0-1) ... 335s Selecting previously unselected package libpangocairo-1.0-0:arm64. 335s Preparing to unpack .../033-libpangocairo-1.0-0_1.57.0-1_arm64.deb ... 335s Unpacking libpangocairo-1.0-0:arm64 (1.57.0-1) ... 335s Selecting previously unselected package libpaper2:arm64. 335s Preparing to unpack .../034-libpaper2_2.2.5-0.3build1_arm64.deb ... 335s Unpacking libpaper2:arm64 (2.2.5-0.3build1) ... 335s Selecting previously unselected package libpaper-utils. 335s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3build1_arm64.deb ... 335s Unpacking libpaper-utils (2.2.5-0.3build1) ... 335s Selecting previously unselected package libsharpyuv0:arm64. 335s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1build1_arm64.deb ... 335s Unpacking libsharpyuv0:arm64 (1.5.0-0.1build1) ... 335s Selecting previously unselected package libsm6:arm64. 335s Preparing to unpack .../037-libsm6_2%3a1.2.6-1build1_arm64.deb ... 335s Unpacking libsm6:arm64 (2:1.2.6-1build1) ... 335s Selecting previously unselected package libtcl8.6:arm64. 335s Preparing to unpack .../038-libtcl8.6_8.6.17+dfsg-1build1_arm64.deb ... 335s Unpacking libtcl8.6:arm64 (8.6.17+dfsg-1build1) ... 335s Selecting previously unselected package libjbig0:arm64. 335s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu3_arm64.deb ... 335s Unpacking libjbig0:arm64 (2.1-6.1ubuntu3) ... 335s Selecting previously unselected package libwebp7:arm64. 335s Preparing to unpack .../040-libwebp7_1.5.0-0.1build1_arm64.deb ... 335s Unpacking libwebp7:arm64 (1.5.0-0.1build1) ... 335s Selecting previously unselected package libtiff6:arm64. 335s Preparing to unpack .../041-libtiff6_4.7.0-3ubuntu3_arm64.deb ... 335s Unpacking libtiff6:arm64 (4.7.0-3ubuntu3) ... 335s Selecting previously unselected package libxft2:arm64. 335s Preparing to unpack .../042-libxft2_2.3.6-1build2_arm64.deb ... 335s Unpacking libxft2:arm64 (2.3.6-1build2) ... 335s Selecting previously unselected package libxss1:arm64. 335s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build4_arm64.deb ... 335s Unpacking libxss1:arm64 (1:1.2.3-1build4) ... 335s Selecting previously unselected package libtk8.6:arm64. 335s Preparing to unpack .../044-libtk8.6_8.6.17-1_arm64.deb ... 335s Unpacking libtk8.6:arm64 (8.6.17-1) ... 335s Selecting previously unselected package libxt6t64:arm64. 335s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.3_arm64.deb ... 335s Unpacking libxt6t64:arm64 (1:1.2.1-1.3) ... 335s Selecting previously unselected package node-normalize.css. 335s Preparing to unpack .../046-node-normalize.css_8.0.1-5.1_all.deb ... 335s Unpacking node-normalize.css (8.0.1-5.1) ... 335s Selecting previously unselected package zip. 335s Preparing to unpack .../047-zip_3.0-15ubuntu3_arm64.deb ... 335s Unpacking zip (3.0-15ubuntu3) ... 335s Selecting previously unselected package unzip. 335s Preparing to unpack .../048-unzip_6.0-29ubuntu1_arm64.deb ... 335s Unpacking unzip (6.0-29ubuntu1) ... 335s Selecting previously unselected package xdg-utils. 335s Preparing to unpack .../049-xdg-utils_1.2.1-2ubuntu2_all.deb ... 335s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 335s Selecting previously unselected package r-base-core. 335s Preparing to unpack .../050-r-base-core_4.5.2-1ubuntu2_arm64.deb ... 335s Unpacking r-base-core (4.5.2-1ubuntu2) ... 336s Selecting previously unselected package r-cran-abind. 336s Preparing to unpack .../051-r-cran-abind_1.4-8-1build1_all.deb ... 336s Unpacking r-cran-abind (1.4-8-1build1) ... 336s Selecting previously unselected package r-cran-cardata. 336s Preparing to unpack .../052-r-cran-cardata_3.0.6-1_all.deb ... 336s Unpacking r-cran-cardata (3.0.6-1) ... 336s Selecting previously unselected package r-cran-formula. 336s Preparing to unpack .../053-r-cran-formula_1.2-5-1_all.deb ... 336s Unpacking r-cran-formula (1.2-5-1) ... 336s Selecting previously unselected package r-cran-mass. 336s Preparing to unpack .../054-r-cran-mass_7.3-65-1_arm64.deb ... 336s Unpacking r-cran-mass (7.3-65-1) ... 336s Selecting previously unselected package r-cran-lattice. 336s Preparing to unpack .../055-r-cran-lattice_0.22-9-1_arm64.deb ... 336s Unpacking r-cran-lattice (0.22-9-1) ... 336s Selecting previously unselected package r-cran-nlme. 336s Preparing to unpack .../056-r-cran-nlme_3.1.168-1_arm64.deb ... 336s Unpacking r-cran-nlme (3.1.168-1) ... 336s Selecting previously unselected package r-cran-matrix. 336s Preparing to unpack .../057-r-cran-matrix_1.7-4-1_arm64.deb ... 336s Unpacking r-cran-matrix (1.7-4-1) ... 336s Selecting previously unselected package r-cran-mgcv. 336s Preparing to unpack .../058-r-cran-mgcv_1.9-4-1_arm64.deb ... 336s Unpacking r-cran-mgcv (1.9-4-1) ... 336s Selecting previously unselected package r-cran-nnet. 336s Preparing to unpack .../059-r-cran-nnet_7.3-20-1_arm64.deb ... 336s Unpacking r-cran-nnet (7.3-20-1) ... 336s Selecting previously unselected package r-cran-boot. 336s Preparing to unpack .../060-r-cran-boot_1.3-32-1_all.deb ... 336s Unpacking r-cran-boot (1.3-32-1) ... 336s Selecting previously unselected package r-cran-littler. 336s Preparing to unpack .../061-r-cran-littler_0.3.22-1_arm64.deb ... 336s Unpacking r-cran-littler (0.3.22-1) ... 336s Selecting previously unselected package r-cran-pkgkitten. 336s Preparing to unpack .../062-r-cran-pkgkitten_0.2.4-1_all.deb ... 336s Unpacking r-cran-pkgkitten (0.2.4-1) ... 336s Selecting previously unselected package r-cran-rcpp. 336s Preparing to unpack .../063-r-cran-rcpp_1.1.0-1_arm64.deb ... 336s Unpacking r-cran-rcpp (1.1.0-1) ... 336s Selecting previously unselected package r-cran-minqa. 336s Preparing to unpack .../064-r-cran-minqa_1.2.8-1_arm64.deb ... 336s Unpacking r-cran-minqa (1.2.8-1) ... 336s Selecting previously unselected package libnlopt0:arm64. 336s Preparing to unpack .../065-libnlopt0_2.7.1-7ubuntu1_arm64.deb ... 336s Unpacking libnlopt0:arm64 (2.7.1-7ubuntu1) ... 336s Selecting previously unselected package r-cran-nloptr. 336s Preparing to unpack .../066-r-cran-nloptr_2.2.1-2_arm64.deb ... 336s Unpacking r-cran-nloptr (2.2.1-2) ... 336s Selecting previously unselected package r-cran-rbibutils. 336s Preparing to unpack .../067-r-cran-rbibutils_2.3-1_arm64.deb ... 336s Unpacking r-cran-rbibutils (2.3-1) ... 336s Selecting previously unselected package r-cran-rdpack. 336s Preparing to unpack .../068-r-cran-rdpack_2.6.3-1_all.deb ... 336s Unpacking r-cran-rdpack (2.6.3-1) ... 336s Selecting previously unselected package r-cran-reformulas. 336s Preparing to unpack .../069-r-cran-reformulas_0.4.4-1_all.deb ... 336s Unpacking r-cran-reformulas (0.4.4-1) ... 337s Selecting previously unselected package r-cran-rlang. 337s Preparing to unpack .../070-r-cran-rlang_1.1.5-3_arm64.deb ... 337s Unpacking r-cran-rlang (1.1.5-3) ... 337s Selecting previously unselected package r-cran-rcppeigen. 337s Preparing to unpack .../071-r-cran-rcppeigen_0.3.4.0.2-1_arm64.deb ... 337s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 337s Selecting previously unselected package r-cran-statmod. 337s Preparing to unpack .../072-r-cran-statmod_1.5.0-1_arm64.deb ... 337s Unpacking r-cran-statmod (1.5.0-1) ... 337s Selecting previously unselected package r-cran-lme4. 337s Preparing to unpack .../073-r-cran-lme4_1.1-38-1_arm64.deb ... 337s Unpacking r-cran-lme4 (1.1-38-1) ... 337s Selecting previously unselected package r-cran-backports. 337s Preparing to unpack .../074-r-cran-backports_1.5.0-2_arm64.deb ... 337s Unpacking r-cran-backports (1.5.0-2) ... 337s Selecting previously unselected package r-cran-cli. 337s Preparing to unpack .../075-r-cran-cli_3.6.4-1_arm64.deb ... 337s Unpacking r-cran-cli (3.6.4-1) ... 337s Selecting previously unselected package r-cran-generics. 337s Preparing to unpack .../076-r-cran-generics_0.1.4-1_all.deb ... 337s Unpacking r-cran-generics (0.1.4-1) ... 337s Selecting previously unselected package r-cran-glue. 337s Preparing to unpack .../077-r-cran-glue_1.8.0-1_arm64.deb ... 337s Unpacking r-cran-glue (1.8.0-1) ... 337s Selecting previously unselected package r-cran-lifecycle. 337s Preparing to unpack .../078-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 337s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 337s Selecting previously unselected package r-cran-magrittr. 337s Preparing to unpack .../079-r-cran-magrittr_2.0.3-1_arm64.deb ... 337s Unpacking r-cran-magrittr (2.0.3-1) ... 337s Selecting previously unselected package r-cran-utf8. 337s Preparing to unpack .../080-r-cran-utf8_1.2.4-1_arm64.deb ... 337s Unpacking r-cran-utf8 (1.2.4-1) ... 337s Selecting previously unselected package r-cran-vctrs. 337s Preparing to unpack .../081-r-cran-vctrs_0.6.5-1_arm64.deb ... 337s Unpacking r-cran-vctrs (0.6.5-1) ... 337s Selecting previously unselected package r-cran-pillar. 337s Preparing to unpack .../082-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 337s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 337s Selecting previously unselected package r-cran-r6. 337s Preparing to unpack .../083-r-cran-r6_2.6.1-1_all.deb ... 337s Unpacking r-cran-r6 (2.6.1-1) ... 337s Selecting previously unselected package r-cran-fansi. 337s Preparing to unpack .../084-r-cran-fansi_1.0.6-2_arm64.deb ... 337s Unpacking r-cran-fansi (1.0.6-2) ... 337s Selecting previously unselected package r-cran-pkgconfig. 337s Preparing to unpack .../085-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 337s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 337s Selecting previously unselected package r-cran-tibble. 337s Preparing to unpack .../086-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 337s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 337s Selecting previously unselected package r-cran-withr. 337s Preparing to unpack .../087-r-cran-withr_3.0.2+dfsg-1_all.deb ... 337s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 337s Selecting previously unselected package r-cran-tidyselect. 337s Preparing to unpack .../088-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 337s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 337s Selecting previously unselected package r-cran-dplyr. 338s Preparing to unpack .../089-r-cran-dplyr_1.1.4-4_arm64.deb ... 338s Unpacking r-cran-dplyr (1.1.4-4) ... 338s Selecting previously unselected package r-cran-purrr. 338s Preparing to unpack .../090-r-cran-purrr_1.0.4-1_arm64.deb ... 338s Unpacking r-cran-purrr (1.0.4-1) ... 338s Selecting previously unselected package r-cran-stringi. 338s Preparing to unpack .../091-r-cran-stringi_1.8.4-1build2_arm64.deb ... 338s Unpacking r-cran-stringi (1.8.4-1build2) ... 338s Selecting previously unselected package r-cran-stringr. 338s Preparing to unpack .../092-r-cran-stringr_1.5.1-1_all.deb ... 338s Unpacking r-cran-stringr (1.5.1-1) ... 338s Selecting previously unselected package r-cran-cpp11. 338s Preparing to unpack .../093-r-cran-cpp11_0.5.3-1_all.deb ... 338s Unpacking r-cran-cpp11 (0.5.3-1) ... 338s Selecting previously unselected package r-cran-tidyr. 338s Preparing to unpack .../094-r-cran-tidyr_1.3.1-1_arm64.deb ... 338s Unpacking r-cran-tidyr (1.3.1-1) ... 338s Selecting previously unselected package r-cran-broom. 338s Preparing to unpack .../095-r-cran-broom_1.0.12+dfsg-1_all.deb ... 338s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 338s Selecting previously unselected package r-cran-numderiv. 338s Preparing to unpack .../096-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 338s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 338s Selecting previously unselected package r-cran-gtable. 338s Preparing to unpack .../097-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 338s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 338s Selecting previously unselected package r-cran-isoband. 338s Preparing to unpack .../098-r-cran-isoband_0.2.7-1_arm64.deb ... 338s Unpacking r-cran-isoband (0.2.7-1) ... 338s Selecting previously unselected package r-cran-farver. 338s Preparing to unpack .../099-r-cran-farver_2.1.2-1_arm64.deb ... 338s Unpacking r-cran-farver (2.1.2-1) ... 338s Selecting previously unselected package r-cran-labeling. 338s Preparing to unpack .../100-r-cran-labeling_0.4.3-1_all.deb ... 338s Unpacking r-cran-labeling (0.4.3-1) ... 338s Selecting previously unselected package r-cran-rcolorbrewer. 338s Preparing to unpack .../101-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 338s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 338s Selecting previously unselected package r-cran-viridislite. 338s Preparing to unpack .../102-r-cran-viridislite_0.4.3-1_all.deb ... 338s Unpacking r-cran-viridislite (0.4.3-1) ... 338s Selecting previously unselected package r-cran-scales. 338s Preparing to unpack .../103-r-cran-scales_1.4.0-1_all.deb ... 338s Unpacking r-cran-scales (1.4.0-1) ... 338s Selecting previously unselected package r-cran-ggplot2. 338s Preparing to unpack .../104-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 338s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 338s Selecting previously unselected package r-cran-cowplot. 338s Preparing to unpack .../105-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 338s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 338s Selecting previously unselected package r-cran-deriv. 338s Preparing to unpack .../106-r-cran-deriv_4.2.0-1_all.deb ... 338s Unpacking r-cran-deriv (4.2.0-1) ... 338s Selecting previously unselected package r-cran-colorspace. 338s Preparing to unpack .../107-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 338s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 338s Selecting previously unselected package r-cran-fracdiff. 338s Preparing to unpack .../108-r-cran-fracdiff_1.5-3-1_arm64.deb ... 338s Unpacking r-cran-fracdiff (1.5-3-1) ... 338s Selecting previously unselected package r-cran-zoo. 339s Preparing to unpack .../109-r-cran-zoo_1.8-15-1_arm64.deb ... 339s Unpacking r-cran-zoo (1.8-15-1) ... 339s Selecting previously unselected package r-cran-lmtest. 339s Preparing to unpack .../110-r-cran-lmtest_0.9.40-1build1_arm64.deb ... 339s Unpacking r-cran-lmtest (0.9.40-1build1) ... 339s Selecting previously unselected package r-cran-timedate. 339s Preparing to unpack .../111-r-cran-timedate_4052.112-1_arm64.deb ... 339s Unpacking r-cran-timedate (4052.112-1) ... 339s Selecting previously unselected package r-cran-quadprog. 339s Preparing to unpack .../112-r-cran-quadprog_1.5-8-1build2_arm64.deb ... 339s Unpacking r-cran-quadprog (1.5-8-1build2) ... 339s Selecting previously unselected package r-cran-xts. 339s Preparing to unpack .../113-r-cran-xts_0.14.1-1_arm64.deb ... 339s Unpacking r-cran-xts (0.14.1-1) ... 339s Selecting previously unselected package r-cran-curl. 339s Preparing to unpack .../114-r-cran-curl_7.0.0+dfsg-1_arm64.deb ... 339s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 339s Selecting previously unselected package r-cran-ttr. 339s Preparing to unpack .../115-r-cran-ttr_0.24.4-1_arm64.deb ... 339s Unpacking r-cran-ttr (0.24.4-1) ... 339s Selecting previously unselected package r-cran-jsonlite. 339s Preparing to unpack .../116-r-cran-jsonlite_1.9.1+dfsg-1_arm64.deb ... 339s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 339s Selecting previously unselected package r-cran-quantmod. 339s Preparing to unpack .../117-r-cran-quantmod_0.4.28-1_all.deb ... 339s Unpacking r-cran-quantmod (0.4.28-1) ... 339s Selecting previously unselected package r-cran-tseries. 339s Preparing to unpack .../118-r-cran-tseries_0.10-59-3_arm64.deb ... 339s Unpacking r-cran-tseries (0.10-59-3) ... 339s Selecting previously unselected package r-cran-urca. 339s Preparing to unpack .../119-r-cran-urca_1.3-4-1build1_arm64.deb ... 339s Unpacking r-cran-urca (1.3-4-1build1) ... 339s Selecting previously unselected package r-cran-rcpparmadillo. 339s Preparing to unpack .../120-r-cran-rcpparmadillo_15.2.3-1-1_arm64.deb ... 339s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 339s Selecting previously unselected package r-cran-forecast. 339s Preparing to unpack .../121-r-cran-forecast_8.23.0-1_arm64.deb ... 339s Unpacking r-cran-forecast (8.23.0-1) ... 339s Selecting previously unselected package r-cran-modelr. 339s Preparing to unpack .../122-r-cran-modelr_0.1.11-1_all.deb ... 339s Unpacking r-cran-modelr (0.1.11-1) ... 339s Selecting previously unselected package r-cran-microbenchmark. 339s Preparing to unpack .../123-r-cran-microbenchmark_1.5.0-1_arm64.deb ... 339s Unpacking r-cran-microbenchmark (1.5.0-1) ... 339s Selecting previously unselected package r-cran-doby. 339s Preparing to unpack .../124-r-cran-doby_4.7.1-3_all.deb ... 339s Unpacking r-cran-doby (4.7.1-3) ... 339s Selecting previously unselected package r-cran-evaluate. 339s Preparing to unpack .../125-r-cran-evaluate_1.0.5-1_all.deb ... 339s Unpacking r-cran-evaluate (1.0.5-1) ... 339s Selecting previously unselected package r-cran-xfun. 339s Preparing to unpack .../126-r-cran-xfun_0.55+dfsg-1_arm64.deb ... 339s Unpacking r-cran-xfun (0.55+dfsg-1) ... 339s Selecting previously unselected package r-cran-highr. 339s Preparing to unpack .../127-r-cran-highr_0.11+dfsg-1_all.deb ... 339s Unpacking r-cran-highr (0.11+dfsg-1) ... 339s Selecting previously unselected package r-cran-yaml. 339s Preparing to unpack .../128-r-cran-yaml_2.3.10-1_arm64.deb ... 339s Unpacking r-cran-yaml (2.3.10-1) ... 340s Selecting previously unselected package libjs-mathjax. 340s Preparing to unpack .../129-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 340s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 340s Selecting previously unselected package r-cran-knitr. 340s Preparing to unpack .../130-r-cran-knitr_1.51+dfsg-1_all.deb ... 340s Unpacking r-cran-knitr (1.51+dfsg-1) ... 340s Selecting previously unselected package r-cran-pbkrtest. 340s Preparing to unpack .../131-r-cran-pbkrtest_0.5.5-1_all.deb ... 340s Unpacking r-cran-pbkrtest (0.5.5-1) ... 340s Selecting previously unselected package r-cran-sparsem. 340s Preparing to unpack .../132-r-cran-sparsem_1.84-2-1_arm64.deb ... 340s Unpacking r-cran-sparsem (1.84-2-1) ... 340s Selecting previously unselected package r-cran-matrixmodels. 340s Preparing to unpack .../133-r-cran-matrixmodels_0.5-4-1_all.deb ... 340s Unpacking r-cran-matrixmodels (0.5-4-1) ... 340s Selecting previously unselected package r-cran-survival. 340s Preparing to unpack .../134-r-cran-survival_3.8-6-1_arm64.deb ... 340s Unpacking r-cran-survival (3.8-6-1) ... 340s Selecting previously unselected package r-cran-matrixstats. 340s Preparing to unpack .../135-r-cran-matrixstats_1.5.0-1_arm64.deb ... 340s Unpacking r-cran-matrixstats (1.5.0-1) ... 340s Selecting previously unselected package r-cran-class. 340s Preparing to unpack .../136-r-cran-class_7.3-23-1_arm64.deb ... 340s Unpacking r-cran-class (7.3-23-1) ... 340s Selecting previously unselected package r-cran-proxy. 340s Preparing to unpack .../137-r-cran-proxy_0.4-27-1_arm64.deb ... 340s Unpacking r-cran-proxy (0.4-27-1) ... 340s Selecting previously unselected package r-cran-e1071. 341s Preparing to unpack .../138-r-cran-e1071_1.7-17-1_arm64.deb ... 341s Unpacking r-cran-e1071 (1.7-17-1) ... 341s Selecting previously unselected package r-cran-codetools. 341s Preparing to unpack .../139-r-cran-codetools_0.2-20-1build1_all.deb ... 341s Unpacking r-cran-codetools (0.2-20-1build1) ... 341s Selecting previously unselected package r-cran-iterators. 341s Preparing to unpack .../140-r-cran-iterators_1.0.14-1build1_all.deb ... 341s Unpacking r-cran-iterators (1.0.14-1build1) ... 341s Selecting previously unselected package r-cran-foreach. 341s Preparing to unpack .../141-r-cran-foreach_1.5.2-1build1_all.deb ... 341s Unpacking r-cran-foreach (1.5.2-1build1) ... 341s Selecting previously unselected package r-cran-data.table. 341s Preparing to unpack .../142-r-cran-data.table_1.17.0+dfsg-1_arm64.deb ... 341s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 341s Selecting previously unselected package r-cran-modelmetrics. 341s Preparing to unpack .../143-r-cran-modelmetrics_1.2.2.2-1build2_arm64.deb ... 341s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ... 341s Selecting previously unselected package r-cran-plyr. 341s Preparing to unpack .../144-r-cran-plyr_1.8.9-1_arm64.deb ... 341s Unpacking r-cran-plyr (1.8.9-1) ... 341s Selecting previously unselected package r-cran-proc. 341s Preparing to unpack .../145-r-cran-proc_1.18.5-1_arm64.deb ... 341s Unpacking r-cran-proc (1.18.5-1) ... 341s Selecting previously unselected package r-cran-tzdb. 341s Preparing to unpack .../146-r-cran-tzdb_0.5.0-1_arm64.deb ... 341s Unpacking r-cran-tzdb (0.5.0-1) ... 341s Selecting previously unselected package r-cran-clock. 341s Preparing to unpack .../147-r-cran-clock_0.7.2-1_arm64.deb ... 341s Unpacking r-cran-clock (0.7.2-1) ... 341s Selecting previously unselected package r-cran-gower. 341s Preparing to unpack .../148-r-cran-gower_1.0.2-1_arm64.deb ... 341s Unpacking r-cran-gower (1.0.2-1) ... 341s Selecting previously unselected package r-cran-sparsevctrs. 341s Preparing to unpack .../149-r-cran-sparsevctrs_0.2.0-2_arm64.deb ... 341s Unpacking r-cran-sparsevctrs (0.2.0-2) ... 341s Selecting previously unselected package r-cran-hardhat. 341s Preparing to unpack .../150-r-cran-hardhat_1.4.2+dfsg-1_all.deb ... 341s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ... 341s Selecting previously unselected package r-cran-rpart. 341s Preparing to unpack .../151-r-cran-rpart_4.1.24-1build1_arm64.deb ... 341s Unpacking r-cran-rpart (4.1.24-1build1) ... 341s Selecting previously unselected package r-cran-shape. 341s Preparing to unpack .../152-r-cran-shape_1.4.6.1-1_all.deb ... 341s Unpacking r-cran-shape (1.4.6.1-1) ... 341s Selecting previously unselected package r-cran-diagram. 341s Preparing to unpack .../153-r-cran-diagram_1.6.5-2_all.deb ... 341s Unpacking r-cran-diagram (1.6.5-2) ... 341s Selecting previously unselected package r-cran-kernsmooth. 341s Preparing to unpack .../154-r-cran-kernsmooth_2.23-26-1build1_arm64.deb ... 341s Unpacking r-cran-kernsmooth (2.23-26-1build1) ... 341s Selecting previously unselected package r-cran-digest. 341s Preparing to unpack .../155-r-cran-digest_0.6.39-1_arm64.deb ... 341s Unpacking r-cran-digest (0.6.39-1) ... 341s Selecting previously unselected package r-cran-globals. 341s Preparing to unpack .../156-r-cran-globals_0.19.0-1_all.deb ... 341s Unpacking r-cran-globals (0.19.0-1) ... 341s Selecting previously unselected package r-cran-listenv. 341s Preparing to unpack .../157-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 341s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 341s Selecting previously unselected package r-cran-parallelly. 341s Preparing to unpack .../158-r-cran-parallelly_1.42.0-1_arm64.deb ... 341s Unpacking r-cran-parallelly (1.42.0-1) ... 341s Selecting previously unselected package r-cran-future. 341s Preparing to unpack .../159-r-cran-future_1.34.0+dfsg-1_all.deb ... 341s Unpacking r-cran-future (1.34.0+dfsg-1) ... 341s Selecting previously unselected package r-cran-future.apply. 341s Preparing to unpack .../160-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 341s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 342s Selecting previously unselected package r-cran-progressr. 342s Preparing to unpack .../161-r-cran-progressr_0.15.1-1_all.deb ... 342s Unpacking r-cran-progressr (0.15.1-1) ... 342s Selecting previously unselected package r-cran-squarem. 342s Preparing to unpack .../162-r-cran-squarem_2021.1-1build1_all.deb ... 342s Unpacking r-cran-squarem (2021.1-1build1) ... 342s Selecting previously unselected package r-cran-lava. 342s Preparing to unpack .../163-r-cran-lava_1.8.2+dfsg-1_all.deb ... 342s Unpacking r-cran-lava (1.8.2+dfsg-1) ... 342s Selecting previously unselected package r-cran-prodlim. 342s Preparing to unpack .../164-r-cran-prodlim_2024.06.25-1_arm64.deb ... 342s Unpacking r-cran-prodlim (2024.06.25-1) ... 342s Selecting previously unselected package r-cran-ipred. 342s Preparing to unpack .../165-r-cran-ipred_0.9-15-1_arm64.deb ... 342s Unpacking r-cran-ipred (0.9-15-1) ... 342s Selecting previously unselected package r-cran-timechange. 342s Preparing to unpack .../166-r-cran-timechange_0.3.0-2_arm64.deb ... 342s Unpacking r-cran-timechange (0.3.0-2) ... 342s Selecting previously unselected package r-cran-lubridate. 342s Preparing to unpack .../167-r-cran-lubridate_1.9.4+dfsg-1_arm64.deb ... 342s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 342s Selecting previously unselected package r-cran-recipes. 342s Preparing to unpack .../168-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 342s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 342s Selecting previously unselected package r-cran-reshape2. 342s Preparing to unpack .../169-r-cran-reshape2_1.4.4-2build2_arm64.deb ... 342s Unpacking r-cran-reshape2 (1.4.4-2build2) ... 342s Selecting previously unselected package r-cran-caret. 342s Preparing to unpack .../170-r-cran-caret_7.0-1+dfsg-1_arm64.deb ... 342s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 342s Selecting previously unselected package r-cran-conquer. 342s Preparing to unpack .../171-r-cran-conquer_1.3.3-1_arm64.deb ... 342s Unpacking r-cran-conquer (1.3.3-1) ... 342s Selecting previously unselected package r-cran-quantreg. 342s Preparing to unpack .../172-r-cran-quantreg_6.1-1_arm64.deb ... 342s Unpacking r-cran-quantreg (6.1-1) ... 342s Selecting previously unselected package r-cran-car. 342s Preparing to unpack .../173-r-cran-car_3.1-5-1_all.deb ... 342s Unpacking r-cran-car (3.1-5-1) ... 342s Selecting previously unselected package r-cran-sandwich. 342s Preparing to unpack .../174-r-cran-sandwich_3.1-1-1build1_all.deb ... 342s Unpacking r-cran-sandwich (3.1-1-1build1) ... 342s Selecting previously unselected package r-cran-aer. 342s Preparing to unpack .../175-r-cran-aer_1.2-15-1_all.deb ... 342s Unpacking r-cran-aer (1.2-15-1) ... 342s Selecting previously unselected package r-cran-bit. 342s Preparing to unpack .../176-r-cran-bit_4.6.0+dfsg-1_arm64.deb ... 342s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 342s Selecting previously unselected package r-cran-bit64. 342s Preparing to unpack .../177-r-cran-bit64_4.6.0-1-4_arm64.deb 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previously unselected package r-cran-r.utils. 343s Preparing to unpack .../189-r-cran-r.utils_2.13.0-1_all.deb ... 343s Unpacking r-cran-r.utils (2.13.0-1) ... 343s Selecting previously unselected package r-cran-r.cache. 343s Preparing to unpack .../190-r-cran-r.cache_0.17.0-1_all.deb ... 343s Unpacking r-cran-r.cache (0.17.0-1) ... 343s Selecting previously unselected package tcl8.6. 343s Preparing to unpack .../191-tcl8.6_8.6.17+dfsg-1build1_arm64.deb ... 343s Unpacking tcl8.6 (8.6.17+dfsg-1build1) ... 343s Selecting previously unselected package tcl. 343s Preparing to unpack .../192-tcl_8.6.16build1_arm64.deb ... 343s Unpacking tcl (8.6.16build1) ... 343s Selecting previously unselected package r-cran-r.rsp. 343s Preparing to unpack .../193-r-cran-r.rsp_0.46.0+ds-1_all.deb ... 343s Unpacking r-cran-r.rsp (0.46.0+ds-1) ... 343s Selecting previously unselected package r-cran-rsqlite. 343s Preparing to unpack .../194-r-cran-rsqlite_2.3.9-1_arm64.deb ... 343s Unpacking r-cran-rsqlite 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344s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 344s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 344s Setting up zip (3.0-15ubuntu3) ... 344s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 344s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 344s Setting up fonts-dejavu-mono (2.37-8build1) ... 344s Setting up libtcl8.6:arm64 (8.6.17+dfsg-1build1) ... 344s Setting up fonts-dejavu-core (2.37-8build1) ... 344s Setting up libjpeg-turbo8:arm64 (2.1.5-4ubuntu3) ... 344s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 344s Setting up libwebp7:arm64 (1.5.0-0.1build1) ... 344s Setting up libjs-highlight.js (10.7.3+dfsg-2) ... 344s Setting up libharfbuzz0b:arm64 (12.3.2-1) ... 344s Setting up libthai-data (0.1.30-1) ... 344s Setting up libxss1:arm64 (1:1.2.3-1build4) ... 344s Setting up libpaper2:arm64 (2.2.5-0.3build1) ... 344s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 344s Setting up node-normalize.css (8.0.1-5.1) ... 344s Setting up xdg-utils (1.2.1-2ubuntu2) ... 344s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 344s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 344s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 344s Setting up libice6:arm64 (2:1.1.1-1build1) ... 344s Setting up tcl8.6 (8.6.17+dfsg-1build1) ... 344s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 344s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 344s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 344s Setting up libpaper-utils (2.2.5-0.3build1) ... 344s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 344s Setting up libthai0:arm64 (0.1.30-1) ... 344s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 344s Setting up tcl (8.6.16build1) ... 344s Setting up 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r-cran-forecast (8.23.0-1) ... 347s Setting up r-cran-quantreg (6.1-1) ... 347s Setting up r-cran-modelr (0.1.11-1) ... 347s Setting up r-cran-doby (4.7.1-3) ... 347s Setting up r-cran-pbkrtest (0.5.5-1) ... 347s Setting up r-cran-car (3.1-5-1) ... 347s Setting up r-cran-aer (1.2-15-1) ... 347s Processing triggers for libc-bin (2.42-2ubuntu4) ... 347s Processing triggers for man-db (2.13.1-1build1) ... 347s Processing triggers for install-info (7.2-5) ... 348s autopkgtest [23:16:52]: test run-unit-test: [----------------------- 348s BEGIN TEST 3stage2phase.R 348s 348s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 348s Copyright (C) 2025 The R Foundation for Statistical Computing 348s Platform: aarch64-unknown-linux-gnu 348s 348s R is free software and comes with ABSOLUTELY NO WARRANTY. 348s You are welcome to redistribute it under certain conditions. 348s Type 'license()' or 'licence()' for distribution details. 348s 348s R is a collaborative project with many contributors. 348s Type 'contributors()' for more information and 348s 'citation()' on how to cite R or R packages in publications. 348s 348s Type 'demo()' for some demos, 'help()' for on-line help, or 348s 'help.start()' for an HTML browser interface to help. 348s Type 'q()' to quit R. 348s 348s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 348s > ## motivated by dietary biomarker substudy in HCHS 348s > 348s > library(survey) 348s Loading required package: grid 348s Loading required package: Matrix 349s Loading required package: survival 349s 349s Attaching package: 'survey' 349s 349s The following object is masked from 'package:graphics': 349s 349s dotchart 349s 349s > 349s > load("simdata1.RData") 349s > 349s > twophase.full = twophase(id=list(~block+house+ind,~1), 349s + strata=list(~strat,NULL), 349s + probs=list(~P.block+P.house+P.ind,NULL), 350s + subset=~phase2, 350s + data=simdata1,method='full') 350s > 350s > twophase.approx = twophase(id=list(~block+house+ind,~1), 350s + strata=list(~strat,NULL), 350s + probs=list(~P.block+P.house+P.ind,NULL), 350s + subset=~phase2, 350s + data=simdata1,method='approx') 350s > 350s > twophase.rep = twophase(id=list(~block,~1), 350s + strata=list(~strat,NULL), 350s + probs=list(~I(P.block*P.house*P.ind),NULL), 350s + subset=~phase2, 350s + data=simdata1,method='full') 350s > 350s > 350s > twophase.repapprox = twophase(id=list(~block,~1), 350s + strata=list(~strat,NULL), 350s + probs=list(~I(P.block*P.house*P.ind),NULL), 350s + subset=~phase2, 350s + data=simdata1,method='approx') 350s > 350s > 350s > svymean(~age, twophase.full) 350s mean SE 350s age 41.116 0.8114 350s > svymean(~age, twophase.approx) 350s mean SE 350s age 41.116 0.6693 350s > svymean(~age, twophase.rep) 350s mean SE 350s age 41.116 0.784 350s > svymean(~age, twophase.repapprox) 350s mean SE 350s age 41.116 0.6592 350s > 350s BEGIN TEST DBIcheck.R 350s 350s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 350s Copyright (C) 2025 The R Foundation for Statistical Computing 350s Platform: aarch64-unknown-linux-gnu 350s 350s R is free software and comes with ABSOLUTELY NO WARRANTY. 350s You are welcome to redistribute it under certain conditions. 350s Type 'license()' or 'licence()' for distribution details. 350s 350s R is a collaborative project with many contributors. 350s Type 'contributors()' for more information and 350s 'citation()' on how to cite R or R packages in publications. 