0s autopkgtest [23:21:12]: starting date and time: 2026-02-09 23:21:12+0000
  0s autopkgtest [23:21:12]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [23:21:12]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8ppo16f2/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-ppc64el-21.secgroup --name adt-resolute-ppc64el-r-cran-survey-20260209-225139-juju-7f2275-prod-proposed-migration-environment-20-d693738a-f9ca-42d5-a83b-5b9a18676834 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  4s Creating nova instance adt-resolute-ppc64el-r-cran-survey-20260209-225139-juju-7f2275-prod-proposed-migration-environment-20-d693738a-f9ca-42d5-a83b-5b9a18676834 from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)...
124s autopkgtest [23:23:16]: testbed dpkg architecture: ppc64el
124s autopkgtest [23:23:16]: testbed apt version: 3.1.15
125s autopkgtest [23:23:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup
125s autopkgtest [23:23:17]: testbed release detected to be: None
126s autopkgtest [23:23:18]: updating testbed package index (apt update)
126s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
126s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
126s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
126s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
126s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB]
126s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB]
126s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB]
129s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB]
129s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB]
132s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB]
132s Fetched 3774 kB in 6s (619 kB/s)
133s Reading package lists...
133s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
133s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
134s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
134s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
134s Reading package lists...
134s Reading package lists...
135s Building dependency tree...
135s Reading state information...
135s Calculating upgrade...
135s The following packages will be upgraded:
135s   cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2
135s   libip6tc2 libxtables12 wget
135s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
135s Need to get 3125 kB of archives.
135s After this operation, 78.8 kB of additional disk space will be used.
135s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB]
135s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB]
135s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB]
135s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB]
135s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB]
139s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB]
139s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB]
139s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB]
139s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB]
140s dpkg-preconfigure: unable to re-open stdin: No such file or directory
140s Fetched 3125 kB in 4s (698 kB/s)
140s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 122003 files and directories currently installed.)
140s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ...
140s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
140s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ...
140s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
140s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ...
140s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
140s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ...
140s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ...
140s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ...
140s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ...
141s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ...
141s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ...
141s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ...
141s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ...
141s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ...
141s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ...
141s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ...
141s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ...
141s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ...
141s Setting up wget (1.25.0-2ubuntu4) ...
141s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ...
141s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ...
141s Setting up dracut-install (109-11ubuntu1) ...
141s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ...
141s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
141s Setting up iptables (1.8.11-2ubuntu3) ...
141s Setting up iproute2 (6.18.0-1ubuntu1) ...
141s Processing triggers for man-db (2.13.1-1build1) ...
142s Processing triggers for install-info (7.2-5) ...
143s Processing triggers for libc-bin (2.42-2ubuntu4) ...
143s autopkgtest [23:23:35]: upgrading testbed (apt dist-upgrade and autopurge)
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
143s Calculating upgrade...
143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
144s Solving dependencies...
144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
146s autopkgtest [23:23:38]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:13:51 UTC 2026
146s autopkgtest [23:23:38]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey
153s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (dsc) [2340 B]
153s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (tar) [2341 kB]
153s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (diff) [4580 B]
153s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC
153s gpgv:                using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
153s gpgv:                issuer "plessy@debian.org"
153s gpgv: Can't check signature: No public key
153s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found
153s autopkgtest [23:23:45]: testing package r-cran-survey version 4.4-2-2
154s autopkgtest [23:23:46]: build not needed
155s autopkgtest [23:23:47]: test run-unit-test: preparing testbed
155s Reading package lists...
155s Building dependency tree...
155s Reading state information...
155s Solving dependencies...
155s The following NEW packages will be installed:
155s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
155s   fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1
155s   libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
155s   libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap
155s   libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
155s   liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0
155s   libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6
155s   libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0
155s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css
155s   r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64
155s   r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata
155s   r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools
155s   r-cran-colorspace r-cran-conquer r-cran-cowplot r-cran-cpp11 r-cran-curl
155s   r-cran-data.table r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest
155s   r-cran-doby r-cran-dplyr r-cran-e1071 r-cran-evaluate r-cran-fansi
155s   r-cran-farver r-cran-fastmap r-cran-foreach r-cran-forecast r-cran-foreign
155s   r-cran-formula r-cran-fracdiff r-cran-future r-cran-future.apply
155s   r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower
155s   r-cran-gtable r-cran-hardhat r-cran-hexbin r-cran-highr r-cran-ipred
155s   r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kernsmooth
155s   r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle
155s   r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate
155s   r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels
155s   r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark
155s   r-cran-minqa r-cran-mitools r-cran-modelmetrics r-cran-modelr r-cran-nlme
155s   r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pbkrtest
155s   r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr
155s   r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr
155s   r-cran-quadprog r-cran-quantmod r-cran-quantreg r-cran-r.cache
155s   r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6
155s   r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo
155s   r-cran-rcppeigen r-cran-rdpack r-cran-recipes r-cran-reformulas
155s   r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-rsqlite r-cran-sandwich
155s   r-cran-scales r-cran-shape r-cran-sparsem r-cran-sparsevctrs r-cran-squarem
155s   r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival
155s   r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange
155s   r-cran-timedate r-cran-tseries r-cran-ttr r-cran-tzdb r-cran-urca
155s   r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun
155s   r-cran-xts r-cran-yaml r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip
155s 0 upgraded, 196 newly installed, 0 to remove and 0 not upgraded.
155s Need to get 174 MB of archives.
155s After this operation, 357 MB of additional disk space will be used.
155s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB]
156s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB]
157s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB]
157s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB]
157s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB]
157s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
157s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
161s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB]
161s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB]
161s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB]
161s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B]
161s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB]
161s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB]
162s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB]
162s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB]
162s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB]
163s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB]
163s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB]
163s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB]
164s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB]
164s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB]
164s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB]
164s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
164s Get:24 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
164s Get:25 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
164s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
164s Get:27 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
164s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB]
169s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB]
169s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB]
169s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB]
169s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB]
169s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB]
169s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB]
169s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB]
169s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB]
169s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB]
169s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB]
169s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB]
171s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB]
171s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB]
171s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB]
171s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB]
171s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B]
171s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB]
173s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB]
173s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-normalize.css all 8.0.1-5.1 [10.4 kB]
173s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB]
173s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB]
173s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
173s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB]
223s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-abind all 1.4-8-1build1 [67.0 kB]
223s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cardata all 3.0.6-1 [1687 kB]
226s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-formula all 1.2-5-1 [158 kB]
226s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB]
228s Get:56 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-lattice ppc64el 0.22-9-1 [1399 kB]
230s Get:57 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB]
234s Get:58 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB]
248s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mgcv ppc64el 1.9-4-1 [3694 kB]
253s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nnet ppc64el 7.3-20-1 [119 kB]
253s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-boot all 1.3-32-1 [636 kB]
254s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB]
254s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
254s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB]
257s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-minqa ppc64el 1.2.8-1 [141 kB]
257s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libnlopt0 ppc64el 2.7.1-7ubuntu1 [292 kB]
257s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nloptr ppc64el 2.2.1-2 [251 kB]
258s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rbibutils ppc64el 2.3-1 [1047 kB]
260s Get:69 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rdpack all 2.6.3-1 [636 kB]
261s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-reformulas all 0.4.4-1 [151 kB]
262s Get:71 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB]
265s Get:72 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcppeigen ppc64el 0.3.4.0.2-1 [1477 kB]
268s Get:73 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-statmod ppc64el 1.5.0-1 [298 kB]
268s Get:74 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lme4 ppc64el 1.1-38-1 [4220 kB]
275s Get:75 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-backports ppc64el 1.5.0-2 [122 kB]
275s Get:76 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB]
277s Get:77 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-generics all 0.1.4-1 [84.0 kB]
277s Get:78 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB]
277s Get:79 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
277s Get:80 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB]
277s Get:81 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB]
277s Get:82 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB]
280s Get:83 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.11.1+dfsg-1 [456 kB]
280s Get:84 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB]
280s Get:85 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB]
281s Get:86 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
281s Get:87 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB]
282s Get:88 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB]
282s Get:89 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyselect ppc64el 1.2.1+dfsg-1 [222 kB]
282s Get:90 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dplyr ppc64el 1.1.4-4 [1542 kB]
285s Get:91 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-purrr ppc64el 1.0.4-1 [555 kB]
285s Get:92 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringi ppc64el 1.8.4-1build2 [947 kB]
286s Get:93 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB]
286s Get:94 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB]
287s Get:95 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB]
288s Get:96 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-broom all 1.0.12+dfsg-1 [1708 kB]
291s Get:97 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-numderiv all 2016.8-1.1-3build1 [116 kB]
291s Get:98 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
291s Get:99 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB]
294s Get:100 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB]
296s Get:101 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB]
296s Get:102 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
296s Get:103 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB]
297s Get:104 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB]
299s Get:105 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
306s Get:106 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cowplot all 1.1.3+dfsg-1 [614 kB]
308s Get:107 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-deriv all 4.2.0-1 [154 kB]
308s Get:108 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-colorspace ppc64el 2.1-1+dfsg-1 [1570 kB]
311s Get:109 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fracdiff ppc64el 1.5-3-1 [118 kB]
311s Get:110 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-zoo ppc64el 1.8-15-1 [1028 kB]
312s Get:111 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lmtest ppc64el 0.9.40-1build1 [401 kB]
312s Get:112 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-timedate ppc64el 4052.112-1 [1299 kB]
314s Get:113 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quadprog ppc64el 1.5-8-1build2 [38.8 kB]
314s Get:114 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xts ppc64el 0.14.1-1 [1209 kB]
316s Get:115 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-curl ppc64el 7.0.0+dfsg-1 [205 kB]
316s Get:116 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ttr ppc64el 0.24.4-1 [516 kB]
316s Get:117 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-jsonlite ppc64el 1.9.1+dfsg-1 [452 kB]
316s Get:118 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quantmod all 0.4.28-1 [1037 kB]
318s Get:119 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tseries ppc64el 0.10-59-3 [390 kB]
318s Get:120 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-urca ppc64el 1.3-4-1build1 [1056 kB]
320s Get:121 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpparmadillo ppc64el 15.2.3-1-1 [935 kB]
322s Get:122 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-forecast ppc64el 8.23.0-1 [1598 kB]
325s Get:123 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-modelr all 0.1.11-1 [195 kB]
325s Get:124 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-microbenchmark ppc64el 1.5.0-1 [67.9 kB]
325s Get:125 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-doby all 4.7.1-3 [4741 kB]
333s Get:126 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-evaluate all 1.0.5-1 [117 kB]
333s Get:127 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xfun ppc64el 0.55+dfsg-1 [589 kB]
334s Get:128 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB]
334s Get:129 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB]
334s Get:130 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
347s Get:131 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-knitr all 1.51+dfsg-1 [847 kB]
350s Get:132 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pbkrtest all 0.5.5-1 [217 kB]
350s Get:133 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sparsem ppc64el 1.84-2-1 [832 kB]
353s Get:134 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrixmodels all 0.5-4-1 [351 kB]
353s Get:135 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-survival ppc64el 3.8-6-1 [8312 kB]
372s Get:136 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrixstats ppc64el 1.5.0-1 [578 kB]
373s Get:137 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-class ppc64el 7.3-23-1 [94.5 kB]
373s Get:138 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-proxy ppc64el 0.4-27-1 [185 kB]
373s Get:139 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-e1071 ppc64el 1.7-17-1 [595 kB]
374s Get:140 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-codetools all 0.2-20-1build1 [91.1 kB]
374s Get:141 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-iterators all 1.0.14-1build1 [336 kB]
374s Get:142 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-foreach all 1.5.2-1build1 [124 kB]
374s Get:143 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-data.table ppc64el 1.17.0+dfsg-1 [2197 kB]
378s Get:144 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-modelmetrics ppc64el 1.2.2.2-1build2 [147 kB]
378s Get:145 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-plyr ppc64el 1.8.9-1 [834 kB]
379s Get:146 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-proc ppc64el 1.18.5-1 [965 kB]
381s Get:147 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tzdb ppc64el 0.5.0-1 [540 kB]
382s Get:148 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-clock ppc64el 0.7.2-1 [1910 kB]
385s Get:149 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gower ppc64el 1.0.2-1 [211 kB]
385s Get:150 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sparsevctrs ppc64el 0.2.0-2 [172 kB]
385s Get:151 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-hardhat all 1.4.2+dfsg-1 [596 kB]
386s Get:152 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rpart ppc64el 4.1.24-1build1 [678 kB]
388s Get:153 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-shape all 1.4.6.1-1 [749 kB]
390s Get:154 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-diagram all 1.6.5-2 [656 kB]
391s Get:155 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-kernsmooth ppc64el 2.23-26-1build1 [96.8 kB]
391s Get:156 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-digest ppc64el 0.6.39-1 [238 kB]
391s Get:157 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-globals all 0.19.0-1 [160 kB]
391s Get:158 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-listenv all 0.10.0+dfsg-1 [113 kB]
391s Get:159 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-parallelly ppc64el 1.42.0-1 [540 kB]
392s Get:160 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-future all 1.34.0+dfsg-1 [646 kB]
394s Get:161 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-future.apply all 1.11.3+dfsg-1 [175 kB]
394s Get:162 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-progressr all 0.15.1-1 [353 kB]
394s Get:163 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-squarem all 2021.1-1build1 [180 kB]
394s Get:164 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lava all 1.8.2+dfsg-1 [2210 kB]
397s Get:165 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-prodlim ppc64el 2024.06.25-1 [420 kB]
397s Get:166 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ipred ppc64el 0.9-15-1 [386 kB]
397s Get:167 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-timechange ppc64el 0.3.0-2 [211 kB]
397s Get:168 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lubridate ppc64el 1.9.4+dfsg-1 [1011 kB]
399s Get:169 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-recipes all 1.1.0+dfsg-1 [2035 kB]
403s Get:170 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-reshape2 ppc64el 1.4.4-2build2 [124 kB]
403s Get:171 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-caret ppc64el 7.0-1+dfsg-1 [3461 kB]
409s Get:172 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-conquer ppc64el 1.3.3-1 [468 kB]
409s Get:173 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quantreg ppc64el 6.1-1 [1463 kB]
412s Get:174 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-car all 3.1-5-1 [1526 kB]
415s Get:175 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sandwich all 3.1-1-1build1 [1483 kB]
417s Get:176 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-aer all 1.2-15-1 [2607 kB]
422s Get:177 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bit ppc64el 4.6.0+dfsg-1 [475 kB]
422s Get:178 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bit64 ppc64el 4.6.0-1-4 [507 kB]
422s Get:179 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-blob all 1.3.0-1 [54.1 kB]
422s Get:180 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fastmap ppc64el 1.2.0-1 [75.0 kB]
422s Get:181 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cachem ppc64el 1.1.0-1 [74.1 kB]
422s Get:182 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dbi all 1.2.3-1build1 [855 kB]
424s Get:183 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-foreign ppc64el 0.8.91-1 [255 kB]
424s Get:184 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-hexbin ppc64el 1.28.5-1 [1583 kB]
426s Get:185 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-memoise all 2.0.1-1build1 [54.5 kB]
426s Get:186 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mitools all 2.4-2build2 [266 kB]
426s Get:187 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-plogr all 0.2.0-3build2 [15.8 kB]
426s Get:188 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.methodss3 all 1.8.2-1 [84.0 kB]
426s Get:189 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.oo all 1.27.1-1 [978 kB]
428s Get:190 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.utils all 2.13.0-1 [1423 kB]
431s Get:191 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.cache all 0.17.0-1 [117 kB]
431s Get:192 http://ftpmaster.internal/ubuntu resolute/main ppc64el tcl8.6 ppc64el 8.6.17+dfsg-1build1 [14.8 kB]
431s Get:193 http://ftpmaster.internal/ubuntu resolute/main ppc64el tcl ppc64el 8.6.16build1 [4204 B]
431s Get:194 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r.rsp all 0.46.0+ds-1 [1412 kB]
434s Get:195 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rsqlite ppc64el 2.3.9-1 [1572 kB]
437s Get:196 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-survey ppc64el 4.4-2-2 [3458 kB]
443s Preconfiguring packages ...
443s Fetched 174 MB in 4min 47s (607 kB/s)
443s Selecting previously unselected package fonts-dejavu-mono.
443s (Reading database ... 
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(Reading database ... 122006 files and directories currently installed.)
443s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ...
443s Unpacking fonts-dejavu-mono (2.37-8build1) ...
443s Selecting previously unselected package fonts-dejavu-core.
443s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ...
443s Unpacking fonts-dejavu-core (2.37-8build1) ...
443s Selecting previously unselected package fontconfig-config.
443s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ...
444s Unpacking fontconfig-config (2.17.1-3ubuntu1) ...
444s Selecting previously unselected package libfontconfig1:ppc64el.
444s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ...
444s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ...
444s Selecting previously unselected package fontconfig.
444s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ...
444s Unpacking fontconfig (2.17.1-3ubuntu1) ...
444s Selecting previously unselected package fonts-glyphicons-halflings.
444s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ...
444s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
444s Selecting previously unselected package fonts-mathjax.
444s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ...
444s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ...
444s Selecting previously unselected package libblas3:ppc64el.
444s Preparing to unpack .../007-libblas3_3.12.1-7ubuntu1_ppc64el.deb ...
444s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ...
444s Selecting previously unselected package libpixman-1-0:ppc64el.
444s Preparing to unpack .../008-libpixman-1-0_0.46.4-1_ppc64el.deb ...
444s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ...
444s Selecting previously unselected package libxcb-render0:ppc64el.
444s Preparing to unpack .../009-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ...
444s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ...
444s Selecting previously unselected package libxcb-shm0:ppc64el.
444s Preparing to unpack .../010-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ...
444s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ...
444s Selecting previously unselected package libxrender1:ppc64el.
444s Preparing to unpack .../011-libxrender1_1%3a0.9.12-1_ppc64el.deb ...
444s Unpacking libxrender1:ppc64el (1:0.9.12-1) ...
444s Selecting previously unselected package libcairo2:ppc64el.
444s Preparing to unpack .../012-libcairo2_1.18.4-3_ppc64el.deb ...
444s Unpacking libcairo2:ppc64el (1.18.4-3) ...
444s Selecting previously unselected package libdatrie1:ppc64el.
444s Preparing to unpack .../013-libdatrie1_0.2.14-1_ppc64el.deb ...
444s Unpacking libdatrie1:ppc64el (0.2.14-1) ...
444s Selecting previously unselected package libdeflate0:ppc64el.
444s Preparing to unpack .../014-libdeflate0_1.23-2build1_ppc64el.deb ...
444s Unpacking libdeflate0:ppc64el (1.23-2build1) ...
444s Selecting previously unselected package libgfortran5:ppc64el.
444s Preparing to unpack .../015-libgfortran5_15.2.0-12ubuntu1_ppc64el.deb ...
444s Unpacking libgfortran5:ppc64el (15.2.0-12ubuntu1) ...
444s Selecting previously unselected package libgomp1:ppc64el.
444s Preparing to unpack .../016-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ...
444s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ...
444s Selecting previously unselected package libgraphite2-3:ppc64el.
444s Preparing to unpack .../017-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ...
444s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ...
444s Selecting previously unselected package libharfbuzz0b:ppc64el.
444s Preparing to unpack .../018-libharfbuzz0b_12.3.2-1_ppc64el.deb ...
444s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ...
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447s Selecting previously unselected package r-cran-timedate.
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447s Selecting previously unselected package r-cran-quadprog.
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447s Selecting previously unselected package r-cran-xts.
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447s Selecting previously unselected package r-cran-jsonlite.
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447s Selecting previously unselected package r-cran-quantmod.
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447s Selecting previously unselected package r-cran-rcpparmadillo.
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447s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ...
447s Selecting previously unselected package r-cran-forecast.
447s Preparing to unpack .../121-r-cran-forecast_8.23.0-1_ppc64el.deb ...
447s Unpacking r-cran-forecast (8.23.0-1) ...
447s Selecting previously unselected package r-cran-modelr.
447s Preparing to unpack .../122-r-cran-modelr_0.1.11-1_all.deb ...
447s Unpacking r-cran-modelr (0.1.11-1) ...
447s Selecting previously unselected package r-cran-microbenchmark.
447s Preparing to unpack .../123-r-cran-microbenchmark_1.5.0-1_ppc64el.deb ...
447s Unpacking r-cran-microbenchmark (1.5.0-1) ...
447s Selecting previously unselected package r-cran-doby.
447s Preparing to unpack .../124-r-cran-doby_4.7.1-3_all.deb ...
447s Unpacking r-cran-doby (4.7.1-3) ...
447s Selecting previously unselected package r-cran-evaluate.
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447s Unpacking r-cran-evaluate (1.0.5-1) ...
447s Selecting previously unselected package r-cran-xfun.
447s Preparing to unpack .../126-r-cran-xfun_0.55+dfsg-1_ppc64el.deb ...
447s Unpacking r-cran-xfun (0.55+dfsg-1) ...
447s Selecting previously unselected package r-cran-highr.
447s Preparing to unpack .../127-r-cran-highr_0.11+dfsg-1_all.deb ...
447s Unpacking r-cran-highr (0.11+dfsg-1) ...
447s Selecting previously unselected package r-cran-yaml.
447s Preparing to unpack .../128-r-cran-yaml_2.3.10-1_ppc64el.deb ...
447s Unpacking r-cran-yaml (2.3.10-1) ...
447s Selecting previously unselected package libjs-mathjax.
447s Preparing to unpack .../129-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ...
447s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ...
448s Selecting previously unselected package r-cran-knitr.
448s Preparing to unpack .../130-r-cran-knitr_1.51+dfsg-1_all.deb ...
448s Unpacking r-cran-knitr (1.51+dfsg-1) ...
448s Selecting previously unselected package r-cran-pbkrtest.
448s Preparing to unpack .../131-r-cran-pbkrtest_0.5.5-1_all.deb ...
448s Unpacking r-cran-pbkrtest (0.5.5-1) ...
448s Selecting previously unselected package r-cran-sparsem.
448s Preparing to unpack .../132-r-cran-sparsem_1.84-2-1_ppc64el.deb ...
448s Unpacking r-cran-sparsem (1.84-2-1) ...
448s Selecting previously unselected package r-cran-matrixmodels.
448s Preparing to unpack .../133-r-cran-matrixmodels_0.5-4-1_all.deb ...
448s Unpacking r-cran-matrixmodels (0.5-4-1) ...
448s Selecting previously unselected package r-cran-survival.
448s Preparing to unpack .../134-r-cran-survival_3.8-6-1_ppc64el.deb ...
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448s Selecting previously unselected package r-cran-matrixstats.
448s Preparing to unpack .../135-r-cran-matrixstats_1.5.0-1_ppc64el.deb ...
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448s Selecting previously unselected package r-cran-class.
448s Preparing to unpack .../136-r-cran-class_7.3-23-1_ppc64el.deb ...
448s Unpacking r-cran-class (7.3-23-1) ...
448s Selecting previously unselected package r-cran-proxy.
448s Preparing to unpack .../137-r-cran-proxy_0.4-27-1_ppc64el.deb ...
448s Unpacking r-cran-proxy (0.4-27-1) ...
448s Selecting previously unselected package r-cran-e1071.
448s Preparing to unpack .../138-r-cran-e1071_1.7-17-1_ppc64el.deb ...
448s Unpacking r-cran-e1071 (1.7-17-1) ...
448s Selecting previously unselected package r-cran-codetools.
448s Preparing to unpack .../139-r-cran-codetools_0.2-20-1build1_all.deb ...
448s Unpacking r-cran-codetools (0.2-20-1build1) ...
448s Selecting previously unselected package r-cran-iterators.
448s Preparing to unpack .../140-r-cran-iterators_1.0.14-1build1_all.deb ...
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448s Selecting previously unselected package r-cran-foreach.
448s Preparing to unpack .../141-r-cran-foreach_1.5.2-1build1_all.deb ...
448s Unpacking r-cran-foreach (1.5.2-1build1) ...
448s Selecting previously unselected package r-cran-data.table.
448s Preparing to unpack .../142-r-cran-data.table_1.17.0+dfsg-1_ppc64el.deb ...
448s Unpacking r-cran-data.table (1.17.0+dfsg-1) ...
448s Selecting previously unselected package r-cran-modelmetrics.
448s Preparing to unpack .../143-r-cran-modelmetrics_1.2.2.2-1build2_ppc64el.deb ...
448s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ...
448s Selecting previously unselected package r-cran-plyr.
448s Preparing to unpack .../144-r-cran-plyr_1.8.9-1_ppc64el.deb ...
448s Unpacking r-cran-plyr (1.8.9-1) ...
448s Selecting previously unselected package r-cran-proc.
448s Preparing to unpack .../145-r-cran-proc_1.18.5-1_ppc64el.deb ...
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448s Selecting previously unselected package r-cran-tzdb.
448s Preparing to unpack .../146-r-cran-tzdb_0.5.0-1_ppc64el.deb ...
448s Unpacking r-cran-tzdb (0.5.0-1) ...
448s Selecting previously unselected package r-cran-clock.
448s Preparing to unpack .../147-r-cran-clock_0.7.2-1_ppc64el.deb ...
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448s Selecting previously unselected package r-cran-gower.
448s Preparing to unpack .../148-r-cran-gower_1.0.2-1_ppc64el.deb ...
448s Unpacking r-cran-gower (1.0.2-1) ...