350s 350s Type 'demo()' for some demos, 'help()' for on-line help, or 350s 'help.start()' for an HTML browser interface to help. 350s Type 'q()' to quit R. 350s 350s > 350s > library(survey) 350s Loading required package: grid 350s Loading required package: Matrix 351s Loading required package: survival 351s 351s Attaching package: 'survey' 351s 351s > library(RSQLite) 351s The following object is masked from 'package:graphics': 351s 351s dotchart 351s 352s > 352s > data(api) 352s > apiclus1$api_stu<-apiclus1$api.stu 352s > apiclus1$comp_imp<-apiclus1$comp.imp 352s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 352s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 352s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 352s > 352s > m<-svymean(~api00+stype,dclus1) 352s > m.db<-svymean(~api00+stype, dbclus1) 352s > all.equal(coef(m),coef(m.db)) 352s [1] TRUE 352s > all.equal(vcov(m), vcov(m.db)) 352s [1] TRUE 352s > 352s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 352s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 352s > all.equal(coef(r), coef(r.db)) 352s [1] TRUE 352s > all.equal(SE(r), SE(r.db)) 352s [1] TRUE 352s > 352s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 352s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 352s > all.equal(coef(b), coef(b.db)) 352s [1] TRUE 352s > all.equal(SE(b), SE(b.db)) 352s [1] TRUE 352s > all.equal(deff(b), deff(b.db)) 352s [1] TRUE 352s > 352s > l<-svyglm(api00~api99+mobility, design=dclus1) 352s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 352s > all.equal(coef(l),coef(l.db)) 352s [1] TRUE 352s > all.equal(vcov(l), vcov(l.db)) 352s [1] TRUE 352s > 352s > dclus1<-update(dclus1, apidiff=api00-api99) 352s > dclus1<-update(dclus1, apipct= apidiff/api99) 352s > dbclus1<-update(dbclus1, apidiff=api00-api99) 352s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 352s > 352s > u<-svymean(~api00+apidiff+apipct, dclus1) 352s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 352s > all.equal(u, u.db) 352s [1] TRUE 352s > 352s > all.equal(nrow(dclus1),nrow(dbclus1)) 352s [1] TRUE 352s > all.equal(nrow(subset(dclus1,stype=="E")), 352s + nrow(subset(dbclus1,stype=="E"))) 352s [1] "Mean relative difference: 0.2708333" 352s > 352s > ## replicate weights 352s > rclus1<-as.svrepdesign(dclus1) 352s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 352s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 352s > m<-svymean(~api00+api99,rclus1) 352s > m.db<-svymean(~api00+api99,db_rclus1) 352s > all.equal(m,m.db) 352s [1] TRUE 352s > 352s > summary(db_rclus1) 352s DB-backed replicate weight design 352s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 352s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 352s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 352s Unstratified cluster jacknife (JK1) with 15 replicates. 352s Variables: 352s [1] "row_names" "cds" "stype" "name" "sname" 352s [6] "snum" "dname" "dnum" "cname" "cnum" 352s [11] "flag" "pcttest" "api00" "api99" "target" 352s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 352s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 352s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 352s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 352s [36] "emer" "enroll" "api_stu" "fpc" "pw" 352s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 352s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 352s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 352s [56] "wt15" 352s > 352s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 352s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 352s > all.equal(s,s.db) 352s [1] TRUE 352s > 352s BEGIN TEST anova-svycoxph.R 352s 352s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 352s Copyright (C) 2025 The R Foundation for Statistical Computing 352s Platform: aarch64-unknown-linux-gnu 352s 352s R is free software and comes with ABSOLUTELY NO WARRANTY. 352s You are welcome to redistribute it under certain conditions. 352s Type 'license()' or 'licence()' for distribution details. 352s 352s R is a collaborative project with many contributors. 352s Type 'contributors()' for more information and 352s 'citation()' on how to cite R or R packages in publications. 352s 352s Type 'demo()' for some demos, 'help()' for on-line help, or 352s 'help.start()' for an HTML browser interface to help. 352s Type 'q()' to quit R. 352s 352s > 352s > library(survey) 352s Loading required package: grid 352s Loading required package: Matrix 353s Loading required package: survival 353s 353s Attaching package: 'survey' 353s 353s The following object is masked from 'package:graphics': 353s 353s dotchart 353s 353s > example(svycoxph, ask=FALSE) 353s 353s svycxp> ## Somewhat unrealistic example of nonresponse bias. 353s svycxp> data(pbc, package="survival") 353s 353s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 353s 353s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 353s 353s svycxp> pbc$randprob<-fitted(biasmodel) 353s 353s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 353s 353s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 353s 353s svycxp> rpbc<-as.svrepdesign(dpbc) 353s 353s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 353s Call: 353s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 353s albumin, design = dpbc) 353s 353s coef exp(coef) se(coef) robust se z p 353s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 353s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 353s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 353s 353s Likelihood ratio test= on 3 df, p= 353s n= 312, number of events= 144 353s 353s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 353s Call: 353s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 353s protime + albumin, design = rpbc) 353s 353s coef exp(coef) se(coef) z p 353s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 353s protime 0.24487 1.27745 0.09373 2.612 0.00899 353s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 353s 353s Likelihood ratio test=NA on 3 df, p=NA 353s n= 312, number of events= 144 353s 353s svycxp> s<-predict(model,se=TRUE, type="curve", 353s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 354s 354s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 354s 354s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 354s 354s svycxp> quantile(s[[1]], ci=TRUE) 354s 0.75 0.5 0.25 354s 1435 2503 3574 354s attr(,"ci") 354s 0.025 0.975 354s 0.75 1217 1786 354s 0.5 2256 3170 354s 0.25 3222 Inf 354s 354s svycxp> confint(s[[2]], parm=365*(1:5)) 354s 0.025 0.975 354s 365 0.8375139 0.9453781 354s 730 0.7382750 0.8999016 354s 1095 0.4784105 0.7478460 354s 1460 0.3192009 0.6206764 354s 1825 0.2149475 0.5292978 354s > m<-update(model, .~.+I(protime^2)) 354s > a<-anova(m,model) 354s > b<-anova(m, model,force=TRUE) 354s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 354s > 354s BEGIN TEST api.R 354s 354s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 354s Copyright (C) 2025 The R Foundation for Statistical Computing 354s Platform: aarch64-unknown-linux-gnu 354s 354s R is free software and comes with ABSOLUTELY NO WARRANTY. 354s You are welcome to redistribute it under certain conditions. 354s Type 'license()' or 'licence()' for distribution details. 354s 354s R is a collaborative project with many contributors. 354s Type 'contributors()' for more information and 354s 'citation()' on how to cite R or R packages in publications. 354s 354s Type 'demo()' for some demos, 'help()' for on-line help, or 354s 'help.start()' for an HTML browser interface to help. 354s Type 'q()' to quit R. 354s 354s > library(survey) 354s Loading required package: grid 354s Loading required package: Matrix 355s Loading required package: survival 355s 355s Attaching package: 'survey' 355s 355s The following object is masked from 'package:graphics': 355s 355s dotchart 355s 355s > options(survey.replicates.mse=TRUE) 355s > example(api) 355s 355s api> library(survey) 355s 355s api> data(api) 355s 355s api> mean(apipop$api00) 355s [1] 664.7126 355s 355s api> sum(apipop$enroll, na.rm=TRUE) 355s [1] 3811472 355s 355s api> #stratified sample 355s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 355s 355s api> summary(dstrat) 355s Stratified Independent Sampling design 355s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 355s Stratum Sizes: 355s E H M 355s obs 100 50 50 355s design.PSU 100 50 50 355s actual.PSU 100 50 50 355s Population stratum sizes (PSUs): 355s E H M 355s 4421 755 1018 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "pw" "fpc" 355s 355s api> svymean(~api00, dstrat) 355s mean SE 355s api00 662.29 9.4089 355s 355s api> svytotal(~enroll, dstrat, na.rm=TRUE) 355s total SE 355s enroll 3687178 114642 355s 355s api> # one-stage cluster sample 355s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 355s 355s api> summary(dclus1) 355s 1 - level Cluster Sampling design 355s With (15) clusters. 355s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 355s Population size (PSUs): 757 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> svymean(~api00, dclus1) 355s mean SE 355s api00 644.17 23.542 355s 355s api> svytotal(~enroll, dclus1, na.rm=TRUE) 355s total SE 355s enroll 3404940 932235 355s 355s api> # two-stage cluster sample 355s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 355s 355s api> summary(dclus2) 355s 2 - level Cluster Sampling design 355s With (40, 126) clusters. 355s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 355s Population size (PSUs): 757 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "pw" "fpc1" "fpc2" 355s 355s api> svymean(~api00, dclus2) 355s mean SE 355s api00 670.81 30.099 355s 355s api> svytotal(~enroll, dclus2, na.rm=TRUE) 355s total SE 355s enroll 2639273 799638 355s 355s api> # two-stage `with replacement' 355s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 355s 355s api> summary(dclus2wr) 355s 2 - level Cluster Sampling design (with replacement) 355s With (40, 126) clusters. 355s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "pw" "fpc1" "fpc2" 355s 355s api> svymean(~api00, dclus2wr) 355s mean SE 355s api00 670.81 30.712 355s 355s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 355s total SE 355s enroll 2639273 820261 355s 355s api> # convert to replicate weights 355s api> rclus1<-as.svrepdesign(dclus1) 355s 355s api> summary(rclus1) 355s Call: as.svrepdesign.default(dclus1) 355s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 355s Variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> svymean(~api00, rclus1) 355s mean SE 355s api00 644.17 26.335 355s 355s api> svytotal(~enroll, rclus1, na.rm=TRUE) 355s total SE 355s enroll 3404940 932235 355s 355s api> # post-stratify on school type 355s api> pop.types<-xtabs(~stype, data=apipop) 355s 355s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 355s 355s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 355s 355s api> summary(dclus1p) 355s 1 - level Cluster Sampling design 355s With (15) clusters. 355s dclus1p<-postStratify(dclus1, ~stype, pop.types) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 355s Population size (PSUs): 757 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> summary(rclus1p) 355s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 355s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 355s Variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> svymean(~api00, dclus1p) 355s mean SE 355s api00 642.31 23.921 355s 355s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 355s total SE 355s enroll 3680893 406293 355s 355s api> svymean(~api00, rclus1p) 355s mean SE 355s api00 642.31 26.936 355s 355s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 355s total SE 355s enroll 3680893 473434 355s > 355s > options(survey.replicates.mse=FALSE) 355s > example(api) 355s 355s api> library(survey) 355s 355s api> data(api) 355s 355s api> mean(apipop$api00) 355s [1] 664.7126 355s 355s api> sum(apipop$enroll, na.rm=TRUE) 355s [1] 3811472 355s 355s api> #stratified sample 355s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 355s 355s api> summary(dstrat) 355s Stratified Independent Sampling design 355s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 355s Stratum Sizes: 355s E H M 355s obs 100 50 50 355s design.PSU 100 50 50 355s actual.PSU 100 50 50 355s Population stratum sizes (PSUs): 355s E H M 355s 4421 755 1018 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "pw" "fpc" 355s 355s api> svymean(~api00, dstrat) 355s mean SE 355s api00 662.29 9.4089 355s 355s api> svytotal(~enroll, dstrat, na.rm=TRUE) 355s total SE 355s enroll 3687178 114642 355s 355s api> # one-stage cluster sample 355s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 355s 355s api> summary(dclus1) 355s 1 - level Cluster Sampling design 355s With (15) clusters. 355s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 355s Population size (PSUs): 757 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> svymean(~api00, dclus1) 355s mean SE 355s api00 644.17 23.542 355s 355s api> svytotal(~enroll, dclus1, na.rm=TRUE) 355s total SE 355s enroll 3404940 932235 355s 355s api> # two-stage cluster sample 355s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 355s 355s api> summary(dclus2) 355s 2 - level Cluster Sampling design 355s With (40, 126) clusters. 355s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 355s Population size (PSUs): 757 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "pw" "fpc1" "fpc2" 355s 355s api> svymean(~api00, dclus2) 355s mean SE 355s api00 670.81 30.099 355s 355s api> svytotal(~enroll, dclus2, na.rm=TRUE) 355s total SE 355s enroll 2639273 799638 355s 355s api> # two-stage `with replacement' 355s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 355s 355s api> summary(dclus2wr) 355s 2 - level Cluster Sampling design (with replacement) 355s With (40, 126) clusters. 355s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "pw" "fpc1" "fpc2" 355s 355s api> svymean(~api00, dclus2wr) 355s mean SE 355s api00 670.81 30.712 355s 355s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 355s total SE 355s enroll 2639273 820261 355s 355s api> # convert to replicate weights 355s api> rclus1<-as.svrepdesign(dclus1) 355s 355s api> summary(rclus1) 355s Call: as.svrepdesign.default(dclus1) 355s Unstratified cluster jacknife (JK1) with 15 replicates. 355s Variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> svymean(~api00, rclus1) 355s mean SE 355s api00 644.17 26.329 355s 355s api> svytotal(~enroll, rclus1, na.rm=TRUE) 355s total SE 355s enroll 3404940 932235 355s 355s api> # post-stratify on school type 355s api> pop.types<-xtabs(~stype, data=apipop) 355s 355s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 355s 355s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 355s 355s api> summary(dclus1p) 355s 1 - level Cluster Sampling design 355s With (15) clusters. 355s dclus1p<-postStratify(dclus1, ~stype, pop.types) 355s Probabilities: 355s Min. 1st Qu. Median Mean 3rd Qu. Max. 355s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 355s Population size (PSUs): 757 355s Data variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> summary(rclus1p) 355s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 355s Unstratified cluster jacknife (JK1) with 15 replicates. 355s Variables: 355s [1] "cds" "stype" "name" "sname" "snum" "dname" 355s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 355s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 355s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 355s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 355s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 355s [37] "api.stu" "fpc" "pw" 355s 355s api> svymean(~api00, dclus1p) 355s mean SE 355s api00 642.31 23.921 355s 355s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 355s total SE 355s enroll 3680893 406293 355s 355s api> svymean(~api00, rclus1p) 355s mean SE 355s api00 642.31 26.934 355s 355s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 355s total SE 355s enroll 3680893 473431 355s > 355s BEGIN TEST badcal.R 355s 355s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 355s Copyright (C) 2025 The R Foundation for Statistical Computing 355s Platform: aarch64-unknown-linux-gnu 355s 355s R is free software and comes with ABSOLUTELY NO WARRANTY. 355s You are welcome to redistribute it under certain conditions. 355s Type 'license()' or 'licence()' for distribution details. 355s 355s R is a collaborative project with many contributors. 355s Type 'contributors()' for more information and 355s 'citation()' on how to cite R or R packages in publications. 355s 355s Type 'demo()' for some demos, 'help()' for on-line help, or 355s 'help.start()' for an HTML browser interface to help. 355s Type 'q()' to quit R. 355s 355s > ## 355s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 355s > ## 355s > library(survey) 355s Loading required package: grid 356s Loading required package: Matrix 356s Loading required package: survival 356s 356s Attaching package: 'survey' 356s 356s The following object is masked from 'package:graphics': 356s 356s dotchart 356s 356s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 356s > des <- svydesign(ids=~1, weights=~w, data=data) 356s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 356s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 356s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 356s > 357s BEGIN TEST brewer_cpp.R 357s 357s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 357s Copyright (C) 2025 The R Foundation for Statistical Computing 357s Platform: aarch64-unknown-linux-gnu 357s 357s R is free software and comes with ABSOLUTELY NO WARRANTY. 357s You are welcome to redistribute it under certain conditions. 357s Type 'license()' or 'licence()' for distribution details. 357s 357s R is a collaborative project with many contributors. 357s Type 'contributors()' for more information and 357s 'citation()' on how to cite R or R packages in publications. 357s 357s Type 'demo()' for some demos, 'help()' for on-line help, or 357s 'help.start()' for an HTML browser interface to help. 357s Type 'q()' to quit R. 357s 357s > ## pps="brewer" can't use rcpp 357s > ## this checks that it doesn't 357s > library(survey) 357s Loading required package: grid 357s Loading required package: Matrix 357s Loading required package: survival 358s 358s Attaching package: 'survey' 358s 358s The following object is masked from 'package:graphics': 358s 358s dotchart 358s 358s > data(election) 358s > 358s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 358s > options(survey.use_rcpp=TRUE) 358s > a<-svytotal(~Bush+Kerry+Nader, dpps_br) 358s > options(survey.use_rcpp=FALSE) 358s > b<-svytotal(~Bush+Kerry+Nader, dpps_br) 358s > 358s > stopifnot(identical(a,b)) 358s > 358s BEGIN TEST bycovmat.R 358s 358s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 358s Copyright (C) 2025 The R Foundation for Statistical Computing 358s Platform: aarch64-unknown-linux-gnu 358s 358s R is free software and comes with ABSOLUTELY NO WARRANTY. 358s You are welcome to redistribute it under certain conditions. 358s Type 'license()' or 'licence()' for distribution details. 358s 358s R is a collaborative project with many contributors. 358s Type 'contributors()' for more information and 358s 'citation()' on how to cite R or R packages in publications. 358s 358s Type 'demo()' for some demos, 'help()' for on-line help, or 358s 'help.start()' for an HTML browser interface to help. 358s Type 'q()' to quit R. 358s 358s > 358s > library(survey) 358s Loading required package: grid 358s Loading required package: Matrix 359s Loading required package: survival 359s 359s Attaching package: 'survey' 359s 359s > data(api) 359s The following object is masked from 'package:graphics': 359s 359s dotchart 359s 359s > options(survey.replicates.mse=TRUE) 359s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 359s > rclus1<-as.svrepdesign(dclus1) 359s > 359s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 359s + covmat=TRUE,drop.empty.groups=FALSE) 359s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 359s + covmat=TRUE,drop.empty.groups=TRUE) 359s > 359s > stopifnot(all.equal( 359s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 359s + )) 359s > stopifnot(all.equal( 359s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 359s + )) 359s > 359s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 359s > all <- svytotal(~ell+mobility+meals, dclus1) 359s > 359s > stopifnot(all(abs(vcov(svycontrast(all, 359s + list(quote(ell/mobility), 359s + quote(mobility/mobility), 359s + quote(ell/meals),quote(mobility/meals)))) 359s + -vcov(rat))<1e-10)) 359s > 359s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 359s > 359s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 359s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 359s > 359s > con<-svycontrast(all, 359s + list(quote(ell/mobility), 359s + quote(mobility/mobility), 359s + quote(ell/meals),quote(mobility/meals))) 359s > 359s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 359s > 359s > options(survey.replicates.mse=FALSE) 359s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 359s > rclus1<-as.svrepdesign(dclus1) 359s > 359s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 359s + covmat=TRUE,drop.empty.groups=FALSE) 359s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 359s + covmat=TRUE,drop.empty.groups=TRUE) 359s > 359s > stopifnot(all.equal( 359s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 359s + )) 359s > stopifnot(all.equal( 359s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 359s + )) 359s > 359s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 359s > all <- svytotal(~ell+mobility+meals, dclus1) 359s > 359s > stopifnot(all(abs(vcov(svycontrast(all, 359s + list(quote(ell/mobility), 359s + quote(mobility/mobility), 359s + quote(ell/meals),quote(mobility/meals)))) 359s + -vcov(rat))<1e-10)) 359s > 359s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 359s > 359s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 359s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 359s > 359s > con<-svycontrast(all, 359s + list(quote(ell/mobility), 359s + quote(mobility/mobility), 359s + quote(ell/meals),quote(mobility/meals))) 359s > 359s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 359s > 359s > 359s > 359s BEGIN TEST caleg.R 359s 359s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 359s Copyright (C) 2025 The R Foundation for Statistical Computing 359s Platform: aarch64-unknown-linux-gnu 359s 359s R is free software and comes with ABSOLUTELY NO WARRANTY. 359s You are welcome to redistribute it under certain conditions. 359s Type 'license()' or 'licence()' for distribution details. 359s 359s R is a collaborative project with many contributors. 359s Type 'contributors()' for more information and 359s 'citation()' on how to cite R or R packages in publications. 359s 359s Type 'demo()' for some demos, 'help()' for on-line help, or 359s 'help.start()' for an HTML browser interface to help. 359s Type 'q()' to quit R. 359s 359s > ## 359s > ## Calibration examples 359s > ## 359s > 359s > 359s > ## Example of calibration to first-stage clusters 359s > library(survey) 359s Loading required package: grid 359s Loading required package: Matrix 360s Loading required package: survival 360s 360s Attaching package: 'survey' 360s 360s The following object is masked from 'package:graphics': 360s 360s dotchart 360s 360s > data(api) 360s > 360s > clusters<-table(apiclus2$dnum) 360s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 360s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 360s > 360s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 361s > 361s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 361s > 361s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 361s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 361s > 361s > names(pop)<-names(clusters) 361s > 361s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 361s > 361s > svymean(~api99, dclus2) 361s mean SE 361s api99 642.14 31.434 361s > svymean(~api99, dclus2g) 361s mean SE 361s api99 654.49 29.82 361s > 361s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 361s dnum api99 se 361s 83 83 694.3333 0.0000 361s 132 132 505.0000 0.0000 361s 152 152 574.0000 0.0000 361s 173 173 894.7500 0.0000 361s 198 198 533.7500 0.0000 361s 200 200 589.8000 6.8335 361s 228 228 477.0000 0.0000 361s 295 295 646.4000 0.0000 361s 302 302 903.5000 0.0000 361s 403 403 852.4000 0.0000 361s 452 452 533.0000 0.0000 361s 480 480 614.2000 0.0000 361s 523 523 580.5000 0.0000 361s 534 534 564.6000 0.0000 361s 549 549 896.2000 0.0000 361s 552 552 730.0000 0.0000 361s 570 570 518.4000 7.5478 361s 575 575 800.8000 4.2513 361s 596 596 785.6000 2.4155 361s 620 620 591.6000 10.5869 361s 638 638 560.2000 4.0954 361s 674 674 760.0000 0.0000 361s 679 679 610.2500 0.0000 361s 687 687 718.6667 0.0000 361s 701 701 651.5000 0.0000 361s 711 711 690.5000 0.0000 361s 731 731 702.0000 2.1744 361s 768 768 562.5000 0.0000 361s 781 781 854.4000 0.7456 361s > 361s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 361s dnum api99 se 361s 83 83 694.3333 0 361s 132 132 505.0000 0 361s 152 152 574.0000 0 361s 173 173 894.7500 0 361s 198 198 533.7500 0 361s 200 200 567.5455 0 361s 228 228 477.0000 0 361s 295 295 646.4000 0 361s 302 302 903.5000 0 361s 403 403 852.4000 0 361s 452 452 533.0000 0 361s 480 480 614.2000 0 361s 523 523 580.5000 0 361s 534 534 564.6000 0 361s 549 549 896.2000 0 361s 552 552 730.0000 0 361s 570 570 548.9444 0 361s 575 575 824.5357 0 361s 596 596 787.5714 0 361s 620 620 609.3750 0 361s 638 638 585.6429 0 361s 674 674 760.0000 0 361s 679 679 610.2500 0 361s 687 687 718.6667 0 361s 701 701 651.5000 0 361s 711 711 690.5000 0 361s 731 731 700.6667 0 361s 768 768 562.5000 0 361s 781 781 851.0000 0 361s > 361s > ## Averaging to first stage 361s > 361s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 361s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 361s > 361s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 361s > 361s > svytotal(~enroll,dclus1g) 361s total SE 361s enroll 3811472 0 361s > svytotal(~api.stu,dclus1g) 361s total SE 361s api.stu 3242857 38967 361s > 361s > #variation within clusters should be zero 361s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 361s [1] TRUE 361s > 361s > ##bounded weights 361s > dclus1g<-calibrate(dclus1, ~enroll, pop) 361s > range(weights(dclus1g)/weights(dclus1)) 361s [1] 0.7906782 1.7891164 361s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 361s > range(weights(dclus1gb)/weights(dclus1)) 361s [1] 0.7198751 1.5000000 361s > 361s > ## Ratio estimators 361s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 361s > svytotal(~api.stu,dstrat) 361s total SE 361s api.stu 3086009 99477 361s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 361s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 361s > predict(common, total=total.enroll) 361s $total 361s enroll 361s api.stu 3190038 361s 361s $se 361s enroll 361s api.stu 29565.98 361s 361s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 361s > svytotal(~api.stu, dstratg) 361s total SE 361s api.stu 3190038 29566 361s > 361s > ## postStratify vs calibrate in stratified sample (Ben French) 361s > set.seed(17) 361s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 361s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 361s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 361s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 361s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 361s > postStratify(des,~w,popw)->dps 361s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 361s > 361s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 361s [1] TRUE 361s > 361s > ## missing data in calibrated design 361s > dps$variables$z[1]<-NA 361s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 361s 361s Call: 361s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 361s 361s Survey design: 361s postStratify(des, ~w, popw) 361s 361s Coefficients: 361s Estimate Std. Error t value Pr(>|t|) 361s (Intercept) -0.1203 0.3380 -0.356 0.722 361s z 6.2118 0.6451 9.630 <2e-16 *** 361s x 2.2602 0.2514 8.992 <2e-16 *** 361s --- 361s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 361s 361s (Dispersion parameter for quasibinomial family taken to be 1.919987) 361s 361s Number of Fisher Scoring iterations: 9 361s 361s > 361s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 361s > # should match the ratio estmate above 361s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 361s > svytotal(~api.stu, dstratgh) 361s total SE 361s api.stu 3190038 29566 361s > 361s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 361s > bnds <- list( 361s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 361s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 361s > lapply(bnds, head) 361s $lower 361s [1] 1 1 -Inf -Inf -Inf -Inf 361s 361s $upper 361s [1] 1 1 Inf Inf Inf Inf 361s 361s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 361s > svytotal(~api.stu, dstratg1) 361s total SE 361s api.stu 3190133 29561 361s > head(weights(dstrat)) 361s 1 2 3 4 5 6 361s 44.21 44.21 44.21 44.21 44.21 44.21 361s > head(weights(dstratg1)) 361s 1 2 3 4 5 6 361s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 361s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 361s [1] TRUE 361s > 361s > ## individual boundary constraints as constant values (Daniel Oehm) 361s > bnds <- list( 361s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 361s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 361s > lapply(bnds, head) 361s $lower 361s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 361s 361s $upper 361s [1] 44.21 44.21 Inf Inf Inf Inf 361s 361s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 361s > svytotal(~api.stu, dstratg2) 361s total SE 361s api.stu 3190133 29561 361s > head(weights(dstrat)) 361s 1 2 3 4 5 6 361s 44.21 44.21 44.21 44.21 44.21 44.21 361s > head(weights(dstratg2)) 361s 1 2 3 4 5 6 361s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 361s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 361s [1] TRUE 361s > 361s > # sparse matrix support (Daniel Oehm) 361s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 361s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 361s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 361s > svymean(~api00, dclus1g) 361s mean SE 361s api00 642.31 23.921 361s > svytotal(~enroll, dclus1g) 361s total SE 361s enroll 3680893 406293 361s > 361s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 361s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 361s > svymean(~api00, dclus1g) 361s mean SE 361s api00 642.31 23.921 361s > svytotal(~enroll, dclus1g) 361s total SE 361s enroll 3680893 406293 361s > 361s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 361s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 361s > svymean(~api00, dclus1g) 361s mean SE 361s api00 642.31 23.921 361s > svytotal(~enroll, dclus1g) 361s total SE 361s enroll 3680893 406293 361s > 361s BEGIN TEST check.R 362s 362s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 362s Copyright (C) 2025 The R Foundation for Statistical Computing 362s Platform: aarch64-unknown-linux-gnu 362s 362s R is free software and comes with ABSOLUTELY NO WARRANTY. 362s You are welcome to redistribute it under certain conditions. 362s Type 'license()' or 'licence()' for distribution details. 362s 362s R is a collaborative project with many contributors. 362s Type 'contributors()' for more information and 362s 'citation()' on how to cite R or R packages in publications. 362s 362s Type 'demo()' for some demos, 'help()' for on-line help, or 362s 'help.start()' for an HTML browser interface to help. 362s Type 'q()' to quit R. 362s 362s > library(survey) 362s Loading required package: grid 362s Loading required package: Matrix 362s Loading required package: survival 363s 363s Attaching package: 'survey' 363s 363s The following object is masked from 'package:graphics': 363s 363s dotchart 363s 363s > data(fpc) 363s > ## test various possibilities for svydesign 363s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 363s variables = ~x, data = fpc, nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7413 363s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 363s data = fpc, nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7413 363s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 363s data = fpc, nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 44.2 6.237 363s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 363s Warning message: 363s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 363s No weights or probabilities supplied, assuming equal probability 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 363s nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.525 0.7796 363s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 363s data = fpc, nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7413 363s > Warning message: 363s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 363s No weights or probabilities supplied, assuming equal probability 363s Warning message: 363s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 363s No weights or probabilities supplied, assuming equal probability 363s a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 363s nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.525 0.7796 363s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 363s > a 363s 1 - level Cluster Sampling design (with replacement) 363s With (5) clusters. 363s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.525 0.838Warning message: 363s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 363s No weights or probabilities supplied, assuming equal probability 363s 363s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 363s > a 363s 1 - level Cluster Sampling design (with replacement) 363s With (5) clusters. 363s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 363s nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7938 363s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 363s > a 363s 2 - level Cluster Sampling design (with replacement) 363s With (2, 8) clusters. 363s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 363s data = fpc) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.5465 363s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 363s > a 363s 2 - level Cluster Sampling design (with replacement) 363s With (2, 8) clusters. 363s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 363s > svymean(~x,a) 363s mean SE 363s x 5.525 0.5188 363s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 363s variables = fpc[, "x", drop = FALSE], nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7413 363s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 363s > a 363s Stratified Independent Sampling design (with replacement) 363s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 363s variables = fpc[, 4:6], nest = TRUE) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7413 363s > 363s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 363s > a 363s 1 - level Cluster Sampling design 363s With (5) clusters. 363s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 363s 4:6], fpc = rep(27, 8)) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.7165 363s > 363s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 363s > a 363s Stratified Independent Sampling design 363s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 363s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 363s > svymean(~x,a) 363s mean SE 363s x 5.4481 0.616 363s > 363s BEGIN TEST confintrep.R 363s 363s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 363s Copyright (C) 2025 The R Foundation for Statistical Computing 363s Platform: aarch64-unknown-linux-gnu 363s 363s R is free software and comes with ABSOLUTELY NO WARRANTY. 363s You are welcome to redistribute it under certain conditions. 363s Type 'license()' or 'licence()' for distribution details. 363s 363s R is a collaborative project with many contributors. 363s Type 'contributors()' for more information and 363s 'citation()' on how to cite R or R packages in publications. 363s 363s Type 'demo()' for some demos, 'help()' for on-line help, or 363s 'help.start()' for an HTML browser interface to help. 363s Type 'q()' to quit R. 363s 363s > library(survey) 363s Loading required package: grid 363s Loading required package: Matrix 364s Loading required package: survival 364s 364s Attaching package: 'survey' 364s 364s The following object is masked from 'package:graphics': 364s 364s dotchart 364s 364s > data(api) 364s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 364s > rclus2<-as.svrepdesign(dclus2) 364s > 364s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial) 364s Warning message: 364s In as.svrepdesign.default(dclus2) : 364s Finite population corrections after first stage have been dropped 364s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint") 364s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial) 364s > if(anyNA(confint(mrep))) stop("NA in confint") 364s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint") 364s > 364s BEGIN TEST contrast-replicates.R 364s 364s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 364s Copyright (C) 2025 The R Foundation for Statistical Computing 364s Platform: aarch64-unknown-linux-gnu 364s 364s R is free software and comes with ABSOLUTELY NO WARRANTY. 364s You are welcome to redistribute it under certain conditions. 364s Type 'license()' or 'licence()' for distribution details. 364s 364s R is a collaborative project with many contributors. 364s Type 'contributors()' for more information and 364s 'citation()' on how to cite R or R packages in publications. 364s 364s Type 'demo()' for some demos, 'help()' for on-line help, or 364s 'help.start()' for an HTML browser interface to help. 364s Type 'q()' to quit R. 364s 364s > ## test use of replicates in svyby, svycontrast 364s > library(survey) 364s Loading required package: grid 364s Loading required package: Matrix 365s Loading required package: survival 365s 365s Attaching package: 'survey' 365s 365s > 365s > data(api) 365s The following object is masked from 'package:graphics': 365s 365s dotchart 365s 365s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 365s > rclus1<-as.svrepdesign(dclus1) 365s > 365s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 365s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 365s > vcov(c_without) 365s contrast 365s contrast 0.06862947 365s > 365s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 365s > 365s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 365s > 365s > v_with<- vcov(rclus1, c_with$replicates) 365s > 365s > r<- attr(meanlogs_with, "replicates") 365s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 365s > 365s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 365s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 365s > 365s BEGIN TEST coxph-termtest.R 366s 366s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 366s Copyright (C) 2025 The R Foundation for Statistical Computing 366s Platform: aarch64-unknown-linux-gnu 366s 366s R is free software and comes with ABSOLUTELY NO WARRANTY. 366s You are welcome to redistribute it under certain conditions. 366s Type 'license()' or 'licence()' for distribution details. 366s 366s R is a collaborative project with many contributors. 366s Type 'contributors()' for more information and 366s 'citation()' on how to cite R or R packages in publications. 366s 366s Type 'demo()' for some demos, 'help()' for on-line help, or 366s 'help.start()' for an HTML browser interface to help. 366s Type 'q()' to quit R. 366s 366s > library(survey) 366s Loading required package: grid 366s Loading required package: Matrix 366s Loading required package: survival 367s 367s Attaching package: 'survey' 367s 367s > library(survival) 367s > set.seed(2021-6-25) 367s > test1 <- list(time=c(4,3,1,1,2,2,3), 367s The following object is masked from 'package:graphics': 367s 367s dotchart 367s 367s + status=c(1,1,1,0,1,1,0), 367s + x1=as.factor(rbinom(7, 2, 0.5)), 367s + x=c(0,2,1,1,1,0,0)) 367s > # Fit a stratified model 367s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 367s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 367s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 367s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 367s > 367s > data(pbc, package="survival") 367s > 367s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 367s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 367s > pbc$randprob<-fitted(biasmodel) 367s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 367s > 367s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 367s > library(splines) 367s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 367s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 367s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 367s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 367s > 367s BEGIN TEST deff.R 367s 367s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 367s Copyright (C) 2025 The R Foundation for Statistical Computing 367s Platform: aarch64-unknown-linux-gnu 367s 367s R is free software and comes with ABSOLUTELY NO WARRANTY. 367s You are welcome to redistribute it under certain conditions. 367s Type 'license()' or 'licence()' for distribution details. 367s 367s R is a collaborative project with many contributors. 367s Type 'contributors()' for more information and 367s 'citation()' on how to cite R or R packages in publications. 367s 367s Type 'demo()' for some demos, 'help()' for on-line help, or 367s 'help.start()' for an HTML browser interface to help. 367s Type 'q()' to quit R. 367s 367s > ## from Takahiro Tsuchiya 367s > library(survey) 367s Loading required package: grid 367s Loading required package: Matrix 368s Loading required package: survival 368s 368s Attaching package: 'survey' 368s 368s The following object is masked from 'package:graphics': 368s 368s dotchart 368s 368s > kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 368s + 1 1 15 100 20 368s + 2 2 143 100 200 368s + 3 3 21 100 11 368s + 4 4 51 100 25 368s + 5 5 337 100 550 368s + 6 6 50 100 30 368s + 7 7 274 100 250 368s + 8 8 145 100 100 368s + 9 9 15 100 10 368s + 10 10 86 100 55 368s + ",open="r"),header=TRUE) 368s > close(tmp) 368s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 368s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 368s mean SE DEff 368s uriage 113.700 35.626 1.0101 368s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 368s uriage 368s uriage 1.010101 368s > 368s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 368s total SE DEff 368s uriage 113700 35626 1.0101 368s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 368s uriage 368s uriage 1.010101 368s > 368s > 368s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 368s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 368s mean SE DEff 368s uriage 243.914 48.752 1.9741 368s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 368s uriage 368s uriage 1.974067 368s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 368s total SE DEff 368s uriage 305136 184965 18.157 368s > (N.hat <- sum(weights(des.pps))) 368s [1] 1251 368s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 368s uriage 368s uriage 18.15669 368s > 368s BEGIN TEST defftest.R 368s 368s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 368s Copyright (C) 2025 The R Foundation for Statistical Computing 368s Platform: aarch64-unknown-linux-gnu 368s 368s R is free software and comes with ABSOLUTELY NO WARRANTY. 368s You are welcome to redistribute it under certain conditions. 368s Type 'license()' or 'licence()' for distribution details. 368s 368s R is a collaborative project with many contributors. 368s Type 'contributors()' for more information and 368s 'citation()' on how to cite R or R packages in publications. 368s 368s Type 'demo()' for some demos, 'help()' for on-line help, or 368s 'help.start()' for an HTML browser interface to help. 368s Type 'q()' to quit R. 368s 368s > library(survey) 368s Loading required package: grid 368s Loading required package: Matrix 369s Loading required package: survival 369s 369s Attaching package: 'survey' 369s 369s The following object is masked from 'package:graphics': 369s 369s dotchart 369s 369s > 369s > data(api) 369s > 369s > ## one-stage cluster sample 369s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 369s > 369s > # svyglm model 369s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 369s > 369s > #deffs returned from svyglm model - implausibly high 369s > deff(mod) 369s (Intercept) enroll api.stu 369s 1.919945 2.500983 2.686102 369s > #> (Intercept) enroll api.stu 369s > #> 351.3500 457.6799 491.5567 369s > 369s > # run mod with same data and glm() 369s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 369s > 369s > # manually calculate deffs 369s > 369s > clust_se <- summary(mod)$coefficients[,2] 369s > srs_se <- summary(srs_mod)$coefficients[,2] 369s > 369s > deffs <- clust_se^2 / srs_se^2 369s > stopifnot(all.equal(deffs, deff(mod))) 369s > 369s > 369s BEGIN TEST degf-svrepdesign.R 369s 369s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 369s Copyright (C) 2025 The R Foundation for Statistical Computing 369s Platform: aarch64-unknown-linux-gnu 369s 369s R is free software and comes with ABSOLUTELY NO WARRANTY. 369s You are welcome to redistribute it under certain conditions. 369s Type 'license()' or 'licence()' for distribution details. 369s 369s R is a collaborative project with many contributors. 369s Type 'contributors()' for more information and 369s 'citation()' on how to cite R or R packages in publications. 369s 369s Type 'demo()' for some demos, 'help()' for on-line help, or 369s 'help.start()' for an HTML browser interface to help. 369s Type 'q()' to quit R. 369s 370s > library(survey) 370s Loading required package: grid 370s Loading required package: Matrix 370s Loading required package: survival 371s 371s Attaching package: 'survey' 371s 371s > data(scd) 371s The following object is masked from 'package:graphics': 371s 371s dotchart 371s 371s > 371s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1), 371s + c(0,1,0,1,1,0)) 371s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights) 371s Warning message: 371s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) : 371s No sampling weights provided: equal probability assumed 371s > 371s > stopifnot(degf(scdrep)==3) 371s > 371s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4) 371s Warning message: 371s > stopifnot(degf(scdrep)==4) 371s > 371s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2) 371s > stopifnot(degf(scdrep)==2) 371s > 371s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 371s + warning=function(w) w) 371s > 371s > stopifnot(inherits(msg,"warning")) 371s > 371s > 371s > 371s > 371s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 371s No sampling weights provided: equal probability assumed 371s Warning message: 371s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 371s No sampling weights provided: equal probability assumed 371s BEGIN TEST domain.R 371s 371s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 371s Copyright (C) 2025 The R Foundation for Statistical Computing 371s Platform: aarch64-unknown-linux-gnu 371s 371s R is free software and comes with ABSOLUTELY NO WARRANTY. 371s You are welcome to redistribute it under certain conditions. 371s Type 'license()' or 'licence()' for distribution details. 371s 371s R is a collaborative project with many contributors. 371s Type 'contributors()' for more information and 371s 'citation()' on how to cite R or R packages in publications. 371s 371s Type 'demo()' for some demos, 'help()' for on-line help, or 371s 'help.start()' for an HTML browser interface to help. 371s Type 'q()' to quit R. 371s 371s > ## 371s > ## Domain means can be written as ratio estimators or as regression coefficients 371s > ## 371s > ## This code checks that subsetting the design object gives the same results as 371s > ## these approaches. 371s > ## 371s > 371s > 371s > library(survey) 371s Loading required package: grid 371s Loading required package: Matrix 372s Loading required package: survival 372s 372s Attaching package: 'survey' 372s 372s The following object is masked from 'package:graphics': 372s 372s dotchart 372s 372s > data(fpc) 372s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 372s > dsub<-subset(dfpc,x>4) 372s > (m1<-svymean(~x,design=dsub)) 372s mean SE 372s x 6.195 0.7555 372s > 372s > ## These should give the same domain estimates and standard errors 372s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 372s I(x > 4) x se 372s FALSE FALSE 3.314286 0.3117042 372s TRUE TRUE 6.195000 0.7555129 372s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 372s > summary(m3) 372s 372s Call: 372s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 372s 372s Survey design: 372s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 372s nest = TRUE) 372s 372s Coefficients: 372s Estimate Std. Error t value Pr(>|t|) 372s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 372s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 372s --- 372s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 372s 372s (Dispersion parameter for gaussian family taken to be 2.557379) 372s 372s Number of Fisher Scoring iterations: 2 372s 372s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 372s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 372s dfpc) 372s Ratios= 372s as.numeric(x > 4) 372s I(x * (x > 4)) 6.195 372s SEs= 372s as.numeric(x > 4) 372s I(x * (x > 4)) 0.7555129 372s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 372s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 372s > 372s > ## with strata 372s > data(api) 372s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 372s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 372s > m2<-svyglm(enroll~comp.imp-1, dstrat) 372s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 372s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 372s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 372s > 372s > ## with calibration 372s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 372s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 372s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 372s 1 - level Cluster Sampling design 372s With (15) clusters. 372s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 372s > 372s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 372s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 372s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 372s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 372s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 372s > 372s > ## with raking 372s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 372s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 372s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 372s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 372s > m2<-svyglm(api00~comp.imp-1, dclus1r) 372s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 372s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 372s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 372s > 372s > 372s > 372s > ## 372s > ## based on bug report from Takahiro Tsuchiya for version 3.4 372s > ## 372s > rei<-read.table(tmp<-textConnection( 372s + " id N n.a h n.ah n.h sub y 372s + 1 1 300 20 1 12 5 TRUE 1 372s + 2 2 300 20 1 12 5 TRUE 2 372s + 3 3 300 20 1 12 5 TRUE 3 372s + 4 4 300 20 1 12 5 TRUE 4 372s + 5 5 300 20 1 12 5 TRUE 5 372s + 6 6 300 20 1 12 5 FALSE NA 372s + 7 7 300 20 1 12 5 FALSE NA 372s + 8 8 300 20 1 12 5 FALSE NA 372s + 9 9 300 20 1 12 5 FALSE NA 372s + 10 10 300 20 1 12 5 FALSE NA 372s + 11 11 300 20 1 12 5 FALSE NA 372s + 12 12 300 20 1 12 5 FALSE NA 372s + 13 13 300 20 2 8 3 TRUE 6 372s + 14 14 300 20 2 8 3 TRUE 7 372s + 15 15 300 20 2 8 3 TRUE 8 372s + 16 16 300 20 2 8 3 FALSE NA 372s + 17 17 300 20 2 8 3 FALSE NA 372s + 18 18 300 20 2 8 3 FALSE NA 372s + 19 19 300 20 2 8 3 FALSE NA 372s + 20 20 300 20 2 8 3 FALSE NA 372s + "), header=TRUE) 372s > close(tmp) 372s > 372s > 372s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 372s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 372s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 372s > 372s > rei$y<-rei$y*(rei$y>3) 372s > ## based on Sarndal et al (9.4.14) 372s > rei$w.ah <- rei$n.ah / rei$n.a 372s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 372s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 372s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 372s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 372s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 372s > 372s > a.rei$f.h<-with(a.rei, n.h/n.ah) 372s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 372s > 372s > a.rei$f<-with(a.rei, n.a/N) 372s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 372s > 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))) 372s > 372s > V 372s [1] 70761.47 372s > Vphase1 372s [1] 44325.47 372s > Vphase2 372s [1] 26436 372s > vcov(tot2) 372s [,1] 372s [1,] 70761.47 372s attr(,"phases") 372s attr(,"phases")$phase1 372s [,1] 372s [1,] 44325.47 372s 372s attr(,"phases")$phase2 372s [,1] 372s [1,] 26436 372s 372s > 372s > ## comparing to regression 372s > reg<-svyglm(y~I(y<4), design=des.rei2) 372s > mn<-svymean(~y, subset(des.rei2,y>3)) 372s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 372s [1] TRUE 372s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 372s [1] TRUE 372s > vcov(mn) 372s [,1] 372s [1,] 0.3292258 372s attr(,"phases") 372s attr(,"phases")$phase1 372s [,1] 372s [1,] 0.1599264 372s 372s attr(,"phases")$phase2 372s [,1] 372s [1,] 0.1692994 372s 372s > vcov(reg) 372s (Intercept) I(y < 4)TRUE 372s (Intercept) 0.3292258 -0.3292258 372s I(y < 4)TRUE -0.3292258 0.5901907 372s attr(,"phases") 372s attr(,"phases")$phase1 372s (Intercept) I(y < 4)TRUE 372s (Intercept) 0.1599264 -0.1599264 372s I(y < 4)TRUE -0.1599264 0.2588542 372s 372s attr(,"phases")$phase2 372s (Intercept) I(y < 4)TRUE 372s (Intercept) 0.1692994 -0.1692994 372s I(y < 4)TRUE -0.1692994 0.3313365 372s 372s > 372s > 372s BEGIN TEST fpc.R 372s 372s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 372s Copyright (C) 2025 The R Foundation for Statistical Computing 372s Platform: aarch64-unknown-linux-gnu 372s 372s R is free software and comes with ABSOLUTELY NO WARRANTY. 372s You are welcome to redistribute it under certain conditions. 372s Type 'license()' or 'licence()' for distribution details. 372s 372s R is a collaborative project with many contributors. 372s Type 'contributors()' for more information and 372s 'citation()' on how to cite R or R packages in publications. 372s 372s Type 'demo()' for some demos, 'help()' for on-line help, or 372s 'help.start()' for an HTML browser interface to help. 372s Type 'q()' to quit R. 372s 372s > library(survey) 372s Loading required package: grid 372s Loading required package: Matrix 373s Loading required package: survival 373s 373s Attaching package: 'survey' 373s 373s > ## check many permutations of fpc specification 373s > example(fpc) 373s The following object is masked from 'package:graphics': 373s 373s dotchart 373s 373s 373s fpc> data(fpc) 373s 373s fpc> fpc 373s stratid psuid weight nh Nh x 373s 1 1 1 3 5 15 2.8 373s 2 1 2 3 5 15 4.1 373s 3 1 3 3 5 15 6.8 373s 4 1 4 3 5 15 6.8 373s 5 1 5 3 5 15 9.2 373s 6 2 1 4 3 12 3.7 373s 7 2 2 4 3 12 6.6 373s 8 2 3 4 3 12 4.2 373s 373s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 373s fpc+ data=fpc, nest=TRUE) 373s 373s fpc> withoutfpc 373s Stratified Independent Sampling design (with replacement) 373s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 373s data=fpc, nest=TRUE) 373s 373s fpc> svymean(~x, withoutfpc) 373s mean SE 373s x 5.4481 0.7413 373s 373s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 373s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 373s 373s fpc> withfpc 373s Stratified Independent Sampling design 373s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 373s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 373s 373s fpc> svymean(~x, withfpc) 373s mean SE 373s x 5.4481 0.616 373s 373s fpc> ## Other equivalent forms 373s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 373s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 373s 373s fpc> svymean(~x, withfpc) 373s mean SE 373s x 5.4481 0.616 373s 373s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 373s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 373s 373s fpc> svymean(~x, withfpc) 373s mean SE 373s x 5.4481 0.616 373s 373s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 373s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 373s 373s fpc> svymean(~x, withfpc) 373s mean SE 373s x 5.4481 0.616 373s 373s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 373s fpc+ variables=~x,data=fpc,nest=TRUE) 373s 373s fpc> svymean(~x, withfpc) 373s mean SE 373s x 5.4481 0.616 373s 373s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 373s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 373s 373s fpc> svymean(~x, withfpc) 373s mean SE 373s x 5.4481 0.616 373s > 373s > 373s BEGIN TEST glm-scoping.R 373s 373s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 373s Copyright (C) 2025 The R Foundation for Statistical Computing 373s Platform: aarch64-unknown-linux-gnu 373s 373s R is free software and comes with ABSOLUTELY NO WARRANTY. 373s You are welcome to redistribute it under certain conditions. 373s Type 'license()' or 'licence()' for distribution details. 373s 373s R is a collaborative project with many contributors. 373s Type 'contributors()' for more information and 373s 'citation()' on how to cite R or R packages in publications. 373s 373s Type 'demo()' for some demos, 'help()' for on-line help, or 373s 'help.start()' for an HTML browser interface to help. 373s Type 'q()' to quit R. 373s 374s > ## bug report from Thomas Leeper, fixed in version 3.32-3 374s > 374s > library("survey") 374s Loading required package: grid 374s Loading required package: Matrix 374s Loading required package: survival 375s 375s Attaching package: 'survey' 375s 375s > data(api) 375s The following object is masked from 'package:graphics': 375s 375s dotchart 375s 375s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 375s > 375s > # pass `family` directly (WORKS!) 375s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 375s Stratified Independent Sampling design 375s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 375s fpc = ~fpc) 375s 375s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 375s family = gaussian()) 375s 375s Coefficients: 375s (Intercept) ell meals mobility 375s 820.8873 -0.4806 -3.1415 0.2257 375s 375s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 375s Null Deviance: 3023000 375s Residual Deviance: 1029000 AIC: 2308 375s > 375s > # passing `family` via ... (WORKS!) 375s > myfun1 <- function(formula, design, ...) { 375s + svyglm(formula, design = design, ...) 375s + } 375s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 375s Stratified Independent Sampling design 375s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 375s fpc = ~fpc) 375s 375s Call: svyglm(formula = formula, design = design, family = ..1) 375s 375s Coefficients: 375s (Intercept) ell meals mobility 375s 820.8873 -0.4806 -3.1415 0.2257 375s 375s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 375s Null Deviance: 3023000 375s Residual Deviance: 1029000 AIC: 2308 375s > 375s > # passing `family` via default argument (DOES NOT WORK!) 375s > myfun2 <- function(formula, design, family = gaussian()) { 375s + svyglm(formula, design = design, family = family) 375s + } 375s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 375s Stratified Independent Sampling design 375s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 375s fpc = ~fpc) 375s 375s Call: svyglm(formula = formula, design = design, family = family) 375s 375s Coefficients: 375s (Intercept) ell meals mobility 375s 820.8873 -0.4806 -3.1415 0.2257 375s 375s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 375s Null Deviance: 3023000 375s Residual Deviance: 1029000 AIC: 2308 375s > 375s BEGIN TEST kalton.R 375s 375s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 375s Copyright (C) 2025 The R Foundation for Statistical Computing 375s Platform: aarch64-unknown-linux-gnu 375s 375s R is free software and comes with ABSOLUTELY NO WARRANTY. 375s You are welcome to redistribute it under certain conditions. 375s Type 'license()' or 'licence()' for distribution details. 375s 375s R is a collaborative project with many contributors. 375s Type 'contributors()' for more information and 375s 'citation()' on how to cite R or R packages in publications. 375s 375s Type 'demo()' for some demos, 'help()' for on-line help, or 375s 'help.start()' for an HTML browser interface to help. 375s Type 'q()' to quit R. 375s 375s > library(survey) 375s Loading required package: grid 375s Loading required package: Matrix 376s Loading required package: survival 376s > 376s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 376s 376s Attaching package: 'survey' 376s 376s The following object is masked from 'package:graphics': 376s 376s dotchart 376s 376s Warning message: 376s In svydesign.default(id = ~1, data = kaltonsample) : 376s No weights or probabilities supplied, assuming equal probability 376s > 376s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 376s > 376s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 376s > 376s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 376s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 376s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 376s > 376s > dkalton<-svydesign(id=~1,data=kaltonsample) 376s > 376s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 376s > 376s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 376s > 376s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 376s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 376s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 376s > 376s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 376s > 376s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 376s > 376s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 376s > 376s > 376s > #table A 376s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 4.00 1.00 1.38 376s 2 1.20 1.07 1.10 376s 3 1.70 1.20 4.00 376s 4 1.83 1.65 1.79 376s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 4.00 1.00 1.37 376s 2 1.20 1.07 1.10 376s 3 1.70 1.20 4.00 376s 4 1.83 1.65 1.79 376s > 376s > #table B 376s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 1.81 1.45 2.02 376s 2 1.08 0.87 1.21 376s 3 2.20 1.76 2.45 376s 4 1.83 1.47 2.04 376s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 1.81 1.45 2.02 376s 2 1.08 0.87 1.21 376s 3 2.20 1.76 2.45 376s 4 1.83 1.47 2.04 376s > 376s > #table C 376s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 1.82 1.50 1.97 376s 2 1.09 0.78 1.24 376s 3 2.19 1.88 2.34 376s 4 1.83 1.52 1.98 376s > 376s > #table D 376s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 1.21 1.17 1.14 376s 2 1.43 1.40 1.36 376s 3 1.66 1.62 1.59 376s 4 1.88 1.85 1.81 376s > 376s > #table G 376s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 1.87 1.46 1.98 376s 2 1.08 0.74 1.27 376s 3 2.17 2.09 2.18 376s 4 1.89 1.49 1.99 376s > 376s > #table G 376s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 376s b 376s a 1 2 3 376s 1 1.81 1.48 1.99 376s 2 1.08 0.75 1.26 376s 3 2.20 2.00 2.20 376s 4 1.83 1.50 2.00 376s > 376s BEGIN TEST logranktest.R 376s 376s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 376s Copyright (C) 2025 The R Foundation for Statistical Computing 376s Platform: aarch64-unknown-linux-gnu 376s 376s R is free software and comes with ABSOLUTELY NO WARRANTY. 376s You are welcome to redistribute it under certain conditions. 376s Type 'license()' or 'licence()' for distribution details. 376s 376s R is a collaborative project with many contributors. 376s Type 'contributors()' for more information and 376s 'citation()' on how to cite R or R packages in publications. 376s 376s Type 'demo()' for some demos, 'help()' for on-line help, or 376s 'help.start()' for an HTML browser interface to help. 376s Type 'q()' to quit R. 376s 376s > ## StackOverflow 63333282 376s > 376s > library(survey) 376s Loading required package: grid 376s Loading required package: Matrix 377s Loading required package: survival 377s 377s Attaching package: 'survey' 377s 377s The following object is masked from 'package:graphics': 377s 377s dotchart 377s 377s > D = data.frame(unique_id = 1:135, 377s + 377s + weights = rep(1,135), 377s + 377s + 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 , 377s + 377s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 377s + 377s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 377s + 377s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 377s + 377s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 377s + 377s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 377s + 377s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 377s + 377s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 377s + 377s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 377s + 377s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 377s + 377s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 377s + 377s + 2.35699896, 2.94956000, 8.85381736), 377s + 377s + 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, 377s + 377s + 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, 377s + 377s + 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), 377s + 377s + group = c(rep("group1", 40), rep("group2", 95))) 377s > 377s > 377s > 377s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 377s > 377s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 377s > 377s > a<-svylogrank(formula = svykm_formula, design = svy_design) 377s > 377s > ii<-with(D, order(event_time, event_flag)) 377s > 377s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 377s > 377s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 377s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 377s > 377s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 377s > 377s > 377s > stopifnot(all.equal(a[[2]],b[[2]])) 377s > 377s > stopifnot(all.equal(a[[2]],d[[2]])) 377s > 377s > stopifnot(all.equal(a[[2]],f[-1])) 377s > 377s > 377s BEGIN TEST lonely.psu.R 377s 377s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 377s Copyright (C) 2025 The R Foundation for Statistical Computing 377s Platform: aarch64-unknown-linux-gnu 377s 377s R is free software and comes with ABSOLUTELY NO WARRANTY. 