448s Selecting previously unselected package r-cran-sparsevctrs.
448s Preparing to unpack .../149-r-cran-sparsevctrs_0.2.0-2_ppc64el.deb ...
448s Unpacking r-cran-sparsevctrs (0.2.0-2) ...
448s Selecting previously unselected package r-cran-hardhat.
448s Preparing to unpack .../150-r-cran-hardhat_1.4.2+dfsg-1_all.deb ...
448s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ...
448s Selecting previously unselected package r-cran-rpart.
448s Preparing to unpack .../151-r-cran-rpart_4.1.24-1build1_ppc64el.deb ...
448s Unpacking r-cran-rpart (4.1.24-1build1) ...
448s Selecting previously unselected package r-cran-shape.
448s Preparing to unpack .../152-r-cran-shape_1.4.6.1-1_all.deb ...
448s Unpacking r-cran-shape (1.4.6.1-1) ...
448s Selecting previously unselected package r-cran-diagram.
448s Preparing to unpack .../153-r-cran-diagram_1.6.5-2_all.deb ...
448s Unpacking r-cran-diagram (1.6.5-2) ...
449s Selecting previously unselected package r-cran-kernsmooth.
449s Preparing to unpack .../154-r-cran-kernsmooth_2.23-26-1build1_ppc64el.deb ...
449s Unpacking r-cran-kernsmooth (2.23-26-1build1) ...
449s Selecting previously unselected package r-cran-digest.
449s Preparing to unpack .../155-r-cran-digest_0.6.39-1_ppc64el.deb ...
449s Unpacking r-cran-digest (0.6.39-1) ...
449s Selecting previously unselected package r-cran-globals.
449s Preparing to unpack .../156-r-cran-globals_0.19.0-1_all.deb ...
449s Unpacking r-cran-globals (0.19.0-1) ...
449s Selecting previously unselected package r-cran-listenv.
449s Preparing to unpack .../157-r-cran-listenv_0.10.0+dfsg-1_all.deb ...
449s Unpacking r-cran-listenv (0.10.0+dfsg-1) ...
449s Selecting previously unselected package r-cran-parallelly.
449s Preparing to unpack .../158-r-cran-parallelly_1.42.0-1_ppc64el.deb ...
449s Unpacking r-cran-parallelly (1.42.0-1) ...
449s Selecting previously unselected package r-cran-future.
449s Preparing to unpack .../159-r-cran-future_1.34.0+dfsg-1_all.deb ...
449s Unpacking r-cran-future (1.34.0+dfsg-1) ...
449s Selecting previously unselected package r-cran-future.apply.
449s Preparing to unpack .../160-r-cran-future.apply_1.11.3+dfsg-1_all.deb ...
449s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ...
449s Selecting previously unselected package r-cran-progressr.
449s Preparing to unpack .../161-r-cran-progressr_0.15.1-1_all.deb ...
449s Unpacking r-cran-progressr (0.15.1-1) ...
449s Selecting previously unselected package r-cran-squarem.
449s Preparing to unpack .../162-r-cran-squarem_2021.1-1build1_all.deb ...
449s Unpacking r-cran-squarem (2021.1-1build1) ...
449s Selecting previously unselected package r-cran-lava.
449s Preparing to unpack .../163-r-cran-lava_1.8.2+dfsg-1_all.deb ...
449s Unpacking r-cran-lava (1.8.2+dfsg-1) ...
449s Selecting previously unselected package r-cran-prodlim.
449s Preparing to unpack .../164-r-cran-prodlim_2024.06.25-1_ppc64el.deb ...
449s Unpacking r-cran-prodlim (2024.06.25-1) ...
449s Selecting previously unselected package r-cran-ipred.
449s Preparing to unpack .../165-r-cran-ipred_0.9-15-1_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-timechange.
449s Preparing to unpack .../166-r-cran-timechange_0.3.0-2_ppc64el.deb ...
449s Unpacking r-cran-timechange (0.3.0-2) ...
449s Selecting previously unselected package r-cran-lubridate.
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449s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ...
449s Selecting previously unselected package r-cran-recipes.
449s Preparing to unpack .../168-r-cran-recipes_1.1.0+dfsg-1_all.deb ...
449s Unpacking r-cran-recipes (1.1.0+dfsg-1) ...
449s Selecting previously unselected package r-cran-reshape2.
449s Preparing to unpack .../169-r-cran-reshape2_1.4.4-2build2_ppc64el.deb ...
449s Unpacking r-cran-reshape2 (1.4.4-2build2) ...
449s Selecting previously unselected package r-cran-caret.
449s Preparing to unpack .../170-r-cran-caret_7.0-1+dfsg-1_ppc64el.deb ...
449s Unpacking r-cran-caret (7.0-1+dfsg-1) ...
449s Selecting previously unselected package r-cran-conquer.
449s Preparing to unpack .../171-r-cran-conquer_1.3.3-1_ppc64el.deb ...
449s Unpacking r-cran-conquer (1.3.3-1) ...
449s Selecting previously unselected package r-cran-quantreg.
449s Preparing to unpack .../172-r-cran-quantreg_6.1-1_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-car.
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449s Selecting previously unselected package r-cran-sandwich.
449s Preparing to unpack .../174-r-cran-sandwich_3.1-1-1build1_all.deb ...
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449s Selecting previously unselected package r-cran-aer.
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449s Selecting previously unselected package r-cran-bit.
449s Preparing to unpack .../176-r-cran-bit_4.6.0+dfsg-1_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-bit64.
449s Preparing to unpack .../177-r-cran-bit64_4.6.0-1-4_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-blob.
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449s Selecting previously unselected package r-cran-fastmap.
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449s Selecting previously unselected package r-cran-cachem.
449s Preparing to unpack .../180-r-cran-cachem_1.1.0-1_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-dbi.
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449s Selecting previously unselected package r-cran-foreign.
449s Preparing to unpack .../182-r-cran-foreign_0.8.91-1_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-hexbin.
449s Preparing to unpack .../183-r-cran-hexbin_1.28.5-1_ppc64el.deb ...
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449s Selecting previously unselected package r-cran-memoise.
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449s Selecting previously unselected package r-cran-mitools.
449s Preparing to unpack .../185-r-cran-mitools_2.4-2build2_all.deb ...
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449s Selecting previously unselected package r-cran-plogr.
449s Preparing to unpack .../186-r-cran-plogr_0.2.0-3build2_all.deb ...
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449s Selecting previously unselected package r-cran-r.methodss3.
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449s Selecting previously unselected package r-cran-r.oo.
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450s Setting up libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ...
450s Setting up libpixman-1-0:ppc64el (0.46.4-1) ...
450s Setting up libsharpyuv0:ppc64el (1.5.0-0.1build1) ...
450s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ...
450s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu2) ...
450s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ...
450s Setting up libxrender1:ppc64el (1:0.9.12-1) ...
450s Setting up libdatrie1:ppc64el (0.2.14-1) ...
450s Setting up libxcb-render0:ppc64el (1.17.0-2ubuntu1) ...
450s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
450s Setting up unzip (6.0-29ubuntu1) ...
450s Setting up x11-common (1:7.7+24ubuntu1) ...
450s Setting up libdeflate0:ppc64el (1.23-2build1) ...
450s Setting up libnlopt0:ppc64el (2.7.1-7ubuntu1) ...
450s Setting up libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ...
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450s Setting up libjbig0:ppc64el (2.1-6.1ubuntu3) ...
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450s Setting up libblas3:ppc64el (3.12.1-7ubuntu1) ...
450s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
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450s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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453s Setting up r-base-core (4.5.2-1ubuntu2) ...
453s Creating config file /etc/R/Renviron with new version
453s Setting up r-cran-squarem (2021.1-1build1) ...
453s Setting up r-cran-labeling (0.4.3-1) ...
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453s Setting up r-cran-hexbin (1.28.5-1) ...
453s Setting up r-cran-viridislite (0.4.3-1) ...
453s Setting up r-cran-sparsem (1.84-2-1) ...
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453s Setting up r-cran-nnet (7.3-20-1) ...
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453s Setting up r-cran-numderiv (2016.8-1.1-3build1) ...
453s Setting up r-cran-magrittr (2.0.3-1) ...
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453s Setting up r-cran-quadprog (1.5-8-1build2) ...
453s Setting up r-cran-littler (0.3.22-1) ...
453s Setting up r-cran-rcpp (1.1.0-1) ...
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453s Setting up r-cran-codetools (0.2-20-1build1) ...
453s Setting up r-cran-nloptr (2.2.1-2) ...
453s Setting up r-cran-boot (1.3-32-1) ...
453s Setting up r-cran-rlang (1.1.5-3) ...
453s Setting up r-cran-matrixstats (1.5.0-1) ...
453s Setting up r-cran-listenv (0.10.0+dfsg-1) ...
453s Setting up r-cran-xfun (0.55+dfsg-1) ...
453s Setting up r-cran-urca (1.3-4-1build1) ...
453s Setting up r-cran-plogr (0.2.0-3build2) ...
453s Setting up r-cran-withr (3.0.2+dfsg-1) ...
453s Setting up r-cran-backports (1.5.0-2) ...
453s Setting up r-cran-deriv (4.2.0-1) ...
453s Setting up r-cran-generics (0.1.4-1) ...
453s Setting up r-cran-iterators (1.0.14-1build1) ...
453s Setting up r-cran-abind (1.4-8-1build1) ...
453s Setting up r-cran-digest (0.6.39-1) ...
453s Setting up r-cran-yaml (2.3.10-1) ...
453s Setting up r-cran-gower (1.0.2-1) ...
453s Setting up r-cran-evaluate (1.0.5-1) ...
453s Setting up r-cran-dbi (1.2.3-1build1) ...
453s Setting up r-cran-timedate (4052.112-1) ...
453s Setting up r-cran-highr (0.11+dfsg-1) ...
453s Setting up r-cran-foreach (1.5.2-1build1) ...
453s Setting up r-cran-fansi (1.0.6-2) ...
453s Setting up r-cran-cardata (3.0.6-1) ...
453s Setting up r-cran-mass (7.3-65-1) ...
453s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
453s Setting up r-cran-glue (1.8.0-1) ...
453s Setting up r-cran-foreign (0.8.91-1) ...
453s Setting up r-cran-fracdiff (1.5-3-1) ...
453s Setting up r-cran-bit (4.6.0+dfsg-1) ...
453s Setting up r-cran-cli (3.6.4-1) ...
453s Setting up r-cran-rbibutils (2.3-1) ...
453s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
453s Setting up r-cran-bit64 (4.6.0-1-4) ...
453s Setting up r-cran-progressr (0.15.1-1) ...
453s Setting up r-cran-shape (1.4.6.1-1) ...
453s Setting up r-cran-fastmap (1.2.0-1) ...
453s Setting up r-cran-r.methodss3 (1.8.2-1) ...
453s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
453s Setting up r-cran-pkgconfig (2.0.3-2build2) ...
453s Setting up r-cran-utf8 (1.2.4-1) ...
453s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
453s Setting up r-cran-parallelly (1.42.0-1) ...
453s Setting up r-cran-stringi (1.8.4-1build2) ...
453s Setting up r-cran-cpp11 (0.5.3-1) ...
453s Setting up r-cran-plyr (1.8.9-1) ...
453s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
453s Setting up r-cran-isoband (0.2.7-1) ...
453s Setting up r-cran-diagram (1.6.5-2) ...
453s Setting up r-cran-scales (1.4.0-1) ...
453s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
453s Setting up r-cran-zoo (1.8-15-1) ...
453s Setting up r-cran-matrix (1.7-4-1) ...
453s Setting up r-cran-kernsmooth (2.23-26-1build1) ...
453s Setting up r-cran-knitr (1.51+dfsg-1) ...
453s Setting up r-cran-mgcv (1.9-4-1) ...
453s Setting up r-cran-cachem (1.1.0-1) ...
453s Setting up r-cran-lmtest (0.9.40-1build1) ...
453s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ...
453s Setting up r-cran-tzdb (0.5.0-1) ...
453s Setting up r-cran-globals (0.19.0-1) ...
453s Setting up r-cran-vctrs (0.6.5-1) ...
453s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ...
453s Setting up r-cran-mitools (2.4-2build2) ...
453s Setting up r-cran-pillar (1.11.1+dfsg-1) ...
453s Setting up r-cran-minqa (1.2.8-1) ...
453s Setting up r-cran-stringr (1.5.1-1) ...
453s Setting up r-cran-class (7.3-23-1) ...
453s Setting up r-cran-modelmetrics (1.2.2.2-1build2) ...
453s Setting up r-cran-matrixmodels (0.5-4-1) ...
453s Setting up r-cran-sparsevctrs (0.2.0-2) ...
453s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
453s Setting up r-cran-clock (0.7.2-1) ...
453s Setting up r-cran-sandwich (3.1-1-1build1) ...
453s Setting up r-cran-proc (1.18.5-1) ...
453s Setting up r-cran-survival (3.8-6-1) ...
453s Setting up r-cran-xts (0.14.1-1) ...
453s Setting up r-cran-survey (4.4-2-2) ...
453s Setting up r-cran-r.oo (1.27.1-1) ...
453s Setting up r-cran-rdpack (2.6.3-1) ...
453s Setting up r-cran-future (1.34.0+dfsg-1) ...
453s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
453s Setting up r-cran-reshape2 (1.4.4-2build2) ...
453s Setting up r-cran-future.apply (1.11.3+dfsg-1) ...
453s Setting up r-cran-timechange (0.3.0-2) ...
453s Setting up r-cran-memoise (2.0.1-1build1) ...
453s Setting up r-cran-lava (1.8.2+dfsg-1) ...
453s Setting up r-cran-purrr (1.0.4-1) ...
453s Setting up r-cran-e1071 (1.7-17-1) ...
453s Setting up r-cran-blob (1.3.0-1) ...
453s Setting up r-cran-hardhat (1.4.2+dfsg-1) ...
453s Setting up r-cran-dplyr (1.1.4-4) ...
453s Setting up r-cran-reformulas (0.4.4-1) ...
453s Setting up r-cran-rsqlite (2.3.9-1) ...
453s Setting up r-cran-ttr (0.24.4-1) ...
453s Setting up r-cran-lubridate (1.9.4+dfsg-1) ...
453s Setting up r-cran-r.utils (2.13.0-1) ...
453s Setting up r-cran-prodlim (2024.06.25-1) ...
453s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
453s Setting up r-cran-rpart (4.1.24-1build1) ...
453s Setting up r-cran-ipred (0.9-15-1) ...
453s Setting up r-cran-lme4 (1.1-38-1) ...
453s Setting up r-cran-tidyr (1.3.1-1) ...
453s Setting up r-cran-recipes (1.1.0+dfsg-1) ...
453s Setting up r-cran-quantmod (0.4.28-1) ...
453s Setting up r-cran-r.cache (0.17.0-1) ...
453s Setting up r-cran-cowplot (1.1.3+dfsg-1) ...
453s Setting up r-cran-caret (7.0-1+dfsg-1) ...
453s Setting up r-cran-tseries (0.10-59-3) ...
453s Setting up r-cran-broom (1.0.12+dfsg-1) ...
453s Setting up r-cran-conquer (1.3.3-1) ...
453s Setting up r-cran-r.rsp (0.46.0+ds-1) ...
453s Setting up r-cran-forecast (8.23.0-1) ...
453s Setting up r-cran-quantreg (6.1-1) ...
453s Setting up r-cran-modelr (0.1.11-1) ...
453s Setting up r-cran-doby (4.7.1-3) ...
453s Setting up r-cran-pbkrtest (0.5.5-1) ...
453s Setting up r-cran-car (3.1-5-1) ...
453s Setting up r-cran-aer (1.2-15-1) ...
453s Processing triggers for libc-bin (2.42-2ubuntu4) ...
453s Processing triggers for man-db (2.13.1-1build1) ...
454s Processing triggers for install-info (7.2-5) ...
454s autopkgtest [23:28:46]: test run-unit-test: [-----------------------
455s BEGIN TEST 3stage2phase.R
455s 
455s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
455s Copyright (C) 2025 The R Foundation for Statistical Computing
455s Platform: powerpc64le-unknown-linux-gnu
455s 
455s R is free software and comes with ABSOLUTELY NO WARRANTY.
455s You are welcome to redistribute it under certain conditions.
455s Type 'license()' or 'licence()' for distribution details.
455s 
455s R is a collaborative project with many contributors.
455s Type 'contributors()' for more information and
455s 'citation()' on how to cite R or R packages in publications.
455s 
455s Type 'demo()' for some demos, 'help()' for on-line help, or
455s 'help.start()' for an HTML browser interface to help.
455s Type 'q()' to quit R.
455s 
455s > ## simulated data with three-stage sample at phase 1, SRS at phase 2
455s > ## motivated by dietary biomarker substudy in HCHS
455s > 
455s > library(survey)
455s Loading required package: grid
455s Loading required package: Matrix
456s Loading required package: survival
456s 
456s Attaching package: 'survey'
456s 
456s The following object is masked from 'package:graphics':
456s 
456s     dotchart
456s 
456s > 
456s > load("simdata1.RData")
456s > 
456s > twophase.full = twophase(id=list(~block+house+ind,~1),
456s +                          strata=list(~strat,NULL),
456s +                          probs=list(~P.block+P.house+P.ind,NULL),
456s +                          subset=~phase2,
456s +                          data=simdata1,method='full')
456s > 
456s > twophase.approx = twophase(id=list(~block+house+ind,~1),
456s +                          strata=list(~strat,NULL),
456s +                          probs=list(~P.block+P.house+P.ind,NULL),
456s +                          subset=~phase2,
456s +                          data=simdata1,method='approx')
456s > 
456s > twophase.rep = twophase(id=list(~block,~1),
456s +                          strata=list(~strat,NULL),
456s +                          probs=list(~I(P.block*P.house*P.ind),NULL),
456s +                          subset=~phase2,
456s +                          data=simdata1,method='full')
457s > 
457s > 
457s > twophase.repapprox = twophase(id=list(~block,~1),
457s +                          strata=list(~strat,NULL),
457s +                          probs=list(~I(P.block*P.house*P.ind),NULL),
457s +                          subset=~phase2,
457s +                          data=simdata1,method='approx')
457s > 
457s > 
457s > svymean(~age, twophase.full)
457s       mean     SE
457s age 41.116 0.8114
457s > svymean(~age, twophase.approx)
457s       mean     SE
457s age 41.116 0.6693
457s > svymean(~age, twophase.rep)
457s       mean    SE
457s age 41.116 0.784
457s > svymean(~age, twophase.repapprox)
457s       mean     SE
457s age 41.116 0.6592
457s > 
457s BEGIN TEST DBIcheck.R
457s 
457s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
457s Copyright (C) 2025 The R Foundation for Statistical Computing
457s Platform: powerpc64le-unknown-linux-gnu
457s 
457s R is free software and comes with ABSOLUTELY NO WARRANTY.
457s You are welcome to redistribute it under certain conditions.
457s Type 'license()' or 'licence()' for distribution details.
457s 
457s R is a collaborative project with many contributors.
457s Type 'contributors()' for more information and
457s 'citation()' on how to cite R or R packages in publications.
457s 
457s Type 'demo()' for some demos, 'help()' for on-line help, or
457s 'help.start()' for an HTML browser interface to help.
457s Type 'q()' to quit R.
457s 
457s > 
457s > library(survey)
457s Loading required package: grid
457s Loading required package: Matrix
458s Loading required package: survival
458s 
458s Attaching package: 'survey'
458s 
458s > library(RSQLite)
458s The following object is masked from 'package:graphics':
458s 
458s     dotchart
458s 
458s > 
458s > data(api)
458s > apiclus1$api_stu<-apiclus1$api.stu
458s > apiclus1$comp_imp<-apiclus1$comp.imp
458s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1)
458s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,
458s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey"))
458s > 
458s > m<-svymean(~api00+stype,dclus1)
458s > m.db<-svymean(~api00+stype, dbclus1)
458s > all.equal(coef(m),coef(m.db))
458s [1] TRUE
458s > all.equal(vcov(m), vcov(m.db))
458s [1] TRUE
458s > 
458s > r<-svyratio(~api_stu, ~enroll, design=dclus1)
458s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1)
458s > all.equal(coef(r), coef(r.db))
458s [1] TRUE
458s > all.equal(SE(r), SE(r.db))
458s [1] TRUE
458s > 
458s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE)
458s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE)
458s > all.equal(coef(b), coef(b.db))
458s [1] TRUE
458s > all.equal(SE(b), SE(b.db))
458s [1] TRUE
458s > all.equal(deff(b), deff(b.db))
458s [1] TRUE
458s > 
458s > l<-svyglm(api00~api99+mobility, design=dclus1)
458s > l.db<-svyglm(api00~api99+mobility, design=dbclus1)
458s > all.equal(coef(l),coef(l.db))
458s [1] TRUE
458s > all.equal(vcov(l), vcov(l.db))
458s [1] TRUE
458s > 
458s > dclus1<-update(dclus1, apidiff=api00-api99)
458s > dclus1<-update(dclus1, apipct= apidiff/api99)
458s > dbclus1<-update(dbclus1, apidiff=api00-api99)
458s > dbclus1<-update(dbclus1, apipct= apidiff/api99)
458s > 
458s > u<-svymean(~api00+apidiff+apipct, dclus1)
458s > u.db<-svymean(~api00+apidiff+apipct, dbclus1)
458s > all.equal(u, u.db)
458s [1] TRUE
458s > 
458s > all.equal(nrow(dclus1),nrow(dbclus1))
458s [1] TRUE
458s > all.equal(nrow(subset(dclus1,stype=="E")),
458s +           nrow(subset(dbclus1,stype=="E")))
458s [1] "Mean relative difference: 0.2708333"
458s > 
458s > ## replicate weights
458s > rclus1<-as.svrepdesign(dclus1)
458s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15,
458s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE)
458s > m<-svymean(~api00+api99,rclus1)
458s > m.db<-svymean(~api00+api99,db_rclus1)
458s > all.equal(m,m.db)
458s [1] TRUE
458s > 
458s > summary(db_rclus1)
458s DB-backed replicate weight design
458s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 
458s     scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 
458s     dbname = system.file("api.db", package = "survey"), combined.weights = FALSE)
458s Unstratified cluster jacknife (JK1) with 15 replicates.
458s Variables: 
458s  [1] "row_names"   "cds"         "stype"       "name"        "sname"      
458s  [6] "snum"        "dname"       "dnum"        "cname"       "cnum"       
458s [11] "flag"        "pcttest"     "api00"       "api99"       "target"     
458s [16] "growth"      "sch_wide"    "comp_imp"    "both"        "awards"     
458s [21] "meals"       "ell"         "yr_rnd"      "mobility"    "acs_k3"     
458s [26] "acs_46"      "acs_core"    "pct_resp"    "not_hsg"     "hsg"        
458s [31] "some_col"    "col_grad"    "grad_sch"    "avg_ed"      "full__1"    
458s [36] "emer"        "enroll"      "api_stu"     "fpc"         "pw"         
458s [41] "row_names:1" "wt1"         "wt2"         "wt3"         "wt4"        
458s [46] "wt5"         "wt6"         "wt7"         "wt8"         "wt9"        
458s [51] "wt10"        "wt11"        "wt12"        "wt13"        "wt14"       
458s [56] "wt15"       
458s > 
458s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes"))
458s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes"))
458s > all.equal(s,s.db)
458s [1] TRUE
458s > 
458s BEGIN TEST anova-svycoxph.R
458s 
458s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
458s Copyright (C) 2025 The R Foundation for Statistical Computing
458s Platform: powerpc64le-unknown-linux-gnu
458s 
458s R is free software and comes with ABSOLUTELY NO WARRANTY.
458s You are welcome to redistribute it under certain conditions.
458s Type 'license()' or 'licence()' for distribution details.
458s 
458s R is a collaborative project with many contributors.
458s Type 'contributors()' for more information and
458s 'citation()' on how to cite R or R packages in publications.
458s 
458s Type 'demo()' for some demos, 'help()' for on-line help, or
458s 'help.start()' for an HTML browser interface to help.
458s Type 'q()' to quit R.
458s 
459s > 
459s >  library(survey)
459s Loading required package: grid
459s Loading required package: Matrix
459s Loading required package: survival
460s > example(svycoxph, ask=FALSE)
460s 
460s Attaching package: 'survey'
460s 
460s The following object is masked from 'package:graphics':
460s 
460s     dotchart
460s 
460s 
460s svycxp> ## Somewhat unrealistic example of nonresponse bias.