377s You are welcome to redistribute it under certain conditions. 377s Type 'license()' or 'licence()' for distribution details. 377s 377s R is a collaborative project with many contributors. 377s Type 'contributors()' for more information and 377s 'citation()' on how to cite R or R packages in publications. 377s 377s Type 'demo()' for some demos, 'help()' for on-line help, or 377s 'help.start()' for an HTML browser interface to help. 377s Type 'q()' to quit R. 377s 377s > 377s > ## lonely PSUs by design 377s > library(survey) 377s Loading required package: grid 377s Loading required package: Matrix 378s Loading required package: survival 379s 379s Attaching package: 'survey' 379s 379s > data(api) 379s The following object is masked from 'package:graphics': 379s 379s dotchart 379s 379s > ## not certainty PSUs by fpc 379s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 379s > summary(ds) 379s Stratified Independent Sampling design (with replacement) 379s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 379s Probabilities: 379s Min. 1st Qu. Median Mean 3rd Qu. Max. 379s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 379s Stratum Sizes: 379s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 379s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 379s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 379s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 379s Data variables: 379s [1] "cds" "stype" "name" "sname" "snum" "dname" 379s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 379s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 379s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 379s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 379s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 379s [37] "api.stu" "fpc" "pw" 379s > 379s > options(survey.lonely.psu="fail") 379s > try(svymean(~api00,ds)) 379s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 379s Stratum (413) has only one PSU at stage 1 379s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 379s Stratum413has only one PSU 379s > try(svymean(~api00, as.svrepdesign(ds))) 379s > options(survey.lonely.psu="remove") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.8058 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.8058 379s > options(survey.lonely.psu="certainty") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.8058 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.8058 379s > options(survey.lonely.psu="adjust") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.8281 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.8267 379s > options(survey.lonely.psu="average") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 6.0096 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.8217 379s > 379s > ## fpc specified 379s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 379s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 379s > summary(ds) 379s Stratified Independent Sampling design 379s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 379s fpc = fpc) 379s Probabilities: 379s Min. 1st Qu. Median Mean 3rd Qu. Max. 379s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 379s Stratum Sizes: 379s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 379s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 379s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 379s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 379s Population stratum sizes (PSUs): 379s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 379s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 379s Data variables: 379s [1] "cds" "stype" "name" "sname" "snum" "dname" 379s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 379s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 379s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 379s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 379s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 379s [37] "api.stu" "fpc" "pw" 379s > 379s > options(survey.lonely.psu="fail") 379s > try(svymean(~api00,ds)) 379s mean SE 379s api00 644.17 5.7344 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.7344 379s > options(survey.lonely.psu="remove") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.7344 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.7344 379s > options(survey.lonely.psu="certainty") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.7344 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.7344 379s > options(survey.lonely.psu="adjust") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.7344 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.7344 379s > options(survey.lonely.psu="average") 379s > svymean(~api00,ds) 379s mean SE 379s api00 644.17 5.7344 379s > svymean(~api00, as.svrepdesign(ds)) 379s mean SE 379s api00 644.17 5.7501 379s > 379s > rs<-as.svrepdesign(ds) 379s > svytotal(~api00,rs) 379s total SE 379s api00 3989986 35616 379s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 379s [1] TRUE 379s > 379s > ## lonely PSUs after subsetting 379s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 379s > ds1<-ds[-31,] 379s > summary(ds1) 379s Stratified Independent Sampling design (with replacement) 379s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 379s dnum != 413)) 379s Probabilities: 379s Min. 1st Qu. Median Mean 3rd Qu. Max. 379s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 379s Stratum Sizes: 379s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 379s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 379s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 379s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 379s Data variables: 379s [1] "cds" "stype" "name" "sname" "snum" "dname" 379s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 379s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 379s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 379s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 379s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 379s [37] "api.stu" "fpc" "pw" 379s > 379s > options(survey.lonely.psu="fail") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="remove") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="certainty") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="adjust") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="average") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > 379s > ## with adjustment 379s > options(survey.adjust.domain.lonely=TRUE) 379s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 379s > ds1<-ds[-31,] 379s > summary(ds1) 379s Stratified Independent Sampling design (with replacement) 379s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 379s dnum != 413)) 379s Probabilities: 379s Min. 1st Qu. Median Mean 3rd Qu. Max. 379s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 379s Stratum Sizes: 379s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 379s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 379s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 379s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 379s Data variables: 379s [1] "cds" "stype" "name" "sname" "snum" "dname" 379s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 379s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 379s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 379s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 379s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 379s [37] "api.stu" "fpc" "pw" 379s > 379s > options(survey.lonely.psu="fail") 379s > try(svymean(~api00,ds1)) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="remove") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="certainty") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.8909 379s > options(survey.lonely.psu="adjust") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 5.9119 379s > options(survey.lonely.psu="average") 379s > svymean(~api00,ds1) 379s mean SE 379s api00 645.14 6.0914 379s > 379s > ## checks for `svytotal()` 379s > 379s > df_w_singleton <- data.frame( 379s + Stratum = c(1, 1, 2, 2, 3), 379s + PSU = c(1, 2, 3, 4, 5), 379s + Design_Weight = c(10.5, 10.5, 20, 20, 15), 379s + Sex = c("M", "F", "F", "M", "M"), 379s + Age = c(30.5, 40.5, 35, 52, 44), 379s + Height = c(6.2, 5.0, 5.3, 5.7, 5.5) 379s + ) 379s Warning message: 379s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 379s Stratum (406) has only one PSU at stage 1 379s Warning message: 379s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 379s Stratum (406) has only one PSU at stage 1 379s Warning message: 379s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 379s Stratum (406) has only one PSU at stage 1 379s Warning message: 379s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 379s Stratum (406) has only one PSU at stage 1 379s Warning message: 379s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 379s Stratum (406) has only one PSU at stage 1 379s > 379s > design_w_singleton <- survey::svydesign( 379s + data = df_w_singleton, 379s + ids = ~ PSU, strata = ~ Stratum, 379s + weights = ~ Design_Weight 379s + ) 379s > 379s > options("survey.lonely.psu" = "remove") 379s > 379s > stopifnot(all.equal( 379s + target = 126625, 379s + current = as.numeric( 379s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 379s + ) 379s + )) 379s > 379s > options("survey.lonely.psu" = "certainty") 379s > 379s > stopifnot(all.equal( 379s + target = 126625, 379s + current = as.numeric( 379s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 379s + ) 379s + )) 379s > 379s > options("survey.lonely.psu" = "adjust") 379s > 379s > stopifnot(all.equal( 379s + target = 127579.8, 379s + current = as.numeric( 379s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 379s + ), 379s + scale = 127579.8, tolerance = 0.000001 379s + )) 379s > 379s BEGIN TEST mtcars-var.R 379s 379s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 379s Copyright (C) 2025 The R Foundation for Statistical Computing 379s Platform: aarch64-unknown-linux-gnu 379s 379s R is free software and comes with ABSOLUTELY NO WARRANTY. 379s You are welcome to redistribute it under certain conditions. 379s Type 'license()' or 'licence()' for distribution details. 379s 379s R is a collaborative project with many contributors. 379s Type 'contributors()' for more information and 379s 'citation()' on how to cite R or R packages in publications. 379s 379s Type 'demo()' for some demos, 'help()' for on-line help, or 379s 'help.start()' for an HTML browser interface to help. 379s Type 'q()' to quit R. 379s 379s > library(survey) 379s Loading required package: grid 379s Loading required package: Matrix 380s Loading required package: survival 380s 380s Attaching package: 'survey' 380s 380s > 380s > # don't throw an error on domains of size 1, just return NA 380s > input <- mtcars 380s > input$carb <- factor(input$carb) 380s The following object is masked from 'package:graphics': 380s 380s dotchart 380s 380s > design <- svydesign(ids = ~0, weights = NULL, data = input) 380s > svyby( 380s + ~mpg, 380s + ~carb, 380s + design, 380s + svyvar 380s + ) 380s carb mpg se 380s 1 1 36.01619 11.2823286 380s 2 2 29.94444 9.0030898 380s 3 3 1.11000 0.4604066 380s 4 4 15.29656 4.3174617 380s 6 6 NA NA 380s 8 8 NA NA 380s > 380s > 380s > ## same n with na.rm=TRUE as subset(, !is.na) 380s > input$mpg[1]<-NA 380s > design <- svydesign(ids = ~0, weights = NULL, data = input) 380s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 380s + svyvar(~mpg, subset(design, !is.na(mpg))))) 380s > 380s BEGIN TEST multistage-rcpp.R 380s 380s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 380s Copyright (C) 2025 The R Foundation for Statistical Computing 380s Platform: aarch64-unknown-linux-gnu 380s 380s R is free software and comes with ABSOLUTELY NO WARRANTY. 380s You are welcome to redistribute it under certain conditions. 380s Type 'license()' or 'licence()' for distribution details. 380s 380s R is a collaborative project with many contributors. 380s Type 'contributors()' for more information and 380s 'citation()' on how to cite R or R packages in publications. 380s 380s Type 'demo()' for some demos, 'help()' for on-line help, or 380s 'help.start()' for an HTML browser interface to help. 380s Type 'q()' to quit R. 380s 380s > ## temporarily disable while it's being fixed 380s > ## q("no") 380s > 380s > ## 380s > ## Check that multistage() and multistage_rcpp() give same results 380s > ## for different options. 380s > ## 380s > library(survey) 380s Loading required package: grid 380s Loading required package: Matrix 381s Loading required package: survival 381s 381s Attaching package: 'survey' 381s 381s The following object is masked from 'package:graphics': 381s 381s dotchart 381s 381s > 381s > # Check for a simple random sample ---- 381s > 381s > data('api', package = 'survey') 381s > api_srs_design <- svydesign( 381s + data = apisrs, 381s + ids = ~ 1, 381s + weights = ~ 1 381s + ) 381s > 381s > x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob) 381s > 381s > base_r_result <- survey:::multistage(x = x, 381s + clusters = api_srs_design$cluster, 381s + stratas = api_srs_design$strata, 381s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=TRUE, stage = 1, cal = NULL) 381s > 381s > rcpp_result <- survey:::multistage_rcpp(x = x, 381s + clusters = api_srs_design$cluster, 381s + stratas = api_srs_design$strata, 381s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=TRUE, stage = 1, cal = NULL) 381s > 381s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 381s + stop("Differences between `multistage()` and `multistage_rcpp()` for SRS") 381s + } 381s > 381s > # Check for a stratified simple random sample ---- 381s > 381s > apistrat_design <- svydesign( 381s + data = apistrat, 381s + id =~ 1, 381s + strata =~ stype, 381s + weights =~ pw, 381s + fpc =~ fpc 381s + ) 381s > 381s > x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob) 381s > 381s > base_r_result <- survey:::multistage(x = x, 381s + clusters = apistrat_design$cluster, 381s + stratas = apistrat_design$strata, 381s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=TRUE, stage = 1, cal = NULL) 381s > 381s > rcpp_result <- survey:::multistage_rcpp(x = x, 381s + clusters = apistrat_design$cluster, 381s + stratas = apistrat_design$strata, 381s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=TRUE, stage = 1, cal = NULL) 381s > 381s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 381s + stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample") 381s + } 381s > 381s > ##_ Check whether expected true zeroes are actually computed as zeroes ---- 381s > 381s > x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob)) 381s > 381s > base_r_result <- survey:::multistage(x = x, 381s + clusters = apistrat_design$cluster, 381s + stratas = apistrat_design$strata, 381s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=TRUE, stage = 1, cal = NULL) 381s > 381s > rcpp_result <- survey:::multistage_rcpp(x = x, 381s + clusters = apistrat_design$cluster, 381s + stratas = apistrat_design$strata, 381s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=TRUE, stage = 1, cal = NULL) 381s > 381s > if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) { 381s + stop("Computations which should equal zero do not.") 381s + } 381s > 381s > # Create a stratified, multistage design ---- 381s > 381s > data(mu284) 381s > 381s > ## Create three strata, the third of which has only one PSU 381s > mu284_stratified <- rbind( 381s + transform(mu284, stratum = 1, 381s + y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)), 381s + transform(mu284, stratum = 2, 381s + y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)), 381s + transform(mu284[1,], stratum = 3, 381s + y2 = y1 + 2) 381s + ) 381s > 381s > ## Create domain variables which yield a lonely PSU or a lonely SSU 381s > mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19) 381s > mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1) 381s > 381s > ## Create a survey design object with no lonely PSUs 381s > dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3), 381s + strata = ~ stratum, nest = TRUE, 381s + id = ~ id1 + id2, fpc = ~ n1 + n2) 381s > ## Create a survey design with one lonely PSU 381s > dmu284_strat_w_lonely <- svydesign(data = mu284_stratified, 381s + strata = ~ stratum, nest = TRUE, 381s + id = ~ id1 + id2, fpc = ~ n1 + n2) 381s > ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU 381s > dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU) 381s > dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU) 381s > 381s > 381s > # Check same results for different values of 'lonely PSU' options ---- 381s > 381s > lonely_psu_options <- c(certainty = 'certainty', 381s + remove = 'remove', 381s + average = 'average', 381s + adjust = 'adjust') 381s > one_stage_options <- c(TRUE, FALSE) 381s > 381s > design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 381s + 'one.stage' = one_stage_options, 381s + stringsAsFactors = FALSE) 381s > design_lonely_psu_comparisons[['results_match']] <- NA 381s > 381s > ##_ Check for lonely PSUs caused by design ---- 381s > for (i in seq_len(nrow(design_lonely_psu_comparisons))) { 381s + survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i] 381s + one.stage <- design_lonely_psu_comparisons[['one.stage']][i] 381s + options('survey.lonely.psu' = survey.lonely.psu) 381s + 381s + x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob) 381s + 381s + base_r_result <- survey:::multistage(x = x, 381s + clusters = dmu284_strat_w_lonely$cluster, 381s + stratas = dmu284_strat_w_lonely$strata, 381s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=one.stage, stage = 1, cal = NULL) 381s + 381s + rcpp_result <- survey:::multistage_rcpp(x = x, 381s + clusters = dmu284_strat_w_lonely$cluster, 381s + stratas = dmu284_strat_w_lonely$strata, 381s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 381s + lonely.psu=getOption("survey.lonely.psu"), 381s + one.stage=one.stage, stage = 1, cal = NULL) 381s + 381s + design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 381s + } 382s > 382s > print(design_lonely_psu_comparisons) 382s survey.lonely.psu one.stage results_match 382s 1 certainty TRUE TRUE 382s 2 remove TRUE TRUE 382s 3 average TRUE TRUE 382s 4 adjust TRUE TRUE 382s 5 certainty FALSE TRUE 382s 6 remove FALSE TRUE 382s 7 average FALSE TRUE 382s 8 adjust FALSE TRUE 382s > if (!all(design_lonely_psu_comparisons$results_match)) { 382s + stop("Results for design lonely PSUs differ between base R and Rcpp implementations.") 382s + } 382s > 382s > ##_ Check for domain lonely PSUs caused by subsetting ---- 382s > 382s > domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 382s + 'survey.adjust.domain.lonely' = c(FALSE, TRUE), 382s + 'one.stage' = one_stage_options, 382s + stringsAsFactors = FALSE) 382s > domain_lonely_psu_comparisons[['results_match']] <- NA 382s > 382s > for (i in seq_len(nrow(domain_lonely_psu_comparisons))) { 382s + 382s + options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i]) 382s + options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i]) 382s + one.stage <- domain_lonely_psu_comparisons[['one.stage']][i] 382s + 382s + 382s + x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob) 382s + suppressWarnings({ 382s + base_r_result <- survey:::multistage(x = x, 382s + clusters = dmu284_strat_domain_lonely_psu$cluster, 382s + stratas = dmu284_strat_domain_lonely_psu$strata, 382s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 382s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 382s + lonely.psu=getOption("survey.lonely.psu"), 382s + one.stage=one.stage, stage = 1, cal = NULL) 382s + }) 382s + 382s + rcpp_result <- survey:::multistage_rcpp(x = x, 382s + clusters = dmu284_strat_domain_lonely_psu$cluster, 382s + stratas = dmu284_strat_domain_lonely_psu$strata, 382s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 382s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 382s + lonely.psu=getOption("survey.lonely.psu"), 382s + one.stage=one.stage, stage = 1, cal = NULL) 382s + 382s + domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 382s + } 382s Warning messages: 382s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s > 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 382s At least one stratum contains only one PSU at stage 1 382s 382s > print(domain_lonely_psu_comparisons) 382s survey.lonely.psu survey.adjust.domain.lonely one.stage results_match 382s 1 certainty FALSE TRUE TRUE 382s 2 remove FALSE TRUE TRUE 382s 3 average FALSE TRUE TRUE 382s 4 adjust FALSE TRUE TRUE 382s 5 certainty TRUE TRUE TRUE 382s 6 remove TRUE TRUE TRUE 382s 7 average TRUE TRUE TRUE 382s 8 adjust TRUE TRUE TRUE 382s 9 certainty FALSE FALSE TRUE 382s 10 remove FALSE FALSE TRUE 382s 11 average FALSE FALSE TRUE 382s 12 adjust FALSE FALSE TRUE 382s 13 certainty TRUE FALSE TRUE 382s 14 remove TRUE FALSE TRUE 382s 15 average TRUE FALSE TRUE 382s 16 adjust TRUE FALSE TRUE 382s > if (!all(domain_lonely_psu_comparisons$results_match)) { 382s + stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.") 382s + } 382s > 382s > # Checks for edge cases ---- 382s > 382s > ## Zero records ---- 382s > 382s > zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent") 382s > 382s > zero_row_result <- survey:::multistage_rcpp( 382s + x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]), 382s + clusters = zero_row_design$cluster, 382s + stratas = zero_row_design$strata, 382s + nPSUs = zero_row_design$fpc$sampsize, 382s + fpcs = zero_row_design$fpc$popsize, 382s + lonely.psu=getOption("survey.lonely.psu"), 382s + one.stage=one.stage, stage = 1, cal = NULL 382s + ) 382s > 382s > if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) { 382s + stop("`multistage_rcpp()` should return zeros for zero-row inputs.") 382s + } 382s > 382s > 382s BEGIN TEST multistage.R 382s 382s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 382s Copyright (C) 2025 The R Foundation for Statistical Computing 382s Platform: aarch64-unknown-linux-gnu 382s 382s R is free software and comes with ABSOLUTELY NO WARRANTY. 382s You are welcome to redistribute it under certain conditions. 382s Type 'license()' or 'licence()' for distribution details. 382s 382s R is a collaborative project with many contributors. 382s Type 'contributors()' for more information and 382s 'citation()' on how to cite R or R packages in publications. 382s 382s Type 'demo()' for some demos, 'help()' for on-line help, or 382s 'help.start()' for an HTML browser interface to help. 382s Type 'q()' to quit R. 382s 382s > ## 382s > ## Check that multistage samples still work 382s > ## 382s > library(survey) 382s Loading required package: grid 382s Loading required package: Matrix 383s Loading required package: survival 383s 383s Attaching package: 'survey' 383s 383s The following object is masked from 'package:graphics': 383s 383s dotchart 383s 383s > example(mu284) 383s 383s mu284> data(mu284) 383s 383s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 383s 2 - level Cluster Sampling design 383s With (5, 15) clusters. 383s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 383s 383s mu284> (ytotal<-svytotal(~y1, dmu284)) 383s total SE 383s y1 15080 2274.3 383s 383s mu284> vcov(ytotal) 383s y1 383s y1 5172234 383s > 383s > 383s BEGIN TEST na_action.R 383s 383s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 383s Copyright (C) 2025 The R Foundation for Statistical Computing 383s Platform: aarch64-unknown-linux-gnu 383s 383s R is free software and comes with ABSOLUTELY NO WARRANTY. 383s You are welcome to redistribute it under certain conditions. 383s Type 'license()' or 'licence()' for distribution details. 383s 383s R is a collaborative project with many contributors. 383s Type 'contributors()' for more information and 383s 'citation()' on how to cite R or R packages in publications. 383s 383s Type 'demo()' for some demos, 'help()' for on-line help, or 383s 'help.start()' for an HTML browser interface to help. 383s Type 'q()' to quit R. 383s 383s > ## from Terry Therneau 383s > library(survey) 383s Loading required package: grid 383s Loading required package: Matrix 384s Loading required package: survival 384s 384s Attaching package: 'survey' 384s 384s > load("naa.rda") 384s The following object is masked from 'package:graphics': 384s 384s dotchart 384s 384s > 384s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 384s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 384s > all.equal(coef(fit1e),coef(fit1o)) 384s [1] TRUE 384s > all.equal(vcov(fit1e),vcov(fit1o)) 384s [1] TRUE 384s > 384s BEGIN TEST newquantile.R 384s 384s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 384s Copyright (C) 2025 The R Foundation for Statistical Computing 384s Platform: aarch64-unknown-linux-gnu 384s 384s R is free software and comes with ABSOLUTELY NO WARRANTY. 384s You are welcome to redistribute it under certain conditions. 384s Type 'license()' or 'licence()' for distribution details. 384s 384s R is a collaborative project with many contributors. 384s Type 'contributors()' for more information and 384s 'citation()' on how to cite R or R packages in publications. 384s 384s Type 'demo()' for some demos, 'help()' for on-line help, or 384s 'help.start()' for an HTML browser interface to help. 384s Type 'q()' to quit R. 384s 384s > ## quantiles with equal weights 384s > 384s > library(survey) 384s Loading required package: grid 384s Loading required package: Matrix 385s Loading required package: survival 386s 386s Attaching package: 'survey' 386s 386s The following object is masked from 'package:graphics': 386s 386s dotchart 386s 386s > data(api) 386s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 386s > 386s > 386s > for(i in 1:9){ 386s + print(i) 386s + all.equal( 386s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 386s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 386s + ) 386s + 386s + } 386s [1] 1 386s [1] 2 386s [1] 3 386s [1] 4 386s [1] 5 386s [1] 6 386s [1] 7 386s [1] 8 386s [1] 9 386s > 386s BEGIN TEST nwts-cch.R 386s 386s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 386s Copyright (C) 2025 The R Foundation for Statistical Computing 386s Platform: aarch64-unknown-linux-gnu 386s 386s R is free software and comes with ABSOLUTELY NO WARRANTY. 386s You are welcome to redistribute it under certain conditions. 386s Type 'license()' or 'licence()' for distribution details. 386s 386s R is a collaborative project with many contributors. 386s Type 'contributors()' for more information and 386s 'citation()' on how to cite R or R packages in publications. 386s 386s Type 'demo()' for some demos, 'help()' for on-line help, or 386s 'help.start()' for an HTML browser interface to help. 386s Type 'q()' to quit R. 386s 386s > library(survey) 386s Loading required package: grid 386s Loading required package: Matrix 387s Loading required package: survival 387s 387s Attaching package: 'survey' 387s 387s The following object is masked from 'package:graphics': 387s 387s dotchart 387s 387s > library(survival) 387s > data(nwtco) 387s > 387s > ntwco<-subset(nwtco, !is.na(edrel)) 387s > 387s > load("nwtco-subcohort.rda") 387s > nwtco$subcohort<-subcohort 387s > 387s > d_BorganII <- twophase(id=list(~seqno,~seqno), 387s + strata=list(NULL,~interaction(instit,rel)), 387s + data=nwtco, subset=~I(rel |subcohort)) 387s > 387s > ##Coefficient results same as Splus with code from 387s > ## http://faculty.washington.edu/norm/software.html 387s > ## SE slightly larger due to using sandwich variance. 387s > 387s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 388s Call: 388s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 388s I(age/12), design = d_BorganII) 388s 388s coef exp(coef) se(coef) robust se z p 388s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 388s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 388s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 388s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 388s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 388s 388s Likelihood ratio test= on 5 df, p= 388s n= 1062, number of events= 571 388s > 388s > ## 388s > ## This gives higher standard errors. calibrate() does not recompute the 388s > ## finite population correction if a calibration variable happens to predict 388s > ## sampling perfectly. It probably should. 388s > ## 388s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 388s + strata=list(NULL,~rel), 388s + data=nwtco, subset=~I(rel |subcohort)), 388s + phase=2, formula=~interaction(instit,rel), 388s + epsilon=1e-10) 388s > 388s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 388s Call: 388s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 388s I(age/12), design = d_BorganIIps) 388s 388s coef exp(coef) se(coef) robust se z p 388s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 388s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 388s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 388s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 388s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 388s 388s Likelihood ratio test= on 5 df, p= 388s n= 1062, number of events= 571 388s > 388s BEGIN TEST nwts.R 388s 388s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 388s Copyright (C) 2025 The R Foundation for Statistical Computing 388s Platform: aarch64-unknown-linux-gnu 388s 388s R is free software and comes with ABSOLUTELY NO WARRANTY. 388s You are welcome to redistribute it under certain conditions. 388s Type 'license()' or 'licence()' for distribution details. 388s 388s R is a collaborative project with many contributors. 388s Type 'contributors()' for more information and 388s 'citation()' on how to cite R or R packages in publications. 