460s svycxp> data(pbc, package="survival")
460s 
460s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
460s 
460s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
460s 
460s svycxp> pbc$randprob<-fitted(biasmodel)
460s 
460s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0
460s 
460s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))
460s 
460s svycxp> rpbc<-as.svrepdesign(dpbc)
460s 
460s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc))
460s Call:
460s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 
460s     albumin, design = dpbc)
460s 
460s               coef exp(coef) se(coef) robust se      z        p
460s log(bili)  0.88592   2.42522  0.09140   0.09048  9.791  < 2e-16
460s protime    0.24487   1.27745  0.07825   0.08122  3.015  0.00257
460s albumin   -1.04298   0.35240  0.21211   0.20454 -5.099 3.41e-07
460s 
460s Likelihood ratio test=  on 3 df, p=
460s n= 312, number of events= 144 
460s 
460s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc)
460s Call:
460s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 
460s     protime + albumin, design = rpbc)
460s 
460s               coef exp(coef) se(coef)      z        p
460s log(bili)  0.88592   2.42522  0.09838  9.005  < 2e-16
460s protime    0.24487   1.27745  0.09373  2.612  0.00899
460s albumin   -1.04298   0.35240  0.21966 -4.748 2.05e-06
460s 
460s Likelihood ratio test=NA  on 3 df, p=NA
460s n= 312, number of events= 144 
460s 
460s svycxp> s<-predict(model,se=TRUE, type="curve",
460s svycxp+      newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5)))
460s 
460s svycxp> plot(s[[1]],ci=TRUE,col="sienna")
460s 
460s svycxp> lines(s[[2]], ci=TRUE,col="royalblue")
460s 
460s svycxp> quantile(s[[1]], ci=TRUE)
460s 0.75  0.5 0.25 
460s 1435 2503 3574 
460s attr(,"ci")
460s      0.025 0.975
460s 0.75  1217  1786
460s 0.5   2256  3170
460s 0.25  3222   Inf
460s 
460s svycxp> confint(s[[2]], parm=365*(1:5))
460s          0.025     0.975
460s 365  0.8375139 0.9453781
460s 730  0.7382750 0.8999016
460s 1095 0.4784105 0.7478460
460s 1460 0.3192009 0.6206764
460s 1825 0.2149475 0.5292978
460s > m<-update(model, .~.+I(protime^2))
460s > a<-anova(m,model)
460s > b<-anova(m, model,force=TRUE)
460s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)])))
460s > 
460s BEGIN TEST api.R
460s 
460s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
460s Copyright (C) 2025 The R Foundation for Statistical Computing
460s Platform: powerpc64le-unknown-linux-gnu
460s 
460s R is free software and comes with ABSOLUTELY NO WARRANTY.
460s You are welcome to redistribute it under certain conditions.
460s Type 'license()' or 'licence()' for distribution details.
460s 
460s R is a collaborative project with many contributors.
460s Type 'contributors()' for more information and
460s 'citation()' on how to cite R or R packages in publications.
460s 
460s Type 'demo()' for some demos, 'help()' for on-line help, or
460s 'help.start()' for an HTML browser interface to help.
460s Type 'q()' to quit R.
460s 
460s > library(survey)
460s Loading required package: grid
460s Loading required package: Matrix
461s Loading required package: survival
461s 
461s Attaching package: 'survey'
461s 
461s The following object is masked from 'package:graphics':
461s 
461s     dotchart
461s 
461s > options(survey.replicates.mse=TRUE)
461s > example(api)
461s 
461s api> library(survey)
461s 
461s api> data(api)
462s 
462s api> mean(apipop$api00)
462s [1] 664.7126
462s 
462s api> sum(apipop$enroll, na.rm=TRUE)
462s [1] 3811472
462s 
462s api> #stratified sample
462s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
462s 
462s api> summary(dstrat)
462s Stratified Independent Sampling design
462s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
462s Probabilities:
462s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
462s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 
462s Stratum Sizes: 
462s              E  H  M
462s obs        100 50 50
462s design.PSU 100 50 50
462s actual.PSU 100 50 50
462s Population stratum sizes (PSUs): 
462s    E    H    M 
462s 4421  755 1018 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "pw"       "fpc"     
462s 
462s api> svymean(~api00, dstrat)
462s         mean     SE
462s api00 662.29 9.4089
462s 
462s api> svytotal(~enroll, dstrat, na.rm=TRUE)
462s          total     SE
462s enroll 3687178 114642
462s 
462s api> # one-stage cluster sample
462s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
462s 
462s api> summary(dclus1)
462s 1 - level Cluster Sampling design
462s With (15) clusters.
462s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
462s Probabilities:
462s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
462s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
462s Population size (PSUs): 757 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> svymean(~api00, dclus1)
462s         mean     SE
462s api00 644.17 23.542
462s 
462s api> svytotal(~enroll, dclus1, na.rm=TRUE)
462s          total     SE
462s enroll 3404940 932235
462s 
462s api> # two-stage cluster sample
462s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
462s 
462s api> summary(dclus2)
462s 2 - level Cluster Sampling design
462s With (40, 126) clusters.
462s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
462s Probabilities:
462s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
462s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
462s Population size (PSUs): 757 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
462s 
462s api> svymean(~api00, dclus2)
462s         mean     SE
462s api00 670.81 30.099
462s 
462s api> svytotal(~enroll, dclus2, na.rm=TRUE)
462s          total     SE
462s enroll 2639273 799638
462s 
462s api> # two-stage `with replacement'
462s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
462s 
462s api> summary(dclus2wr)
462s 2 - level Cluster Sampling design (with replacement)
462s With (40, 126) clusters.
462s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
462s Probabilities:
462s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
462s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
462s 
462s api> svymean(~api00, dclus2wr)
462s         mean     SE
462s api00 670.81 30.712
462s 
462s api> svytotal(~enroll, dclus2wr, na.rm=TRUE)
462s          total     SE
462s enroll 2639273 820261
462s 
462s api> # convert to replicate weights
462s api> rclus1<-as.svrepdesign(dclus1)
462s 
462s api> summary(rclus1)
462s Call: as.svrepdesign.default(dclus1)
462s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances.
462s Variables: 
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> svymean(~api00, rclus1)
462s         mean     SE
462s api00 644.17 26.335
462s 
462s api> svytotal(~enroll, rclus1, na.rm=TRUE)
462s          total     SE
462s enroll 3404940 932235
462s 
462s api> # post-stratify on school type
462s api> pop.types<-xtabs(~stype, data=apipop)
462s 
462s api> rclus1p<-postStratify(rclus1, ~stype, pop.types)
462s 
462s api> dclus1p<-postStratify(dclus1, ~stype, pop.types)
462s 
462s api> summary(dclus1p)
462s 1 - level Cluster Sampling design
462s With (15) clusters.
462s dclus1p<-postStratify(dclus1, ~stype, pop.types)
462s Probabilities:
462s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
462s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 
462s Population size (PSUs): 757 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> summary(rclus1p)
462s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types)
462s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances.
462s Variables: 
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> svymean(~api00, dclus1p)
462s         mean    SE
462s api00 642.31 23.92
462s 
462s api> svytotal(~enroll, dclus1p, na.rm=TRUE)
462s          total     SE
462s enroll 3680893 406293
462s 
462s api> svymean(~api00, rclus1p)
462s         mean     SE
462s api00 642.31 26.936
462s 
462s api> svytotal(~enroll, rclus1p, na.rm=TRUE)
462s          total     SE
462s enroll 3680893 473434
462s > 
462s > options(survey.replicates.mse=FALSE)
462s > example(api)
462s 
462s api> library(survey)
462s 
462s api> data(api)
462s 
462s api> mean(apipop$api00)
462s [1] 664.7126
462s 
462s api> sum(apipop$enroll, na.rm=TRUE)
462s [1] 3811472
462s 
462s api> #stratified sample
462s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
462s 
462s api> summary(dstrat)
462s Stratified Independent Sampling design
462s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
462s Probabilities:
462s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
462s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 
462s Stratum Sizes: 
462s              E  H  M
462s obs        100 50 50
462s design.PSU 100 50 50
462s actual.PSU 100 50 50
462s Population stratum sizes (PSUs): 
462s    E    H    M 
462s 4421  755 1018 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "pw"       "fpc"     
462s 
462s api> svymean(~api00, dstrat)
462s         mean     SE
462s api00 662.29 9.4089
462s 
462s api> svytotal(~enroll, dstrat, na.rm=TRUE)
462s          total     SE
462s enroll 3687178 114642
462s 
462s api> # one-stage cluster sample
462s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
462s 
462s api> summary(dclus1)
462s 1 - level Cluster Sampling design
462s With (15) clusters.
462s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
462s Probabilities:
462s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
462s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
462s Population size (PSUs): 757 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> svymean(~api00, dclus1)
462s         mean     SE
462s api00 644.17 23.542
462s 
462s api> svytotal(~enroll, dclus1, na.rm=TRUE)
462s          total     SE
462s enroll 3404940 932235
462s 
462s api> # two-stage cluster sample
462s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
462s 
462s api> summary(dclus2)
462s 2 - level Cluster Sampling design
462s With (40, 126) clusters.
462s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
462s Probabilities:
462s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
462s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
462s Population size (PSUs): 757 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
462s 
462s api> svymean(~api00, dclus2)
462s         mean     SE
462s api00 670.81 30.099
462s 
462s api> svytotal(~enroll, dclus2, na.rm=TRUE)
462s          total     SE
462s enroll 2639273 799638
462s 
462s api> # two-stage `with replacement'
462s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
462s 
462s api> summary(dclus2wr)
462s 2 - level Cluster Sampling design (with replacement)
462s With (40, 126) clusters.
462s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
462s Probabilities:
462s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
462s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
462s 
462s api> svymean(~api00, dclus2wr)
462s         mean     SE
462s api00 670.81 30.712
462s 
462s api> svytotal(~enroll, dclus2wr, na.rm=TRUE)
462s          total     SE
462s enroll 2639273 820261
462s 
462s api> # convert to replicate weights
462s api> rclus1<-as.svrepdesign(dclus1)
462s 
462s api> summary(rclus1)
462s Call: as.svrepdesign.default(dclus1)
462s Unstratified cluster jacknife (JK1) with 15 replicates.
462s Variables: 
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> svymean(~api00, rclus1)
462s         mean     SE
462s api00 644.17 26.329
462s 
462s api> svytotal(~enroll, rclus1, na.rm=TRUE)
462s          total     SE
462s enroll 3404940 932235
462s 
462s api> # post-stratify on school type
462s api> pop.types<-xtabs(~stype, data=apipop)
462s 
462s api> rclus1p<-postStratify(rclus1, ~stype, pop.types)
462s 
462s api> dclus1p<-postStratify(dclus1, ~stype, pop.types)
462s 
462s api> summary(dclus1p)
462s 1 - level Cluster Sampling design
462s With (15) clusters.
462s dclus1p<-postStratify(dclus1, ~stype, pop.types)
462s Probabilities:
462s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
462s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 
462s Population size (PSUs): 757 
462s Data variables:
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> summary(rclus1p)
462s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types)
462s Unstratified cluster jacknife (JK1) with 15 replicates.
462s Variables: 
462s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
462s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
462s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
462s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
462s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
462s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
462s [37] "api.stu"  "fpc"      "pw"      
462s 
462s api> svymean(~api00, dclus1p)
462s         mean    SE
462s api00 642.31 23.92
462s 
462s api> svytotal(~enroll, dclus1p, na.rm=TRUE)
462s          total     SE
462s enroll 3680893 406293
462s 
462s api> svymean(~api00, rclus1p)
462s         mean     SE
462s api00 642.31 26.934
462s 
462s api> svytotal(~enroll, rclus1p, na.rm=TRUE)
462s          total     SE
462s enroll 3680893 473431
462s > 
462s BEGIN TEST badcal.R
462s 
462s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
462s Copyright (C) 2025 The R Foundation for Statistical Computing
462s Platform: powerpc64le-unknown-linux-gnu
462s 
462s R is free software and comes with ABSOLUTELY NO WARRANTY.
462s You are welcome to redistribute it under certain conditions.
462s Type 'license()' or 'licence()' for distribution details.
462s 
462s R is a collaborative project with many contributors.
462s Type 'contributors()' for more information and
462s 'citation()' on how to cite R or R packages in publications.
462s 
462s Type 'demo()' for some demos, 'help()' for on-line help, or
462s 'help.start()' for an HTML browser interface to help.
462s Type 'q()' to quit R.
462s 
462s > ##
462s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya)
462s > ##
462s > library(survey)
462s Loading required package: grid
462s Loading required package: Matrix
463s Loading required package: survival
463s 
463s Attaching package: 'survey'
463s 
463s The following object is masked from 'package:graphics':
463s 
463s     dotchart
463s 
463s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10))
463s > des <- svydesign(ids=~1, weights=~w, data=data)
463s > des.c <- calibrate(des, ~factor(x), c(10000, 5000))
463s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking')
463s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r)))
463s > 
463s BEGIN TEST brewer_cpp.R
463s 
463s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
463s Copyright (C) 2025 The R Foundation for Statistical Computing
463s Platform: powerpc64le-unknown-linux-gnu
463s 
463s R is free software and comes with ABSOLUTELY NO WARRANTY.
463s You are welcome to redistribute it under certain conditions.
463s Type 'license()' or 'licence()' for distribution details.
463s 
463s R is a collaborative project with many contributors.
463s Type 'contributors()' for more information and
463s 'citation()' on how to cite R or R packages in publications.
463s 
463s Type 'demo()' for some demos, 'help()' for on-line help, or
463s 'help.start()' for an HTML browser interface to help.
463s Type 'q()' to quit R.
463s 
463s > ## pps="brewer" can't use rcpp
463s > ## this checks that it doesn't
463s > library(survey)
463s Loading required package: grid
463s Loading required package: Matrix
464s Loading required package: survival
464s 
464s Attaching package: 'survey'
464s 
464s The following object is masked from 'package:graphics':
464s 
464s     dotchart
464s 
464s > data(election)
464s > 
464s > dpps_br<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="brewer")
464s > options(survey.use_rcpp=TRUE)
464s > a<-svytotal(~Bush+Kerry+Nader, dpps_br)
464s > options(survey.use_rcpp=FALSE)
464s > b<-svytotal(~Bush+Kerry+Nader, dpps_br)
464s > 
464s > stopifnot(identical(a,b))
464s > 
464s BEGIN TEST bycovmat.R
464s 
464s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
464s Copyright (C) 2025 The R Foundation for Statistical Computing
464s Platform: powerpc64le-unknown-linux-gnu
464s 
464s R is free software and comes with ABSOLUTELY NO WARRANTY.
464s You are welcome to redistribute it under certain conditions.
464s Type 'license()' or 'licence()' for distribution details.
464s 
464s R is a collaborative project with many contributors.
464s Type 'contributors()' for more information and
464s 'citation()' on how to cite R or R packages in publications.
464s 
464s Type 'demo()' for some demos, 'help()' for on-line help, or
464s 'help.start()' for an HTML browser interface to help.
464s Type 'q()' to quit R.
464s 
464s > 
464s > library(survey)
464s Loading required package: grid
464s Loading required package: Matrix
465s Loading required package: survival
466s 
466s Attaching package: 'survey'
466s 
466s The following object is masked from 'package:graphics':
466s 
466s     dotchart
466s 
466s > data(api)
466s > options(survey.replicates.mse=TRUE)
466s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
466s > rclus1<-as.svrepdesign(dclus1)
466s > 
466s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
466s +          covmat=TRUE,drop.empty.groups=FALSE)
466s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
466s +          covmat=TRUE,drop.empty.groups=TRUE)
466s > 
466s > stopifnot(all.equal(
466s +               as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a))))
466s + ))
466s > stopifnot(all.equal(
466s +               as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b))))
466s +               ))
466s > 
466s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE)
466s > all <- svytotal(~ell+mobility+meals, dclus1)
466s > 
466s > stopifnot(all(abs(vcov(svycontrast(all,
466s +                                    list(quote(ell/mobility),
466s +                                         quote(mobility/mobility),
466s +                                         quote(ell/meals),quote(mobility/meals))))
466s +                   -vcov(rat))<1e-10))
466s > 
466s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10))
466s > 
466s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE)
466s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE)
466s > 
466s > con<-svycontrast(all,
466s +                  list(quote(ell/mobility),
466s +                       quote(mobility/mobility),
466s +                       quote(ell/meals),quote(mobility/meals)))
466s > 
466s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10))
466s > 
466s > options(survey.replicates.mse=FALSE)
466s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
466s > rclus1<-as.svrepdesign(dclus1)
466s > 
466s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
466s +          covmat=TRUE,drop.empty.groups=FALSE)
466s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
466s +          covmat=TRUE,drop.empty.groups=TRUE)
466s > 
466s > stopifnot(all.equal(
466s +               as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a))))
466s + ))
466s > stopifnot(all.equal(
466s +               as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b))))
466s +               ))
466s > 
466s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE)
466s > all <- svytotal(~ell+mobility+meals, dclus1)
466s > 
466s > stopifnot(all(abs(vcov(svycontrast(all,
466s +                                    list(quote(ell/mobility),
466s +                                         quote(mobility/mobility),
466s +                                         quote(ell/meals),quote(mobility/meals))))
466s +                   -vcov(rat))<1e-10))
466s > 
466s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10))
466s > 
466s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE)
466s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE)
466s > 
466s > con<-svycontrast(all,
466s +                  list(quote(ell/mobility),
466s +                       quote(mobility/mobility),
466s +                       quote(ell/meals),quote(mobility/meals)))
466s > 
466s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10))
466s > 
466s > 
466s > 
466s BEGIN TEST caleg.R
466s 
466s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
466s Copyright (C) 2025 The R Foundation for Statistical Computing
466s Platform: powerpc64le-unknown-linux-gnu
466s 
466s R is free software and comes with ABSOLUTELY NO WARRANTY.
466s You are welcome to redistribute it under certain conditions.
466s Type 'license()' or 'licence()' for distribution details.
466s 
466s R is a collaborative project with many contributors.
466s Type 'contributors()' for more information and
466s 'citation()' on how to cite R or R packages in publications.
466s 
466s Type 'demo()' for some demos, 'help()' for on-line help, or
466s 'help.start()' for an HTML browser interface to help.
466s Type 'q()' to quit R.
466s 
466s > ##
466s > ## Calibration examples
466s > ##
466s > 
466s > 
466s > ## Example of calibration to first-stage clusters
466s > library(survey)
466s Loading required package: grid
466s Loading required package: Matrix
467s Loading required package: survival
467s 
467s Attaching package: 'survey'
467s 
467s The following object is masked from 'package:graphics':
467s 
467s     dotchart
467s 
467s > data(api)
467s > 
467s > clusters<-table(apiclus2$dnum)
467s > clusters<-clusters[clusters>1 & names(clusters)!="639"]
467s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters)))
467s > 
467s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a)
467s > 
467s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters)))
467s > 
467s > pop<-lapply(as.numeric(names(clusters)), function(cluster) {
467s +   colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))})
467s > 
467s > names(pop)<-names(clusters)
467s > 
467s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1)
467s > 
467s > svymean(~api99, dclus2)
467s         mean     SE
467s api99 642.14 31.434
467s > svymean(~api99, dclus2g)
467s         mean    SE
467s api99 654.49 29.82
467s > 
467s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4)
467s     dnum    api99      se
467s 83    83 694.3333  0.0000
467s 132  132 505.0000  0.0000
467s 152  152 574.0000  0.0000
467s 173  173 894.7500  0.0000
467s 198  198 533.7500  0.0000
467s 200  200 589.8000  6.8335
467s 228  228 477.0000  0.0000
467s 295  295 646.4000  0.0000
467s 302  302 903.5000  0.0000
467s 403  403 852.4000  0.0000
467s 452  452 533.0000  0.0000
467s 480  480 614.2000  0.0000
467s 523  523 580.5000  0.0000
467s 534  534 564.6000  0.0000
467s 549  549 896.2000  0.0000
467s 552  552 730.0000  0.0000
467s 570  570 518.4000  7.5478
467s 575  575 800.8000  4.2513
467s 596  596 785.6000  2.4155
467s 620  620 591.6000 10.5869
467s 638  638 560.2000  4.0954
467s 674  674 760.0000  0.0000
467s 679  679 610.2500  0.0000
467s 687  687 718.6667  0.0000
467s 701  701 651.5000  0.0000
467s 711  711 690.5000  0.0000
467s 731  731 702.0000  2.1744
467s 768  768 562.5000  0.0000
467s 781  781 854.4000  0.7456
467s > 
467s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4)
468s     dnum    api99 se
468s 83    83 694.3333  0
468s 132  132 505.0000  0
468s 152  152 574.0000  0
468s 173  173 894.7500  0
468s 198  198 533.7500  0
468s 200  200 567.5455  0
468s 228  228 477.0000  0
468s 295  295 646.4000  0
468s 302  302 903.5000  0
468s 403  403 852.4000  0
468s 452  452 533.0000  0
468s 480  480 614.2000  0
468s 523  523 580.5000  0
468s 534  534 564.6000  0
468s 549  549 896.2000  0
468s 552  552 730.0000  0
468s 570  570 548.9444  0
468s 575  575 824.5357  0
468s 596  596 787.5714  0
468s 620  620 609.3750  0
468s 638  638 585.6429  0
468s 674  674 760.0000  0
468s 679  679 610.2500  0
468s 687  687 718.6667  0
468s 701  701 651.5000  0
468s 711  711 690.5000  0
468s 731  731 700.6667  0
468s 768  768 562.5000  0
468s 781  781 851.0000  0
468s > 
468s > ## Averaging to first stage
468s > 
468s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
468s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE)
468s > 
468s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1)
468s > 
468s > svytotal(~enroll,dclus1g)
468s          total SE
468s enroll 3811472  0
468s > svytotal(~api.stu,dclus1g)
468s           total    SE
468s api.stu 3242857 38967
468s > 
468s > #variation within clusters should be zero
468s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE))
468s [1] TRUE
468s > 
468s > ##bounded weights
468s >  dclus1g<-calibrate(dclus1, ~enroll, pop)
468s >  range(weights(dclus1g)/weights(dclus1))
468s [1] 0.7906782 1.7891164
468s >  dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5))
468s >  range(weights(dclus1gb)/weights(dclus1))
468s [1] 0.7198751 1.5000000
468s > 
468s > ## Ratio estimators
468s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
468s > svytotal(~api.stu,dstrat)
468s           total    SE
468s api.stu 3086009 99477
468s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE)
468s > total.enroll<-sum(apipop$enroll,na.rm=TRUE)
468s > predict(common, total=total.enroll)
468s $total
468s          enroll
468s api.stu 3190038
468s 
468s $se
468s           enroll
468s api.stu 29565.98
468s 
468s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1)
468s > svytotal(~api.stu, dstratg)
468s           total    SE
468s api.stu 3190038 29566
468s > 
468s > ## postStratify vs calibrate in stratified sample (Ben French)
468s > set.seed(17)
468s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100),
468s +                 z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100))
468s > dat$w<-ifelse(dat$y,dat$z,1-dat$z)
468s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000))
468s >  des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y)
468s > postStratify(des,~w,popw)->dps
468s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000))
468s > 
468s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps)))
468s [1] TRUE
468s > 
468s > ## missing data in calibrated design
468s > dps$variables$z[1]<-NA
468s > summary(svyglm(y~z+x,design=dps,family=quasibinomial))
468s 
468s Call:
468s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial)
468s 
468s Survey design:
468s postStratify(des, ~w, popw)
468s 
468s Coefficients:
468s             Estimate Std. Error t value Pr(>|t|)    
468s (Intercept)  -0.1203     0.3380  -0.356    0.722    
468s z             6.2118     0.6451   9.630   <2e-16 ***
468s x             2.2602     0.2514   8.992   <2e-16 ***
468s ---
468s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
468s 
468s (Dispersion parameter for quasibinomial family taken to be 1.919987)
468s 
468s Number of Fisher Scoring iterations: 9
468s 
468s > 
468s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm)
468s > # should match the ratio estmate above
468s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll)
468s > svytotal(~api.stu, dstratgh)
468s           total    SE
468s api.stu 3190038 29566
468s > 
468s > ## individual boundary constraints as multiplicative values (Daniel Oehm)
468s > bnds <- list(
468s +   lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 
468s +   upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move
468s > lapply(bnds, head)
468s $lower
468s [1]    1    1 -Inf -Inf -Inf -Inf
468s 
468s $upper
468s [1]   1   1 Inf Inf Inf Inf
468s 
468s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll)
468s > svytotal(~api.stu, dstratg1)
468s           total    SE
468s api.stu 3190133 29561
468s > head(weights(dstrat))
468s     1     2     3     4     5     6 
468s 44.21 44.21 44.21 44.21 44.21 44.21 
468s > head(weights(dstratg1))
468s        1        2        3        4        5        6 
468s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 
468s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2])
468s [1] TRUE
468s > 
468s > ## individual boundary constraints as constant values (Daniel Oehm)
468s > bnds <- list(
468s +   lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 
468s +   upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged
468s > lapply(bnds, head)
468s $lower
468s [1] 44.21 44.21  -Inf  -Inf  -Inf  -Inf
468s 
468s $upper
468s [1] 44.21 44.21   Inf   Inf   Inf   Inf
468s 
468s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll)
468s > svytotal(~api.stu, dstratg2)
468s           total    SE
468s api.stu 3190133 29561
468s > head(weights(dstrat))
468s     1     2     3     4     5     6 
468s 44.21 44.21 44.21 44.21 44.21 44.21 
468s > head(weights(dstratg2))
468s        1        2        3        4        5        6 
468s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 
468s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good
468s [1] TRUE
468s > 
468s > # sparse matrix support (Daniel Oehm)
468s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
468s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
468s > dclus1g<-calibrate(dclus1, ~stype, pop.totals)
468s > svymean(~api00, dclus1g)
468s         mean    SE
468s api00 642.31 23.92
468s > svytotal(~enroll, dclus1g)
468s          total     SE
468s enroll 3680893 406293
468s > 
468s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
468s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE)
468s > svymean(~api00, dclus1g)
468s         mean    SE
468s api00 642.31 23.92
468s > svytotal(~enroll, dclus1g)
468s          total     SE
468s enroll 3680893 406293
468s > 
468s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
468s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking")
468s > svymean(~api00, dclus1g)
468s         mean    SE
468s api00 642.31 23.92
468s > svytotal(~enroll, dclus1g)
468s          total     SE
468s enroll 3680893 406293
468s > 
468s BEGIN TEST check.R
468s 
468s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
468s Copyright (C) 2025 The R Foundation for Statistical Computing
468s Platform: powerpc64le-unknown-linux-gnu
468s 
468s R is free software and comes with ABSOLUTELY NO WARRANTY.
468s You are welcome to redistribute it under certain conditions.
468s Type 'license()' or 'licence()' for distribution details.
468s 
468s R is a collaborative project with many contributors.
468s Type 'contributors()' for more information and
468s 'citation()' on how to cite R or R packages in publications.
468s 
468s Type 'demo()' for some demos, 'help()' for on-line help, or
468s 'help.start()' for an HTML browser interface to help.
468s Type 'q()' to quit R.
468s 
468s > library(survey)
468s Loading required package: grid
468s Loading required package: Matrix
469s Loading required package: survival
469s 
469s Attaching package: 'survey'
469s 
469s The following object is masked from 'package:graphics':
469s 
469s     dotchart
469s 
469s > data(fpc)
469s > ## test various possibilities for svydesign
469s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 
469s     variables = ~x, data = fpc, nest = TRUE)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7413
469s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 
469s     data = fpc, nest = TRUE)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7413
469s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 
469s     data = fpc, nest = TRUE)
469s > svymean(~x,a)
469s   mean    SE
469s x 44.2 6.237
469s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
469s > a
469s Stratified Warning message:
469s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x,  :
469s   No weights or probabilities supplied, assuming equal probability
469s Independent Sampling design (with replacement)
469s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 
469s     nest = TRUE)
469s > svymean(~x,a)
469s Warning message:
469s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x,  :
469s   No weights or probabilities supplied, assuming equal probability
469s Warning message:
469s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) :
469s   No weights or probabilities supplied, assuming equal probability
469s    mean     SE
469s x 5.525 0.7796
469s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 
469s     data = fpc, nest = TRUE)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7413
469s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 
469s     nest = TRUE)
469s > svymean(~x,a)
469s    mean     SE
469s x 5.525 0.7796
469s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE)
469s > a
469s 1 - level Cluster Sampling design (with replacement)
469s With (5) clusters.
469s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE)
469s > svymean(~x,a)
469s    mean    SE
469s x 5.525 0.838
469s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE)
469s > a
469s 1 - level Cluster Sampling design (with replacement)
469s With (5) clusters.
469s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 
469s     nest = TRUE)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7938
469s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc)
469s > a
469s 2 - level Cluster Sampling design (with replacement)
469s With (2, 8) clusters.
469s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 
469s     data = fpc)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.5465
469s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc)
469s Warning message:
469s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) :
469s   No weights or probabilities supplied, assuming equal probability
469s > a
469s 2 - level Cluster Sampling design (with replacement)
469s With (2, 8) clusters.
469s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc)
469s > svymean(~x,a)
469s    mean     SE
469s x 5.525 0.5188
469s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE],  nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
469s     variables = fpc[, "x", drop = FALSE], nest = TRUE)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7413
469s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6],  nest=TRUE)
469s > a
469s Stratified Independent Sampling design (with replacement)
469s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
469s     variables = fpc[, 4:6], nest = TRUE)
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7413
469s > 
469s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid,  variables=fpc[,4:6], fpc=rep(27,8))
469s > a
469s 1 - level Cluster Sampling design
469s With (5) clusters.
469s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 
469s     4:6], fpc = rep(27, 8))
469s > svymean(~x,a)
469s     mean     SE
469s x 5.4481 0.7165
469s > 
469s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid,  strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh)
469s > a
469s Stratified Independent Sampling design
469s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
469s     nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh)
469s > svymean(~x,a)
469s     mean    SE
469s x 5.4481 0.616
469s > 
469s BEGIN TEST confintrep.R
469s 
469s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
469s Copyright (C) 2025 The R Foundation for Statistical Computing
469s Platform: powerpc64le-unknown-linux-gnu
469s 
469s R is free software and comes with ABSOLUTELY NO WARRANTY.
469s You are welcome to redistribute it under certain conditions.
469s Type 'license()' or 'licence()' for distribution details.
469s 
469s R is a collaborative project with many contributors.
469s Type 'contributors()' for more information and
469s 'citation()' on how to cite R or R packages in publications.
469s 
469s Type 'demo()' for some demos, 'help()' for on-line help, or
469s 'help.start()' for an HTML browser interface to help.
469s Type 'q()' to quit R.
469s 
469s > library(survey)
469s Loading required package: grid
469s Loading required package: Matrix
470s Loading required package: survival
470s 
470s Attaching package: 'survey'
470s 
470s The following object is masked from 'package:graphics':
470s 
470s     dotchart
470s 
470s > data(api)
471s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
471s > rclus2<-as.svrepdesign(dclus2)
471s Warning message:
471s In as.svrepdesign.default(dclus2) :
471s   Finite population corrections after first stage have been dropped
471s > 
471s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial)
471s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint")
471s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial)
471s > if(anyNA(confint(mrep))) stop("NA in confint")
471s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint")
471s > 
471s BEGIN TEST contrast-replicates.R
471s 
471s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
471s Copyright (C) 2025 The R Foundation for Statistical Computing
471s Platform: powerpc64le-unknown-linux-gnu
471s 
471s R is free software and comes with ABSOLUTELY NO WARRANTY.
471s You are welcome to redistribute it under certain conditions.
471s Type 'license()' or 'licence()' for distribution details.
471s 
471s R is a collaborative project with many contributors.
471s Type 'contributors()' for more information and
471s 'citation()' on how to cite R or R packages in publications.
471s 
471s Type 'demo()' for some demos, 'help()' for on-line help, or
471s 'help.start()' for an HTML browser interface to help.
471s Type 'q()' to quit R.
471s 
471s > ## test use of replicates in svyby, svycontrast
471s > library(survey)
471s Loading required package: grid
471s Loading required package: Matrix
472s Loading required package: survival
472s 
472s Attaching package: 'survey'
472s 
472s > 
472s > data(api)
472s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
472s > rclus1<-as.svrepdesign(dclus1)
472s > 
472s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE)
472s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H)))
472s > vcov(c_without)
472s            contrast
472s contrast 0.06862947
472s > 
472s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE)
472s > 
472s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H)))
472s The following object is masked from 'package:graphics':
472s 
472s     dotchart
472s 
472s > 
472s > v_with<- vcov(rclus1, c_with$replicates)
472s > 
472s > r<- attr(meanlogs_with, "replicates")
472s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2]))
472s > 
472s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with)))
472s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with))))
472s > 
472s BEGIN TEST coxph-termtest.R
472s 
472s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
472s Copyright (C) 2025 The R Foundation for Statistical Computing
472s Platform: powerpc64le-unknown-linux-gnu
472s 
472s R is free software and comes with ABSOLUTELY NO WARRANTY.
472s You are welcome to redistribute it under certain conditions.
472s Type 'license()' or 'licence()' for distribution details.
472s 
472s R is a collaborative project with many contributors.
472s Type 'contributors()' for more information and
472s 'citation()' on how to cite R or R packages in publications.
472s 
472s Type 'demo()' for some demos, 'help()' for on-line help, or
472s 'help.start()' for an HTML browser interface to help.
472s Type 'q()' to quit R.
472s 
472s > library(survey)
472s Loading required package: grid
472s Loading required package: Matrix
473s Loading required package: survival
473s 
473s Attaching package: 'survey'
473s 
473s The following object is masked from 'package:graphics':
473s 
473s     dotchart
473s 
473s > library(survival)
473s > set.seed(2021-6-25)
473s > test1 <- list(time=c(4,3,1,1,2,2,3),
473s +               status=c(1,1,1,0,1,1,0),
473s +               x1=as.factor(rbinom(7, 2, 0.5)),
473s +               x=c(0,2,1,1,1,0,0))
473s > # Fit a stratified model
473s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1)
473s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1)
473s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")],
473s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")]))
473s > 
473s > data(pbc, package="survival")
473s > 
473s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
473s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
473s > pbc$randprob<-fitted(biasmodel)
473s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0
473s > 
473s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))
473s > library(splines)
473s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc)
473s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT")
473s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4))
473s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4))
473s > 
473s BEGIN TEST deff.R
473s 
473s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
473s Copyright (C) 2025 The R Foundation for Statistical Computing
473s Platform: powerpc64le-unknown-linux-gnu
473s 
473s R is free software and comes with ABSOLUTELY NO WARRANTY.
473s You are welcome to redistribute it under certain conditions.
473s Type 'license()' or 'licence()' for distribution details.
473s 
473s R is a collaborative project with many contributors.
473s Type 'contributors()' for more information and
473s 'citation()' on how to cite R or R packages in publications.
473s 
473s Type 'demo()' for some demos, 'help()' for on-line help, or
473s 'help.start()' for an HTML browser interface to help.
473s Type 'q()' to quit R.
473s 
473s > ## from Takahiro Tsuchiya
473s > library(survey)
473s Loading required package: grid
473s Loading required package: Matrix
474s Loading required package: survival
474s 
474s Attaching package: 'survey'
474s 
474s > kigyo<-read.table(tmp<-textConnection("  obs uriage srs.w pps.w
474s + 1    1     15   100    20
474s + 2    2    143   100   200
474s + 3    3     21   100    11
474s + 4    4     51   100    25
474s + 5    5    337   100   550
474s + 6    6     50   100    30
474s + 7    7    274   100   250
474s + 8    8    145   100   100
474s + 9    9     15   100    10
474s + 10  10     86   100    55
474s + ",open="r"),header=TRUE)
474s > close(tmp)
474s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo)
474s The following object is masked from 'package:graphics':
474s 
474s     dotchart
474s 
474s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE))
474s           mean      SE   DEff
474s uriage 113.700  35.626 1.0101
474s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10)
474s          uriage
474s uriage 1.010101
474s > 
474s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE))
474s         total     SE   DEff
474s uriage 113700  35626 1.0101
474s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10)
474s          uriage
474s uriage 1.010101
474s > 
474s > 
474s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo)
474s > (res.pps <- svymean(~uriage, des.pps, deff='replace'))
474s           mean      SE   DEff
474s uriage 243.914  48.752 1.9741
474s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10)
474s          uriage
474s uriage 1.974067
474s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace'))
474s         total     SE   DEff
474s uriage 305136 184965 18.157
474s > (N.hat <- sum(weights(des.pps)))
474s [1] 1251
474s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10)
475s          uriage
475s uriage 18.15669
475s > 
475s BEGIN TEST defftest.R
475s 
475s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
475s Copyright (C) 2025 The R Foundation for Statistical Computing
475s Platform: powerpc64le-unknown-linux-gnu
475s 
475s R is free software and comes with ABSOLUTELY NO WARRANTY.
475s You are welcome to redistribute it under certain conditions.
475s Type 'license()' or 'licence()' for distribution details.
475s 
475s R is a collaborative project with many contributors.
475s Type 'contributors()' for more information and
475s 'citation()' on how to cite R or R packages in publications.
475s 
475s Type 'demo()' for some demos, 'help()' for on-line help, or
475s 'help.start()' for an HTML browser interface to help.
475s Type 'q()' to quit R.
475s 
475s > library(survey)
475s Loading required package: grid
475s Loading required package: Matrix
476s Loading required package: survival
476s 
476s Attaching package: 'survey'
476s 
476s The following object is masked from 'package:graphics':
476s 
476s     dotchart
476s 
476s > 
476s > data(api)
476s > 
476s > ## one-stage cluster sample
476s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
476s > 
476s > # svyglm model
476s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE)
476s > 
476s > #deffs returned from svyglm model - implausibly high
476s > deff(mod)
476s (Intercept)      enroll     api.stu 
476s    1.919945    2.500983    2.686102 
476s > #> (Intercept)      enroll     api.stu 
476s > #>    351.3500    457.6799    491.5567
476s > 
476s > # run mod with same data and glm()
476s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1)
476s > 
476s > # manually calculate deffs
476s > 
476s > clust_se <- summary(mod)$coefficients[,2]
476s > srs_se <- summary(srs_mod)$coefficients[,2]
476s > 
476s > deffs <- clust_se^2 / srs_se^2
476s > stopifnot(all.equal(deffs, deff(mod)))
476s > 
476s > 
476s BEGIN TEST degf-svrepdesign.R
476s 
476s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
476s Copyright (C) 2025 The R Foundation for Statistical Computing
476s Platform: powerpc64le-unknown-linux-gnu
476s 
476s R is free software and comes with ABSOLUTELY NO WARRANTY.
476s You are welcome to redistribute it under certain conditions.
476s Type 'license()' or 'licence()' for distribution details.
476s 
476s R is a collaborative project with many contributors.
476s Type 'contributors()' for more information and
476s 'citation()' on how to cite R or R packages in publications.
476s 
476s Type 'demo()' for some demos, 'help()' for on-line help, or
476s 'help.start()' for an HTML browser interface to help.
476s Type 'q()' to quit R.
476s 
476s > library(survey)
476s Loading required package: grid
476s Loading required package: Matrix
477s Loading required package: survival
477s 
477s Attaching package: 'survey'
477s 
477s The following object is masked from 'package:graphics':
477s 
477s     dotchart
477s 
477s > data(scd)
477s > 
477s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1),
477s + c(0,1,0,1,1,0))
477s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights)
477s Warning message:
477s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) :
477s   No sampling weights provided: equal probability assumed
477s > 
477s > stopifnot(degf(scdrep)==3)
477s > 
477s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4)
477s > stopifnot(degf(scdrep)==4)
477s > Warning message:
477s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights,  :
477s   No sampling weights provided: equal probability assumed
477s 
477s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2)
477s > stopifnot(degf(scdrep)==2)
477s > 
477s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 
477s +    warning=function(w) w)
477s > 
477s > stopifnot(inherits(msg,"warning"))
477s > 
477s > 
477s > 
477s > 
477s BEGIN TEST domain.R
477s Warning message:
477s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights,  :
477s   No sampling weights provided: equal probability assumed
477s 
477s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
477s Copyright (C) 2025 The R Foundation for Statistical Computing
477s Platform: powerpc64le-unknown-linux-gnu
477s 
477s R is free software and comes with ABSOLUTELY NO WARRANTY.
477s You are welcome to redistribute it under certain conditions.
477s Type 'license()' or 'licence()' for distribution details.
477s 
477s R is a collaborative project with many contributors.
477s Type 'contributors()' for more information and
477s 'citation()' on how to cite R or R packages in publications.
477s 
477s Type 'demo()' for some demos, 'help()' for on-line help, or
477s 'help.start()' for an HTML browser interface to help.
477s Type 'q()' to quit R.
477s 
477s > ##
477s > ## Domain means can be written as ratio estimators or as regression coefficients
477s > ##
477s > ## This code checks that subsetting the design object gives the same results as
477s > ## these approaches.
477s > ##
477s > 
477s > 
477s > library(survey)
477s Loading required package: grid
477s Loading required package: Matrix
478s Loading required package: survival
478s 
478s Attaching package: 'survey'
478s 
478s The following object is masked from 'package:graphics':
478s 
478s     dotchart
478s 
478s > data(fpc)
478s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE)
478s > dsub<-subset(dfpc,x>4)
478s > (m1<-svymean(~x,design=dsub))
478s    mean     SE
478s x 6.195 0.7555
478s > 
478s > ## These should give the same domain estimates and standard errors
478s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE))
478s       I(x > 4)        x        se
478s FALSE    FALSE 3.314286 0.3117042
478s TRUE      TRUE 6.195000 0.7555129
478s > m3<-svyglm(x~I(x>4)+0,design=dfpc)
478s > summary(m3)
478s 
478s Call:
478s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc)
478s 
478s Survey design:
478s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 
478s     nest = TRUE)
478s 
478s Coefficients:
478s               Estimate Std. Error t value Pr(>|t|)    
478s I(x > 4)FALSE   3.3143     0.3117   10.63 0.000127 ***
478s I(x > 4)TRUE    6.1950     0.7555    8.20 0.000439 ***
478s ---
478s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
478s 
478s (Dispersion parameter for gaussian family taken to be 2.557379)
478s 
478s Number of Fisher Scoring iterations: 2
478s 
478s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc))
478s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 
478s     dfpc)
478s Ratios=
478s                as.numeric(x > 4)
478s I(x * (x > 4))             6.195
478s SEs=
478s                as.numeric(x > 4)
478s I(x * (x > 4))         0.7555129
478s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3)))))
478s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4)))))
478s > 
478s > ## with strata
478s > data(api)
478s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
478s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes"))
478s > m2<-svyglm(enroll~comp.imp-1, dstrat)
478s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat)
478s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
478s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
478s > 
478s > ## with calibration
478s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
478s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
478s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069)))
478s 1 - level Cluster Sampling design
478s With (15) clusters.
478s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069))
478s > 
478s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes"))
479s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3)
479s > m2<-svyglm(api00~comp.imp-1, dclus1g3)
479s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
479s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
479s > 
479s > ## with raking
479s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
479s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
479s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
479s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes"))
479s > m2<-svyglm(api00~comp.imp-1, dclus1r)
479s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r)
479s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
479s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
479s > 
479s > 
479s > 
479s > ##
479s > ## based on bug report from Takahiro Tsuchiya for version 3.4
479s > ## 
479s > rei<-read.table(tmp<-textConnection(
479s + "  id   N n.a h n.ah n.h   sub  y
479s + 1   1 300  20 1   12   5  TRUE  1
479s + 2   2 300  20 1   12   5  TRUE  2
479s + 3   3 300  20 1   12   5  TRUE  3
479s + 4   4 300  20 1   12   5  TRUE  4
479s + 5   5 300  20 1   12   5  TRUE  5
479s + 6   6 300  20 1   12   5 FALSE NA
479s + 7   7 300  20 1   12   5 FALSE NA
479s + 8   8 300  20 1   12   5 FALSE NA
479s + 9   9 300  20 1   12   5 FALSE NA
479s + 10 10 300  20 1   12   5 FALSE NA
479s + 11 11 300  20 1   12   5 FALSE NA
479s + 12 12 300  20 1   12   5 FALSE NA
479s + 13 13 300  20 2    8   3  TRUE  6
479s + 14 14 300  20 2    8   3  TRUE  7
479s + 15 15 300  20 2    8   3  TRUE  8
479s + 16 16 300  20 2    8   3 FALSE NA
479s + 17 17 300  20 2    8   3 FALSE NA
479s + 18 18 300  20 2    8   3 FALSE NA
479s + 19 19 300  20 2    8   3 FALSE NA
479s + 20 20 300  20 2    8   3 FALSE NA
479s + "), header=TRUE)
479s > close(tmp)
479s > 
479s > 
479s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h),
479s +                     fpc=list(~N,NULL), subset=~sub, data=rei, method="full")
479s > tot2<- svytotal(~y, subset(des.rei2, y>3))
479s > 
479s > rei$y<-rei$y*(rei$y>3)
479s > ## based on Sarndal et al (9.4.14)
479s > rei$w.ah <- rei$n.ah / rei$n.a
479s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE)
479s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE)
479s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y)
479s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h))
479s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1)))
479s > 
479s > a.rei$f.h<-with(a.rei, n.h/n.ah)
479s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh))
479s > 
479s > a.rei$f<-with(a.rei, n.a/N)
479s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1))
479s > 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)))
479s > 
479s > V
479s [1] 70761.47
479s > Vphase1
479s [1] 44325.47
479s > Vphase2
479s [1] 26436
479s > vcov(tot2)
479s          [,1]
479s [1,] 70761.47
479s attr(,"phases")
479s attr(,"phases")$phase1
479s          [,1]
479s [1,] 44325.47
479s 
479s attr(,"phases")$phase2
479s       [,1]
479s [1,] 26436
479s 
479s > 
479s > ## comparing to regression
479s > reg<-svyglm(y~I(y<4), design=des.rei2)
479s > mn<-svymean(~y, subset(des.rei2,y>3))
479s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn)))
479s [1] TRUE
479s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn)))
479s [1] TRUE
479s > vcov(mn)
479s           [,1]
479s [1,] 0.3292258
479s attr(,"phases")
479s attr(,"phases")$phase1
479s           [,1]
479s [1,] 0.1599264
479s 
479s attr(,"phases")$phase2
479s           [,1]
479s [1,] 0.1692994
479s 
479s > vcov(reg)
479s              (Intercept) I(y < 4)TRUE
479s (Intercept)    0.3292258   -0.3292258
479s I(y < 4)TRUE  -0.3292258    0.5901907
479s attr(,"phases")
479s attr(,"phases")$phase1
479s              (Intercept) I(y < 4)TRUE
479s (Intercept)    0.1599264   -0.1599264
479s I(y < 4)TRUE  -0.1599264    0.2588542
479s 
479s attr(,"phases")$phase2
479s              (Intercept) I(y < 4)TRUE
479s (Intercept)    0.1692994   -0.1692994
479s I(y < 4)TRUE  -0.1692994    0.3313365
479s 
479s > 
479s > 
479s BEGIN TEST fpc.R
479s 
479s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
479s Copyright (C) 2025 The R Foundation for Statistical Computing
479s Platform: powerpc64le-unknown-linux-gnu
479s 
479s R is free software and comes with ABSOLUTELY NO WARRANTY.
479s You are welcome to redistribute it under certain conditions.
479s Type 'license()' or 'licence()' for distribution details.
479s 
479s R is a collaborative project with many contributors.
479s Type 'contributors()' for more information and
479s 'citation()' on how to cite R or R packages in publications.
479s 
479s Type 'demo()' for some demos, 'help()' for on-line help, or
479s 'help.start()' for an HTML browser interface to help.
479s Type 'q()' to quit R.
479s 
479s > Loading required package: grid
479s library(survey)
479s Loading required package: Matrix
480s Loading required package: survival
480s 
480s Attaching package: 'survey'
480s 
480s The following object is masked from 'package:graphics':
480s 
480s     dotchart
480s 
480s > ## check many permutations of fpc specification
480s > example(fpc)
480s 
480s fpc> data(fpc)
480s 
480s fpc> fpc
480s   stratid psuid weight nh Nh   x
480s 1       1     1      3  5 15 2.8
480s 2       1     2      3  5 15 4.1
480s 3       1     3      3  5 15 6.8
480s 4       1     4      3  5 15 6.8
480s 5       1     5      3  5 15 9.2
480s 6       2     1      4  3 12 3.7
480s 7       2     2      4  3 12 6.6
480s 8       2     3      4  3 12 4.2
480s 
480s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 
480s fpc+    data=fpc, nest=TRUE)
480s 
480s fpc> withoutfpc
480s Stratified Independent Sampling design (with replacement)
480s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 
480s    data=fpc, nest=TRUE)
480s 
480s fpc> svymean(~x, withoutfpc)
480s     mean     SE
480s x 5.4481 0.7413
480s 
480s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
480s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
480s 
480s fpc> withfpc
480s Stratified Independent Sampling design
480s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
480s fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
480s 
480s fpc> svymean(~x, withfpc)
480s     mean    SE
480s x 5.4481 0.616
480s 
480s fpc> ## Other equivalent forms 
480s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid,
480s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
480s 
480s fpc> svymean(~x, withfpc)
480s     mean    SE
480s x 5.4481 0.616
480s 
480s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
480s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE)
480s 
480s fpc> svymean(~x, withfpc)
480s     mean    SE
480s x 5.4481 0.616
480s 
480s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid),
480s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc)
480s 
480s fpc> svymean(~x, withfpc)
480s     mean    SE
480s x 5.4481 0.616
480s 
480s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh,
480s fpc+  variables=~x,data=fpc,nest=TRUE)
480s 
480s fpc> svymean(~x, withfpc)
480s     mean    SE
480s x 5.4481 0.616
480s 
480s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid,
480s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE)
480s 
480s fpc> svymean(~x, withfpc)
480s     mean    SE
480s x 5.4481 0.616
480s > 
480s > 
480s BEGIN TEST glm-scoping.R
480s 
480s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
480s Copyright (C) 2025 The R Foundation for Statistical Computing
480s Platform: powerpc64le-unknown-linux-gnu
480s 
480s R is free software and comes with ABSOLUTELY NO WARRANTY.
480s You are welcome to redistribute it under certain conditions.
480s Type 'license()' or 'licence()' for distribution details.
480s 
480s R is a collaborative project with many contributors.
480s Type 'contributors()' for more information and
480s 'citation()' on how to cite R or R packages in publications.
480s 
480s Type 'demo()' for some demos, 'help()' for on-line help, or
480s 'help.start()' for an HTML browser interface to help.
480s Type 'q()' to quit R.
480s 
480s > ## bug report from Thomas Leeper, fixed in version 3.32-3
480s > 
480s > library("survey")
480s Loading required package: grid
480s Loading required package: Matrix
481s Loading required package: survival
481s > data(api)
481s 
481s Attaching package: 'survey'
481s 
481s The following object is masked from 'package:graphics':
481s 
481s     dotchart
481s 
481s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
481s > 
481s > # pass `family` directly (WORKS!)