388s 388s Type 'demo()' for some demos, 'help()' for on-line help, or 388s 'help.start()' for an HTML browser interface to help. 388s Type 'q()' to quit R. 388s 388s > 388s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 388s > ## data from Norman Breslow's web page. 388s > library(survey) 388s Loading required package: grid 388s Loading required package: Matrix 389s Loading required package: survival 389s 389s Attaching package: 'survey' 389s 389s The following object is masked from 'package:graphics': 389s 389s dotchart 389s 389s > load("nwts.rda") 389s > nwtsnb<-nwts 389s > nwtsnb$case<-nwts$case-nwtsb$case 389s > nwtsnb$control<-nwts$control-nwtsb$control 389s > 389s > a<-rbind(nwtsb,nwtsnb) 389s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 389s > 389s > b<-rbind(a,a) 389s > b$rel<-rep(c(1,0),each=32) 389s > b$n<-ifelse(b$rel,b$case,b$control) 389s > 389s > index<-rep(1:64,b$n) 389s > 389s > nwt.exp<-b[index,c(1:3,6,7)] 389s > nwt.exp$id<-1:4088 389s > 389s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 389s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 390s > 390s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 390s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 390s > 390s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 390s > 390s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 390s 390s Call: 390s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 390s family = quasibinomial) 390s 390s Survey design: 390s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 390s subset = subset, data = data, pps = pps) 390s 390s Coefficients: 390s Estimate Std. Error t value Pr(>|t|) 390s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 390s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 390s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 390s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 390s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 390s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 390s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 390s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 390s --- 390s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 390s 390s (Dispersion parameter for quasibinomial family taken to be 1.000876) 390s 390s Number of Fisher Scoring iterations: 4 390s 390s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 390s 390s Call: 390s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 390s family = quasibinomial) 390s 390s Survey design: 390s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 390s subset = subset, data = data, pps = pps) 390s 390s Coefficients: 390s Estimate Std. Error t value Pr(>|t|) 390s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 390s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 390s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 390s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 390s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 390s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 390s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 390s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 390s --- 390s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 390s 390s (Dispersion parameter for quasibinomial family taken to be 1.000876) 390s 390s Number of Fisher Scoring iterations: 4 390s 390s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 390s 390s Call: 390s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 390s family = quasibinomial) 390s 390s Survey design: 390s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 390s rel)) 390s 390s Coefficients: 390s Estimate Std. Error t value Pr(>|t|) 390s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 390s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 390s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 390s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 390s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 390s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 390s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 390s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 390s --- 390s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 390s 390s (Dispersion parameter for quasibinomial family taken to be 1.000876) 390s 390s Number of Fisher Scoring iterations: 4 390s 390s > 390s > ## check subsets of calibrated designs. 390s > summary(svyglm(rel~factor(stage), 390s + family=quasibinomial,design=subset(dccs8,histol==1))) 390s 390s Call: 390s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 390s histol == 1), family = quasibinomial) 390s 390s Survey design: 390s subset(dccs8, histol == 1) 390s 390s Coefficients: 390s Estimate Std. Error t value Pr(>|t|) 390s (Intercept) -2.7160 0.1083 -25.085 < 2e-16 *** 390s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 390s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 390s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 390s --- 390s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 390s 390s (Dispersion parameter for quasibinomial family taken to be 1.001333) 390s 390s Number of Fisher Scoring iterations: 4 390s 390s > summary(svyglm(rel~factor(stage), 390s + family=quasibinomial,design=subset(gccs8,histol==1))) 390s Warning messages: 390s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 390s 2: In summary.glm(g) : 390s observations with zero weight not used for calculating dispersion 390s 3: In summary.glm(glm.object) : 390s observations with zero weight not used for calculating dispersion 390s 4: In `[.twophase2`(design, nas == 0, ) : 390s 1 strata have only one PSU in this subset. 390s 5: In `[.twophase2`(design, nas == 0, ) : 390s 1 strata have only one PSU in this subset. 390s 390s Call: 390s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 390s histol == 1), family = quasibinomial) 390s 390s Survey design: 390s subset(gccs8, histol == 1) 390s 390s Coefficients: 390s Estimate Std. Error t value Pr(>|t|) 390s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 390s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 390s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 390s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 390s --- 390s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1Warning messages: 390s 1: In summary.glm(g) : 390s observations with zero weight not used for calculating dispersion 390s 2: In summary.glm(glm.object) : 390s observations with zero weight not used for calculating dispersion 390s 390s 390s (Dispersion parameter for quasibinomial family taken to be 1.001333) 390s 390s Number of Fisher Scoring iterations: 4 390s 390s > 390s > 390s BEGIN TEST poisson.R 390s 390s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 390s Copyright (C) 2025 The R Foundation for Statistical Computing 390s Platform: aarch64-unknown-linux-gnu 390s 390s R is free software and comes with ABSOLUTELY NO WARRANTY. 390s You are welcome to redistribute it under certain conditions. 390s Type 'license()' or 'licence()' for distribution details. 390s 390s R is a collaborative project with many contributors. 390s Type 'contributors()' for more information and 390s 'citation()' on how to cite R or R packages in publications. 390s 390s Type 'demo()' for some demos, 'help()' for on-line help, or 390s 'help.start()' for an HTML browser interface to help. 390s Type 'q()' to quit R. 390s 390s > ## check poisson sampling 390s > library(survey) 390s Loading required package: grid 390s Loading required package: Matrix 391s Loading required package: survival 391s 391s Attaching package: 'survey' 391s 391s The following object is masked from 'package:graphics': 391s 391s dotchart 391s 391s > data(api) 391s > set.seed(2021-7-15) 391s > apipop$prob<-apipop$api00/1000 391s > insample<-rbinom(nrow(apipop),1,apipop$prob) 391s > apipois<-apipop[insample,] 391s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 391s > 391s > stopifnot(isTRUE(all.equal( 391s + as.vector(SE(svytotal(~api00,design=des))), 391s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 391s + ))) 392s > 392s > 392s BEGIN TEST pps.R 392s 392s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 392s Copyright (C) 2025 The R Foundation for Statistical Computing 392s Platform: aarch64-unknown-linux-gnu 392s 392s R is free software and comes with ABSOLUTELY NO WARRANTY. 392s You are welcome to redistribute it under certain conditions. 392s Type 'license()' or 'licence()' for distribution details. 392s 392s R is a collaborative project with many contributors. 392s Type 'contributors()' for more information and 392s 'citation()' on how to cite R or R packages in publications. 392s 392s Type 'demo()' for some demos, 'help()' for on-line help, or 392s 'help.start()' for an HTML browser interface to help. 392s Type 'q()' to quit R. 392s 392s > library(survey) 392s Loading required package: grid 392s Loading required package: Matrix 393s Loading required package: survival 393s 393s Attaching package: 'survey' 393s 393s The following object is masked from 'package:graphics': 393s 393s dotchart 393s 393s > data(election) 393s > 393s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 393s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 393s > svytotal(~Bush+Kerry+Nader, dpps) 393s total SE 393s Bush 64518472 2447629 393s Kerry 51202102 2450787 393s Nader 478530 102420 393s > svytotal(~Bush+Kerry+Nader, dppswr) 393s total SE 393s Bush 64518472 2671455 393s Kerry 51202102 2679433 393s Nader 478530 105303 393s > 393s > ##subsets 393s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 393s total SE 393s Bush 34944285 5399833 393s Kerry 25581714 4028434 393s Nader 478530 102420 393s > 393s > ##multistage: should agree with STRS analysis 393s > data(api) 393s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 393s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 393s > 393s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 393s [1] TRUE 393s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 393s [1] TRUE 393s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 393s [1] TRUE 393s > 393s > ## the new without-replacement methods 393s > data(election) 393s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 393s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 393s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 393s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 393s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 393s > ## Yates-Grundy type 393s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 393s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 393s > 393s > ## The with-replacement approximation 393s > svytotal(~Bush+Kerry+Nader, dpps_ht) 393s total SE 393s Bush 64518472 2604404 393s Kerry 51202102 2523712 393s Nader 478530 102326 393s > svytotal(~Bush+Kerry+Nader, dpps_yg) 393s total SE 393s Bush 64518472 2406526 393s Kerry 51202102 2408091 393s Nader 478530 101664 393s > svytotal(~Bush+Kerry+Nader, dpps_hr) 393s total SE 393s Bush 64518472 2624662 393s Kerry 51202102 2525222 393s Nader 478530 102793 393s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 393s total SE 393s Bush 64518472 2436738 393s Kerry 51202102 2439845 393s Nader 478530 102016 393s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 393s total SE 393s Bush 64518472 2472753 393s Kerry 51202102 2426842 393s Nader 478530 102595 393s > svytotal(~Bush+Kerry+Nader, dpps_br) 393s total SE 393s Bush 64518472 2447629 393s Kerry 51202102 2450787 393s Nader 478530 102420 393s > svytotal(~Bush+Kerry+Nader, dpps_ov) 393s total SE 393s Bush 64518472 2939608 393s Kerry 51202102 1964632 393s Nader 478530 104373 393s > 393s > ## subsets 393s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 393s total SE 393s Bush 34944285 5406348 393s Kerry 25581714 4047741 393s Nader 478530 102326 393s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 393s total SE 393s Bush 34944285 5377659 393s Kerry 25581714 4010908 393s Nader 478530 102016 393s > 393s > ## counts 393s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 393s I(Nader > 0) counts se 393s FALSE FALSE 19 0 393s TRUE TRUE 21 0 393s > 393s BEGIN TEST qrule-swiss.R 393s 393s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 393s Copyright (C) 2025 The R Foundation for Statistical Computing 393s Platform: aarch64-unknown-linux-gnu 393s 393s R is free software and comes with ABSOLUTELY NO WARRANTY. 393s You are welcome to redistribute it under certain conditions. 393s Type 'license()' or 'licence()' for distribution details. 393s 393s R is a collaborative project with many contributors. 393s Type 'contributors()' for more information and 393s 'citation()' on how to cite R or R packages in publications. 393s 393s Type 'demo()' for some demos, 'help()' for on-line help, or 393s 'help.start()' for an HTML browser interface to help. 393s Type 'q()' to quit R. 393s 393s > library(survey) 393s Loading required package: grid 393s Loading required package: Matrix 394s Loading required package: survival 394s 394s Attaching package: 'survey' 394s 394s The following object is masked from 'package:graphics': 394s 394s dotchart 394s 394s > 394s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1) 394s > 394s > design_no_strat <- svydesign(id = ~id, 394s + probs = ~probs, 394s + data = data_no_strat, 394s + fpc = ~fpc) 394s > 394s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99) 394s > 394s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE, 394s + interval.type = "mean", qrule = "hf1") 394s > 394s > stopifnot(all(diff(res$x[,"quantile"])>=0)) 394s > 394s > 394s > 394s BEGIN TEST quantile.R 394s 394s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 394s Copyright (C) 2025 The R Foundation for Statistical Computing 394s Platform: aarch64-unknown-linux-gnu 394s 394s R is free software and comes with ABSOLUTELY NO WARRANTY. 394s You are welcome to redistribute it under certain conditions. 394s Type 'license()' or 'licence()' for distribution details. 394s 394s R is a collaborative project with many contributors. 394s Type 'contributors()' for more information and 394s 'citation()' on how to cite R or R packages in publications. 394s 394s Type 'demo()' for some demos, 'help()' for on-line help, or 394s 'help.start()' for an HTML browser interface to help. 394s Type 'q()' to quit R. 394s 395s > library(survey) 395s Loading required package: grid 395s Loading required package: Matrix 395s Loading required package: survival 396s 396s Attaching package: 'survey' 396s 396s The following object is masked from 'package:graphics': 396s 396s dotchart 396s 396s > set.seed(42) 396s > 396s > df<-data.frame(x=exp(rnorm(1000))) 396s > df$y<-round(df$x,1) 396s > ddf<-svydesign(id=~1,data=df) 396s Warning message: 396s In svydesign.default(id = ~1, data = df) : 396s No weights or probabilities supplied, assuming equal probability 396s > rdf<-as.svrepdesign(ddf) 396s > 396s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 396s 0.01 0.1 0.5 0.9 0.99 396s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 396s > 396s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 396s x 396s q0.01 0.01554946 396s q0.1 0.01425828 396s q0.5 0.03428012 396s q0.9 0.16457488 396s q0.99 1.88672412 396s > 396s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 396s 0.01 0.1 0.5 0.9 0.99 396s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 396s > 396s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 396s x 396s q0.01 0.01556240 396s q0.1 0.01420086 396s q0.5 0.03430175 396s q0.9 0.16461019 396s q0.99 1.88818131 396s > 396s > 396s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 396s $quantiles 396s 0.01 0.1 0.5 0.9 0.99 396s y 0.02352941 0.2230769 0.9340909 3.55 9.4 396s 396s $CIs 396s , , y 396s 396s 0.01 0.1 0.5 0.9 0.99 396s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 396s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 396s 396s 396s > 396s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 397s Statistic: 397s y 397s q0.01 0.1 397s q0.1 0.3 397s q0.5 1.0 397s q0.9 3.6 397s q0.99 9.4 397s SE: 397s y 397s q0.01 0.02547977 397s q0.1 0.02547977 397s q0.5 0.02547977 397s q0.9 0.15287859 397s q0.99 1.88302540 397s > 397s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 397s $quantiles 397s 0.01 0.1 0.5 0.9 0.99 397s y 0.02352941 0.2230769 0.9340909 3.55 9.4 397s 397s $CIs 397s , , y 397s 397s 0.01 0.1 0.5 0.9 0.99 397s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 397s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 397s 397s 397s > 397s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 397s Statistic: 397s y 397s q0.01 0.1 397s q0.1 0.3 397s q0.5 1.0 397s q0.9 3.6 397s q0.99 9.4 397s SE: 397s y 397s q0.01 0.02551067 397s q0.1 0.02551067 397s q0.5 0.02551067 397s q0.9 0.15306404 397s q0.99 1.88450896 397s > 397s > 397s > 397s > df<-data.frame(x=exp(rnorm(20))) 397s > df$y<-round(df$x,1) 397s > ddf<-svydesign(id=~1,data=df) 397s Warning message: 397s In svydesign.default(id = ~1, data = df) : 397s No weights or probabilities supplied, assuming equal probability 397s > rdf<-as.svrepdesign(ddf) 397s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 397s 0.01 0.1 0.5 0.9 0.99 397s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 397s > 397s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 397s x 397s q0.01 0.00000000 397s q0.1 0.04598541 397s q0.5 0.25943731 397s q0.9 2.12343073 397s q0.99 1.91998924 397s > 397s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 397s 0.01 0.1 0.5 0.9 0.99 397s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 397s > 397s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 397s x 397s q0.01 0.00000000 397s q0.1 0.04732818 397s q0.5 0.24957966 397s q0.9 2.25211815 397s q0.99 2.04043154 397s > 397s > 397s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 397s $quantiles 397s 0.01 0.1 0.5 0.9 0.99 397s y 0.1 0.15 0.75 2.4 8.68 397s 397s $CIs 397s , , y 397s 397s 0.01 0.1 0.5 0.9 0.99 397s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 397s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 397s 397s 397s > 397s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 397s Statistic: 397s y 397s q0.01 0.10 397s q0.1 0.20 397s q0.5 0.80 397s q0.9 2.40 397s q0.99 8.68 397s SE: 397s y 397s q0.01 0.00000000 397s q0.1 0.02611112 397s q0.5 0.26542051 397s q0.9 2.10908603 397s q0.99 1.91777710 397s > 397s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 397s $quantiles 397s 0.01 0.1 0.5 0.9 0.99 397s y 0.1 0.15 0.75 2.4 8.68 397s 397s $CIs 397s , , y 397s 397s 0.01 0.1 0.5 0.9 0.99 397s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 397s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 397s 397s 397s > 397s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 397s Statistic: 397s y 397s q0.01 0.10 397s q0.1 0.20 397s q0.5 0.80 397s q0.9 2.40 397s q0.99 8.68 397s SE: 397s y 397s q0.01 0.00000000 397s q0.1 0.02551067 397s q0.5 0.25244616 397s q0.9 2.23558589 397s q0.99 2.03881114 397s > 397s BEGIN TEST quantiles-chile.R 397s 397s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 397s Copyright (C) 2025 The R Foundation for Statistical Computing 397s Platform: aarch64-unknown-linux-gnu 397s 397s R is free software and comes with ABSOLUTELY NO WARRANTY. 397s You are welcome to redistribute it under certain conditions. 397s Type 'license()' or 'licence()' for distribution details. 397s 397s R is a collaborative project with many contributors. 397s Type 'contributors()' for more information and 397s 'citation()' on how to cite R or R packages in publications. 397s 397s Type 'demo()' for some demos, 'help()' for on-line help, or 397s 'help.start()' for an HTML browser interface to help. 397s Type 'q()' to quit R. 397s 397s > library(survey) 397s Loading required package: grid 397s Loading required package: Matrix 398s Loading required package: survival 398s 398s Attaching package: 'survey' 398s 398s The following object is masked from 'package:graphics': 398s 398s dotchart 398s 398s > datos <- readRDS("datos_ejemplo.rds") 398s > 398s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 398s > set.seed(234262762) 398s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 398s > options(survey.lonely.psu="remove") 398s > 398s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 398s > 398s > suppressWarnings({ 398s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 398s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 398s + }) 398s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 398s [1] TRUE 398s > 398s > suppressWarnings({ 398s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 398s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 398s + }) 398s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 398s [1] TRUE 398s > 398s BEGIN TEST rakecheck.R 398s 398s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 398s Copyright (C) 2025 The R Foundation for Statistical Computing 398s Platform: aarch64-unknown-linux-gnu 398s 398s R is free software and comes with ABSOLUTELY NO WARRANTY. 398s You are welcome to redistribute it under certain conditions. 398s Type 'license()' or 'licence()' for distribution details. 398s 398s R is a collaborative project with many contributors. 398s Type 'contributors()' for more information and 398s 'citation()' on how to cite R or R packages in publications. 398s 398s Type 'demo()' for some demos, 'help()' for on-line help, or 398s 'help.start()' for an HTML browser interface to help. 398s Type 'q()' to quit R. 398s 398s > library(survey) 398s Loading required package: grid 398s Loading required package: Matrix 399s Loading required package: survival 400s 400s Attaching package: 'survey' 400s 400s The following object is masked from 'package:graphics': 400s 400s dotchart 400s 400s > 400s > data(api) 400s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 400s > rclus1 <- as.svrepdesign(dclus1) 400s > 400s > ## population marginal totals for each stratum 400s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 400s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 400s > 400s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 400s > 400s > svymean(~api00, rclus1r) 400s mean SE 400s api00 641.23 26.873 400s > svytotal(~enroll, rclus1r) 400s total SE 400s enroll 3647300 463511 400s > 400s > ff<-~stype+sch.wide 400s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 400s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 400s > 400s > svymean(~api00,rclus1g) 400s mean SE 400s api00 641.23 26.874 400s > svytotal(~enroll,rclus1g) 400s total SE 400s enroll 3647280 463582 400s > 400s > summary(weights(rclus1g)/weights(rclus1r)) 400s V1 V2 V3 V4 V5 V6 400s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 400s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 400s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 400s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 400s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 400s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 400s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 400s V7 V8 V9 V10 V11 400s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 400s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 400s Median :1 Median :1 Median :1 Median :1 Median :1 400s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 400s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 400s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 400s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 400s V12 V13 V14 V15 400s Min. :0.9997 Min. :1 Min. :1 Min. :1 400s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 400s Median :1.0001 Median :1 Median :1 Median :1 400s Mean :1.0000 Mean :1 Mean :1 Mean :1 400s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 400s Max. :1.0002 Max. :1 Max. :1 Max. :1 400s NA's :37 NA's :13 NA's :1 NA's :12 400s > 400s > 400s > ## Do it for a design without replicate weights 400s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 400s > 400s > svymean(~api00, dclus1r) 400s mean SE 400s api00 641.23 23.704 400s > svytotal(~enroll, dclus1r) 400s total SE 400s enroll 3647300 400603 400s > 400s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 400s > 400s > svymean(~api00,dclus1g) 400s mean SE 400s api00 641.23 23.704 400s > svytotal(~enroll,dclus1g) 400s total SE 400s enroll 3647280 400603 400s > 400s > summary(weights(dclus1g)/weights(dclus1r)) 400s Min. 1st Qu. Median Mean 3rd Qu. Max. 400s 1 1 1 1 1 1 400s > 400s > 400s > 400s > ## Example of raking with partial joint distributions 400s > pop.table <- xtabs(~stype+sch.wide,apipop) 400s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 400s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 400s + list(pop.table, pop.imp)) 400s > svymean(~api00, dclus1r2) 400s mean SE 400s api00 642.62 22.732 400s > 400s > ff1 <-~stype*sch.wide+comp.imp 400s > 400s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 400s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 400s > 400s > svymean(~api00, dclus1g2) 400s mean SE 400s api00 642.61 22.731 400s > 400s > summary(weights(dclus1r2)/weights(dclus1g2)) 400s Min. 1st Qu. Median Mean 3rd Qu. Max. 400s 0.999 1.000 1.000 1.000 1.000 1.002 400s > 400s BEGIN TEST raowuboot.R 400s 400s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 400s Copyright (C) 2025 The R Foundation for Statistical Computing 400s Platform: aarch64-unknown-linux-gnu 400s 400s R is free software and comes with ABSOLUTELY NO WARRANTY. 400s You are welcome to redistribute it under certain conditions. 400s Type 'license()' or 'licence()' for distribution details. 400s 400s R is a collaborative project with many contributors. 400s Type 'contributors()' for more information and 400s 'citation()' on how to cite R or R packages in publications. 400s 400s Type 'demo()' for some demos, 'help()' for on-line help, or 400s 'help.start()' for an HTML browser interface to help. 400s Type 'q()' to quit R. 400s 400s > ## regression test for bug reported by Richard Valliant 400s > library(survey) 400s Loading required package: grid 400s Loading required package: Matrix 401s Loading required package: survival 401s 401s Attaching package: 'survey' 401s 401s The following object is masked from 'package:graphics': 401s 401s dotchart 401s 401s > s<-subbootweights(c(1,1),1:2, 50) 401s > stopifnot(all(s$repweights$weights %in% c(0,2))) 401s > 401s BEGIN TEST regTermTest-missing.R 401s 401s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 401s Copyright (C) 2025 The R Foundation for Statistical Computing 401s Platform: aarch64-unknown-linux-gnu 401s 401s R is free software and comes with ABSOLUTELY NO WARRANTY. 401s You are welcome to redistribute it under certain conditions. 401s Type 'license()' or 'licence()' for distribution details. 401s 401s R is a collaborative project with many contributors. 401s Type 'contributors()' for more information and 401s 'citation()' on how to cite R or R packages in publications. 401s 401s Type 'demo()' for some demos, 'help()' for on-line help, or 401s 'help.start()' for an HTML browser interface to help. 401s Type 'q()' to quit R. 401s 401s Loading required package: grid 401s Loading required package: Matrix 401s > library(survey) 402s Loading required package: survival 402s 402s Attaching package: 'survey' 402s 402s The following object is masked from 'package:graphics': 402s 402s dotchart 402s 402s > data(nhanes) 402s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 402s > 402s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 403s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 403s > 403s > ta<-regTermTest(a, ~HI_CHOL) 403s > tb<-regTermTest(b, ~HI_CHOL) 403s > 403s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 403s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 403s > 403s BEGIN TEST regpredict.R 403s 403s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 403s Copyright (C) 2025 The R Foundation for Statistical Computing 403s Platform: aarch64-unknown-linux-gnu 403s 403s R is free software and comes with ABSOLUTELY NO WARRANTY. 403s You are welcome to redistribute it under certain conditions. 403s Type 'license()' or 'licence()' for distribution details. 403s 403s R is a collaborative project with many contributors. 403s Type 'contributors()' for more information and 403s 'citation()' on how to cite R or R packages in publications. 403s 403s Type 'demo()' for some demos, 'help()' for on-line help, or 403s 'help.start()' for an HTML browser interface to help. 403s Type 'q()' to quit R. 403s 403s > library(survey) 403s Loading required package: grid 403s Loading required package: Matrix 404s Loading required package: survival 404s 404s Attaching package: 'survey' 404s 404s The following object is masked from 'package:graphics': 404s 404s dotchart 404s 404s > data(api) 404s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 404s > 404s > 404s > ## regression estimator of total, three ways 404s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 404s > npop <- sum(!is.na(apipop$enroll)) 404s > 404s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 404s > a <- predict(api.reg, newdata=pop, total=npop) 404s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 404s > 404s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 404s [1] TRUE 404s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 404s [1] TRUE 404s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 404s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 404s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 404s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 404s + } 404s > 404s > ## classical ratio estimator, four ways. 404s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 404s + family=quasi(link="identity", var="mu")) 404s > 404s > a <- predict(api.reg2, newdata=pop, total=npop) 404s > b <- svytotal(~api.stu, 404s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 404s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 404s > 404s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 404s [1] TRUE 404s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 404s [1] TRUE 404s > all.equal(as.vector(coef(a)),as.vector(e$total)) 404s [1] TRUE 404s > all.equal(as.vector(SE(a)), as.vector(e$se)) 404s [1] TRUE 404s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 404s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 404s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 404s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 404s + } 404s > 404s BEGIN TEST rss_scores.R 404s 404s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 404s Copyright (C) 2025 The R Foundation for Statistical Computing 404s Platform: aarch64-unknown-linux-gnu 404s 404s R is free software and comes with ABSOLUTELY NO WARRANTY. 404s You are welcome to redistribute it under certain conditions. 404s Type 'license()' or 'licence()' for distribution details. 404s 404s R is a collaborative project with many contributors. 404s Type 'contributors()' for more information and 404s 'citation()' on how to cite R or R packages in publications. 404s 404s Type 'demo()' for some demos, 'help()' for on-line help, or 404s 'help.start()' for an HTML browser interface to help. 404s Type 'q()' to quit R. 404s 404s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 404s > library(survey) 404s Loading required package: grid 404s Loading required package: Matrix 405s Loading required package: survival 405s 405s Attaching package: 'survey' 405s 405s > data(myco) 405s The following object is masked from 'package:graphics': 405s 405s dotchart 405s 405s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 405s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 405s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 405s > 405s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 405s > 405s > s<-svyscoretest(m_full, ~Scar) 405s > stopifnot(abs(s[1]-10.73)<0.05) 405s > 405s > t<-svyscoretest(m_full,~Scar,method="individual") 405s > stopifnot(abs(coef(t)- -32.61)<0.1) 405s > stopifnot(abs(vcov(t)-99.1)<0.1) 405s > 405s > 405s BEGIN TEST scoping.R 405s 405s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 405s Copyright (C) 2025 The R Foundation for Statistical Computing 405s Platform: aarch64-unknown-linux-gnu 405s 405s R is free software and comes with ABSOLUTELY NO WARRANTY. 405s You are welcome to redistribute it under certain conditions. 405s Type 'license()' or 'licence()' for distribution details. 405s 405s R is a collaborative project with many contributors. 405s Type 'contributors()' for more information and 405s 'citation()' on how to cite R or R packages in publications. 405s 405s Type 'demo()' for some demos, 'help()' for on-line help, or 405s 'help.start()' for an HTML browser interface to help. 405s Type 'q()' to quit R. 405s 406s > 406s > ## regression test for testing regression 406s > 406s > library(survey) 406s Loading required package: grid 406s Loading required package: Matrix 406s Loading required package: survival 407s 407s Attaching package: 'survey' 407s 407s > data(api) 407s The following object is masked from 'package:graphics': 407s 407s dotchart 407s 407s > 407s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 407s > 407s > 407s > f<-function(){ 407s + form<-acs.46~stype 407s + svyglm(formula=form, design = dstrat) 407s + } 407s > 407s > g<-function(form){ 407s + svyglm(formula=form, design = dstrat) 407s + } 407s > f() 407s Stratified Independent Sampling design 407s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 407s fpc = ~fpc) 407s 407s Call: svyglm(formula = form, design = dstrat) 407s 407s Coefficients: 407s (Intercept) stypeH stypeM 407s 28.7449 0.7551 0.4022 407s 407s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 407s (66 observations deleted due to missingness) 407s Null Deviance: 1838 407s Residual Deviance: 1835 AIC: 719.8 407s > g(acs.46~stype) 407s Stratified Independent Sampling design 407s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 407s fpc = ~fpc) 407s 407s Call: svyglm(formula = form, design = dstrat) 407s 407s Coefficients: 407s (Intercept) stypeH stypeM 407s 28.7449 0.7551 0.4022 407s 407s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 407s (66 observations deleted due to missingness) 407s Null Deviance: 1838 407s Residual Deviance: 1835 AIC: 719.8 407s > 407s > f<-function(){ 407s + form<-Surv(acs.46)~stype 407s + svycoxph(formula=form, design = dstrat) 407s + } 407s > 407s > g<-function(form){ 407s + svycoxph(formula=form, design = dstrat) 407s + } 407s > 407s > f() 407s Call: 407s svycoxph(formula = form, design = dstrat) 407s 407s coef exp(coef) se(coef) robust se z p 407s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 407s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 407s 407s Likelihood ratio test= on 2 df, p= 407s n= 134, number of events= 134 407s (66 observations deleted due to missingness) 407s > g(Surv(acs.46)~stype) 407s Call: 407s svycoxph(formula = form, design = dstrat) 407s 407s coef exp(coef) se(coef) robust se z p 407s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 407s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 407s 407s Likelihood ratio test= on 2 df, p= 407s n= 134, number of events= 134 407s (66 observations deleted due to missingness) 407s > 407s > ## check coxph for a single predictor 407s > svycoxph(Surv(acs.46)~api00,design=dstrat) 407s Call: 407s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 407s 407s coef exp(coef) se(coef) robust se z p 407s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 407s 407s Likelihood ratio test= on 1 df, p= 407s n= 134, number of events= 134 407s (66 observations deleted due to missingness) 407s > 407s BEGIN TEST survcurve.R 407s 407s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 407s Copyright (C) 2025 The R Foundation for Statistical Computing 407s Platform: aarch64-unknown-linux-gnu 407s 407s R is free software and comes with ABSOLUTELY NO WARRANTY. 