481s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian())
481s Stratified Independent Sampling design
481s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
481s     fpc = ~fpc)
481s 
481s Call:  svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 
481s     family = gaussian())
481s 
481s Coefficients:
481s (Intercept)          ell        meals     mobility  
481s    820.8873      -0.4806      -3.1415       0.2257  
481s 
481s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
481s Null Deviance:	    3023000 
481s Residual Deviance: 1029000 	AIC: 2308
481s > 
481s > # passing `family` via ... (WORKS!)
481s > myfun1 <- function(formula, design, ...) {
481s +     svyglm(formula, design = design, ...)
481s + }
481s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian())
481s Stratified Independent Sampling design
481s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
481s     fpc = ~fpc)
481s 
481s Call:  svyglm(formula = formula, design = design, family = ..1)
481s 
481s Coefficients:
481s (Intercept)          ell        meals     mobility  
481s    820.8873      -0.4806      -3.1415       0.2257  
481s 
481s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
481s Null Deviance:	    3023000 
481s Residual Deviance: 1029000 	AIC: 2308
481s > 
481s > # passing `family` via default argument (DOES NOT WORK!)
481s > myfun2 <- function(formula, design, family = gaussian()) {
481s +     svyglm(formula, design = design, family = family)
481s + }
481s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian())
481s Stratified Independent Sampling design
481s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
481s     fpc = ~fpc)
481s 
481s Call:  svyglm(formula = formula, design = design, family = family)
481s 
481s Coefficients:
481s (Intercept)          ell        meals     mobility  
481s    820.8873      -0.4806      -3.1415       0.2257  
481s 
481s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
481s Null Deviance:	    3023000 
481s Residual Deviance: 1029000 	AIC: 2308
481s > 
481s BEGIN TEST kalton.R
481s 
481s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
481s Copyright (C) 2025 The R Foundation for Statistical Computing
481s Platform: powerpc64le-unknown-linux-gnu
481s 
481s R is free software and comes with ABSOLUTELY NO WARRANTY.
481s You are welcome to redistribute it under certain conditions.
481s Type 'license()' or 'licence()' for distribution details.
481s 
481s R is a collaborative project with many contributors.
481s Type 'contributors()' for more information and
481s 'citation()' on how to cite R or R packages in publications.
481s 
481s Type 'demo()' for some demos, 'help()' for on-line help, or
481s 'help.start()' for an HTML browser interface to help.
481s Type 'q()' to quit R.
481s 
481s > library(survey)
481s Loading required package: grid
482s Loading required package: Matrix
483s Loading required package: survival
483s 
483s Attaching package: 'survey'
483s 
483s The following object is masked from 'package:graphics':
483s 
483s     dotchart
483s 
483s > 
483s > ab<-expand.grid(a=factor(1:4),b=factor(1:3))
483s > 
483s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),]
483s > 
483s Warning message:
483s In svydesign.default(id = ~1, data = kaltonsample) :
483s   No weights or probabilities supplied, assuming equal probability
483s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),]
483s > 
483s > jointpop<-colSums(model.matrix(~a*b,kaltonpop))
483s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop))
483s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop))
483s > 
483s > dkalton<-svydesign(id=~1,data=kaltonsample)
483s > 
483s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop))
483s > 
483s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001))
483s > 
483s > dcalps<-calibrate(dkalton, ~a*b, jointpop)
483s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking")
483s > dlinear<-calibrate(dkalton, ~a+b, marginalpop)
483s > 
483s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2))
483s > 
483s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit")
483s > 
483s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop)
483s > 
483s > 
483s > #table A
483s >  round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 4.00 1.00 1.38
483s   2 1.20 1.07 1.10
483s   3 1.70 1.20 4.00
483s   4 1.83 1.65 1.79
483s >  round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 4.00 1.00 1.37
483s   2 1.20 1.07 1.10
483s   3 1.70 1.20 4.00
483s   4 1.83 1.65 1.79
483s > 
483s > #table B
483s >  round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 1.81 1.45 2.02
483s   2 1.08 0.87 1.21
483s   3 2.20 1.76 2.45
483s   4 1.83 1.47 2.04
483s >  round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 1.81 1.45 2.02
483s   2 1.08 0.87 1.21
483s   3 2.20 1.76 2.45
483s   4 1.83 1.47 2.04
483s > 
483s > #table C
483s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 1.82 1.50 1.97
483s   2 1.09 0.78 1.24
483s   3 2.19 1.88 2.34
483s   4 1.83 1.52 1.98
483s > 
483s > #table D
483s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 1.21 1.17 1.14
483s   2 1.43 1.40 1.36
483s   3 1.66 1.62 1.59
483s   4 1.88 1.85 1.81
483s > 
483s > #table G
483s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 1.87 1.46 1.98
483s   2 1.08 0.74 1.27
483s   3 2.17 2.09 2.18
483s   4 1.89 1.49 1.99
483s > 
483s > #table G
483s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2)
483s    b
483s a      1    2    3
483s   1 1.81 1.48 1.99
483s   2 1.08 0.75 1.26
483s   3 2.20 2.00 2.20
483s   4 1.83 1.50 2.00
483s > 
483s BEGIN TEST logranktest.R
483s 
483s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
483s Copyright (C) 2025 The R Foundation for Statistical Computing
483s Platform: powerpc64le-unknown-linux-gnu
483s 
483s R is free software and comes with ABSOLUTELY NO WARRANTY.
483s You are welcome to redistribute it under certain conditions.
483s Type 'license()' or 'licence()' for distribution details.
483s 
483s R is a collaborative project with many contributors.
483s Type 'contributors()' for more information and
483s 'citation()' on how to cite R or R packages in publications.
483s 
483s Type 'demo()' for some demos, 'help()' for on-line help, or
483s 'help.start()' for an HTML browser interface to help.
483s Type 'q()' to quit R.
483s 
483s > ## StackOverflow 63333282
483s > 
483s > library(survey)
483s Loading required package: grid
483s Loading required package: Matrix
484s Loading required package: survival
484s 
484s Attaching package: 'survey'
484s 
484s > D = data.frame(unique_id = 1:135,
484s The following object is masked from 'package:graphics':
484s 
484s     dotchart
484s 
484s +                
484s +                weights = rep(1,135),
484s +                
484s +                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 ,
484s +                               
484s +                               6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522,
484s +                               
484s +                               15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263,
484s +                               
484s +                               23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409,
484s +                               
484s +                               9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009,
484s +                               
484s +                               2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540,
484s +                               
484s +                               1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679,
484s +                               
484s +                               0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630,
484s +                               
484s +                               2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901,
484s +                               
484s +                               2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354,
484s +                               
484s +                               11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594,
484s +                               
484s +                               2.35699896, 2.94956000, 8.85381736),
484s +                
484s +                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,
484s +                               
484s +                               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,
484s +                               
484s +                               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),
484s +                
484s +                group = c(rep("group1", 40), rep("group2", 95)))
484s > 
484s > 
484s > 
484s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group")
484s > 
484s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D )
484s > 
484s > a<-svylogrank(formula = svykm_formula, design = svy_design)
484s > 
484s > ii<-with(D, order(event_time, event_flag))
484s > 
484s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] )
484s > 
484s > b<-svylogrank(formula = svykm_formula, design = svy_design2)
484s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large")
484s > 
484s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score")
484s > 
484s > 
484s > stopifnot(all.equal(a[[2]],b[[2]]))
484s > 
484s > stopifnot(all.equal(a[[2]],d[[2]]))
484s > 
484s > stopifnot(all.equal(a[[2]],f[-1]))
484s > 
484s > 
484s BEGIN TEST lonely.psu.R
484s 
484s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
484s Copyright (C) 2025 The R Foundation for Statistical Computing
484s Platform: powerpc64le-unknown-linux-gnu
484s 
484s R is free software and comes with ABSOLUTELY NO WARRANTY.
484s You are welcome to redistribute it under certain conditions.
484s Type 'license()' or 'licence()' for distribution details.
484s 
484s R is a collaborative project with many contributors.
484s Type 'contributors()' for more information and
484s 'citation()' on how to cite R or R packages in publications.
484s 
484s Type 'demo()' for some demos, 'help()' for on-line help, or
484s 'help.start()' for an HTML browser interface to help.
484s Type 'q()' to quit R.
484s 
484s > 
484s > ## lonely PSUs by design
484s > library(survey)
484s Loading required package: grid
484s Loading required package: Matrix
485s Loading required package: survival
485s 
485s Attaching package: 'survey'
485s 
485s > data(api)
485s The following object is masked from 'package:graphics':
485s 
485s     dotchart
485s 
485s > ## not certainty PSUs by fpc
485s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1)
485s > summary(ds)
485s Stratified Independent Sampling design (with replacement)
485s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1)
485s Probabilities:
485s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  : 
485s   Stratum (413) has only one PSU at stage 1
485s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc,  : 
485s   Stratum413has only one PSU
485s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
485s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
485s Stratum Sizes: 
485s            61 135 178 197 255 406 413 437 448 510 568 637 716 778 815
485s obs        13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
485s design.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
485s actual.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
485s Data variables:
485s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
485s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
485s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
485s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
485s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
485s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
485s [37] "api.stu"  "fpc"      "pw"      
485s > 
485s > options(survey.lonely.psu="fail")
485s > try(svymean(~api00,ds))
485s > try(svymean(~api00, as.svrepdesign(ds)))
485s > options(survey.lonely.psu="remove")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.8058
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.8058
485s > options(survey.lonely.psu="certainty")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.8058
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.8058
485s > options(survey.lonely.psu="adjust")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.8281
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.8267
485s > options(survey.lonely.psu="average")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 6.0096
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.8217
485s > 
485s > ## fpc specified
485s > fpc<-ifelse(apiclus1$dnum==413, 1,1000)
485s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc)
485s > summary(ds)
485s Stratified Independent Sampling design
485s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 
485s     fpc = fpc)
485s Probabilities:
485s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
485s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
485s Stratum Sizes: 
485s            61 135 178 197 255 406 413 437 448 510 568 637 716 778 815
485s obs        13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
485s design.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
485s actual.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
485s Population stratum sizes (PSUs): 
485s  135  178  197  255  406  413  437  448  510  568   61  637  716  778  815 
485s 1000 1000 1000 1000 1000    1 1000 1000 1000 1000 1000 1000 1000 1000 1000 
485s Data variables:
485s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
485s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
485s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
485s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
485s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
485s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
485s [37] "api.stu"  "fpc"      "pw"      
485s > 
485s > options(survey.lonely.psu="fail")
485s > try(svymean(~api00,ds))
485s         mean     SE
485s api00 644.17 5.7344
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.7344
485s > options(survey.lonely.psu="remove")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.7344
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.7344
485s > options(survey.lonely.psu="certainty")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.7344
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.7344
485s > options(survey.lonely.psu="adjust")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.7344
485s > svymean(~api00, as.svrepdesign(ds))
485s         mean     SE
485s api00 644.17 5.7344
485s > options(survey.lonely.psu="average")
485s > svymean(~api00,ds)
485s         mean     SE
485s api00 644.17 5.7344
485s > svymean(~api00, as.svrepdesign(ds))
486s         mean     SE
486s api00 644.17 5.7501
486s > 
486s > rs<-as.svrepdesign(ds)
486s > svytotal(~api00,rs)
486s         total    SE
486s api00 3989986 35616
486s > SE(svytotal(~api00,subset(rs, dnum==413)))==0
486s [1] TRUE
486s > 
486s > ## lonely PSUs after subsetting
486s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413))
486s > ds1<-ds[-31,]
486s > summary(ds1)
486s Stratified Independent Sampling design (with replacement)
486s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 
486s     dnum != 413))
486s Probabilities:
486s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
486s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
486s Stratum Sizes: 
486s            61 135 178 197 255 406 437 448 510 568 637 716 778 815
486s obs        13  34   4  13  16   1   4  12  21   9  11  37   2   4
486s design.PSU 13  34   4  13  16   2   4  12  21   9  11  37   2   4
486s actual.PSU 13  34   4  13  16   1   4  12  21   9  11  37   2   4
486s Data variables:
486s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
486s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
486s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
486s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
486s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
486s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
486s [37] "api.stu"  "fpc"      "pw"      
486s > 
486s > options(survey.lonely.psu="fail")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 5.8909
486s > options(survey.lonely.psu="remove")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 5.8909
486s > options(survey.lonely.psu="certainty")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 5.8909
486s > options(survey.lonely.psu="adjust")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 5.8909
486s > options(survey.lonely.psu="average")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 5.8909
486s > 
486s > ## with adjustment
486s > options(survey.adjust.domain.lonely=TRUE)
486s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413))
486s > ds1<-ds[-31,]
486s > summary(ds1)
486s Stratified Independent Sampling design (with replacement)
486s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 
486s     dnum != 413))
486s Probabilities:
486s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
486s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
486s Stratum Sizes: 
486s            61 135 178 197 255 406 437 448 510 568 637 716 778 815
486s obs        13  34   4  13  16   1   4  12  21   9  11  37   2   4
486s design.PSU 13  34   4  13  16   2   4  12  21   9  11  37   2   4
486s actual.PSU 13  34   4  13  16   1   4  12  21   9  11  37   2   4
486s Data variables:
486s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
486s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
486s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
486s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
486s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
486s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
486s [37] "api.stu"  "fpc"      "pw"      
486s > 
486s > options(survey.lonely.psu="fail")
486s > try(svymean(~api00,ds1))
486s Warning message:
486s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
486s   Stratum (406) has only one PSU at stage 1
486s         mean     SE
486s api00 645.14 5.8909
486s > options(survey.lonely.psu="remove")
486s > svymean(~api00,ds1)
486s Warning message:
486s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
486s   Stratum (406) has only one PSU at stage 1
486s         mean     SE
486s api00 645.14 5.8909
486s > options(survey.lonely.psu="certainty")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 5.8909
486s Warning message:
486s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
486s   Stratum (406) has only one PSU at stage 1
486s > options(survey.lonely.psu="adjust")
486s > svymean(~api00,ds1)
486s Warning message:
486s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
486s   Stratum (406) has only one PSU at stage 1
486s         mean     SE
486s api00 645.14 5.9119
486s > options(survey.lonely.psu="average")
486s > svymean(~api00,ds1)
486s         mean     SE
486s api00 645.14 6.0914
486s > 
486s > ## checks for `svytotal()`
486s > 
486s > df_w_singleton <- data.frame(
486s +   Stratum = c(1, 1, 2, 2, 3),
486s +   PSU = c(1, 2, 3, 4, 5),
486s +   Design_Weight = c(10.5, 10.5, 20, 20, 15),
486s +   Sex = c("M", "F", "F", "M",  "M"),
486s +   Age = c(30.5, 40.5, 35, 52, 44),
486s +   Height = c(6.2, 5.0, 5.3, 5.7, 5.5)
486s + )
486s > 
486s > design_w_singleton <- survey::svydesign(
486s +   data = df_w_singleton,
486s Warning message:
486s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
486s   Stratum (406) has only one PSU at stage 1
486s +   ids = ~ PSU, strata = ~ Stratum,
486s +   weights = ~ Design_Weight
486s + )
486s > 
486s > options("survey.lonely.psu" = "remove")
486s > 
486s > stopifnot(all.equal(
486s +   target = 126625,
486s +   current = as.numeric(
486s +     vcov(svytotal(x = ~ Age, design = design_w_singleton))
486s +   )
486s + ))
486s > 
486s > options("survey.lonely.psu" = "certainty")
486s > 
486s > stopifnot(all.equal(
486s +   target = 126625,
486s +   current = as.numeric(
486s +     vcov(svytotal(x = ~ Age, design = design_w_singleton))
486s +   )
486s + ))
486s > 
486s > options("survey.lonely.psu" = "adjust")
486s > 
486s > stopifnot(all.equal(
486s +   target = 127579.8,
486s +   current = as.numeric(
486s +     vcov(svytotal(x = ~ Age, design = design_w_singleton))
486s +   ),
486s +   scale = 127579.8, tolerance = 0.000001
486s + ))
486s > 
486s BEGIN TEST mtcars-var.R
486s 
486s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
486s Copyright (C) 2025 The R Foundation for Statistical Computing
486s Platform: powerpc64le-unknown-linux-gnu
486s 
486s R is free software and comes with ABSOLUTELY NO WARRANTY.
486s You are welcome to redistribute it under certain conditions.
486s Type 'license()' or 'licence()' for distribution details.
486s 
486s R is a collaborative project with many contributors.
486s Type 'contributors()' for more information and
486s 'citation()' on how to cite R or R packages in publications.
486s 
486s Type 'demo()' for some demos, 'help()' for on-line help, or
486s 'help.start()' for an HTML browser interface to help.
486s Type 'q()' to quit R.
486s 
486s > library(survey)
486s Loading required package: grid
486s Loading required package: Matrix
487s Loading required package: survival
487s > 
487s > # don't throw an error on domains of size 1, just return NA
487s > input <- mtcars
487s > input$carb <- factor(input$carb)
487s > design <- svydesign(ids = ~0, weights = NULL, data = input)
487s 
487s Attaching package: 'survey'
487s 
487s The following object is masked from 'package:graphics':
487s 
487s     dotchart
487s 
487s > svyby(
487s +   ~mpg,
487s +   ~carb,
487s +   design,
487s +   svyvar
487s + )
487s   carb      mpg         se
487s 1    1 36.01619 11.2823286
487s 2    2 29.94444  9.0030898
487s 3    3  1.11000  0.4604066
487s 4    4 15.29656  4.3174617
487s 6    6       NA         NA
487s 8    8       NA         NA
487s > 
487s > 
487s > ## same n with na.rm=TRUE as subset(, !is.na)
487s > input$mpg[1]<-NA
487s > design <- svydesign(ids = ~0, weights = NULL, data = input)
487s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE),
487s +           svyvar(~mpg, subset(design, !is.na(mpg)))))
487s > 
487s BEGIN TEST multistage-rcpp.R
487s 
487s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
487s Copyright (C) 2025 The R Foundation for Statistical Computing
487s Platform: powerpc64le-unknown-linux-gnu
487s 
487s R is free software and comes with ABSOLUTELY NO WARRANTY.
487s You are welcome to redistribute it under certain conditions.
487s Type 'license()' or 'licence()' for distribution details.
487s 
487s R is a collaborative project with many contributors.
487s Type 'contributors()' for more information and
487s 'citation()' on how to cite R or R packages in publications.
487s 
487s Type 'demo()' for some demos, 'help()' for on-line help, or
487s 'help.start()' for an HTML browser interface to help.
487s Type 'q()' to quit R.
487s 
487s > ## temporarily disable while it's being fixed
487s > ## q("no")
487s > 
487s > ## 
487s > ## Check that multistage() and multistage_rcpp() give same results
487s > ## for different options.
487s > ##
487s > library(survey)
487s Loading required package: grid
487s Loading required package: Matrix
488s Loading required package: survival
488s 
488s Attaching package: 'survey'
488s 
488s > 
488s > # Check for a simple random sample ----
488s > 
488s >   data('api', package = 'survey')
488s The following object is masked from 'package:graphics':
488s 
488s     dotchart
488s 
488s >   api_srs_design <- svydesign(
488s +     data = apisrs,
488s +     ids = ~ 1,
488s +     weights = ~ 1
488s +   )
488s >   
488s >   x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob)
488s >   
488s >   base_r_result <- survey:::multistage(x = x,
488s +                                        clusters = api_srs_design$cluster,
488s +                                        stratas = api_srs_design$strata,
488s +                                        nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize,
488s +                                        lonely.psu=getOption("survey.lonely.psu"),
488s +                                        one.stage=TRUE, stage = 1, cal = NULL)
488s >   
488s >   rcpp_result <- survey:::multistage_rcpp(x = x,
488s +                                           clusters = api_srs_design$cluster,
488s +                                           stratas = api_srs_design$strata,
488s +                                           nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize,
488s +                                           lonely.psu=getOption("survey.lonely.psu"),
488s +                                           one.stage=TRUE, stage = 1, cal = NULL)
488s >   
488s >   if (!isTRUE(all.equal(base_r_result, rcpp_result))) {
488s +     stop("Differences between `multistage()` and `multistage_rcpp()` for SRS")
488s +   }
488s >   
488s > # Check for a stratified simple random sample ----
488s >   
488s >   apistrat_design <- svydesign(
488s +     data = apistrat,
488s +     id =~ 1,
488s +     strata =~ stype,
488s +     weights =~ pw,
488s +     fpc =~ fpc
488s +   )
488s >   
488s >   x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob)
488s >   
488s >   base_r_result <- survey:::multistage(x = x,
488s +                                        clusters = apistrat_design$cluster,
488s +                                        stratas = apistrat_design$strata,
488s +                                        nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
488s +                                        lonely.psu=getOption("survey.lonely.psu"),
488s +                                        one.stage=TRUE, stage = 1, cal = NULL)
488s >   
488s >   rcpp_result <- survey:::multistage_rcpp(x = x,
488s +                                           clusters = apistrat_design$cluster,
488s +                                           stratas = apistrat_design$strata,
488s +                                           nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
488s +                                           lonely.psu=getOption("survey.lonely.psu"),
488s +                                           one.stage=TRUE, stage = 1, cal = NULL)
488s >   
488s >   if (!isTRUE(all.equal(base_r_result, rcpp_result))) {
488s +     stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample")
488s +   }
488s >   
488s >   ##_ Check whether expected true zeroes are actually computed as zeroes ----
488s >   
488s >   x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob))
488s >   
488s >   base_r_result <- survey:::multistage(x = x,
488s +                                        clusters = apistrat_design$cluster,
488s +                                        stratas = apistrat_design$strata,
488s +                                        nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
488s +                                        lonely.psu=getOption("survey.lonely.psu"),
488s +                                        one.stage=TRUE, stage = 1, cal = NULL)
488s >   
488s >   rcpp_result <- survey:::multistage_rcpp(x = x,
488s +                                           clusters = apistrat_design$cluster,
488s +                                           stratas = apistrat_design$strata,
488s +                                           nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
488s +                                           lonely.psu=getOption("survey.lonely.psu"),
488s +                                           one.stage=TRUE, stage = 1, cal = NULL)
488s >   
488s >   if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) {
488s +     stop("Computations which should equal zero do not.")
488s +   }
488s > 
488s > # Create a stratified, multistage design ----
488s >   
488s >   data(mu284)
488s >   
488s >   ## Create three strata, the third of which has only one PSU
488s >   mu284_stratified <- rbind(
488s +     transform(mu284, stratum = 1,
488s +               y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)),
488s +     transform(mu284, stratum = 2,
488s +               y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)),
488s +     transform(mu284[1,], stratum = 3,
488s +               y2 = y1 + 2)
488s +   )
488s >   
488s >   ## Create domain variables which yield a lonely PSU or a lonely SSU
488s >   mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19)
488s >   mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1)
488s >   
488s >   ## Create a survey design object with no lonely PSUs
488s >   dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3),
488s +                             strata = ~ stratum, nest = TRUE,
488s +                             id = ~ id1 + id2, fpc = ~ n1 + n2)
488s >   ## Create a survey design with one lonely PSU
488s >   dmu284_strat_w_lonely <- svydesign(data = mu284_stratified,
488s +                                      strata = ~ stratum, nest = TRUE,
488s +                                      id = ~ id1 + id2, fpc = ~ n1 + n2)
488s >   ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU
488s >   dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU)
488s >   dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU)
488s >   
488s >   
488s > # Check same results for different values of 'lonely PSU' options ----
488s >   
488s >   lonely_psu_options <- c(certainty = 'certainty',
488s +                           remove    = 'remove',
488s +                           average   = 'average',
488s +                           adjust    = 'adjust')
488s >   one_stage_options <- c(TRUE, FALSE)
488s >   
488s >   design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options,
488s +                                                'one.stage' = one_stage_options,
488s +                                                stringsAsFactors = FALSE)
488s >   design_lonely_psu_comparisons[['results_match']] <- NA
488s >   
488s >   ##_ Check for lonely PSUs caused by design ----
488s >   for (i in seq_len(nrow(design_lonely_psu_comparisons))) {
488s +     survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i]
488s +     one.stage <- design_lonely_psu_comparisons[['one.stage']][i]
488s +     options('survey.lonely.psu' = survey.lonely.psu)
488s +     
488s +     x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob)
488s +     
488s +     base_r_result <- survey:::multistage(x = x,
488s +                                          clusters = dmu284_strat_w_lonely$cluster,
488s +                                          stratas = dmu284_strat_w_lonely$strata,
488s +                                          nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize,
488s +                                          lonely.psu=getOption("survey.lonely.psu"),
488s +                                          one.stage=one.stage, stage = 1, cal = NULL)
488s +     
488s +     rcpp_result <- survey:::multistage_rcpp(x = x,
488s +                                             clusters = dmu284_strat_w_lonely$cluster,
488s +                                             stratas = dmu284_strat_w_lonely$strata,
488s +                                             nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize,
488s +                                             lonely.psu=getOption("survey.lonely.psu"),
488s +                                             one.stage=one.stage, stage = 1, cal = NULL)
488s +     
488s +       design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result))
488s +   }
488s >   
488s >   print(design_lonely_psu_comparisons)
488s   survey.lonely.psu one.stage results_match
488s 1         certainty      TRUE          TRUE
488s 2            remove      TRUE          TRUE
488s 3           average      TRUE          TRUE
488s 4            adjust      TRUE          TRUE
488s 5         certainty     FALSE          TRUE
488s 6            remove     FALSE          TRUE
488s 7           average     FALSE          TRUE
488s 8            adjust     FALSE          TRUE
488s >   if (!all(design_lonely_psu_comparisons$results_match)) {
488s +     stop("Results for design lonely PSUs differ between base R and Rcpp implementations.")
488s +   }
488s > 
488s >   ##_ Check for domain lonely PSUs caused by subsetting ----
488s >   
488s >   domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options,
488s +                                                'survey.adjust.domain.lonely' = c(FALSE, TRUE),
488s +                                                'one.stage' = one_stage_options,
488s +                                                stringsAsFactors = FALSE)
488s >   domain_lonely_psu_comparisons[['results_match']] <- NA
488s >   
488s >   for (i in seq_len(nrow(domain_lonely_psu_comparisons))) {
488s +       
488s +     options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i])
488s +     options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i])
488s +     one.stage <- domain_lonely_psu_comparisons[['one.stage']][i]
488s +     
488s +     
488s +     x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob)
488s +     suppressWarnings({
488s +       base_r_result <- survey:::multistage(x = x,
488s +                                            clusters = dmu284_strat_domain_lonely_psu$cluster,
488s +                                            stratas = dmu284_strat_domain_lonely_psu$strata,
488s +                                            nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize,
488s +                                            fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize,
488s +                                            lonely.psu=getOption("survey.lonely.psu"),
488s +                                            one.stage=one.stage, stage = 1, cal = NULL)
488s +     })
488s +     
488s +     rcpp_result <- survey:::multistage_rcpp(x = x,
488s +                                             clusters = dmu284_strat_domain_lonely_psu$cluster,
488s +                                             stratas = dmu284_strat_domain_lonely_psu$strata,
488s +                                             nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize,
488s +                                             fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize,
488s +                                             lonely.psu=getOption("survey.lonely.psu"),
488s +                                             one.stage=one.stage, stage = 1, cal = NULL)
488s +     
488s +     domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result))
488s +   }
488s Warning messages:
488s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :>   
488s >   print(domain_lonely_psu_comparisons)
488s    survey.lonely.psu survey.adjust.domain.lonely one.stage results_match
488s 1          certainty                       FALSE      TRUE          TRUE
488s   At least one stratum contains only one PSU at stage 1
488s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
488s   At least one stratum contains only one PSU at stage 1
488s 
488s 2             remove                       FALSE      TRUE          TRUE
488s 3            average                       FALSE      TRUE          TRUE
488s 4             adjust                       FALSE      TRUE          TRUE
488s 5          certainty                        TRUE      TRUE          TRUE
488s 6             remove                        TRUE      TRUE          TRUE
488s 7            average                        TRUE      TRUE          TRUE
488s 8             adjust                        TRUE      TRUE          TRUE
488s 9          certainty                       FALSE     FALSE          TRUE
488s 10            remove                       FALSE     FALSE          TRUE
488s 11           average                       FALSE     FALSE          TRUE
488s 12            adjust                       FALSE     FALSE          TRUE
488s 13         certainty                        TRUE     FALSE          TRUE
488s 14            remove                        TRUE     FALSE          TRUE
488s 15           average                        TRUE     FALSE          TRUE
488s 16            adjust                        TRUE     FALSE          TRUE
488s >   if (!all(domain_lonely_psu_comparisons$results_match)) {
488s +     stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.")
488s +   }
488s >   
488s > # Checks for edge cases ----
488s >   
488s >   ## Zero records ----
488s >   
488s >   zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent")
488s >   
488s >   zero_row_result <- survey:::multistage_rcpp(
488s +     x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]),
488s +     clusters = zero_row_design$cluster,
488s +     stratas = zero_row_design$strata,
488s +     nPSUs = zero_row_design$fpc$sampsize, 
488s +     fpcs = zero_row_design$fpc$popsize,
488s +     lonely.psu=getOption("survey.lonely.psu"),
488s +     one.stage=one.stage, stage = 1, cal = NULL
488s +   )
488s >   
488s >   if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) {
488s +     stop("`multistage_rcpp()` should return zeros for zero-row inputs.")
488s +   }
488s >   
488s > 
488s BEGIN TEST multistage.R
488s 
488s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
488s Copyright (C) 2025 The R Foundation for Statistical Computing
488s Platform: powerpc64le-unknown-linux-gnu
488s 
488s R is free software and comes with ABSOLUTELY NO WARRANTY.
488s You are welcome to redistribute it under certain conditions.
488s Type 'license()' or 'licence()' for distribution details.
488s 
488s R is a collaborative project with many contributors.
488s Type 'contributors()' for more information and
488s 'citation()' on how to cite R or R packages in publications.
488s 
488s Type 'demo()' for some demos, 'help()' for on-line help, or
488s 'help.start()' for an HTML browser interface to help.
488s Type 'q()' to quit R.
488s 
489s > ## 
489s > ## Check that multistage samples still work
489s > ##
489s > library(survey)
489s Loading required package: grid
489s Loading required package: Matrix
489s Loading required package: survival
490s > example(mu284)
490s 
490s Attaching package: 'survey'
490s 
490s The following object is masked from 'package:graphics':
490s 
490s     dotchart
490s 
490s 
490s mu284> data(mu284)
490s 
490s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284))
490s 2 - level Cluster Sampling design
490s With (5, 15) clusters.
490s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284))
490s 
490s mu284> (ytotal<-svytotal(~y1, dmu284))
490s    total     SE
490s y1 15080 2274.3
490s 
490s mu284> vcov(ytotal)
490s         y1
490s y1 5172234
490s > 
490s > 
490s BEGIN TEST na_action.R
490s 
490s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
490s Copyright (C) 2025 The R Foundation for Statistical Computing
490s Platform: powerpc64le-unknown-linux-gnu
490s 
490s R is free software and comes with ABSOLUTELY NO WARRANTY.
490s You are welcome to redistribute it under certain conditions.
490s Type 'license()' or 'licence()' for distribution details.
490s 
490s R is a collaborative project with many contributors.
490s Type 'contributors()' for more information and
490s 'citation()' on how to cite R or R packages in publications.
490s 
490s Type 'demo()' for some demos, 'help()' for on-line help, or
490s 'help.start()' for an HTML browser interface to help.
490s Type 'q()' to quit R.
490s 
490s > ## from Terry Therneau
490s > library(survey)
490s Loading required package: grid
490s Loading required package: Matrix
491s Loading required package: survival
491s 
491s Attaching package: 'survey'
491s 
491s > load("naa.rda")
491s > 
491s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times),  design= adata.s,na.action=na.exclude)
491s The following object is masked from 'package:graphics':
491s 
491s     dotchart
491s 
491s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times),  design= adata.s)
491s > all.equal(coef(fit1e),coef(fit1o))
491s [1] TRUE
491s > all.equal(vcov(fit1e),vcov(fit1o))
491s [1] TRUE
491s > 
491s BEGIN TEST newquantile.R
491s 
491s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
491s Copyright (C) 2025 The R Foundation for Statistical Computing
491s Platform: powerpc64le-unknown-linux-gnu
491s 
491s R is free software and comes with ABSOLUTELY NO WARRANTY.
491s You are welcome to redistribute it under certain conditions.
491s Type 'license()' or 'licence()' for distribution details.
491s 
491s R is a collaborative project with many contributors.
491s Type 'contributors()' for more information and
491s 'citation()' on how to cite R or R packages in publications.
491s 
491s Type 'demo()' for some demos, 'help()' for on-line help, or
491s 'help.start()' for an HTML browser interface to help.
491s Type 'q()' to quit R.
491s 
491s > ## quantiles with equal weights
491s > Loading required package: grid
491s 
491s > library(survey)
491s Loading required package: Matrix
492s Loading required package: survival
492s 
492s Attaching package: 'survey'
492s 
492s The following object is masked from 'package:graphics':
492s 
492s     dotchart
492s 
492s > data(api)
492s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
492s > 
492s > 
492s > for(i in 1:9){
492s +     print(i)
492s +     all.equal(
492s +         as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))),
492s +         as.vector(quantile(apiclus1$ell,  c(0.2,0.5,0.9), type=i))
492s +     )
492s +     
492s + }
492s [1] 1
492s [1] 2
492s [1] 3
492s [1] 4
492s [1] 5
492s [1] 6
492s [1] 7
492s [1] 8
492s [1] 9
492s > 
492s BEGIN TEST nwts-cch.R
492s 
492s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
492s Copyright (C) 2025 The R Foundation for Statistical Computing
492s Platform: powerpc64le-unknown-linux-gnu
492s 
492s R is free software and comes with ABSOLUTELY NO WARRANTY.
492s You are welcome to redistribute it under certain conditions.
492s Type 'license()' or 'licence()' for distribution details.
492s 
492s R is a collaborative project with many contributors.
492s Type 'contributors()' for more information and
492s 'citation()' on how to cite R or R packages in publications.
492s 
492s Type 'demo()' for some demos, 'help()' for on-line help, or
492s 'help.start()' for an HTML browser interface to help.
492s Type 'q()' to quit R.
492s 
494s > library(survey)
494s Loading required package: grid
494s > library(survival)
494s > data(nwtco)
494s > 
494s > ntwco<-subset(nwtco, !is.na(edrel))
494s > 
494s > load("nwtco-subcohort.rda")
494s > nwtco$subcohort<-subcohort
494s > 
494s > d_BorganII <- twophase(id=list(~seqno,~seqno),
494s +                        strata=list(NULL,~interaction(instit,rel)),
494s +                        data=nwtco, subset=~I(rel |subcohort))
494s Loading required package: Matrix
494s Loading required package: survival
494s 
494s Attaching package: 'survey'
494s 
494s The following object is masked from 'package:graphics':
494s 
494s     dotchart
494s 
494s > 
494s > ##Coefficient results same as Splus with code from
494s > ## http://faculty.washington.edu/norm/software.html
494s > ## SE slightly larger due to using sandwich variance.
494s > 
494s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII)
494s Call:
494s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 
494s     I(age/12), design = d_BorganII)
494s 
494s                    coef exp(coef) se(coef) robust se      z        p
494s factor(stage)2  0.46286   1.58861  0.23762   0.18087  2.559  0.01049
494s factor(stage)3  0.58309   1.79156  0.23965   0.17848  3.267  0.00109
494s factor(stage)4  1.05967   2.88541  0.26182   0.20524  5.163 2.43e-07
494s factor(histol)2 1.59744   4.94035  0.17688   0.13342 11.973  < 2e-16
494s I(age/12)       0.02994   1.03039  0.02942   0.03337  0.897  0.36972
494s 
494s Likelihood ratio test=  on 5 df, p=
494s n= 1062, number of events= 571 
494s > 
494s > ##
494s > ## This gives higher standard errors. calibrate() does not recompute the
494s > ## finite population correction if a calibration variable happens to predict
494s > ## sampling perfectly. It probably should.
494s > ##
494s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno),
494s +                            strata=list(NULL,~rel),
494s +                            data=nwtco, subset=~I(rel |subcohort)), 
494s +                         phase=2, formula=~interaction(instit,rel),
494s +                         epsilon=1e-10)
494s > 
494s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps)
494s Call:
494s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 
494s     I(age/12), design = d_BorganIIps)
494s 
494s                    coef exp(coef) se(coef) robust se      z        p
494s factor(stage)2  0.46286   1.58861  0.23762   0.18076  2.561  0.01045
494s factor(stage)3  0.58309   1.79156  0.23965   0.17838  3.269  0.00108
494s factor(stage)4  1.05967   2.88541  0.26182   0.20513  5.166 2.39e-07
494s factor(histol)2 1.59744   4.94035  0.17688   0.13044 12.246  < 2e-16
494s I(age/12)       0.02994   1.03039  0.02942   0.03331  0.899  0.36876
494s 
494s Likelihood ratio test=  on 5 df, p=
494s n= 1062, number of events= 571 
494s > 
494s BEGIN TEST nwts.R
494s 
494s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
494s Copyright (C) 2025 The R Foundation for Statistical Computing
494s Platform: powerpc64le-unknown-linux-gnu
494s 
494s R is free software and comes with ABSOLUTELY NO WARRANTY.
494s You are welcome to redistribute it under certain conditions.
494s Type 'license()' or 'licence()' for distribution details.
494s 
494s R is a collaborative project with many contributors.
494s Type 'contributors()' for more information and
494s 'citation()' on how to cite R or R packages in publications.
494s 
494s Type 'demo()' for some demos, 'help()' for on-line help, or
494s 'help.start()' for an HTML browser interface to help.
494s Type 'q()' to quit R.
494s 
494s > 
494s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458
494s > ## data from Norman Breslow's web page.
494s > library(survey)
494s Loading required package: grid
494s Loading required package: Matrix
495s Loading required package: survival
495s 
495s Attaching package: 'survey'
495s 
495s The following object is masked from 'package:graphics':
495s 
495s     dotchart
495s 
495s > load("nwts.rda")
495s > nwtsnb<-nwts
495s > nwtsnb$case<-nwts$case-nwtsb$case
495s > nwtsnb$control<-nwts$control-nwtsb$control
495s > 
495s > a<-rbind(nwtsb,nwtsnb)
495s > a$in.ccs<-rep(c(TRUE,FALSE),each=16)
496s > 
496s > b<-rbind(a,a)
496s > b$rel<-rep(c(1,0),each=32)
496s > b$n<-ifelse(b$rel,b$case,b$control)
496s > 
496s > index<-rep(1:64,b$n)
496s > 
496s > nwt.exp<-b[index,c(1:3,6,7)]
496s > nwt.exp$id<-1:4088
496s > 
496s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs,
496s +                 strata=list(NULL,~interaction(instit,rel)),data=nwt.exp)
496s > 
496s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs,
496s +                 strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp)
496s > 
496s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel))
496s > 
496s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2))
496s 
496s Call:
496s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 
496s     family = quasibinomial)
496s 
496s Survey design:
496s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
496s     subset = subset, data = data, pps = pps)
496s 
496s Coefficients:
496s                                Estimate Std. Error t value Pr(>|t|)    
496s (Intercept)                     -2.5701     0.1288 -19.955  < 2e-16 ***
496s factor(stage)2                   0.5482     0.1979   2.769 0.005708 ** 
496s factor(stage)3                   0.4791     0.2032   2.359 0.018515 *  
496s factor(stage)4                   1.0037     0.2592   3.872 0.000114 ***
496s factor(histol)2                  1.3505     0.3107   4.346 1.51e-05 ***
496s factor(stage)2:factor(histol)2   0.1152     0.4410   0.261 0.793876    
496s factor(stage)3:factor(histol)2   0.5066     0.4241   1.194 0.232548    
496s factor(stage)4:factor(histol)2   0.9785     0.6214   1.575 0.115615    
496s ---
496s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
496s 
496s (Dispersion parameter for quasibinomial family taken to be 1.000876)
496s 
496s Number of Fisher Scoring iterations: 4
496s 
496s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8))
496s 
496s Call:
496s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 
496s     family = quasibinomial)
496s 
496s Survey design:
496s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
496s     subset = subset, data = data, pps = pps)
496s 
496s Coefficients:
496s                                Estimate Std. Error t value Pr(>|t|)    
496s (Intercept)                    -2.71604    0.10827 -25.085  < 2e-16 ***
496s factor(stage)2                  0.78141    0.14726   5.306 1.35e-07 ***
496s factor(stage)3                  0.80093    0.15250   5.252 1.80e-07 ***
496s factor(stage)4                  1.07293    0.17817   6.022 2.33e-09 ***
496s factor(histol)2                 1.45836    0.31780   4.589 4.96e-06 ***
496s factor(stage)2:factor(histol)2 -0.04743    0.43495  -0.109    0.913    
496s factor(stage)3:factor(histol)2  0.28064    0.41298   0.680    0.497    
496s factor(stage)4:factor(histol)2  0.90983    0.63774   1.427    0.154    
496s ---
496s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
496s 
496s (Dispersion parameter for quasibinomial family taken to be 1.000876)
496s 
496s Number of Fisher Scoring iterations: 4
496s 
496s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8))
496s 
496s Call:
496s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 
496s     family = quasibinomial)
496s 
496s Survey design:
496s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 
496s     rel))
496s 
496s Coefficients:
496s                                Estimate Std. Error t value Pr(>|t|)    
496s (Intercept)                    -2.71604    0.10878 -24.968  < 2e-16 ***
496s factor(stage)2                  0.78141    0.14729   5.305 1.35e-07 ***
496s factor(stage)3                  0.80093    0.15212   5.265 1.68e-07 ***
496s factor(stage)4                  1.07293    0.17905   5.993 2.77e-09 ***
496s factor(histol)2                 1.45836    0.31757   4.592 4.88e-06 ***
496s factor(stage)2:factor(histol)2 -0.04743    0.43432  -0.109    0.913    
496s factor(stage)3:factor(histol)2  0.28064    0.41231   0.681    0.496    
496s factor(stage)4:factor(histol)2  0.90983    0.63187   1.440    0.150    
496s ---
496s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
496s 
496s (Dispersion parameter for quasibinomial family taken to be 1.000876)
496s 
496s Number of Fisher Scoring iterations: 4
496s 
496s > 
496s > ## check subsets of calibrated designs.
496s > summary(svyglm(rel~factor(stage),
496s +                family=quasibinomial,design=subset(dccs8,histol==1)))
496s 
496s Call:
496s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 
496s     histol == 1), family = quasibinomial)
496s 
496s Survey design:
496s subset(dccs8, histol == 1)
496s 
496s Coefficients:
496s                Estimate Std. Error t value Pr(>|t|)    
496s (Intercept)     -2.7160     0.1083 -25.085  < 2e-16 ***
496s factor(stage)2   0.7814     0.1473   5.306 1.48e-07 ***
496s factor(stage)3   0.8009     0.1525   5.252 1.97e-07 ***
496s factor(stage)4   1.0729     0.1782   6.022 2.73e-09 ***
496s ---
496s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
496s 
496s (Dispersion parameter for quasibinomial family taken to be 1.001333)
496s 
496s Number of Fisher Scoring iterations: 4
496s 
496s Warning messages:
496s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset.
496s 2: In summary.glm(g) :
496s   observations with zero weight not used for calculating dispersion
496s 3: In summary.glm(glm.object) :
496s   observations with zero weight not used for calculating dispersion
496s 4: In `[.twophase2`(design, nas == 0, ) :
496s   1 strata have only one PSU in this subset.
496s > summary(svyglm(rel~factor(stage),
496s 5: In `[.twophase2`(design, nas == 0, ) :
496s   1 strata have only one PSU in this subset.
496s +                family=quasibinomial,design=subset(gccs8,histol==1)))
496s 
496s Call:
496s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 
496s     histol == 1), family = quasibinomial)
496s 
496s Survey design:
496s subset(gccs8, histol == 1)
496s 
496s Coefficients:
496s                Estimate Std. Error t value Pr(>|t|)    
496s (Intercept)     -2.7160     0.1082 -25.105  < 2e-16 ***
496s factor(stage)2   0.7814     0.1457   5.363 1.10e-07 ***
496s factor(stage)3   0.8009     0.1504   5.324 1.34e-07 ***
496s factor(stage)4   1.0729     0.1759   6.101 1.70e-09 ***
496s ---
496s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
496s 
496s (Dispersion parameter for quasibinomial family taken to be 1.001333)
496s 
496s Number of Fisher Scoring iterations: 4
496s 
496s > 
496s > 
496s Warning messages:
496s 1: In summary.glm(g) :
496s   observations with zero weight not used for calculating dispersion
496s 2: In summary.glm(glm.object) :
496s   observations with zero weight not used for calculating dispersion
496s BEGIN TEST poisson.R
496s 
496s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
496s Copyright (C) 2025 The R Foundation for Statistical Computing
496s Platform: powerpc64le-unknown-linux-gnu
496s 
496s R is free software and comes with ABSOLUTELY NO WARRANTY.
496s You are welcome to redistribute it under certain conditions.
496s Type 'license()' or 'licence()' for distribution details.
496s 
496s R is a collaborative project with many contributors.
496s Type 'contributors()' for more information and
496s 'citation()' on how to cite R or R packages in publications.
496s 
496s Type 'demo()' for some demos, 'help()' for on-line help, or
496s 'help.start()' for an HTML browser interface to help.
496s Type 'q()' to quit R.
496s 
496s > ## check poisson sampling
496s > library(survey)
496s Loading required package: grid
496s Loading required package: Matrix
497s Loading required package: survival
498s > data(api)
498s 
498s Attaching package: 'survey'
498s 
498s The following object is masked from 'package:graphics':
498s 
498s     dotchart
498s 
498s > set.seed(2021-7-15)
498s > apipop$prob<-apipop$api00/1000
498s > insample<-rbinom(nrow(apipop),1,apipop$prob)
498s > apipois<-apipop[insample,]
498s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois)
498s > 
498s > stopifnot(isTRUE(all.equal(
498s +  as.vector(SE(svytotal(~api00,design=des))),
498s +  as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob))))
498s +  )))
498s >  
498s > 
498s BEGIN TEST pps.R
498s 
498s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
498s Copyright (C) 2025 The R Foundation for Statistical Computing
498s Platform: powerpc64le-unknown-linux-gnu
498s 
498s R is free software and comes with ABSOLUTELY NO WARRANTY.
498s You are welcome to redistribute it under certain conditions.
498s Type 'license()' or 'licence()' for distribution details.
498s 
498s R is a collaborative project with many contributors.
498s Type 'contributors()' for more information and
498s 'citation()' on how to cite R or R packages in publications.
498s 
498s Type 'demo()' for some demos, 'help()' for on-line help, or
498s 'help.start()' for an HTML browser interface to help.
498s Type 'q()' to quit R.
498s 
498s > library(survey)
498s Loading required package: grid
498s Loading required package: Matrix
499s Loading required package: survival
499s 
499s Attaching package: 'survey'
499s 
499s > data(election)
499s The following object is masked from 'package:graphics':
499s 
499s     dotchart
499s 
499s > 
499s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer")
499s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps)
499s > svytotal(~Bush+Kerry+Nader, dpps)
499s          total      SE
499s Bush  64518472 2447629
499s Kerry 51202102 2450787
499s Nader   478530  102420
499s > svytotal(~Bush+Kerry+Nader, dppswr)
499s          total      SE
499s Bush  64518472 2671455
499s Kerry 51202102 2679433
499s Nader   478530  105303
499s > 
499s > ##subsets
499s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0))
499s          total      SE
499s Bush  34944285 5399833
499s Kerry 25581714 4028434
499s Nader   478530  102420
499s > 
499s > ##multistage: should agree with STRS analysis
499s > data(api)
499s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2)
499s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2)
499s > 
499s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps))
499s [1] TRUE
499s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps))
499s [1] TRUE
499s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps))
499s [1] TRUE
499s > 
499s > ## the new without-replacement methods
499s > data(election)
499s > dpps_br<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="brewer")
499s > dpps_ov<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="overton")
499s > dpps_hr<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40))
499s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR())
499s > dpps_ht<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=ppsmat(election_jointprob))
499s > ## Yates-Grundy type
499s > dpps_yg<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG")
499s > dpps_hryg<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG")
499s > 
499s > ## The with-replacement approximation
499s > svytotal(~Bush+Kerry+Nader, dpps_ht)
499s          total      SE
499s Bush  64518472 2604404
499s Kerry 51202102 2523712
499s Nader   478530  102326
499s > svytotal(~Bush+Kerry+Nader, dpps_yg)
499s          total      SE
499s Bush  64518472 2406526
499s Kerry 51202102 2408091
499s Nader   478530  101664
499s > svytotal(~Bush+Kerry+Nader, dpps_hr)
499s          total      SE
499s Bush  64518472 2624662
499s Kerry 51202102 2525222
499s Nader   478530  102793
499s > svytotal(~Bush+Kerry+Nader, dpps_hryg)
499s          total      SE
499s Bush  64518472 2436738
499s Kerry 51202102 2439845
499s Nader   478530  102016
499s > svytotal(~Bush+Kerry+Nader, dpps_hr1)
499s          total      SE
499s Bush  64518472 2472753
499s Kerry 51202102 2426842
499s Nader   478530  102595
499s > svytotal(~Bush+Kerry+Nader, dpps_br)
499s          total      SE
499s Bush  64518472 2447629
499s Kerry 51202102 2450787
499s Nader   478530  102420
499s > svytotal(~Bush+Kerry+Nader, dpps_ov)
499s          total      SE
499s Bush  64518472 2939608
499s Kerry 51202102 1964632
499s Nader   478530  104373
499s > 
499s > ## subsets
499s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0))
499s          total      SE
499s Bush  34944285 5406348
499s Kerry 25581714 4047741
499s Nader   478530  102326
499s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0))
499s          total      SE
499s Bush  34944285 5377659
499s Kerry 25581714 4010908
499s Nader   478530  102016
499s > 
499s > ## counts
499s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht)
499s       I(Nader > 0) counts se
499s FALSE        FALSE     19  0
499s TRUE          TRUE     21  0
499s > 
499s BEGIN TEST qrule-swiss.R
499s 
499s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
499s Copyright (C) 2025 The R Foundation for Statistical Computing
499s Platform: powerpc64le-unknown-linux-gnu
499s 
499s R is free software and comes with ABSOLUTELY NO WARRANTY.