407s You are welcome to redistribute it under certain conditions. 407s Type 'license()' or 'licence()' for distribution details. 407s 407s R is a collaborative project with many contributors. 407s Type 'contributors()' for more information and 407s 'citation()' on how to cite R or R packages in publications. 407s 407s Type 'demo()' for some demos, 'help()' for on-line help, or 407s 'help.start()' for an HTML browser interface to help. 407s Type 'q()' to quit R. 407s 407s > library(survey) 407s Loading required package: grid 407s Loading required package: Matrix 408s Loading required package: survival 408s 408s Attaching package: 'survey' 408s 408s The following object is masked from 'package:graphics': 408s 408s dotchart 408s 408s > library(survival) 408s > 408s > pbc2<-rbind(pbc,pbc) 408s > pbc2$id<-rep(1:418,2) 408s > 408s > dpbc1<-svydesign(id=~1, data=pbc) 408s Warning message: 408s In svydesign.default(id = ~1, data = pbc) :> dpbc2<-svydesign(id=~id, data=pbc2) 408s 408s No weights or probabilities supplied, assuming equal probability 408s Warning message: 408s In svydesign.default(id = ~id, data = pbc2) : 408s No weights or probabilities supplied, assuming equal probability 408s > 408s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 408s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 408s > 408s > (c1<-confint(s1,(1:5)*365)) 408s 0.025 0.975 408s 365 0.6446215 0.8594153 408s 730 0.5410938 0.7766848 408s 1095 0.2683127 0.5103356 408s 1460 0.1444731 0.3722001 408s 1825 0.1009672 0.3204713 408s > (c2<-confint(s2,(1:5)*365)) 408s 0.025 0.975 408s 365 0.6446215 0.8594153 408s 730 0.5410938 0.7766848 408s 1095 0.2683127 0.5103356 408s 1460 0.1444731 0.3722001 408s 1825 0.1009672 0.3204713 408s > all.equal(c1, c2) 408s [1] TRUE 408s > 408s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 408s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 408s > 408s > d<-data.frame(bili=c(5,10)) 408s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 408s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 410s > 410s > (pc1<-confint(p1[[1]],(1:5)*365)) 410s 0.025 0.975 410s 365 0.8410027 0.9266263 410s 730 0.7371114 0.8548312 410s 1095 0.5517779 0.7018583 410s 1460 0.4335073 0.5992819 410s 1825 0.3260899 0.5046241 410s > (pc2<-confint(p2[[1]],(1:5)*365)) 410s 0.025 0.975 410s 365 0.8409490 0.9267054 410s 730 0.7370152 0.8549432 410s 1095 0.5515848 0.7019513 410s 1460 0.4332252 0.5992968 410s 1825 0.3257172 0.5045795 410s > all.equal(pc1, pc2) 410s [1] "Mean relative difference: 0.0002070722" 410s > 410s > (q1<-quantile(p1[[2]])) 410s 0.75 0.5 0.25 410s 489 930 1492 410s > (q2<-quantile(p2[[2]])) 410s 0.75 0.5 0.25 410s 489 930 1492 410s > all.equal(q1,q2) 410s [1] TRUE 410s > 410s BEGIN TEST svyby-strings.R 410s 410s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 410s Copyright (C) 2025 The R Foundation for Statistical Computing 410s Platform: aarch64-unknown-linux-gnu 410s 410s R is free software and comes with ABSOLUTELY NO WARRANTY. 410s You are welcome to redistribute it under certain conditions. 410s Type 'license()' or 'licence()' for distribution details. 410s 410s R is a collaborative project with many contributors. 410s Type 'contributors()' for more information and 410s 'citation()' on how to cite R or R packages in publications. 410s 410s Type 'demo()' for some demos, 'help()' for on-line help, or 410s 'help.start()' for an HTML browser interface to help. 410s Type 'q()' to quit R. 410s 410s > 410s > ## check that stringsAsFactors fixes the string levels problem 410s > data(api, package = "survey") 410s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 411s > est0 <- 411s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 411s > 411s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 411s > 411s BEGIN TEST svyby_bug.R 412s 412s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 412s Copyright (C) 2025 The R Foundation for Statistical Computing 412s Platform: aarch64-unknown-linux-gnu 412s 412s R is free software and comes with ABSOLUTELY NO WARRANTY. 412s You are welcome to redistribute it under certain conditions. 412s Type 'license()' or 'licence()' for distribution details. 412s 412s R is a collaborative project with many contributors. 412s Type 'contributors()' for more information and 412s 'citation()' on how to cite R or R packages in publications. 412s 412s Type 'demo()' for some demos, 'help()' for on-line help, or 412s 'help.start()' for an HTML browser interface to help. 412s Type 'q()' to quit R. 412s 412s > library(survey) 412s Loading required package: grid 412s Loading required package: Matrix 412s Loading required package: survival 413s 413s Attaching package: 'survey' 413s 413s The following object is masked from 'package:graphics': 413s 413s dotchart 413s 413s > options(warn=2) 413s > 413s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 413s > data(api) 413s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 413s > svyby(~api99, ~stype, dclus1, svymean ) 413s stype api99 se 413s E E 607.7917 22.81660 413s H H 595.7143 41.76400 413s M M 608.6000 32.56064 413s > 413s > set.seed(123) 413s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 413s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 413s > 413s > # subsetting w/ na.rm = FALSE... 413s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 413s mean SE 413s api99 NA NA 413s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 413s mean SE 413s api99 595.71 41.764 413s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 413s mean SE 413s api99 NA NA 413s > 413s > # ... looks like this: 413s > svyby(~api99, ~stype, dclus1.na , svymean ) 413s stype api99 se 413s E E NA NA 413s H H 595.7143 41.764 413s M M NA NA 413s > 413s > # subsetting w/ na.rm = TRUE... 413s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 413s mean SE 413s api99 606.53 22.901 413s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 413s mean SE 413s api99 595.71 41.764 413s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 413s mean SE 413s api99 613.39 33.224 413s > 413s > # ... looks like this 413s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 413s stype api99 se 413s E E 606.5319 22.90084 413s H H 595.7143 41.76400 413s M M 613.3913 33.22358 413s > 413s > # Without missing values, this works: 413s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 413s stype api99 se 413s E E 607.7917 22.81660 413s H H 595.7143 41.76400 413s M M 608.6000 32.56064 413s > 413s > # ... but this breaks! 413s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 413s stype api99 se 413s E E 606.5319 22.90084 413s H H 595.7143 41.76400 413s M M 613.3913 33.22358 413s > 413s > # ... and i don't think this is the expected behavior 413s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 413s stype api99 se 413s E E NA NA 413s H H 595.7143 41.764 413s M M NA NA 413s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 413s stype api99 se 413s E E 606.5319 22.90084 413s H H 595.7143 41.76400 413s M M 613.3913 33.22358 413s > 413s > 413s > ## Now some more as tests 413s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 413s stype api99 se 413s E E 2894629.0 792809.8 413s H H 282283.9 101492.9 413s M M 477513.4 107555.5 413s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 413s stype api99/api00 se.api99/api00 413s E E 0.9367750 0.006365702 413s H H 0.9630485 0.010520785 413s M M 0.9682246 0.009390982 413s > 413s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 413s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 413s stype (Intercept) se.(Intercept) 413s E E 606.5319 22.90084 413s H H 595.7143 41.76400 413s M M 613.3913 33.22358 413s > 413s BEGIN TEST svyby_se.R 413s 413s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 413s Copyright (C) 2025 The R Foundation for Statistical Computing 413s Platform: aarch64-unknown-linux-gnu 413s 413s R is free software and comes with ABSOLUTELY NO WARRANTY. 413s You are welcome to redistribute it under certain conditions. 413s Type 'license()' or 'licence()' for distribution details. 413s 413s R is a collaborative project with many contributors. 413s Type 'contributors()' for more information and 413s 'citation()' on how to cite R or R packages in publications. 413s 413s Type 'demo()' for some demos, 'help()' for on-line help, or 413s 'help.start()' for an HTML browser interface to help. 413s Type 'q()' to quit R. 413s 413s > library(survey) 413s Loading required package: grid 413s Loading required package: Matrix 414s Loading required package: survival 414s 414s Attaching package: 'survey' 414s 414s > data(api) 414s The following object is masked from 'package:graphics': 414s 414s dotchart 414s 414s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 414s > 414s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 414s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 414s > 414s > 414s > stopifnot(all.equal(SE(a),SE(b))) 414s > 414s BEGIN TEST svycontrast.R 414s 414s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 414s Copyright (C) 2025 The R Foundation for Statistical Computing 414s Platform: aarch64-unknown-linux-gnu 414s 414s R is free software and comes with ABSOLUTELY NO WARRANTY. 414s You are welcome to redistribute it under certain conditions. 414s Type 'license()' or 'licence()' for distribution details. 414s 414s R is a collaborative project with many contributors. 414s Type 'contributors()' for more information and 414s 'citation()' on how to cite R or R packages in publications. 414s 414s Type 'demo()' for some demos, 'help()' for on-line help, or 414s 'help.start()' for an HTML browser interface to help. 414s Type 'q()' to quit R. 414s 414s > library(survey) 414s Loading required package: grid 414s Loading required package: Matrix 415s Loading required package: survival 416s 416s Attaching package: 'survey' 416s 416s The following object is masked from 'package:graphics': 416s 416s dotchart 416s 416s > data(api) 416s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 416s > rclus2<-as.svrepdesign(dclus2) 416s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 416s > svycontrast(model, c(ell=1,meals=0)) 416s contrast SE 416s contrast -2.0592 1.6177 416s > a<-svycontrast(model, c(0,1,0,0)) 416s > 416s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 416s > svycontrast(model2, c(ell=1,meals=0)) 416s contrast SE 416s contrast -2.0592 1.6177 416s > a2<-svycontrast(model2, c(0,1,0,0)) 416s > stopifnot(!is.null(a2$replicates)) 416s > 416s BEGIN TEST svyivreg-var.R 416s 416s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 416s Copyright (C) 2025 The R Foundation for Statistical Computing 416s Platform: aarch64-unknown-linux-gnu 416s 416s R is free software and comes with ABSOLUTELY NO WARRANTY. 416s You are welcome to redistribute it under certain conditions. 416s Type 'license()' or 'licence()' for distribution details. 416s 416s R is a collaborative project with many contributors. 416s Type 'contributors()' for more information and 416s 'citation()' on how to cite R or R packages in publications. 416s 416s Type 'demo()' for some demos, 'help()' for on-line help, or 416s 'help.start()' for an HTML browser interface to help. 416s Type 'q()' to quit R. 416s 416s > 416s > library(survey) 416s Loading required package: grid 416s Loading required package: Matrix 417s Loading required package: survival 417s 417s Attaching package: 'survey' 417s 417s The following object is masked from 'package:graphics': 417s 417s dotchart 417s 417s > data(api) 417s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 417s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 417s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 417s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 417s > 417s BEGIN TEST svyivreg.R 417s 417s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 417s Copyright (C) 2025 The R Foundation for Statistical Computing 417s Platform: aarch64-unknown-linux-gnu 417s 417s R is free software and comes with ABSOLUTELY NO WARRANTY. 417s You are welcome to redistribute it under certain conditions. 417s Type 'license()' or 'licence()' for distribution details. 417s 417s R is a collaborative project with many contributors. 417s Type 'contributors()' for more information and 417s 'citation()' on how to cite R or R packages in publications. 417s 417s Type 'demo()' for some demos, 'help()' for on-line help, or 417s 'help.start()' for an HTML browser interface to help. 417s Type 'q()' to quit R. 417s 417s > library(survey) 417s Loading required package: grid 417s Loading required package: Matrix 418s Loading required package: survival 418s 418s Attaching package: 'survey' 418s 418s The following object is masked from 'package:graphics': 418s 418s dotchart 418s 418s > library(AER) 418s Loading required package: car 418s Loading required package: carData 418s Loading required package: lmtest 418s Loading required package: zoo 418s 418s Attaching package: 'zoo' 418s 418s The following objects are masked from 'package:base': 418s 418s as.Date, as.Date.numeric 418s 418s Loading required package: sandwich 418s > 418s > load("cigsw.rda") 418s > 418s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 418s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 418s > 418s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 418s [1] TRUE 418s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 418s [1] TRUE 418s > 418s BEGIN TEST svyolr-rake-subset.R 418s 418s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 418s Copyright (C) 2025 The R Foundation for Statistical Computing 418s Platform: aarch64-unknown-linux-gnu 418s 418s R is free software and comes with ABSOLUTELY NO WARRANTY. 418s You are welcome to redistribute it under certain conditions. 418s Type 'license()' or 'licence()' for distribution details. 418s 418s R is a collaborative project with many contributors. 418s Type 'contributors()' for more information and 418s 'citation()' on how to cite R or R packages in publications. 418s 418s Type 'demo()' for some demos, 'help()' for on-line help, or 418s 'help.start()' for an HTML browser interface to help. 418s Type 'q()' to quit R. 418s 419s > library(survey) 419s Loading required package: grid 419s Loading required package: Matrix 419s Loading required package: survival 420s 420s Attaching package: 'survey' 420s 420s The following object is masked from 'package:graphics': 420s 420s dotchart 420s 420s > data(api) 420s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 420s > 420s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 420s > 420s > ## population marginal totals for each stratum 420s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 420s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 420s > 420s > 420s > ## rake with the population totals 420s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 420s > 420s > # works 420s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 420s > 420s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 420s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 420s > 420s > # fails in 4.1 (should work because NA values are subsetted out) 420s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 420s > 420s BEGIN TEST svyolr.R 420s 420s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 420s Copyright (C) 2025 The R Foundation for Statistical Computing 420s Platform: aarch64-unknown-linux-gnu 420s 420s R is free software and comes with ABSOLUTELY NO WARRANTY. 420s You are welcome to redistribute it under certain conditions. 420s Type 'license()' or 'licence()' for distribution details. 420s 420s R is a collaborative project with many contributors. 420s Type 'contributors()' for more information and 420s 'citation()' on how to cite R or R packages in publications. 420s 420s Type 'demo()' for some demos, 'help()' for on-line help, or 420s 'help.start()' for an HTML browser interface to help. 420s Type 'q()' to quit R. 420s 420s > library(survey) 420s Loading required package: grid 420s Loading required package: Matrix 421s Loading required package: survival 421s 421s Attaching package: 'survey' 421s 421s The following object is masked from 'package:graphics': 421s 421s dotchart 421s 421s > 421s > ################################################################################ 421s > # Example from svyolr: runs OK 421s > data(api) 421s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 421s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 421s > 421s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 421s > m 421s Call: 421s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 421s 421s Coefficients: 421s avg.ed mobility stypeH stypeM 421s -2.6999217 0.0325042 -1.7574715 -0.6191463 421s 421s Intercepts: 421s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 421s -8.857919 -6.586464 -4.924938 421s > 421s > ## Use regTermTest for testing multiple parameters 421s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 421s > ################################################################################ 421s > 421s > ################################################################################ 421s > # If we wrap everything into a function: error b/c it looks for design variable 421s > # dclus1 in .GlobalEnv 421s > 421s > foo <- function(x){ 421s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 421s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 421s + 421s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 421s + ## Use regTermTest for testing multiple parameters 421s + regTermTest(m, ~avg.ed+stype, method="LRT") 421s + } 421s > 421s > # OK 421s > foo(apiclus1) 421s Working (Rao-Scott+F) LRT for avg.ed stype 421s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 421s Working 2logLR = 0.6580304 p= 0.73257 421s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 421s > 421s > # Clean-up everything but apiclus1 and foo 421s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 421s > 421s > # Error 421s > test2<-foo(apiclus1) 421s > ################################################################################ 421s > all.equal(test,test2) 421s [1] TRUE 421s > 421s > 421s BEGIN TEST toy_example_for_postStratify.R 421s 421s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 421s Copyright (C) 2025 The R Foundation for Statistical Computing 421s Platform: aarch64-unknown-linux-gnu 421s 421s R is free software and comes with ABSOLUTELY NO WARRANTY. 421s You are welcome to redistribute it under certain conditions. 421s Type 'license()' or 'licence()' for distribution details. 421s 421s R is a collaborative project with many contributors. 421s Type 'contributors()' for more information and 421s 'citation()' on how to cite R or R packages in publications. 421s 421s Type 'demo()' for some demos, 'help()' for on-line help, or 421s 'help.start()' for an HTML browser interface to help. 421s Type 'q()' to quit R. 421s 422s > library(survey) 422s Loading required package: grid 422s Loading required package: Matrix 422s Loading required package: survival 423s 423s Attaching package: 'survey' 423s 423s The following object is masked from 'package:graphics': 423s 423s dotchart 423s 423s > 423s > # Dummy data for testing nonresponse adjustments 423s > toy <- data.frame(id = 1:10, 423s + dummy = 1, 423s + class = c(rep("A", 5), rep("B", 5)), 423s + responded = c(rep(TRUE, 8), FALSE, FALSE), 423s + weight = rep(100, 10)) 423s > 423s > # With jackknife replicate weights 423s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 423s > diag(toy_repweights) <- rep(0, 10) 423s > 423s > # Scramble up which person is in which jackknife group 423s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 423s > 423s > toy_design <- svrepdesign(variables = toy[, 1:4], 423s + weights = toy$weight, 423s + repweights = toy_repweights, 423s + type = "JK1", 423s + scale = 0.9) 423s > 423s > # Get the sum of the weights for the full sample 423s > poptotals <- as.data.frame(svyby(formula = ~dummy, 423s + by = ~class, 423s + design = toy_design, 423s + FUN = survey::svytotal)) 423s > 423s > poptotals$Freq <- poptotals$dummy 423s > poptotals$dummy <- NULL 423s > poptotals$se <- NULL 423s > 423s > # Adjust the weights of the responding sample to match to the full sample 423s > adjusted <- postStratify(design = subset(toy_design, responded), 423s + strata = ~class, 423s + population = poptotals) 423s > 423s > # This works for the weights... 423s > svyby(formula = ~dummy, 423s + by = ~class, 423s + design = adjusted, 423s + FUN = survey::svytotal) 423s class dummy se 423s A A 500 0 423s B B 500 0 423s > 423s > # ...and some, but not all, the replicate weights 423s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 423s > 423s > 423s > 423s BEGIN TEST twophase.R 423s 423s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 423s Copyright (C) 2025 The R Foundation for Statistical Computing 423s Platform: aarch64-unknown-linux-gnu 423s 423s R is free software and comes with ABSOLUTELY NO WARRANTY. 423s You are welcome to redistribute it under certain conditions. 423s Type 'license()' or 'licence()' for distribution details. 423s 423s R is a collaborative project with many contributors. 423s Type 'contributors()' for more information and 423s 'citation()' on how to cite R or R packages in publications. 423s 423s Type 'demo()' for some demos, 'help()' for on-line help, or 423s 'help.start()' for an HTML browser interface to help. 423s Type 'q()' to quit R. 423s 423s > library(survey) 423s Loading required package: grid 423s Loading required package: Matrix 424s Loading required package: survival 424s 424s Attaching package: 'survey' 424s 424s The following object is masked from 'package:graphics': 424s 424s dotchart 424s 424s > 424s > ## two-phase simple random sampling. 424s > data(pbc, package="survival") 424s > pbc$id<-1:nrow(pbc) 424s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 424s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 424s Two-phase sparse-matrix design: 424s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 424s subset = subset, data = data, pps = pps) 424s Phase 1: 424s Independent Sampling design (with replacement) 424s svydesign(ids = ~id) 424s Phase 2: 424s Independent Sampling design 424s svydesign(ids = ~id, fpc = `*phase1*`) 424s > m<-svymean(~bili, d2pbc) 424s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 424s [1] TRUE 424s > all.equal(as.vector(SE(m)), 424s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 424s + tolerance=0.002) 424s [1] TRUE 424s > 424s > ## two-stage sampling as two-phase 424s > data(mu284) 424s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 424s > mu284.1<-mu284[ii,] 424s > mu284.1$id<-1:nrow(mu284.1) 424s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 424s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 424s > ## first phase cluster sample, second phase stratified within cluster 424s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 424s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 424s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 424s NULL), data = mu284.1, subset = ~sub, method = "approx") 424s Phase 1: 424s 1 - level Cluster Sampling design 424s With (5) clusters. 424s svydesign(ids = ~id1, fpc = ~n1) 424s Phase 2: 424s Stratified Independent Sampling design 424s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 424s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 424s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 424s Two-phase sparse-matrix design: 424s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 424s subset = subset, data = data, pps = pps) 424s Phase 1: 424s 1 - level Cluster Sampling design 424s With (5) clusters. 424s svydesign(ids = ~id1, fpc = ~n1) 424s Phase 2: 424s Stratified Independent Sampling design 424s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 424s > summary(d2mu284) 424s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 424s NULL), data = mu284.1, subset = ~sub, method = "approx") 424s Phase 1: 424s 1 - level Cluster Sampling design 424s With (5) clusters. 424s svydesign(ids = ~id1, fpc = ~n1) 424s Probabilities: 424s Min. 1st Qu. Median Mean 3rd Qu. Max. 424s 0.1 0.1 0.1 0.1 0.1 0.1 424s Population size (PSUs): 50 424s Phase 2: 424s Stratified Independent Sampling design 424s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 424s Probabilities: 424s Min. 1st Qu. Median Mean 3rd Qu. Max. 424s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 424s Stratum Sizes: 424s 19 31 45 47 50 424s obs 3 3 3 3 3 424s design.PSU 3 3 3 3 3 424s actual.PSU 3 3 3 3 3 424s Population stratum sizes (PSUs): 424s 19 31 45 47 50 424s 5 7 8 5 9 424s Data variables: 424s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 424s > t1<-svytotal(~y1, dmu284) 424s > t2<-svytotal(~y1, d2mu284) 424s > t22<-svytotal(~y1,d22mu284) 424s > m1<-svymean(~y1, dmu284) 424s > m2<-svymean(~y1, d2mu284) 424s > m22<-svymean(~y1, d22mu284) 424s > all.equal(coef(t1),coef(t2)) 424s [1] TRUE 424s > all.equal(coef(t1),coef(t22)) 424s [1] TRUE 424s > all.equal(coef(m1),coef(m2)) 424s [1] TRUE 424s > all.equal(coef(m1),coef(m22)) 424s [1] TRUE 424s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 424s [1] TRUE 424s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 424s [1] TRUE 424s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 424s [1] TRUE 424s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 424s [1] TRUE 424s > 424s > ## case-cohort design 424s > ##this example requires R 2.3.1 or later for cch and data. 424s > library("survival") 424s > data(nwtco, package="survival") 424s > ## unstratified, equivalent to Lin & Ying (1993) 424s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 424s + subset=~I(in.subcohort | rel), data=nwtco)) 425s Two-phase sparse-matrix design: 425s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 425s subset = subset, data = data, pps = pps) 425s Phase 1: 425s Independent Sampling design (with replacement) 425s svydesign(ids = ~seqno) 425s Phase 2: 425s Stratified Independent Sampling design 425s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 425s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 425s + design=dcchs) 425s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 425s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 425s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 425s + design=dcchs) 425s > all.equal(coef(cch1),coef(cch1.2)) 425s [1] TRUE 425s > all.equal(SE(cch1),SE(cch1.2)) 425s [1] TRUE 425s > ## Using survival::cch 425s > subcoh <- nwtco$in.subcohort 425s > selccoh <- with(nwtco, rel==1|subcoh==1) 425s > ccoh.data <- nwtco[selccoh,] 425s > ccoh.data$subcohort <- subcoh[selccoh] 425s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 425s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 425s + cohort.size=4028, method="LinYing", robust=TRUE) 425s > 425s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 425s [1] TRUE 425s > ## cch has smaller variances by a factor of 1.0005 because 425s > ## there is a (n/(n-1)) in the survey phase1 varianace 425s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 425s [1] TRUE 425s > 425s > 425s > ## bug report from Takahiro Tsuchiya for version 3.4 425s > ## We used to not match Sarndal exactly, because our old phase-one 425s > ## estimator had a small bias for finite populations 425s > rei<-read.table(tmp<-textConnection( 425s + " id N n.a h n.ah n.h sub y 425s + 1 1 300 20 1 12 5 TRUE 1 425s + 2 2 300 20 1 12 5 TRUE 2 425s + 3 3 300 20 1 12 5 TRUE 3 425s + 4 4 300 20 1 12 5 TRUE 4 425s + 5 5 300 20 1 12 5 TRUE 5 425s + 6 6 300 20 1 12 5 FALSE NA 425s + 7 7 300 20 1 12 5 FALSE NA 425s + 8 8 300 20 1 12 5 FALSE NA 425s + 9 9 300 20 1 12 5 FALSE NA 425s + 10 10 300 20 1 12 5 FALSE NA 425s + 11 11 300 20 1 12 5 FALSE NA 425s + 12 12 300 20 1 12 5 FALSE NA 425s + 13 13 300 20 2 8 3 TRUE 6 425s + 14 14 300 20 2 8 3 TRUE 7 425s + 15 15 300 20 2 8 3 TRUE 8 425s + 16 16 300 20 2 8 3 FALSE NA 425s + 17 17 300 20 2 8 3 FALSE NA 425s + 18 18 300 20 2 8 3 FALSE NA 425s + 19 19 300 20 2 8 3 FALSE NA 425s + 20 20 300 20 2 8 3 FALSE NA 425s + "), header=TRUE) 425s > close(tmp) 425s > 425s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 425s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 425s > tot<- svytotal(~y, des.rei) 425s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 425s + fpc=list(~N,NULL), subset=~sub, data=rei) 425s > tot2<- svytotal(~y, des.rei2) 425s > 425s > ## based on Sarndal et al (9.4.14) 425s > rei$w.ah <- rei$n.ah / rei$n.a 425s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 425s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 425s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 425s > 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)) 425s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 425s > 425s > a.rei$f.h<-with(a.rei, n.h/n.ah) 425s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 425s > 425s > a.rei$f<-with(a.rei, n.a/N) 425s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 425s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 425s > 425s > V 425s [1] 36522.63 425s > Vphase1 425s [1] 24072.63 425s > Vphase2 425s [1] 12450 425s > vcov(tot) 425s y 425s y 35911.05 425s attr(,"phases") 425s attr(,"phases")$phase1 425s [,1] 425s [1,] 23461.05 425s 425s attr(,"phases")$phase2 425s y 425s y 12450 425s 425s > vcov(tot2) 425s [,1] 425s [1,] 36522.63 425s attr(,"phases") 425s attr(,"phases")$phase1 425s [,1] 425s [1,] 24072.63 425s 425s attr(,"phases")$phase2 425s [,1] 425s [1,] 12450 425s 425s > ## phase 2 identical 425s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 425s [1] TRUE 425s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 425s [1] TRUE 425s > ## phase 1 differs by 2.6% for old twophase estimator 425s > Vphase1/attr(vcov(tot),"phases")$phase1 425s [,1] 425s [1,] 1.026068 425s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 425s [1] TRUE 425s > 425s > 425s autopkgtest [23:18:09]: test run-unit-test: -----------------------] 426s autopkgtest [23:18:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 426s run-unit-test PASS 426s autopkgtest [23:18:10]: test pkg-r-autopkgtest: preparing testbed 446s Creating nova instance adt-resolute-arm64-r-cran-survey-20260209-231104-juju-7f2275-prod-proposed-migration-environment-15-12b8b94f-6312-4b22-b4e8-be2eb4190e1f from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 575s autopkgtest [23:20:39]: testbed dpkg architecture: arm64 575s autopkgtest [23:20:39]: testbed apt version: 3.1.15 575s autopkgtest [23:20:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 576s autopkgtest [23:20:40]: testbed release detected to be: resolute 576s autopkgtest [23:20:40]: updating testbed package index (apt update) 577s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 577s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 577s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 577s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 577s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 577s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 577s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 580s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 580s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 580s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 580s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 583s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 583s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 583s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 584s Fetched 3862 kB in 6s (605 kB/s) 585s Reading package lists... 