499s You are welcome to redistribute it under certain conditions.
499s Type 'license()' or 'licence()' for distribution details.
499s 
499s R is a collaborative project with many contributors.
499s Type 'contributors()' for more information and
499s 'citation()' on how to cite R or R packages in publications.
499s 
499s Type 'demo()' for some demos, 'help()' for on-line help, or
499s 'help.start()' for an HTML browser interface to help.
499s Type 'q()' to quit R.
499s 
499s > library(survey)
499s Loading required package: grid
499s Loading required package: Matrix
500s Loading required package: survival
500s 
500s Attaching package: 'survey'
500s 
500s > 
500s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1)
500s The following object is masked from 'package:graphics':
500s 
500s     dotchart
500s 
500s > 
500s > design_no_strat <- svydesign(id = ~id, 
500s +                              probs = ~probs, 
500s +                              data = data_no_strat, 
500s +                              fpc = ~fpc)
500s > 
500s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99)
500s > 
500s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE,
500s +             interval.type = "mean", qrule = "hf1")
500s > 
500s > stopifnot(all(diff(res$x[,"quantile"])>=0))
500s > 
500s > 
500s > 
500s BEGIN TEST quantile.R
500s 
500s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
500s Copyright (C) 2025 The R Foundation for Statistical Computing
500s Platform: powerpc64le-unknown-linux-gnu
500s 
500s R is free software and comes with ABSOLUTELY NO WARRANTY.
500s You are welcome to redistribute it under certain conditions.
500s Type 'license()' or 'licence()' for distribution details.
500s 
500s R is a collaborative project with many contributors.
500s Type 'contributors()' for more information and
500s 'citation()' on how to cite R or R packages in publications.
500s 
500s Type 'demo()' for some demos, 'help()' for on-line help, or
500s 'help.start()' for an HTML browser interface to help.
500s Type 'q()' to quit R.
500s 
501s > library(survey)
501s Loading required package: grid
501s Loading required package: Matrix
501s Loading required package: survival
502s 
502s Attaching package: 'survey'
502s 
502s > set.seed(42)
502s The following object is masked from 'package:graphics':
502s 
502s     dotchart
502s 
502s > 
502s > df<-data.frame(x=exp(rnorm(1000)))
502s > df$y<-round(df$x,1)
502s > ddf<-svydesign(id=~1,data=df)
502s Warning message:
502s In svydesign.default(id = ~1, data = df) :
502s   No weights or probabilities supplied, assuming equal probability
502s > rdf<-as.svrepdesign(ddf)
502s > 
502s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
502s       0.01        0.1        0.5        0.9       0.99 
502s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 
502s > 
502s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
503s                x
503s q0.01 0.01554946
503s q0.1  0.01425828
503s q0.5  0.03428012
503s q0.9  0.16457488
503s q0.99 1.88672412
503s > 
503s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
503s       0.01        0.1        0.5        0.9       0.99 
503s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 
503s > 
503s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
503s                x
503s q0.01 0.01556240
503s q0.1  0.01420086
503s q0.5  0.03430175
503s q0.9  0.16461019
503s q0.99 1.88818131
503s > 
503s > 
503s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald")
503s $quantiles
503s         0.01       0.1       0.5  0.9 0.99
503s y 0.02352941 0.2230769 0.9340909 3.55  9.4
503s 
503s $CIs
503s , , y
503s 
503s              0.01       0.1       0.5      0.9      0.99
503s (lower 0.01594200 0.2020115 0.8578143 3.207543  7.568142
503s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632
503s 
503s 
503s > 
503s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)
503s Statistic:
503s         y
503s q0.01 0.1
503s q0.1  0.3
503s q0.5  1.0
503s q0.9  3.6
503s q0.99 9.4
503s SE:
503s                y
503s q0.01 0.02547977
503s q0.1  0.02547977
503s q0.5  0.02547977
503s q0.9  0.15287859
503s q0.99 1.88302540
503s > 
503s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf)
503s $quantiles
503s         0.01       0.1       0.5  0.9 0.99
503s y 0.02352941 0.2230769 0.9340909 3.55  9.4
503s 
503s $CIs
503s , , y
503s 
503s              0.01       0.1       0.5      0.9      0.99
503s (lower 0.01594200 0.2020115 0.8578143 3.207543  7.568142
503s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632
503s 
503s 
503s > 
503s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf)
503s Statistic:
503s         y
503s q0.01 0.1
503s q0.1  0.3
503s q0.5  1.0
503s q0.9  3.6
503s q0.99 9.4
503s SE:
503s                y
503s q0.01 0.02551067
503s q0.1  0.02551067
503s q0.5  0.02551067
503s q0.9  0.15306404
503s q0.99 1.88450896
503s > 
503s > 
503s > 
503s > df<-data.frame(x=exp(rnorm(20)))
503s > df$y<-round(df$x,1)
503s > ddf<-svydesign(id=~1,data=df)
503s Warning message:
503s In svydesign.default(id = ~1, data = df) :
503s   No weights or probabilities supplied, assuming equal probability
503s > rdf<-as.svrepdesign(ddf)
503s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
503s       0.01        0.1        0.5        0.9       0.99 
503s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 
503s > 
503s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
503s                x
503s q0.01 0.00000000
503s q0.1  0.04598541
503s q0.5  0.25943731
503s q0.9  2.12343073
503s q0.99 1.91998924
503s > 
503s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
503s       0.01        0.1        0.5        0.9       0.99 
503s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 
503s > 
503s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
503s                x
503s q0.01 0.00000000
503s q0.1  0.04732818
503s q0.5  0.24957966
503s q0.9  2.25211815
503s q0.99 2.04043154
503s > 
503s > 
503s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald")
503s $quantiles
503s   0.01  0.1  0.5 0.9 0.99
503s y  0.1 0.15 0.75 2.4 8.68
503s 
503s $CIs
503s , , y
503s 
503s            0.01       0.1       0.5      0.9       0.99
503s (lower 0.100000 0.1000000 0.3674054 1.352279  0.5674674
503s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000
503s 
503s 
503s > 
503s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)
503s Statistic:
503s          y
503s q0.01 0.10
503s q0.1  0.20
503s q0.5  0.80
503s q0.9  2.40
503s q0.99 8.68
503s SE:
503s                y
503s q0.01 0.00000000
503s q0.1  0.02611112
503s q0.5  0.26542051
503s q0.9  2.10908603
503s q0.99 1.91777710
503s > 
503s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf)
503s $quantiles
503s   0.01  0.1  0.5 0.9 0.99
503s y  0.1 0.15 0.75 2.4 8.68
503s 
503s $CIs
503s , , y
503s 
503s            0.01       0.1       0.5      0.9       0.99
503s (lower 0.100000 0.1000000 0.3674054 1.352279  0.5674674
503s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000
503s 
503s 
503s > 
503s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf)
503s Statistic:
503s          y
503s q0.01 0.10
503s q0.1  0.20
503s q0.5  0.80
503s q0.9  2.40
503s q0.99 8.68
503s SE:
503s                y
503s q0.01 0.00000000
503s q0.1  0.02551067
503s q0.5  0.25244616
503s q0.9  2.23558589
503s q0.99 2.03881114
503s > 
503s BEGIN TEST quantiles-chile.R
503s 
503s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
503s Copyright (C) 2025 The R Foundation for Statistical Computing
503s Platform: powerpc64le-unknown-linux-gnu
503s 
503s R is free software and comes with ABSOLUTELY NO WARRANTY.
503s You are welcome to redistribute it under certain conditions.
503s Type 'license()' or 'licence()' for distribution details.
503s 
503s R is a collaborative project with many contributors.
503s Type 'contributors()' for more information and
503s 'citation()' on how to cite R or R packages in publications.
503s 
503s Type 'demo()' for some demos, 'help()' for on-line help, or
503s 'help.start()' for an HTML browser interface to help.
503s Type 'q()' to quit R.
503s 
503s > library(survey)
503s Loading required package: grid
503s Loading required package: Matrix
504s Loading required package: survival
504s 
504s Attaching package: 'survey'
504s 
504s The following object is masked from 'package:graphics':
504s 
504s     dotchart
504s 
504s > datos <- readRDS("datos_ejemplo.rds")
504s > 
504s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos)
504s > set.seed(234262762)
504s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20)
504s > options(survey.lonely.psu="remove")
504s > 
504s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"]
504s > 
504s > suppressWarnings({
504s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math"))
504s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school"))
504s + })
504s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5)))
504s [1] TRUE
504s > 
504s > suppressWarnings({
504s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math"))
504s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school"))
504s + })
504s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5)))
504s [1] TRUE
504s > 
504s BEGIN TEST rakecheck.R
504s 
504s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
504s Copyright (C) 2025 The R Foundation for Statistical Computing
504s Platform: powerpc64le-unknown-linux-gnu
504s 
504s R is free software and comes with ABSOLUTELY NO WARRANTY.
504s You are welcome to redistribute it under certain conditions.
504s Type 'license()' or 'licence()' for distribution details.
504s 
504s R is a collaborative project with many contributors.
504s Type 'contributors()' for more information and
504s 'citation()' on how to cite R or R packages in publications.
504s 
504s Type 'demo()' for some demos, 'help()' for on-line help, or
504s 'help.start()' for an HTML browser interface to help.
504s Type 'q()' to quit R.
504s 
504s > library(survey)
504s Loading required package: grid
504s Loading required package: Matrix
505s Loading required package: survival
505s 
505s Attaching package: 'survey'
505s 
505s > 
505s > data(api)
505s The following object is masked from 'package:graphics':
505s 
505s     dotchart
505s 
505s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
505s > rclus1 <- as.svrepdesign(dclus1)
505s > 
505s > ## population marginal totals for each stratum
505s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
505s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
505s > 
505s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
505s > 
505s > svymean(~api00, rclus1r)
505s         mean     SE
505s api00 641.23 26.873
505s > svytotal(~enroll, rclus1r)
505s          total     SE
505s enroll 3647300 463511
505s > 
505s > ff<-~stype+sch.wide
505s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop)))
505s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking")
506s > 
506s > svymean(~api00,rclus1g)
506s         mean     SE
506s api00 641.23 26.874
506s > svytotal(~enroll,rclus1g)
506s          total     SE
506s enroll 3647280 463582
506s > 
506s > summary(weights(rclus1g)/weights(rclus1r))
506s        V1           V2          V3          V4           V5          V6   
506s  Min.   :1    Min.   :1   Min.   :1   Min.   :1    Min.   :1   Min.   :1  
506s  1st Qu.:1    1st Qu.:1   1st Qu.:1   1st Qu.:1    1st Qu.:1   1st Qu.:1  
506s  Median :1    Median :1   Median :1   Median :1    Median :1   Median :1  
506s  Mean   :1    Mean   :1   Mean   :1   Mean   :1    Mean   :1   Mean   :1  
506s  3rd Qu.:1    3rd Qu.:1   3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1  
506s  Max.   :1    Max.   :1   Max.   :1   Max.   :1    Max.   :1   Max.   :1  
506s  NA's   :11   NA's   :4   NA's   :2   NA's   :13   NA's   :2   NA's   :4  
506s        V7          V8           V9         V10          V11    
506s  Min.   :1   Min.   :1    Min.   :1   Min.   :1    Min.   :1   
506s  1st Qu.:1   1st Qu.:1    1st Qu.:1   1st Qu.:1    1st Qu.:1   
506s  Median :1   Median :1    Median :1   Median :1    Median :1   
506s  Mean   :1   Mean   :1    Mean   :1   Mean   :1    Mean   :1   
506s  3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   
506s  Max.   :1   Max.   :1    Max.   :1   Max.   :1    Max.   :1   
506s  NA's   :4   NA's   :16   NA's   :9   NA's   :34   NA's   :21  
506s       V12              V13          V14         V15    
506s  Min.   :0.9997   Min.   :1    Min.   :1   Min.   :1   
506s  1st Qu.:1.0001   1st Qu.:1    1st Qu.:1   1st Qu.:1   
506s  Median :1.0001   Median :1    Median :1   Median :1   
506s  Mean   :1.0000   Mean   :1    Mean   :1   Mean   :1   
506s  3rd Qu.:1.0001   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1   
506s  Max.   :1.0002   Max.   :1    Max.   :1   Max.   :1   
506s  NA's   :37       NA's   :13   NA's   :1   NA's   :12  
506s > 
506s > 
506s > ## Do it for a design without replicate weights
506s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
506s > 
506s > svymean(~api00, dclus1r)
506s         mean     SE
506s api00 641.23 23.704
506s > svytotal(~enroll, dclus1r)
506s          total     SE
506s enroll 3647300 400603
506s > 
506s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking")
506s > 
506s > svymean(~api00,dclus1g)
506s         mean     SE
506s api00 641.23 23.704
506s > svytotal(~enroll,dclus1g)
506s          total     SE
506s enroll 3647280 400603
506s > 
506s > summary(weights(dclus1g)/weights(dclus1r))
506s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
506s       1       1       1       1       1       1 
506s > 
506s > 
506s > 
506s > ## Example of raking with partial joint distributions
506s > pop.table <- xtabs(~stype+sch.wide,apipop)
506s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482))
506s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp),
506s +                list(pop.table, pop.imp))
506s > svymean(~api00, dclus1r2)
506s         mean     SE
506s api00 642.62 22.732
506s > 
506s > ff1 <-~stype*sch.wide+comp.imp
506s > 
506s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop)))
506s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking")
506s > 
506s > svymean(~api00, dclus1g2)
506s         mean     SE
506s api00 642.61 22.731
506s > 
506s > summary(weights(dclus1r2)/weights(dclus1g2))
506s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
506s   0.999   1.000   1.000   1.000   1.000   1.002 
506s > 
506s BEGIN TEST raowuboot.R
506s 
506s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
506s Copyright (C) 2025 The R Foundation for Statistical Computing
506s Platform: powerpc64le-unknown-linux-gnu
506s 
506s R is free software and comes with ABSOLUTELY NO WARRANTY.
506s You are welcome to redistribute it under certain conditions.
506s Type 'license()' or 'licence()' for distribution details.
506s 
506s R is a collaborative project with many contributors.
506s Type 'contributors()' for more information and
506s 'citation()' on how to cite R or R packages in publications.
506s 
506s Type 'demo()' for some demos, 'help()' for on-line help, or
506s 'help.start()' for an HTML browser interface to help.
506s Type 'q()' to quit R.
506s 
506s > ## regression test for bug reported by Richard Valliant
506s > library(survey)
506s Loading required package: grid
506s Loading required package: Matrix
507s Loading required package: survival
507s 
507s Attaching package: 'survey'
507s 
507s The following object is masked from 'package:graphics':
507s 
507s     dotchart
507s 
507s > s<-subbootweights(c(1,1),1:2, 50)
507s > stopifnot(all(s$repweights$weights %in% c(0,2)))
507s > 
507s BEGIN TEST regTermTest-missing.R
507s 
507s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
507s Copyright (C) 2025 The R Foundation for Statistical Computing
507s Platform: powerpc64le-unknown-linux-gnu
507s 
507s R is free software and comes with ABSOLUTELY NO WARRANTY.
507s You are welcome to redistribute it under certain conditions.
507s Type 'license()' or 'licence()' for distribution details.
507s 
507s R is a collaborative project with many contributors.
507s Type 'contributors()' for more information and
507s 'citation()' on how to cite R or R packages in publications.
507s 
507s Type 'demo()' for some demos, 'help()' for on-line help, or
507s 'help.start()' for an HTML browser interface to help.
507s Type 'q()' to quit R.
507s 
507s > library(survey)
507s Loading required package: grid
507s Loading required package: Matrix
508s Loading required package: survival
508s 
508s Attaching package: 'survey'
508s 
508s The following object is masked from 'package:graphics':
508s 
508s     dotchart
508s 
508s > data(nhanes)
508s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes)
508s > 
508s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR,  design = subset(design,!is.na(HI_CHOL)), family=quasibinomial)
508s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR,  design =design , family=quasibinomial)
508s > 
508s > ta<-regTermTest(a, ~HI_CHOL)
508s > tb<-regTermTest(b, ~HI_CHOL)
508s > 
508s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq)))
508s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda)))
508s > 
508s BEGIN TEST regpredict.R
508s 
508s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
508s Copyright (C) 2025 The R Foundation for Statistical Computing
508s Platform: powerpc64le-unknown-linux-gnu
508s 
508s R is free software and comes with ABSOLUTELY NO WARRANTY.
508s You are welcome to redistribute it under certain conditions.
508s Type 'license()' or 'licence()' for distribution details.
508s 
508s R is a collaborative project with many contributors.
508s Type 'contributors()' for more information and
508s 'citation()' on how to cite R or R packages in publications.
508s 
508s Type 'demo()' for some demos, 'help()' for on-line help, or
508s 'help.start()' for an HTML browser interface to help.
508s Type 'q()' to quit R.
508s 
508s > library(survey)
508s Loading required package: grid
508s Loading required package: Matrix
509s Loading required package: survival
510s 
510s Attaching package: 'survey'
510s 
510s The following object is masked from 'package:graphics':
510s 
510s     dotchart
510s 
510s > data(api)
510s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
510s > 
510s > 
510s > ## regression estimator of total, three ways
510s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE))
510s > npop <- sum(!is.na(apipop$enroll))
510s > 
510s > api.reg <- svyglm(api.stu~enroll, design=dstrat)
510s > a <- predict(api.reg, newdata=pop, total=npop)
510s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll)))
510s > 
510s > all.equal(as.vector(coef(a)),as.vector(coef(b)))
510s [1] TRUE
510s > all.equal(as.vector(SE(a)), as.vector(SE(b)))
510s [1] TRUE
510s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix
510s +     d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE]))
510s +     all.equal(as.vector(coef(a)), as.vector(sum(coef(d))))
510s +     all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d)))))
510s + }
510s > 
510s > ## classical ratio estimator, four ways.
510s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat,
510s +                    family=quasi(link="identity", var="mu"))
510s > 
510s > a <- predict(api.reg2, newdata=pop, total=npop)
510s > b <- svytotal(~api.stu,
510s +               calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2))
510s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll)
510s > 
510s > all.equal(as.vector(coef(a)),as.vector(coef(b)))
510s [1] TRUE
510s > all.equal(as.vector(SE(a)), as.vector(SE(b)))
510s [1] TRUE
510s > all.equal(as.vector(coef(a)),as.vector(e$total))
510s [1] TRUE
510s > all.equal(as.vector(SE(a)), as.vector(e$se))
510s [1] TRUE
510s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix
510s +     d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE]))
510s +     all.equal(as.vector(coef(a)), as.vector(sum(coef(d))))
510s +     all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d)))))
510s + }
510s > 
510s BEGIN TEST rss_scores.R
510s 
510s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
510s Copyright (C) 2025 The R Foundation for Statistical Computing
510s Platform: powerpc64le-unknown-linux-gnu
510s 
510s R is free software and comes with ABSOLUTELY NO WARRANTY.
510s You are welcome to redistribute it under certain conditions.
510s Type 'license()' or 'licence()' for distribution details.
510s 
510s R is a collaborative project with many contributors.
510s Type 'contributors()' for more information and
510s 'citation()' on how to cite R or R packages in publications.
510s 
510s Type 'demo()' for some demos, 'help()' for on-line help, or
510s 'help.start()' for an HTML browser interface to help.
510s Type 'q()' to quit R.
510s 
510s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica
510s > library(survey)
510s Loading required package: grid
510s Loading required package: Matrix
511s Loading required package: survival
511s 
511s Attaching package: 'survey'
511s 
511s > data(myco)
511s The following object is masked from 'package:graphics':
511s 
511s     dotchart
511s 
511s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco)
511s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco)
511s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco)
511s > 
511s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2)))
511s > 
511s > s<-svyscoretest(m_full, ~Scar)
511s > stopifnot(abs(s[1]-10.73)<0.05)
511s > 
511s > t<-svyscoretest(m_full,~Scar,method="individual")
511s > stopifnot(abs(coef(t)- -32.61)<0.1)
511s > stopifnot(abs(vcov(t)-99.1)<0.1)
511s >  
511s > 
511s BEGIN TEST scoping.R
511s 
511s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
511s Copyright (C) 2025 The R Foundation for Statistical Computing
511s Platform: powerpc64le-unknown-linux-gnu
511s 
511s R is free software and comes with ABSOLUTELY NO WARRANTY.
511s You are welcome to redistribute it under certain conditions.
511s Type 'license()' or 'licence()' for distribution details.
511s 
511s R is a collaborative project with many contributors.
511s Type 'contributors()' for more information and
511s 'citation()' on how to cite R or R packages in publications.
511s 
511s Type 'demo()' for some demos, 'help()' for on-line help, or
511s 'help.start()' for an HTML browser interface to help.
511s Type 'q()' to quit R.
511s 
511s > 
511s > ## regression test for testing regression
511s > 
511s > library(survey)
511s Loading required package: grid
511s Loading required package: Matrix
512s Loading required package: survival
512s > data(api)
512s 
512s Attaching package: 'survey'
512s 
512s The following object is masked from 'package:graphics':
512s 
512s     dotchart
512s 
512s > 
512s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
512s > 
512s > 
512s > f<-function(){
512s +   form<-acs.46~stype
512s +   svyglm(formula=form, design = dstrat)  
512s + }
512s > 
512s > g<-function(form){
512s +   svyglm(formula=form, design = dstrat)  
512s + }
512s > f()
512s Stratified Independent Sampling design
512s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
512s     fpc = ~fpc)
512s 
512s Call:  svyglm(formula = form, design = dstrat)
512s 
512s Coefficients:
512s (Intercept)       stypeH       stypeM  
512s     28.7449       0.7551       0.4022  
512s 
512s Degrees of Freedom: 133 Total (i.e. Null);  129 Residual
512s   (66 observations deleted due to missingness)
512s Null Deviance:	    1838 
512s Residual Deviance: 1835 	AIC: 719.8
512s > g(acs.46~stype)
512s Stratified Independent Sampling design
512s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
512s     fpc = ~fpc)
512s 
512s Call:  svyglm(formula = form, design = dstrat)
512s 
512s Coefficients:
512s (Intercept)       stypeH       stypeM  
512s     28.7449       0.7551       0.4022  
512s 
512s Degrees of Freedom: 133 Total (i.e. Null);  129 Residual
512s   (66 observations deleted due to missingness)
512s Null Deviance:	    1838 
512s Residual Deviance: 1835 	AIC: 719.8
512s > 
512s > f<-function(){
512s +   form<-Surv(acs.46)~stype
512s +   svycoxph(formula=form, design = dstrat)  
512s + }
512s > 
512s > g<-function(form){
512s +   svycoxph(formula=form, design = dstrat)  
512s + }
512s > 
512s > f()
512s Call:
512s svycoxph(formula = form, design = dstrat)
512s 
512s           coef exp(coef) se(coef) robust se      z     p
512s stypeH -0.6766    0.5083   1.0208    0.6652 -1.017 0.309
512s stypeM -0.2509    0.7781   0.2308    0.2089 -1.201 0.230
512s 
512s Likelihood ratio test=  on 2 df, p=
512s n= 134, number of events= 134 
512s    (66 observations deleted due to missingness)
512s > g(Surv(acs.46)~stype)
512s Call:
512s svycoxph(formula = form, design = dstrat)
512s 
512s           coef exp(coef) se(coef) robust se      z     p
512s stypeH -0.6766    0.5083   1.0208    0.6652 -1.017 0.309
512s stypeM -0.2509    0.7781   0.2308    0.2089 -1.201 0.230
512s 
512s Likelihood ratio test=  on 2 df, p=
512s n= 134, number of events= 134 
512s    (66 observations deleted due to missingness)
512s > 
512s > ## check coxph for a single predictor
512s > svycoxph(Surv(acs.46)~api00,design=dstrat)
512s Call:
512s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat)
512s 
512s            coef exp(coef)  se(coef) robust se     z     p
512s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994
512s 
512s Likelihood ratio test=  on 1 df, p=
512s n= 134, number of events= 134 
512s    (66 observations deleted due to missingness)
512s > 
512s BEGIN TEST survcurve.R
512s 
512s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
512s Copyright (C) 2025 The R Foundation for Statistical Computing
512s Platform: powerpc64le-unknown-linux-gnu
512s 
512s R is free software and comes with ABSOLUTELY NO WARRANTY.
512s You are welcome to redistribute it under certain conditions.
512s Type 'license()' or 'licence()' for distribution details.
512s 
512s R is a collaborative project with many contributors.
512s Type 'contributors()' for more information and
512s 'citation()' on how to cite R or R packages in publications.
512s 
512s Type 'demo()' for some demos, 'help()' for on-line help, or
512s 'help.start()' for an HTML browser interface to help.
512s Type 'q()' to quit R.