586s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 586s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 586s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 586s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 587s Reading package lists... 587s Reading package lists... 587s Building dependency tree... 587s Reading state information... 587s Calculating upgrade... 588s The following packages will be upgraded: 588s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 588s libip6tc2 libxtables12 wget 588s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 588s Need to get 2534 kB of archives. 588s After this operation, 18.4 kB of additional disk space will be used. 588s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 588s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 588s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 588s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 588s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 590s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 590s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 590s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 590s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 590s dpkg-preconfigure: unable to re-open stdin: No such file or directory 590s Fetched 2534 kB in 2s (1207 kB/s) 590s (Reading database ... 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Need to get 268 MB of archives. 598s After this operation, 708 MB of additional disk space will be used. 598s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 598s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 601s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 601s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 601s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 604s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 605s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 605s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 626s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 626s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 626s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 626s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 626s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 626s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 626s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 631s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 633s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 637s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 640s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 642s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 647s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 691s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 691s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 691s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 691s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 696s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 721s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 721s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 721s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 721s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 721s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 721s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 721s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 723s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 723s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 723s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 723s Get:37 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 723s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 727s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 727s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 727s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 750s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 750s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 750s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 750s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 750s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 750s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 750s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 750s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 750s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 750s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 750s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 750s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 751s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 751s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 751s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 751s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 751s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 751s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 751s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 752s Get:61 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 782s Get:62 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 782s Get:63 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 782s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 782s Get:65 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 782s Get:66 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 782s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 782s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 782s Get:69 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 782s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 782s Get:71 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 787s Get:72 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 794s Get:73 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 794s Get:74 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 794s Get:75 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 794s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 794s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 794s Get:78 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 794s Get:79 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 794s Get:80 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 794s Get:81 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 794s Get:82 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 794s Get:83 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 794s Get:84 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 794s Get:85 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 796s Get:86 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 796s Get:87 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 797s Get:88 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 797s Get:89 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 797s Get:90 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 797s Get:91 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 797s Get:92 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 799s Get:93 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 799s Get:94 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 799s Get:95 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 799s Get:96 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 799s Get:97 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 799s Get:98 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 800s Get:99 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 800s Get:100 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 800s Get:101 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 800s Get:102 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 800s Get:103 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 800s Get:104 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 800s Get:105 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 848s Get:106 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 848s Get:107 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 848s Get:108 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 848s Get:109 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 848s Get:110 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 848s Get:111 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 848s Get:112 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-abind all 1.4-8-1build1 [67.0 kB] 848s Get:113 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cardata all 3.0.6-1 [1687 kB] 851s Get:114 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 851s Get:115 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 853s Get:116 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-lattice arm64 0.22-9-1 [1399 kB] 855s Get:117 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 859s Get:118 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 866s Get:119 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-4-1 [3546 kB] 873s Get:120 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 873s Get:121 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-boot all 1.3-32-1 [636 kB] 875s Get:122 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 875s Get:123 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 875s Get:124 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 882s Get:125 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-minqa arm64 1.2.8-1 [112 kB] 882s Get:126 http://ftpmaster.internal/ubuntu resolute/universe arm64 libnlopt0 arm64 2.7.1-7ubuntu1 [177 kB] 882s Get:127 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nloptr arm64 2.2.1-2 [250 kB] 882s Get:128 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rbibutils arm64 2.3-1 [1016 kB] 884s Get:129 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rdpack all 2.6.3-1 [636 kB] 885s Get:130 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reformulas all 0.4.4-1 [151 kB] 885s Get:131 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 889s Get:132 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcppeigen arm64 0.3.4.0.2-1 [1422 kB] 890s Get:133 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 890s Get:134 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lme4 arm64 1.1-38-1 [4177 kB] 897s Get:135 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 897s Get:136 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 899s Get:137 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 899s Get:138 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 899s Get:139 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 899s Get:140 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 899s Get:141 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 899s Get:142 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 901s Get:143 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 901s Get:144 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 901s Get:145 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fansi arm64 1.0.6-2 [627 kB] 902s Get:146 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 902s Get:147 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 902s Get:148 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 902s Get:149 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 902s Get:150 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 905s Get:151 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 906s Get:152 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringi arm64 1.8.4-1build2 [901 kB] 908s Get:153 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 908s Get:154 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 908s Get:155 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 911s Get:156 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 914s Get:157 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 914s Get:158 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 914s Get:159 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 916s Get:160 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 919s Get:161 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 919s Get:162 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 919s Get:163 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-viridislite all 0.4.3-1 [1088 kB] 921s Get:164 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-scales all 1.4.0-1 [725 kB] 922s Get:165 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 929s Get:166 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 930s Get:167 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-deriv all 4.2.0-1 [154 kB] 930s Get:168 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 932s Get:169 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fracdiff arm64 1.5-3-1 [108 kB] 932s Get:170 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-zoo arm64 1.8-15-1 [1025 kB] 934s Get:171 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lmtest arm64 0.9.40-1build1 [400 kB] 934s Get:172 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timedate arm64 4052.112-1 [1298 kB] 936s Get:173 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quadprog arm64 1.5-8-1build2 [31.9 kB] 936s Get:174 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xts arm64 0.14.1-1 [1189 kB] 938s Get:175 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-curl arm64 7.0.0+dfsg-1 [202 kB] 938s Get:176 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ttr arm64 0.24.4-1 [509 kB] 938s Get:177 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB] 939s Get:178 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quantmod all 0.4.28-1 [1037 kB] 940s Get:179 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tseries arm64 0.10-59-3 [381 kB] 940s Get:180 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-urca arm64 1.3-4-1build1 [1050 kB] 942s Get:181 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpparmadillo arm64 15.2.3-1-1 [916 kB] 944s Get:182 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-forecast arm64 8.23.0-1 [1564 kB] 946s Get:183 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 946s Get:184 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-microbenchmark arm64 1.5.0-1 [67.5 kB] 946s Get:185 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-doby all 4.7.1-3 [4741 kB] 957s Get:186 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.5-1 [117 kB] 957s Get:187 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.55+dfsg-1 [587 kB] 958s Get:188 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 958s Get:189 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 958s Get:190 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 969s Get:191 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 971s Get:192 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 971s Get:193 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sparsem arm64 1.84-2-1 [812 kB] 972s Get:194 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrixmodels all 0.5-4-1 [351 kB] 972s Get:195 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survival arm64 3.8-6-1 [8270 kB] 985s Get:196 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB] 985s Get:197 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-class arm64 7.3-23-1 [90.5 kB] 985s Get:198 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-proxy arm64 0.4-27-1 [181 kB] 986s Get:199 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-e1071 arm64 1.7-17-1 [576 kB] 987s Get:200 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-codetools all 0.2-20-1build1 [91.1 kB] 987s Get:201 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-iterators all 1.0.14-1build1 [336 kB] 987s Get:202 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-foreach all 1.5.2-1build1 [124 kB] 987s Get:203 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 990s Get:204 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-modelmetrics arm64 1.2.2.2-1build2 [143 kB] 990s Get:205 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 991s Get:206 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-proc arm64 1.18.5-1 [963 kB] 993s Get:207 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-tzdb arm64 0.5.0-1 [530 kB] 994s Get:208 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-clock arm64 0.7.2-1 [1829 kB] 998s Get:209 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gower arm64 1.0.2-1 [208 kB] 998s Get:210 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sparsevctrs arm64 0.2.0-2 [169 kB] 998s Get:211 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-hardhat all 1.4.2+dfsg-1 [596 kB] 999s Get:212 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rpart arm64 4.1.24-1build1 [665 kB] 1001s Get:213 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-shape all 1.4.6.1-1 [749 kB] 1002s Get:214 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-diagram all 1.6.5-2 [656 kB] 1003s Get:215 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-kernsmooth arm64 2.23-26-1build1 [93.6 kB] 1003s Get:216 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-digest arm64 0.6.39-1 [196 kB] 1003s Get:217 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-globals all 0.19.0-1 [160 kB] 1003s Get:218 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 1003s Get:219 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-parallelly arm64 1.42.0-1 [540 kB] 1004s Get:220 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 1005s Get:221 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 1005s Get:222 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-progressr all 0.15.1-1 [353 kB] 1005s Get:223 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-squarem all 2021.1-1build1 [180 kB] 1005s Get:224 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lava all 1.8.2+dfsg-1 [2210 kB] 1009s Get:225 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-prodlim arm64 2024.06.25-1 [415 kB] 1009s Get:226 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ipred arm64 0.9-15-1 [386 kB] 1009s Get:227 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-timechange arm64 0.3.0-2 [175 kB] 1010s Get:228 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lubridate arm64 1.9.4+dfsg-1 [1009 kB] 1011s Get:229 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 1015s Get:230 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-reshape2 arm64 1.4.4-2build2 [118 kB] 1015s Get:231 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-caret arm64 7.0-1+dfsg-1 [3461 kB] 1021s Get:232 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-conquer arm64 1.3.3-1 [440 kB] 1021s Get:233 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quantreg arm64 6.1-1 [1437 kB] 1024s Get:234 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-car all 3.1-5-1 [1526 kB] 1026s Get:235 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-sandwich all 3.1-1-1build1 [1483 kB] 1029s Get:236 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-aer all 1.2-15-1 [2607 kB] 1033s Get:237 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit arm64 4.6.0+dfsg-1 [450 kB] 1033s Get:238 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-bit64 arm64 4.6.0-1-4 [495 kB] 1033s Get:239 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-blob all 1.3.0-1 [54.1 kB] 1033s Get:240 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB] 1033s Get:241 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB] 1033s Get:242 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-dbi all 1.2.3-1build1 [855 kB] 1035s Get:243 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-foreign arm64 0.8.91-1 [243 kB] 1035s Get:244 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-hexbin arm64 1.28.5-1 [1580 kB] 1039s Get:245 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-memoise all 2.0.1-1build1 [54.5 kB] 1039s Get:246 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mitools all 2.4-2build2 [266 kB] 1039s Get:247 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-plogr all 0.2.0-3build2 [15.8 kB] 1039s Get:248 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rsqlite arm64 2.3.9-1 [1247 kB] 1041s Get:249 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-survey arm64 4.4-2-2 [3448 kB] 1048s Preconfiguring packages ... 1048s Fetched 268 MB in 7min 30s (595 kB/s) 1048s Selecting previously unselected package libc-dev-bin. 1048s (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 ... 136600 files and directories currently installed.) 1048s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 1048s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 1048s Selecting previously unselected package linux-libc-dev:arm64. 1048s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_arm64.deb ... 1048s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 1048s Selecting previously unselected package libcrypt-dev:arm64. 1048s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 1048s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 1048s Selecting previously unselected package rpcsvc-proto. 1049s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 1049s Unpacking rpcsvc-proto (1.4.3-1build1) ... 1049s Selecting previously unselected package libc6-dev:arm64. 1049s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_arm64.deb ... 1049s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 1049s Selecting previously unselected package libisl23:arm64. 1049s Preparing to unpack .../005-libisl23_0.27-1build1_arm64.deb ... 1049s Unpacking libisl23:arm64 (0.27-1build1) ... 1049s Selecting previously unselected package libmpc3:arm64. 1049s Preparing to unpack .../006-libmpc3_1.3.1-2_arm64.deb ... 1049s Unpacking libmpc3:arm64 (1.3.1-2) ... 1049s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 1049s Preparing to unpack .../007-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1049s Selecting previously unselected package cpp-15. 1049s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 1049s Selecting previously unselected package cpp-aarch64-linux-gnu. 1049s Preparing to unpack .../009-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1049s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1049s Selecting previously unselected package cpp. 1049s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 1049s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1049s Selecting previously unselected package libcc1-0:arm64. 1049s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 1049s Selecting previously unselected package libgomp1:arm64. 1049s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 1049s Selecting previously unselected package libitm1:arm64. 1049s Preparing to unpack .../013-libitm1_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 1049s Selecting previously unselected package libasan8:arm64. 1049s Preparing to unpack .../014-libasan8_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 1049s Selecting previously unselected package liblsan0:arm64. 1049s Preparing to unpack .../015-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 1049s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package libtsan2:arm64. 1050s Preparing to unpack .../016-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package libubsan1:arm64. 1050s Preparing to unpack .../017-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package libhwasan0:arm64. 1050s Preparing to unpack .../018-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package libgcc-15-dev:arm64. 1050s Preparing to unpack .../019-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 1050s Preparing to unpack .../020-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package gcc-15. 1050s Preparing to unpack .../021-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 1050s Selecting previously unselected package gcc-aarch64-linux-gnu. 1050s Preparing to unpack .../022-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1050s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1050s Selecting previously unselected package gcc. 1050s Preparing to unpack .../023-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 1050s Unpacking gcc (4:15.2.0-4ubuntu1) ... 1050s Selecting previously unselected package libstdc++-15-dev:arm64. 1050s Preparing to unpack .../024-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1050s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 1051s Selecting previously unselected package g++-15-aarch64-linux-gnu. 1051s Preparing to unpack .../025-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1051s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1051s Selecting previously unselected package g++-15. 1051s Preparing to unpack .../026-g++-15_15.2.0-12ubuntu1_arm64.deb ... 1051s Unpacking g++-15 (15.2.0-12ubuntu1) ... 1051s Selecting previously unselected package g++-aarch64-linux-gnu. 1051s Preparing to unpack .../027-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1051s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1051s Selecting previously unselected package g++. 1051s Preparing to unpack .../028-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 1051s Unpacking g++ (4:15.2.0-4ubuntu1) ... 1051s Selecting previously unselected package build-essential. 1051s Preparing to unpack .../029-build-essential_12.12ubuntu2_arm64.deb ... 1051s Unpacking build-essential (12.12ubuntu2) ... 1051s Selecting previously unselected package dctrl-tools. 1051s Preparing to unpack .../030-dctrl-tools_2.24-3build4_arm64.deb ... 1051s Unpacking dctrl-tools (2.24-3build4) ... 1051s Selecting previously unselected package fonts-dejavu-mono. 1051s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8build1_all.deb ... 1051s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1051s Selecting previously unselected package fonts-dejavu-core. 1051s Preparing to unpack .../032-fonts-dejavu-core_2.37-8build1_all.deb ... 1051s Unpacking fonts-dejavu-core (2.37-8build1) ... 1051s Selecting previously unselected package fontconfig-config. 1051s Preparing to unpack .../033-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 1051s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 1051s Selecting previously unselected package libfontconfig1:arm64. 1051s Preparing to unpack .../034-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 1051s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 1051s Selecting previously unselected package fontconfig. 1051s Preparing to unpack .../035-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 1051s Unpacking fontconfig (2.17.1-3ubuntu1) ... 1051s Selecting previously unselected package fonts-glyphicons-halflings. 1051s Preparing to unpack .../036-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 1051s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 1051s Selecting previously unselected package fonts-mathjax. 1052s Preparing to unpack .../037-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 1052s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 1052s Selecting previously unselected package libgfortran5:arm64. 1052s Preparing to unpack .../038-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 1052s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 1052s Selecting previously unselected package libgfortran-15-dev:arm64. 1052s Preparing to unpack .../039-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 1052s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 1052s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 1052s Preparing to unpack .../040-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 1052s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1052s Selecting previously unselected package gfortran-15. 1052s Preparing to unpack .../041-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 1052s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 1052s Selecting previously unselected package gfortran-aarch64-linux-gnu. 1052s Preparing to unpack .../042-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 1052s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1052s Selecting previously unselected package gfortran. 1052s Preparing to unpack .../043-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 1052s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 1052s Selecting previously unselected package icu-devtools. 1052s Preparing to unpack .../044-icu-devtools_78.2-1ubuntu1_arm64.deb ... 1052s Unpacking icu-devtools (78.2-1ubuntu1) ... 1052s Selecting previously unselected package libblas3:arm64. 1052s Preparing to unpack .../045-libblas3_3.12.1-7ubuntu1_arm64.deb ... 1052s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 1052s Selecting previously unselected package libblas-dev:arm64. 1052s Preparing to unpack .../046-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 1052s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 1052s Selecting previously unselected package libbz2-dev:arm64. 1052s Preparing to unpack .../047-libbz2-dev_1.0.8-6build2_arm64.deb ... 1052s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 1052s Selecting previously unselected package libpixman-1-0:arm64. 1052s Preparing to unpack .../048-libpixman-1-0_0.46.4-1_arm64.deb ... 1052s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 1052s Selecting previously unselected package libxcb-render0:arm64. 1052s Preparing to unpack .../049-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 1052s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 1052s Selecting previously unselected package libxcb-shm0:arm64. 1052s Preparing to unpack .../050-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 1052s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 1052s Selecting previously unselected package libxrender1:arm64. 1052s Preparing to unpack .../051-libxrender1_1%3a0.9.12-1_arm64.deb ... 1052s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 1052s Selecting previously unselected package libcairo2:arm64. 1052s Preparing to unpack .../052-libcairo2_1.18.4-3_arm64.deb ... 1052s Unpacking libcairo2:arm64 (1.18.4-3) ... 1052s Selecting previously unselected package libdatrie1:arm64. 1052s 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unselected package libzstd-dev:arm64. 1055s Preparing to unpack .../099-libzstd-dev_1.5.7+dfsg-3_arm64.deb ... 1055s Unpacking libzstd-dev:arm64 (1.5.7+dfsg-3) ... 1055s Selecting previously unselected package node-normalize.css. 1055s Preparing to unpack .../100-node-normalize.css_8.0.1-5.1_all.deb ... 1055s Unpacking node-normalize.css (8.0.1-5.1) ... 1055s Selecting previously unselected package zip. 1055s Preparing to unpack .../101-zip_3.0-15ubuntu3_arm64.deb ... 1055s Unpacking zip (3.0-15ubuntu3) ... 1055s Selecting previously unselected package unzip. 1055s Preparing to unpack .../102-unzip_6.0-29ubuntu1_arm64.deb ... 1055s Unpacking unzip (6.0-29ubuntu1) ... 1055s Selecting previously unselected package xdg-utils. 1055s Preparing to unpack .../103-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1055s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1055s Selecting previously unselected package r-base-core. 1055s Preparing to unpack .../104-r-base-core_4.5.2-1ubuntu2_arm64.deb ... 1055s Unpacking r-base-core (4.5.2-1ubuntu2) ... 1055s Selecting previously unselected package liblzma-dev:arm64. 1055s Preparing to unpack .../105-liblzma-dev_5.8.2-2_arm64.deb ... 1055s Unpacking liblzma-dev:arm64 (5.8.2-2) ... 1055s Selecting previously unselected package pkgconf-bin. 1055s Preparing to unpack .../106-pkgconf-bin_1.8.1-4build1_arm64.deb ... 1055s Unpacking pkgconf-bin (1.8.1-4build1) ... 1055s Selecting previously unselected package pkgconf:arm64. 1055s Preparing to unpack .../107-pkgconf_1.8.1-4build1_arm64.deb ... 1055s Unpacking pkgconf:arm64 (1.8.1-4build1) ... 1055s Selecting previously unselected package libtirpc-dev:arm64. 1055s Preparing to unpack .../108-libtirpc-dev_1.3.6+ds-1_arm64.deb ... 1055s Unpacking libtirpc-dev:arm64 (1.3.6+ds-1) ... 1055s Selecting previously unselected package r-base-dev. 1055s Preparing to unpack .../109-r-base-dev_4.5.2-1ubuntu2_all.deb ... 1056s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 1056s Selecting previously unselected package pkg-r-autopkgtest. 1056s Preparing to unpack .../110-pkg-r-autopkgtest_20250812_all.deb ... 1056s Unpacking pkg-r-autopkgtest (20250812) ... 1056s Selecting previously unselected package r-cran-abind. 1056s Preparing to unpack .../111-r-cran-abind_1.4-8-1build1_all.deb ... 1056s Unpacking r-cran-abind (1.4-8-1build1) ... 1056s Selecting previously unselected package r-cran-cardata. 1056s Preparing to unpack .../112-r-cran-cardata_3.0.6-1_all.deb ... 1056s Unpacking r-cran-cardata (3.0.6-1) ... 1056s Selecting previously unselected package r-cran-formula. 1056s Preparing to unpack .../113-r-cran-formula_1.2-5-1_all.deb ... 1056s Unpacking r-cran-formula (1.2-5-1) ... 1056s Selecting previously unselected package r-cran-mass. 1056s Preparing to unpack .../114-r-cran-mass_7.3-65-1_arm64.deb ... 1056s Unpacking r-cran-mass (7.3-65-1) ... 1056s Selecting previously unselected package r-cran-lattice. 1056s Preparing to unpack .../115-r-cran-lattice_0.22-9-1_arm64.deb ... 1056s Unpacking r-cran-lattice (0.22-9-1) ... 1056s Selecting previously unselected package r-cran-nlme. 1056s Preparing to unpack .../116-r-cran-nlme_3.1.168-1_arm64.deb ... 1056s Unpacking r-cran-nlme (3.1.168-1) ... 1056s Selecting previously unselected package r-cran-matrix. 1056s Preparing to unpack .../117-r-cran-matrix_1.7-4-1_arm64.deb ... 1056s Unpacking r-cran-matrix (1.7-4-1) ... 1056s Selecting previously unselected package r-cran-mgcv. 1056s Preparing to unpack .../118-r-cran-mgcv_1.9-4-1_arm64.deb ... 1056s Unpacking r-cran-mgcv (1.9-4-1) ... 1056s Selecting previously unselected package r-cran-nnet. 1056s Preparing to unpack .../119-r-cran-nnet_7.3-20-1_arm64.deb ... 1056s Unpacking r-cran-nnet (7.3-20-1) ... 1056s Selecting previously unselected package r-cran-boot. 1056s Preparing to unpack .../120-r-cran-boot_1.3-32-1_all.deb ... 1056s Unpacking r-cran-boot (1.3-32-1) ... 1056s Selecting previously unselected package r-cran-littler. 1056s Preparing to unpack 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previously unselected package r-cran-rbibutils. 1056s Preparing to unpack .../127-r-cran-rbibutils_2.3-1_arm64.deb ... 1056s Unpacking r-cran-rbibutils (2.3-1) ... 1056s Selecting previously unselected package r-cran-rdpack. 1057s Preparing to unpack .../128-r-cran-rdpack_2.6.3-1_all.deb ... 1057s Unpacking r-cran-rdpack (2.6.3-1) ... 1057s Selecting previously unselected package r-cran-reformulas. 1057s Preparing to unpack .../129-r-cran-reformulas_0.4.4-1_all.deb ... 1057s Unpacking r-cran-reformulas (0.4.4-1) ... 1057s Selecting previously unselected package r-cran-rlang. 1057s Preparing to unpack .../130-r-cran-rlang_1.1.5-3_arm64.deb ... 1057s Unpacking r-cran-rlang (1.1.5-3) ... 1057s Selecting previously unselected package r-cran-rcppeigen. 1057s Preparing to unpack .../131-r-cran-rcppeigen_0.3.4.0.2-1_arm64.deb ... 1057s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 1057s Selecting previously unselected package r-cran-statmod. 1057s Preparing to unpack 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package r-cran-lifecycle. 1057s Preparing to unpack .../138-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 1057s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 1057s Selecting previously unselected package r-cran-magrittr. 1057s Preparing to unpack .../139-r-cran-magrittr_2.0.3-1_arm64.deb ... 1057s Unpacking r-cran-magrittr (2.0.3-1) ... 1057s Selecting previously unselected package r-cran-utf8. 1057s Preparing to unpack .../140-r-cran-utf8_1.2.4-1_arm64.deb ... 1057s Unpacking r-cran-utf8 (1.2.4-1) ... 1057s Selecting previously unselected package r-cran-vctrs. 1057s Preparing to unpack .../141-r-cran-vctrs_0.6.5-1_arm64.deb ... 1057s Unpacking r-cran-vctrs (0.6.5-1) ... 1057s Selecting previously unselected package r-cran-pillar. 1057s Preparing to unpack .../142-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 1057s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 1057s Selecting previously unselected package r-cran-r6. 1057s Preparing to unpack .../143-r-cran-r6_2.6.1-1_all.deb ... 1057s Unpacking r-cran-r6 (2.6.1-1) ... 1057s Selecting previously unselected package r-cran-fansi. 1057s Preparing to unpack .../144-r-cran-fansi_1.0.6-2_arm64.deb ... 1057s Unpacking r-cran-fansi (1.0.6-2) ... 1057s Selecting previously unselected package r-cran-pkgconfig. 1057s Preparing to unpack .../145-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 1057s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 1057s Selecting previously unselected package r-cran-tibble. 1057s Preparing to unpack .../146-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 1057s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 1058s Selecting previously unselected package r-cran-withr. 1058s Preparing to unpack .../147-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1058s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1058s Selecting previously unselected package r-cran-tidyselect. 1058s Preparing to unpack .../148-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 1058s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 1058s Selecting previously unselected package r-cran-dplyr. 1058s Preparing to unpack .../149-r-cran-dplyr_1.1.4-4_arm64.deb ... 1058s Unpacking r-cran-dplyr (1.1.4-4) ... 1058s Selecting previously unselected package r-cran-purrr. 1058s Preparing to unpack .../150-r-cran-purrr_1.0.4-1_arm64.deb ... 1058s Unpacking r-cran-purrr (1.0.4-1) ... 1058s Selecting previously unselected package r-cran-stringi. 1058s Preparing to unpack .../151-r-cran-stringi_1.8.4-1build2_arm64.deb ... 1058s Unpacking r-cran-stringi (1.8.4-1build2) ... 1058s Selecting previously unselected package r-cran-stringr. 1058s Preparing to unpack .../152-r-cran-stringr_1.5.1-1_all.deb ... 1058s Unpacking r-cran-stringr (1.5.1-1) ... 1058s Selecting previously unselected package r-cran-cpp11. 1058s Preparing to unpack .../153-r-cran-cpp11_0.5.3-1_all.deb ... 1058s Unpacking r-cran-cpp11 (0.5.3-1) ... 1058s Selecting previously unselected package r-cran-tidyr. 1058s Preparing to unpack .../154-r-cran-tidyr_1.3.1-1_arm64.deb ... 1058s Unpacking r-cran-tidyr (1.3.1-1) ... 1058s Selecting previously unselected package r-cran-broom. 1058s Preparing to unpack .../155-r-cran-broom_1.0.12+dfsg-1_all.deb ... 1058s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 1058s Selecting previously unselected package r-cran-numderiv. 1058s Preparing to unpack .../156-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 1058s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 1058s Selecting previously unselected package r-cran-gtable. 1058s Preparing to unpack .../157-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1058s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 1058s Selecting previously unselected package r-cran-isoband. 1058s Preparing to unpack .../158-r-cran-isoband_0.2.7-1_arm64.deb ... 1058s Unpacking r-cran-isoband (0.2.7-1) ... 1058s Selecting previously unselected package r-cran-farver. 1058s Preparing to unpack .../159-r-cran-farver_2.1.2-1_arm64.deb ... 1058s Unpacking r-cran-farver (2.1.2-1) ... 1058s Selecting previously unselected package r-cran-labeling. 1058s Preparing to unpack .../160-r-cran-labeling_0.4.3-1_all.deb ... 1058s Unpacking r-cran-labeling (0.4.3-1) ... 1058s Selecting previously unselected package r-cran-rcolorbrewer. 1058s Preparing to unpack .../161-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 1058s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 1058s Selecting previously unselected package r-cran-viridislite. 1058s Preparing to unpack .../162-r-cran-viridislite_0.4.3-1_all.deb ... 1058s Unpacking r-cran-viridislite (0.4.3-1) ... 1058s Selecting previously unselected package r-cran-scales. 1058s Preparing to unpack .../163-r-cran-scales_1.4.0-1_all.deb ... 1058s Unpacking r-cran-scales (1.4.0-1) ... 1058s Selecting previously unselected package r-cran-ggplot2. 1058s Preparing to unpack .../164-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 1058s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 1058s Selecting previously unselected package r-cran-cowplot. 1058s Preparing to unpack .../165-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 1058s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 1059s Selecting previously unselected package r-cran-deriv. 1059s Preparing to unpack .../166-r-cran-deriv_4.2.0-1_all.deb ... 1059s Unpacking r-cran-deriv (4.2.0-1) ... 1059s Selecting previously unselected package r-cran-colorspace. 1059s Preparing to unpack .../167-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 1059s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 1059s Selecting previously unselected package r-cran-fracdiff. 1059s Preparing to unpack .../168-r-cran-fracdiff_1.5-3-1_arm64.deb ... 1059s Unpacking r-cran-fracdiff (1.5-3-1) ... 1059s Selecting previously unselected package r-cran-zoo. 1059s Preparing to unpack .../169-r-cran-zoo_1.8-15-1_arm64.deb ... 1059s Unpacking r-cran-zoo (1.8-15-1) ... 1059s Selecting previously unselected package r-cran-lmtest. 1059s Preparing to unpack .../170-r-cran-lmtest_0.9.40-1build1_arm64.deb ... 1059s Unpacking r-cran-lmtest (0.9.40-1build1) ... 1059s Selecting previously unselected package r-cran-timedate. 1059s Preparing to unpack .../171-r-cran-timedate_4052.112-1_arm64.deb ... 1059s Unpacking r-cran-timedate (4052.112-1) ... 1059s Selecting previously unselected package r-cran-quadprog. 1059s Preparing to unpack .../172-r-cran-quadprog_1.5-8-1build2_arm64.deb ... 1059s Unpacking r-cran-quadprog (1.5-8-1build2) ... 1059s Selecting previously unselected package r-cran-xts. 1059s Preparing to unpack .../173-r-cran-xts_0.14.1-1_arm64.deb ... 1059s Unpacking r-cran-xts (0.14.1-1) ... 1059s Selecting previously unselected package r-cran-curl. 1059s Preparing to unpack .../174-r-cran-curl_7.0.0+dfsg-1_arm64.deb ... 1059s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 1059s Selecting previously unselected package r-cran-ttr. 1059s Preparing to unpack .../175-r-cran-ttr_0.24.4-1_arm64.deb ... 1059s Unpacking r-cran-ttr (0.24.4-1) ... 1059s Selecting previously unselected package r-cran-jsonlite. 1059s Preparing to unpack .../176-r-cran-jsonlite_1.9.1+dfsg-1_arm64.deb ... 1059s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 1059s Selecting previously unselected package r-cran-quantmod. 1059s Preparing to unpack .../177-r-cran-quantmod_0.4.28-1_all.deb ... 1059s Unpacking r-cran-quantmod (0.4.28-1) ... 1059s Selecting previously unselected package r-cran-tseries. 1059s Preparing to unpack .../178-r-cran-tseries_0.10-59-3_arm64.deb ... 1059s Unpacking r-cran-tseries (0.10-59-3) ... 1059s Selecting previously unselected package r-cran-urca. 1059s Preparing to unpack .../179-r-cran-urca_1.3-4-1build1_arm64.deb ... 1059s Unpacking r-cran-urca (1.3-4-1build1) ... 1059s Selecting previously unselected package r-cran-rcpparmadillo. 1059s Preparing to unpack .../180-r-cran-rcpparmadillo_15.2.3-1-1_arm64.deb ... 1059s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 1059s Selecting previously unselected package r-cran-forecast. 1059s Preparing to unpack .../181-r-cran-forecast_8.23.0-1_arm64.deb ... 1059s Unpacking r-cran-forecast (8.23.0-1) ... 1059s Selecting previously unselected package r-cran-modelr. 1059s Preparing to unpack .../182-r-cran-modelr_0.1.11-1_all.deb ... 1059s Unpacking r-cran-modelr (0.1.11-1) ... 1059s Selecting previously unselected package r-cran-microbenchmark. 1059s Preparing to unpack .../183-r-cran-microbenchmark_1.5.0-1_arm64.deb ... 1059s Unpacking r-cran-microbenchmark (1.5.0-1) ... 1059s Selecting previously unselected package r-cran-doby. 1060s Preparing to unpack .../184-r-cran-doby_4.7.1-3_all.deb ... 1060s Unpacking r-cran-doby (4.7.1-3) ... 1060s Selecting previously unselected package r-cran-evaluate. 1060s Preparing to unpack .../185-r-cran-evaluate_1.0.5-1_all.deb ... 1060s Unpacking r-cran-evaluate (1.0.5-1) ... 1060s Selecting previously unselected package r-cran-xfun. 1060s Preparing to unpack .../186-r-cran-xfun_0.55+dfsg-1_arm64.deb ... 1060s Unpacking r-cran-xfun (0.55+dfsg-1) ... 1060s Selecting previously unselected package r-cran-highr. 1060s Preparing to unpack .../187-r-cran-highr_0.11+dfsg-1_all.deb ... 1060s Unpacking r-cran-highr (0.11+dfsg-1) ... 1060s Selecting previously unselected package r-cran-yaml. 1060s Preparing to unpack .../188-r-cran-yaml_2.3.10-1_arm64.deb ... 1060s Unpacking r-cran-yaml (2.3.10-1) ... 1060s Selecting previously unselected package libjs-mathjax. 1060s Preparing to unpack .../189-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 1060s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 1062s Selecting previously unselected package r-cran-knitr. 1062s Preparing to unpack .../190-r-cran-knitr_1.51+dfsg-1_all.deb ... 1062s Unpacking r-cran-knitr (1.51+dfsg-1) ... 1062s Selecting previously unselected package r-cran-pbkrtest. 1062s Preparing to unpack .../191-r-cran-pbkrtest_0.5.5-1_all.deb ... 1062s Unpacking r-cran-pbkrtest (0.5.5-1) ... 1062s Selecting previously unselected package r-cran-sparsem. 1062s Preparing to unpack .../192-r-cran-sparsem_1.84-2-1_arm64.deb ... 1062s Unpacking r-cran-sparsem (1.84-2-1) ... 1062s Selecting previously unselected package r-cran-matrixmodels. 1062s Preparing to unpack .../193-r-cran-matrixmodels_0.5-4-1_all.deb ... 1062s Unpacking r-cran-matrixmodels (0.5-4-1) ... 1062s Selecting previously unselected package r-cran-survival. 1062s Preparing to unpack .../194-r-cran-survival_3.8-6-1_arm64.deb ... 1062s Unpacking r-cran-survival (3.8-6-1) ... 1062s Selecting previously unselected package r-cran-matrixstats. 1062s Preparing to unpack .../195-r-cran-matrixstats_1.5.0-1_arm64.deb ... 1062s Unpacking r-cran-matrixstats (1.5.0-1) ... 1062s Selecting previously unselected package r-cran-class. 1062s Preparing to unpack .../196-r-cran-class_7.3-23-1_arm64.deb ... 1062s Unpacking r-cran-class (7.3-23-1) ... 1062s Selecting previously unselected package r-cran-proxy. 1062s Preparing to unpack .../197-r-cran-proxy_0.4-27-1_arm64.deb ... 1062s Unpacking r-cran-proxy (0.4-27-1) ... 1062s Selecting previously unselected package r-cran-e1071. 1062s Preparing to unpack .../198-r-cran-e1071_1.7-17-1_arm64.deb ... 1062s Unpacking r-cran-e1071 (1.7-17-1) ... 1062s Selecting previously unselected package r-cran-codetools. 1062s Preparing to unpack .../199-r-cran-codetools_0.2-20-1build1_all.deb ... 1062s Unpacking r-cran-codetools (0.2-20-1build1) ... 1062s Selecting previously unselected package r-cran-iterators. 1062s Preparing to unpack .../200-r-cran-iterators_1.0.14-1build1_all.deb ... 1062s Unpacking r-cran-iterators (1.0.14-1build1) ... 1062s Selecting previously unselected package r-cran-foreach. 1062s Preparing to unpack .../201-r-cran-foreach_1.5.2-1build1_all.deb ... 1062s Unpacking r-cran-foreach (1.5.2-1build1) ... 1062s Selecting previously unselected package r-cran-data.table. 1062s Preparing to unpack .../202-r-cran-data.table_1.17.0+dfsg-1_arm64.deb ... 1062s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 1062s Selecting previously unselected package r-cran-modelmetrics. 1062s Preparing to unpack .../203-r-cran-modelmetrics_1.2.2.2-1build2_arm64.deb ... 1062s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ... 1062s Selecting previously unselected package r-cran-plyr. 1062s Preparing to unpack .../204-r-cran-plyr_1.8.9-1_arm64.deb ... 1062s Unpacking r-cran-plyr (1.8.9-1) ... 1062s Selecting previously unselected package r-cran-proc. 1062s Preparing to unpack .../205-r-cran-proc_1.18.5-1_arm64.deb ... 1062s Unpacking r-cran-proc (1.18.5-1) ... 1062s Selecting previously unselected package r-cran-tzdb. 1062s Preparing to unpack .../206-r-cran-tzdb_0.5.0-1_arm64.deb ... 1062s Unpacking r-cran-tzdb (0.5.0-1) ... 1062s Selecting previously unselected package r-cran-clock. 1062s Preparing to unpack .../207-r-cran-clock_0.7.2-1_arm64.deb ... 1062s Unpacking r-cran-clock (0.7.2-1) ... 1062s Selecting previously unselected package r-cran-gower. 1062s Preparing to unpack .../208-r-cran-gower_1.0.2-1_arm64.deb ... 1062s Unpacking r-cran-gower (1.0.2-1) ... 1062s Selecting previously unselected package r-cran-sparsevctrs. 1062s Preparing to unpack .../209-r-cran-sparsevctrs_0.2.0-2_arm64.deb ... 1062s Unpacking r-cran-sparsevctrs (0.2.0-2) ... 1062s Selecting previously unselected package r-cran-hardhat. 1062s Preparing to unpack .../210-r-cran-hardhat_1.4.2+dfsg-1_all.deb ... 1062s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ... 1062s Selecting previously unselected package r-cran-rpart. 1062s Preparing to unpack .../211-r-cran-rpart_4.1.24-1build1_arm64.deb ... 1062s Unpacking r-cran-rpart (4.1.24-1build1) ... 1062s Selecting previously unselected package r-cran-shape. 1062s Preparing to unpack .../212-r-cran-shape_1.4.6.1-1_all.deb ... 1062s Unpacking r-cran-shape (1.4.6.1-1) ... 1062s Selecting previously unselected package r-cran-diagram. 1062s Preparing to unpack .../213-r-cran-diagram_1.6.5-2_all.deb ... 1062s Unpacking r-cran-diagram (1.6.5-2) ... 1062s Selecting previously unselected package r-cran-kernsmooth. 1062s Preparing to unpack .../214-r-cran-kernsmooth_2.23-26-1build1_arm64.deb ... 1062s Unpacking r-cran-kernsmooth (2.23-26-1build1) ... 1062s Selecting previously unselected package r-cran-digest. 1062s Preparing to unpack .../215-r-cran-digest_0.6.39-1_arm64.deb ... 1062s Unpacking r-cran-digest (0.6.39-1) ... 1062s Selecting previously unselected package r-cran-globals. 1062s Preparing to unpack .../216-r-cran-globals_0.19.0-1_all.deb ... 1062s Unpacking r-cran-globals (0.19.0-1) ... 1062s Selecting previously unselected package r-cran-listenv. 1062s Preparing to unpack .../217-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 1062s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 1062s Selecting previously unselected package r-cran-parallelly. 1062s Preparing to unpack .../218-r-cran-parallelly_1.42.0-1_arm64.deb ... 1062s Unpacking r-cran-parallelly (1.42.0-1) ... 1062s Selecting previously unselected package r-cran-future. 1062s Preparing to unpack .../219-r-cran-future_1.34.0+dfsg-1_all.deb ... 1062s Unpacking r-cran-future (1.34.0+dfsg-1) ... 1062s Selecting previously unselected package r-cran-future.apply. 1062s Preparing to unpack .../220-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 1062s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 1062s Selecting previously unselected package r-cran-progressr. 1062s Preparing to unpack .../221-r-cran-progressr_0.15.1-1_all.deb ... 1062s Unpacking r-cran-progressr (0.15.1-1) ... 1062s Selecting previously unselected package r-cran-squarem. 1062s Preparing to unpack .../222-r-cran-squarem_2021.1-1build1_all.deb ... 1062s Unpacking r-cran-squarem (2021.1-1build1) ... 1062s Selecting previously unselected package r-cran-lava. 1062s Preparing to unpack .../223-r-cran-lava_1.8.2+dfsg-1_all.deb ... 1062s Unpacking r-cran-lava (1.8.2+dfsg-1) ... 1062s Selecting previously unselected package r-cran-prodlim. 1062s Preparing to unpack .../224-r-cran-prodlim_2024.06.25-1_arm64.deb ... 1062s Unpacking r-cran-prodlim (2024.06.25-1) ... 1062s Selecting previously unselected package r-cran-ipred. 1062s Preparing to unpack .../225-r-cran-ipred_0.9-15-1_arm64.deb ... 1062s Unpacking r-cran-ipred (0.9-15-1) ... 1062s Selecting previously unselected package r-cran-timechange. 1062s Preparing to unpack .../226-r-cran-timechange_0.3.0-2_arm64.deb ... 1062s Unpacking r-cran-timechange (0.3.0-2) ... 1062s Selecting previously unselected package r-cran-lubridate. 1062s Preparing to unpack .../227-r-cran-lubridate_1.9.4+dfsg-1_arm64.deb ... 1062s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 1062s Selecting previously unselected package r-cran-recipes. 1062s Preparing to unpack .../228-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 1062s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 1062s Selecting previously unselected package r-cran-reshape2. 1062s Preparing to unpack .../229-r-cran-reshape2_1.4.4-2build2_arm64.deb ... 1062s Unpacking r-cran-reshape2 (1.4.4-2build2) ... 1062s Selecting previously unselected package r-cran-caret. 1062s Preparing to unpack .../230-r-cran-caret_7.0-1+dfsg-1_arm64.deb ... 1062s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 1062s Selecting previously unselected package r-cran-conquer. 1062s Preparing to unpack .../231-r-cran-conquer_1.3.3-1_arm64.deb ... 1062s Unpacking r-cran-conquer (1.3.3-1) ... 1062s Selecting previously unselected package r-cran-quantreg. 1062s Preparing to unpack .../232-r-cran-quantreg_6.1-1_arm64.deb ... 1062s Unpacking r-cran-quantreg (6.1-1) ... 1062s Selecting previously unselected package r-cran-car. 1063s Preparing to unpack .../233-r-cran-car_3.1-5-1_all.deb ... 1063s Unpacking r-cran-car (3.1-5-1) ... 1063s Selecting previously unselected package r-cran-sandwich. 1063s Preparing to unpack .../234-r-cran-sandwich_3.1-1-1build1_all.deb ... 1063s Unpacking r-cran-sandwich (3.1-1-1build1) ... 1063s Selecting previously unselected package r-cran-aer. 1063s Preparing to unpack .../235-r-cran-aer_1.2-15-1_all.deb ... 1063s Unpacking r-cran-aer (1.2-15-1) ... 1063s Selecting previously unselected package r-cran-bit. 1063s Preparing to unpack .../236-r-cran-bit_4.6.0+dfsg-1_arm64.deb ... 1063s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 1063s Selecting previously unselected package r-cran-bit64. 1063s Preparing to unpack .../237-r-cran-bit64_4.6.0-1-4_arm64.deb ... 1063s Unpacking r-cran-bit64 (4.6.0-1-4) ... 1063s Selecting previously unselected package r-cran-blob. 1063s Preparing to unpack .../238-r-cran-blob_1.3.0-1_all.deb ... 1063s Unpacking r-cran-blob (1.3.0-1) ... 1063s Selecting previously unselected package r-cran-fastmap. 1063s Preparing to unpack .../239-r-cran-fastmap_1.2.0-1_arm64.deb ... 1063s Unpacking r-cran-fastmap (1.2.0-1) ... 1063s Selecting previously unselected package r-cran-cachem. 1063s Preparing to unpack .../240-r-cran-cachem_1.1.0-1_arm64.deb ... 1063s Unpacking r-cran-cachem (1.1.0-1) ... 1063s Selecting previously unselected package r-cran-dbi. 1063s Preparing to unpack .../241-r-cran-dbi_1.2.3-1build1_all.deb ... 1063s Unpacking r-cran-dbi (1.2.3-1build1) ... 1063s Selecting previously unselected package r-cran-foreign. 1063s Preparing to unpack .../242-r-cran-foreign_0.8.91-1_arm64.deb ... 1063s Unpacking r-cran-foreign (0.8.91-1) ... 1063s Selecting previously unselected package r-cran-hexbin. 1063s Preparing to unpack .../243-r-cran-hexbin_1.28.5-1_arm64.deb ... 1063s Unpacking r-cran-hexbin (1.28.5-1) ... 1063s Selecting previously unselected package r-cran-memoise. 1063s Preparing to unpack .../244-r-cran-memoise_2.0.1-1build1_all.deb ... 1063s Unpacking r-cran-memoise (2.0.1-1build1) ... 1063s Selecting previously unselected package r-cran-mitools. 1063s Preparing to unpack .../245-r-cran-mitools_2.4-2build2_all.deb ... 1063s Unpacking r-cran-mitools (2.4-2build2) ... 1063s Selecting previously unselected package r-cran-plogr. 1063s Preparing to unpack .../246-r-cran-plogr_0.2.0-3build2_all.deb ... 1063s Unpacking r-cran-plogr (0.2.0-3build2) ... 1063s Selecting previously unselected package 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(1:7.7+24ubuntu1) ... 1064s Setting up libdeflate0:arm64 (1.23-2build1) ... 1064s Setting up linux-libc-dev:arm64 (6.19.0-3.3) ... 1064s Setting up libnlopt0:arm64 (2.7.1-7ubuntu1) ... 1064s Setting up libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 1064s Setting up libgomp1:arm64 (15.2.0-12ubuntu1) ... 1064s Setting up libjbig0:arm64 (2.1-6.1ubuntu3) ... 1064s Setting up libpcre2-16-0:arm64 (10.46-1) ... 1064s Setting up zip (3.0-15ubuntu3) ... 1064s Setting up libpcre2-32-0:arm64 (10.46-1) ... 1064s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 1064s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 1064s Setting up libtirpc-dev:arm64 (1.3.6+ds-1) ... 1064s Setting up libpkgconf3:arm64 (1.8.1-4build1) ... 1064s Setting up rpcsvc-proto (1.4.3-1build1) ... 1064s Setting up fonts-dejavu-mono (2.37-8build1) ... 1064s Setting up libmpc3:arm64 (1.3.1-2) ... 1064s Setting up 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... 1064s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1064s Setting up libisl23:arm64 (0.27-1build1) ... 1064s Setting up libc-dev-bin (2.42-2ubuntu4) ... 1064s Setting up libdeflate-dev:arm64 (1.23-2build1) ... 1064s Setting up node-normalize.css (8.0.1-5.1) ... 1064s Setting up xdg-utils (1.2.1-2ubuntu2) ... 1064s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1064s Setting up libcc1-0:arm64 (15.2.0-12ubuntu1) ... 1064s Setting up liblsan0:arm64 (15.2.0-12ubuntu1) ... 1064s Setting up libblas-dev:arm64 (3.12.1-7ubuntu1) ... 1064s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 1064s Setting up dctrl-tools (2.24-3build4) ... 1064s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 1064s Setting up libitm1:arm64 (15.2.0-12ubuntu1) ... 1064s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 1064s Setting up cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1064s Setting up libice6:arm64 (2:1.1.1-1build1) ... 1064s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 1064s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 1064s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 1064s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 1064s Setting up libpaper-utils (2.2.5-0.3build1) ... 1064s Setting up libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 1064s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 1064s Setting up pkgconf:arm64 (1.8.1-4build1) ... 1064s Setting up libthai0:arm64 (0.1.30-1) ... 1064s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1064s Setting up liblapack-dev:arm64 (3.12.1-7ubuntu1) ... 1064s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so 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Setting up libcairo2:arm64 (1.18.4-3) ... 1066s Setting up gcc-15 (15.2.0-12ubuntu1) ... 1066s Setting up libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 1066s Setting up gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1066s Setting up g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 1066s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 1066s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1066s Setting up libpangoft2-1.0-0:arm64 (1.57.0-1) ... 1066s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 1066s Setting up g++-15 (15.2.0-12ubuntu1) ... 1066s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 1066s Setting up libpangocairo-1.0-0:arm64 (1.57.0-1) ... 1066s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 1066s Setting up libpng-dev:arm64 (1.6.54-1) ... 1068s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 1068s Setting up gcc (4:15.2.0-4ubuntu1) ... 1068s Setting up r-base-core (4.5.2-1ubuntu2) ... 1068s Creating config file /etc/R/Renviron with new version 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Setting up r-cran-littler (0.3.22-1) ... 1068s Setting up r-cran-rcpp (1.1.0-1) ... 1068s Setting up r-cran-curl (7.0.0+dfsg-1) ... 1068s Setting up r-cran-codetools (0.2-20-1build1) ... 1068s Setting up r-cran-nloptr (2.2.1-2) ... 1068s Setting up r-cran-boot (1.3-32-1) ... 1068s Setting up r-cran-rlang (1.1.5-3) ... 1068s Setting up r-cran-matrixstats (1.5.0-1) ... 1068s Setting up r-cran-listenv (0.10.0+dfsg-1) ... 1068s Setting up r-cran-xfun (0.55+dfsg-1) ... 1068s Setting up r-cran-urca (1.3-4-1build1) ... 1068s Setting up r-cran-plogr (0.2.0-3build2) ... 1068s Setting up r-cran-withr (3.0.2+dfsg-1) ... 1068s Setting up r-cran-backports (1.5.0-2) ... 1068s Setting up r-cran-deriv (4.2.0-1) ... 1068s Setting up r-cran-generics (0.1.4-1) ... 1068s Setting up r-cran-iterators (1.0.14-1build1) ... 1068s Setting up r-cran-abind (1.4-8-1build1) ... 1068s Setting up r-cran-digest (0.6.39-1) ... 1068s Setting up r-cran-yaml (2.3.10-1) ... 1068s Setting up r-cran-gower (1.0.2-1) ... 1068s Setting up r-cran-evaluate (1.0.5-1) ... 1068s Setting up r-cran-dbi (1.2.3-1build1) ... 1068s Setting up r-cran-timedate (4052.112-1) ... 1068s Setting up r-cran-highr (0.11+dfsg-1) ... 1068s Setting up r-cran-foreach (1.5.2-1build1) ... 1068s Setting up r-cran-fansi (1.0.6-2) ... 1068s Setting up r-cran-cardata (3.0.6-1) ... 1068s Setting up r-cran-mass (7.3-65-1) ... 1068s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 1068s Setting up r-cran-glue (1.8.0-1) ... 1068s Setting up r-cran-foreign (0.8.91-1) ... 1068s Setting up r-cran-fracdiff (1.5-3-1) ... 1068s Setting up r-cran-bit (4.6.0+dfsg-1) ... 1068s Setting up r-cran-cli (3.6.4-1) ... 1068s Setting up gfortran (4:15.2.0-4ubuntu1) ... 1068s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1068s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 1068s update-alternatives: 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r-cran-isoband (0.2.7-1) ... 1068s Setting up r-cran-diagram (1.6.5-2) ... 1068s Setting up r-cran-scales (1.4.0-1) ... 1068s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 1068s Setting up r-cran-zoo (1.8-15-1) ... 1068s Setting up r-cran-matrix (1.7-4-1) ... 1068s Setting up r-cran-kernsmooth (2.23-26-1build1) ... 1068s Setting up r-cran-knitr (1.51+dfsg-1) ... 1068s Setting up r-cran-mgcv (1.9-4-1) ... 1068s Setting up g++ (4:15.2.0-4ubuntu1) ... 1068s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1068s Setting up r-cran-cachem (1.1.0-1) ... 1068s Setting up r-cran-lmtest (0.9.40-1build1) ... 1068s Setting up build-essential (12.12ubuntu2) ... 1068s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 1068s Setting up r-cran-tzdb (0.5.0-1) ... 1068s Setting up r-cran-globals (0.19.0-1) ... 1068s Setting up r-cran-vctrs (0.6.5-1) ... 1068s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 1068s Setting up r-cran-mitools (2.4-2build2) ... 1068s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 1068s Setting up r-cran-minqa (1.2.8-1) ... 1068s Setting up r-base-dev (4.5.2-1ubuntu2) ... 1068s Setting up r-cran-stringr (1.5.1-1) ... 1068s Setting up r-cran-class (7.3-23-1) ... 1068s Setting up r-cran-modelmetrics (1.2.2.2-1build2) ... 1068s Setting up r-cran-matrixmodels (0.5-4-1) ... 1068s Setting up r-cran-sparsevctrs (0.2.0-2) ... 1068s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 1068s Setting up r-cran-clock (0.7.2-1) ... 1068s Setting up r-cran-sandwich (3.1-1-1build1) ... 1068s Setting up r-cran-proc (1.18.5-1) ... 1068s Setting up r-cran-survival (3.8-6-1) ... 1068s Setting up r-cran-xts (0.14.1-1) ... 1068s Setting up r-cran-survey (4.4-2-2) ... 1068s Setting up r-cran-rdpack (2.6.3-1) ... 1068s Setting up r-cran-future (1.34.0+dfsg-1) ... 1068s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 1068s Setting up r-cran-reshape2 (1.4.4-2build2) ... 1068s Setting up r-cran-future.apply (1.11.3+dfsg-1) ... 1068s Setting up r-cran-timechange 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(1.1.3+dfsg-1) ... 1068s Setting up r-cran-caret (7.0-1+dfsg-1) ... 1068s Setting up r-cran-tseries (0.10-59-3) ... 1068s Setting up r-cran-broom (1.0.12+dfsg-1) ... 1068s Setting up r-cran-conquer (1.3.3-1) ... 1068s Setting up r-cran-forecast (8.23.0-1) ... 1068s Setting up r-cran-quantreg (6.1-1) ... 1068s Setting up r-cran-modelr (0.1.11-1) ... 1068s Setting up r-cran-doby (4.7.1-3) ... 1068s Setting up r-cran-pbkrtest (0.5.5-1) ... 1068s Setting up r-cran-car (3.1-5-1) ... 1068s Setting up r-cran-aer (1.2-15-1) ... 1068s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1068s Processing triggers for man-db (2.13.1-1build1) ... 1068s Processing triggers for install-info (7.2-5) ... 1070s autopkgtest [23:28:54]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1070s autopkgtest [23:28:54]: test pkg-r-autopkgtest: [----------------------- 1070s Test: Try to load the R library survey 1070s 1070s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 1070s Copyright (C) 2025 The R Foundation for Statistical Computing 1070s Platform: aarch64-unknown-linux-gnu 1070s 1070s R is free software and comes with ABSOLUTELY NO WARRANTY. 1070s You are welcome to redistribute it under certain conditions. 1070s Type 'license()' or 'licence()' for distribution details. 1070s 1070s R is a collaborative project with many contributors. 1070s Type 'contributors()' for more information and 1070s 'citation()' on how to cite R or R packages in publications. 1070s 1070s Type 'demo()' for some demos, 'help()' for on-line help, or 1070s 'help.start()' for an HTML browser interface to help. 1070s Type 'q()' to quit R. 1070s 1071s > library('survey') 1071s Loading required package: grid 1071s Loading required package: Matrix 1071s Loading required package: survival 1072s 1072s Attaching package: ‘survey’ 1072s 1072s > 1072s The following object is masked from ‘package:graphics’: 1072s 1072s dotchart 1072s 1072s autopkgtest [23:28:56]: test pkg-r-autopkgtest: -----------------------] 1072s pkg-r-autopkgtest PASS 1072s autopkgtest [23:28:56]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1073s autopkgtest [23:28:57]: @@@@@@@@@@@@@@@@@@@@ summary 1073s run-unit-test PASS 1073s pkg-r-autopkgtest PASS