512s 
513s > library(survey)
513s Loading required package: grid
513s Loading required package: Matrix
513s Loading required package: survival
514s 
514s Attaching package: 'survey'
514s 
514s The following object is masked from 'package:graphics':
514s 
514s     dotchart
514s 
514s > library(survival)
514s > 
514s > pbc2<-rbind(pbc,pbc)
514s > pbc2$id<-rep(1:418,2)
514s > 
514s > dpbc1<-svydesign(id=~1, data=pbc)
514s Warning message:
514s In svydesign.default(id = ~1, data = pbc) :
514s   No weights or probabilities supplied, assuming equal probability
514s > dpbc2<-svydesign(id=~id, data=pbc2)
514s > 
514s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE)
514s Warning message:
514s In svydesign.default(id = ~id, data = pbc2) :
514s   No weights or probabilities supplied, assuming equal probability
514s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE)
514s > 
514s > (c1<-confint(s1,(1:5)*365))
514s          0.025     0.975
514s 365  0.6446215 0.8594153
514s 730  0.5410938 0.7766848
514s 1095 0.2683127 0.5103356
514s 1460 0.1444731 0.3722001
514s 1825 0.1009672 0.3204713
514s > (c2<-confint(s2,(1:5)*365))
514s          0.025     0.975
514s 365  0.6446215 0.8594153
514s 730  0.5410938 0.7766848
514s 1095 0.2683127 0.5103356
514s 1460 0.1444731 0.3722001
514s 1825 0.1009672 0.3204713
514s > all.equal(c1, c2)
514s [1] TRUE
514s > 
514s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1)
514s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2)
514s > 
514s > d<-data.frame(bili=c(5,10))
514s > p1<-predict(m1, se=TRUE, newdata=d,type="curve")
514s > p2<-predict(m2, se=TRUE, newdata=d,type="curve")
516s > 
516s > (pc1<-confint(p1[[1]],(1:5)*365))
516s          0.025     0.975
516s 365  0.8410027 0.9266263
516s 730  0.7371114 0.8548312
516s 1095 0.5517779 0.7018583
516s 1460 0.4335073 0.5992819
516s 1825 0.3260899 0.5046241
516s > (pc2<-confint(p2[[1]],(1:5)*365))
516s          0.025     0.975
516s 365  0.8409490 0.9267054
516s 730  0.7370152 0.8549432
516s 1095 0.5515848 0.7019513
516s 1460 0.4332252 0.5992968
516s 1825 0.3257172 0.5045795
516s > all.equal(pc1, pc2)
516s [1] "Mean relative difference: 0.0002070722"
516s > 
516s > (q1<-quantile(p1[[2]]))
516s 0.75  0.5 0.25 
516s  489  930 1492 
516s > (q2<-quantile(p2[[2]]))
516s 0.75  0.5 0.25 
516s  489  930 1492 
516s > all.equal(q1,q2)
516s [1] TRUE
516s > 
516s BEGIN TEST svyby-strings.R
516s 
516s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
516s Copyright (C) 2025 The R Foundation for Statistical Computing
516s Platform: powerpc64le-unknown-linux-gnu
516s 
516s R is free software and comes with ABSOLUTELY NO WARRANTY.
516s You are welcome to redistribute it under certain conditions.
516s Type 'license()' or 'licence()' for distribution details.
516s 
516s R is a collaborative project with many contributors.
516s Type 'contributors()' for more information and
516s 'citation()' on how to cite R or R packages in publications.
516s 
516s Type 'demo()' for some demos, 'help()' for on-line help, or
516s 'help.start()' for an HTML browser interface to help.
516s Type 'q()' to quit R.
516s 
516s > 
516s > ## check that stringsAsFactors fixes the string levels problem
516s > data(api, package = "survey")
516s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
517s > est0 <-
517s +   survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 
517s > 
517s > stopifnot(isTRUE(all(dim(est0)==c(2,23))))
517s > 
517s BEGIN TEST svyby_bug.R
517s 
517s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
517s Copyright (C) 2025 The R Foundation for Statistical Computing
517s Platform: powerpc64le-unknown-linux-gnu
517s 
517s R is free software and comes with ABSOLUTELY NO WARRANTY.
517s You are welcome to redistribute it under certain conditions.
517s Type 'license()' or 'licence()' for distribution details.
517s 
517s R is a collaborative project with many contributors.
517s Type 'contributors()' for more information and
517s 'citation()' on how to cite R or R packages in publications.
517s 
517s Type 'demo()' for some demos, 'help()' for on-line help, or
517s 'help.start()' for an HTML browser interface to help.
517s Type 'q()' to quit R.
517s 
517s > library(survey)
517s Loading required package: grid
517s Loading required package: Matrix
518s Loading required package: survival
519s > options(warn=2)
519s > 
519s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob)
519s > data(api)
519s 
519s Attaching package: 'survey'
519s 
519s The following object is masked from 'package:graphics':
519s 
519s     dotchart
519s 
519s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
519s > svyby(~api99, ~stype, dclus1, svymean )
519s   stype    api99       se
519s E     E 607.7917 22.81660
519s H     H 595.7143 41.76400
519s M     M 608.6000 32.56064
519s > 
519s > set.seed(123)
519s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA
519s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
519s > 
519s > # subsetting w/ na.rm = FALSE...
519s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE )
519s       mean SE
519s api99   NA NA
519s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE )
519s         mean     SE
519s api99 595.71 41.764
519s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE )
519s       mean SE
519s api99   NA NA
519s > 
519s > # ... looks like this:
519s > svyby(~api99, ~stype, dclus1.na , svymean )
519s   stype    api99     se
519s E     E       NA     NA
519s H     H 595.7143 41.764
519s M     M       NA     NA
519s > 
519s > # subsetting w/ na.rm = TRUE...
519s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE )
519s         mean     SE
519s api99 606.53 22.901
519s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE )
519s         mean     SE
519s api99 595.71 41.764
519s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE )
519s         mean     SE
519s api99 613.39 33.224
519s > 
519s > # ... looks like this
519s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE )
519s   stype    api99       se
519s E     E 606.5319 22.90084
519s H     H 595.7143 41.76400
519s M     M 613.3913 33.22358
519s > 
519s > # Without missing values, this works:
519s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE )
519s   stype    api99       se
519s E     E 607.7917 22.81660
519s H     H 595.7143 41.76400
519s M     M 608.6000 32.56064
519s > 
519s > # ... but this breaks!
519s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE )
519s   stype    api99       se
519s E     E 606.5319 22.90084
519s H     H 595.7143 41.76400
519s M     M 613.3913 33.22358
519s > 
519s > # ... and i don't think this is the expected behavior
519s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE )
519s   stype    api99     se
519s E     E       NA     NA
519s H     H 595.7143 41.764
519s M     M       NA     NA
519s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE )
519s   stype    api99       se
519s E     E 606.5319 22.90084
519s H     H 595.7143 41.76400
519s M     M 613.3913 33.22358
519s > 
519s > 
519s > ## <TL> Now some more as tests
519s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE )
519s   stype     api99       se
519s E     E 2894629.0 792809.8
519s H     H  282283.9 101492.9
519s M     M  477513.4 107555.5
519s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE )
519s   stype api99/api00 se.api99/api00
519s E     E   0.9367750    0.006365702
519s H     H   0.9630485    0.010520785
519s M     M   0.9682246    0.009390982
519s > 
519s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...)
519s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE )
519s   stype (Intercept) se.(Intercept)
519s E     E    606.5319       22.90084
519s H     H    595.7143       41.76400
519s M     M    613.3913       33.22358
519s > 
519s BEGIN TEST svyby_se.R
519s 
519s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
519s Copyright (C) 2025 The R Foundation for Statistical Computing
519s Platform: powerpc64le-unknown-linux-gnu
519s 
519s R is free software and comes with ABSOLUTELY NO WARRANTY.
519s You are welcome to redistribute it under certain conditions.
519s Type 'license()' or 'licence()' for distribution details.
519s 
519s R is a collaborative project with many contributors.
519s Type 'contributors()' for more information and
519s 'citation()' on how to cite R or R packages in publications.
519s 
519s Type 'demo()' for some demos, 'help()' for on-line help, or
519s 'help.start()' for an HTML browser interface to help.
519s Type 'q()' to quit R.
519s 
519s > library(survey)
519s Loading required package: grid
519s Loading required package: Matrix
520s Loading required package: survival
520s > data(api)
520s 
520s Attaching package: 'survey'
520s 
520s The following object is masked from 'package:graphics':
520s 
520s     dotchart
520s 
520s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
520s > 
520s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se"))
520s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci"))
520s > 
520s > 
520s > stopifnot(all.equal(SE(a),SE(b)))
520s > 
520s BEGIN TEST svycontrast.R
520s 
520s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
520s Copyright (C) 2025 The R Foundation for Statistical Computing
520s Platform: powerpc64le-unknown-linux-gnu
520s 
520s R is free software and comes with ABSOLUTELY NO WARRANTY.
520s You are welcome to redistribute it under certain conditions.
520s Type 'license()' or 'licence()' for distribution details.
520s 
520s R is a collaborative project with many contributors.
520s Type 'contributors()' for more information and
520s 'citation()' on how to cite R or R packages in publications.
520s 
520s Type 'demo()' for some demos, 'help()' for on-line help, or
520s 'help.start()' for an HTML browser interface to help.
520s Type 'q()' to quit R.
520s 
520s > library(survey)
520s Loading required package: grid
520s Loading required package: Matrix
521s Loading required package: survival
521s 
521s Attaching package: 'survey'
521s 
521s > data(api)
521s The following object is masked from 'package:graphics':
521s 
521s     dotchart
521s 
521s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
521s > rclus2<-as.svrepdesign(dclus2)
521s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2)
521s > svycontrast(model, c(ell=1,meals=0))
521s          contrast     SE
521s contrast  -2.0592 1.6177
521s > a<-svycontrast(model, c(0,1,0,0))
521s > 
521s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE)
521s > svycontrast(model2, c(ell=1,meals=0))
521s          contrast     SE
521s contrast  -2.0592 1.6177
521s > a2<-svycontrast(model2, c(0,1,0,0))
521s > stopifnot(!is.null(a2$replicates))
521s > 
521s BEGIN TEST svyivreg-var.R
522s 
522s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
522s Copyright (C) 2025 The R Foundation for Statistical Computing
522s Platform: powerpc64le-unknown-linux-gnu
522s 
522s R is free software and comes with ABSOLUTELY NO WARRANTY.
522s You are welcome to redistribute it under certain conditions.
522s Type 'license()' or 'licence()' for distribution details.
522s 
522s R is a collaborative project with many contributors.
522s Type 'contributors()' for more information and
522s 'citation()' on how to cite R or R packages in publications.
522s 
522s Type 'demo()' for some demos, 'help()' for on-line help, or
522s 'help.start()' for an HTML browser interface to help.
522s Type 'q()' to quit R.
522s 
522s > 
522s > library(survey)
522s Loading required package: grid
522s Loading required package: Matrix
523s Loading required package: survival
523s 
523s Attaching package: 'survey'
523s 
523s > data(api)
523s The following object is masked from 'package:graphics':
523s 
523s     dotchart
523s 
523s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
523s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat))
523s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat))
523s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov)))
523s > 
523s BEGIN TEST svyivreg.R
523s 
523s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
523s Copyright (C) 2025 The R Foundation for Statistical Computing
523s Platform: powerpc64le-unknown-linux-gnu
523s 
523s R is free software and comes with ABSOLUTELY NO WARRANTY.
523s You are welcome to redistribute it under certain conditions.
523s Type 'license()' or 'licence()' for distribution details.
523s 
523s R is a collaborative project with many contributors.
523s Type 'contributors()' for more information and
523s 'citation()' on how to cite R or R packages in publications.
523s 
523s Type 'demo()' for some demos, 'help()' for on-line help, or
523s 'help.start()' for an HTML browser interface to help.
523s Type 'q()' to quit R.
523s 
523s > library(survey)
523s Loading required package: grid
523s Loading required package: Matrix
524s Loading required package: survival
524s 
524s Attaching package: 'survey'
524s 
524s > library(AER)
524s The following object is masked from 'package:graphics':
524s 
524s     dotchart
524s 
524s Loading required package: car
524s Loading required package: carData
524s Loading required package: lmtest
524s Loading required package: zoo
524s 
524s Attaching package: 'zoo'
524s 
524s The following objects are masked from 'package:base':
524s 
524s     as.Date, as.Date.numeric
524s 
524s Loading required package: sandwich
524s > 
524s > load("cigsw.rda")
524s > 
524s > des<-svydesign(id=~1, weights=~wt, data=cigsw)
524s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des)
524s > 
524s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6)
524s [1] TRUE
524s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232,  .3614382 ),tolerance=1e-6)
524s [1] TRUE
524s > 
524s BEGIN TEST svyolr-rake-subset.R
524s 
524s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
524s Copyright (C) 2025 The R Foundation for Statistical Computing
524s Platform: powerpc64le-unknown-linux-gnu
524s 
524s R is free software and comes with ABSOLUTELY NO WARRANTY.
524s You are welcome to redistribute it under certain conditions.
524s Type 'license()' or 'licence()' for distribution details.
524s 
524s R is a collaborative project with many contributors.
524s Type 'contributors()' for more information and
524s 'citation()' on how to cite R or R packages in publications.
524s 
524s Type 'demo()' for some demos, 'help()' for on-line help, or
524s 'help.start()' for an HTML browser interface to help.
524s Type 'q()' to quit R.
524s 
524s > library(survey)
524s Loading required package: grid
524s Loading required package: Matrix
525s Loading required package: survival
526s 
526s Attaching package: 'survey'
526s 
526s The following object is masked from 'package:graphics':
526s 
526s     dotchart
526s 
526s > data(api)
526s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
526s > 
526s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
526s > 
526s > ## population marginal totals for each stratum
526s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
526s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
526s > 
526s > 
526s > ## rake with the population totals
526s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
526s > 
526s > # works
526s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
526s > 
526s > # fails in 4.1 (should work because svyolr's default na.action is na.omit)
526s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r)
526s > 
526s > # fails in 4.1 (should work because NA values are subsetted out)
526s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) )
526s > 
526s BEGIN TEST svyolr.R
526s 
526s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
526s Copyright (C) 2025 The R Foundation for Statistical Computing
526s Platform: powerpc64le-unknown-linux-gnu
526s 
526s R is free software and comes with ABSOLUTELY NO WARRANTY.
526s You are welcome to redistribute it under certain conditions.
526s Type 'license()' or 'licence()' for distribution details.
526s 
526s R is a collaborative project with many contributors.
526s Type 'contributors()' for more information and
526s 'citation()' on how to cite R or R packages in publications.
526s 
526s Type 'demo()' for some demos, 'help()' for on-line help, or
526s 'help.start()' for an HTML browser interface to help.
526s Type 'q()' to quit R.
526s 
526s > library(survey)
526s Loading required package: grid
526s Loading required package: Matrix
527s Loading required package: survival
527s 
527s Attaching package: 'survey'
527s 
527s The following object is masked from 'package:graphics':
527s 
527s     dotchart
527s 
527s > 
527s > ################################################################################
527s > # Example from svyolr: runs OK
527s > data(api)
527s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
527s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
527s > 
527s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
527s > m
527s Call:
527s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1)
527s 
527s Coefficients:
527s     avg.ed   mobility     stypeH     stypeM 
527s -2.6999217  0.0325042 -1.7574715 -0.6191463 
527s 
527s Intercepts:
527s   (0,25]|(25,50]  (25,50]|(50,75] (50,75]|(75,100] 
527s        -8.857919        -6.586464        -4.924938 
527s > 
527s > ## Use regTermTest for testing multiple parameters
527s > test<-regTermTest(m, ~avg.ed+stype, method="LRT")
527s > ################################################################################
527s > 
527s > ################################################################################
527s > # If we wrap everything into a function: error b/c it looks for design variable
527s > # dclus1 in .GlobalEnv
527s > 
527s > foo <- function(x){
527s +   dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc)
527s +   dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
527s + 
527s +   m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
527s +   ## Use regTermTest for testing multiple parameters
527s +   regTermTest(m, ~avg.ed+stype, method="LRT")
527s + }
527s > 
527s > # OK
527s > foo(apiclus1)
527s Working (Rao-Scott+F) LRT for avg.ed stype
527s  in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1)
527s Working 2logLR =  0.6580304 p= 0.73257 
527s (scale factors:  2.7 0.22 0.11 );  denominator df= 10
527s > 
527s > # Clean-up everything but apiclus1 and foo
527s > rm(list = setdiff(ls(),c('apiclus1','foo','test')))
527s > 
527s > # Error
527s > test2<-foo(apiclus1)
527s > ################################################################################
527s > all.equal(test,test2)
527s [1] TRUE
527s > 
527s > 
527s BEGIN TEST toy_example_for_postStratify.R
527s 
527s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
527s Copyright (C) 2025 The R Foundation for Statistical Computing
527s Platform: powerpc64le-unknown-linux-gnu
527s 
527s R is free software and comes with ABSOLUTELY NO WARRANTY.
527s You are welcome to redistribute it under certain conditions.
527s Type 'license()' or 'licence()' for distribution details.
527s 
527s R is a collaborative project with many contributors.
527s Type 'contributors()' for more information and
527s 'citation()' on how to cite R or R packages in publications.
527s 
527s Type 'demo()' for some demos, 'help()' for on-line help, or
527s 'help.start()' for an HTML browser interface to help.
527s Type 'q()' to quit R.
527s 
527s > library(survey)
527s Loading required package: grid
527s Loading required package: Matrix
528s Loading required package: survival
528s 
528s Attaching package: 'survey'
528s 
528s The following object is masked from 'package:graphics':
528s 
528s     dotchart
528s 
528s > 
528s > # Dummy data for testing nonresponse adjustments
528s > toy <- data.frame(id = 1:10,
528s +                   dummy = 1,
528s +                   class = c(rep("A", 5), rep("B", 5)),
528s +                   responded = c(rep(TRUE, 8), FALSE, FALSE),
528s +                   weight = rep(100, 10))
528s > 
528s > # With jackknife replicate weights
528s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10)
528s > diag(toy_repweights) <- rep(0, 10)
528s > 
528s > # Scramble up which person is in which jackknife group
528s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ]
528s > 
528s > toy_design <- svrepdesign(variables = toy[, 1:4],
528s +                           weights = toy$weight,
528s +                           repweights = toy_repweights,
528s +                           type = "JK1",
528s +                           scale = 0.9)
528s > 
528s > # Get the sum of the weights for the full sample
528s > poptotals <- as.data.frame(svyby(formula = ~dummy,
528s +                                  by = ~class,
528s +                                  design = toy_design,
528s +                                  FUN = survey::svytotal))
528s > 
528s > poptotals$Freq <- poptotals$dummy
528s > poptotals$dummy <- NULL
528s > poptotals$se <- NULL
528s > 
528s > # Adjust the weights of the responding sample to match to the full sample
528s > adjusted <-  postStratify(design = subset(toy_design, responded),
528s +                           strata = ~class,
528s +                           population = poptotals)
528s > 
528s > # This works for the weights...
528s > svyby(formula = ~dummy,
528s +       by = ~class,
528s +       design = adjusted,
528s +       FUN = survey::svytotal)
528s   class dummy se
528s A     A   500  0
528s B     B   500  0
528s > 
528s > # ...and some, but not all, the replicate weights
528s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights)))
528s > 
528s > 
528s > 
528s BEGIN TEST twophase.R
529s 
529s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
529s Copyright (C) 2025 The R Foundation for Statistical Computing
529s Platform: powerpc64le-unknown-linux-gnu
529s 
529s R is free software and comes with ABSOLUTELY NO WARRANTY.
529s You are welcome to redistribute it under certain conditions.
529s Type 'license()' or 'licence()' for distribution details.
529s 
529s R is a collaborative project with many contributors.
529s Type 'contributors()' for more information and
529s 'citation()' on how to cite R or R packages in publications.
529s 
529s Type 'demo()' for some demos, 'help()' for on-line help, or
529s 'help.start()' for an HTML browser interface to help.
529s Type 'q()' to quit R.
529s 
529s > Loading required package: grid
529s library(survey)
529s Loading required package: Matrix
529s Loading required package: survival
530s 
530s Attaching package: 'survey'
530s 
530s The following object is masked from 'package:graphics':
530s 
530s     dotchart
530s 
530s > 
530s > ## two-phase simple random sampling.
530s > data(pbc, package="survival")
530s > pbc$id<-1:nrow(pbc)
530s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9)
530s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized)))
530s Two-phase sparse-matrix design:
530s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
530s     subset = subset, data = data, pps = pps)
530s Phase 1:
530s Independent Sampling design (with replacement)
530s svydesign(ids = ~id)
530s Phase 2:
530s Independent Sampling design
530s svydesign(ids = ~id, fpc = `*phase1*`)
530s > m<-svymean(~bili, d2pbc)
530s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized])))
530s [1] TRUE
530s > all.equal(as.vector(SE(m)),
530s +           with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))),
530s +           tolerance=0.002)
530s [1] TRUE
530s > 
530s > ## two-stage sampling as two-phase
530s > data(mu284)
530s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3)))
530s > mu284.1<-mu284[ii,]
530s > mu284.1$id<-1:nrow(mu284.1)
530s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15))
530s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)
530s > ## first phase cluster sample, second phase stratified within cluster
530s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1),
530s +                    fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx"))
530s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 
530s     NULL), data = mu284.1, subset = ~sub, method = "approx")
530s Phase 1:
530s 1 - level Cluster Sampling design
530s With (5) clusters.
530s svydesign(ids = ~id1, fpc = ~n1)
530s Phase 2:
530s Stratified Independent Sampling design
530s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
530s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1),
530s +                    fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full"))
530s Two-phase sparse-matrix design:
530s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
530s     subset = subset, data = data, pps = pps)
530s Phase 1:
530s 1 - level Cluster Sampling design
530s With (5) clusters.
530s svydesign(ids = ~id1, fpc = ~n1)
530s Phase 2:
530s Stratified Independent Sampling design
530s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
530s > summary(d2mu284)
530s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 
530s     NULL), data = mu284.1, subset = ~sub, method = "approx")
530s Phase 1:
530s 1 - level Cluster Sampling design
530s With (5) clusters.
530s svydesign(ids = ~id1, fpc = ~n1)
530s Probabilities:
530s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
530s     0.1     0.1     0.1     0.1     0.1     0.1 
530s Population size (PSUs): 50 
530s Phase 2:
530s Stratified Independent Sampling design
530s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
530s Probabilities:
530s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
530s  0.3333  0.3750  0.4286  0.4674  0.6000  0.6000 
530s Stratum Sizes: 
530s            19 31 45 47 50
530s obs         3  3  3  3  3
530s design.PSU  3  3  3  3  3
530s actual.PSU  3  3  3  3  3
530s Population stratum sizes (PSUs): 
530s 19 31 45 47 50 
530s  5  7  8  5  9 
530s Data variables:
530s [1] "id1" "n1"  "id2" "y1"  "n2"  "id"  "sub"
530s > t1<-svytotal(~y1, dmu284)
530s > t2<-svytotal(~y1, d2mu284)
530s > t22<-svytotal(~y1,d22mu284)
530s > m1<-svymean(~y1, dmu284)
530s > m2<-svymean(~y1, d2mu284)
530s > m22<-svymean(~y1, d22mu284)
530s > all.equal(coef(t1),coef(t2))
530s [1] TRUE
530s > all.equal(coef(t1),coef(t22))
530s [1] TRUE
530s > all.equal(coef(m1),coef(m2))
530s [1] TRUE
530s > all.equal(coef(m1),coef(m22))
530s [1] TRUE
530s > all.equal(as.vector(SE(m1)),as.vector(SE(m2)))
530s [1] TRUE
530s > all.equal(as.vector(SE(m1)),as.vector(SE(m22)))
530s [1] TRUE
530s > all.equal(as.vector(SE(t1)),as.vector(SE(t2)))
530s [1] TRUE
530s > all.equal(as.vector(SE(t1)),as.vector(SE(t22)))
530s [1] TRUE
530s > 
530s > ## case-cohort design
530s > ##this example requires R 2.3.1 or later for cch and data.
530s > library("survival")
530s > data(nwtco, package="survival")
530s > ## unstratified, equivalent to Lin & Ying (1993)
530s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel),
530s +                  subset=~I(in.subcohort | rel), data=nwtco))
530s Two-phase sparse-matrix design:
530s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
530s     subset = subset, data = data, pps = pps)
530s Phase 1:
530s Independent Sampling design (with replacement)
530s svydesign(ids = ~seqno)
530s Phase 2:
530s Stratified Independent Sampling design
530s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`)
530s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12),
530s +                design=dcchs)
530s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel),
530s +                  subset=~I(in.subcohort | rel), data=nwtco,method="approx")
530s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12),
530s +                design=dcchs)
530s > all.equal(coef(cch1),coef(cch1.2))
530s [1] TRUE
530s > all.equal(SE(cch1),SE(cch1.2))
530s [1] TRUE
530s > ## Using survival::cch 
530s > subcoh <- nwtco$in.subcohort
530s > selccoh <- with(nwtco, rel==1|subcoh==1)
530s > ccoh.data <- nwtco[selccoh,]
530s > ccoh.data$subcohort <- subcoh[selccoh]
530s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12),
530s +           data =ccoh.data, subcoh = ~subcohort, id=~seqno,
530s +           cohort.size=4028, method="LinYing", robust=TRUE)
530s > 
530s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2))))
530s [1] TRUE
530s > ## cch has smaller variances by a factor of 1.0005 because
530s > ## there is a (n/(n-1)) in the survey phase1 varianace
530s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006))
530s [1] TRUE
530s > 
530s > 
530s > ## bug report from Takahiro Tsuchiya for version 3.4
530s > ## We used to not match Sarndal exactly, because our old phase-one
530s > ## estimator had a small bias for finite populations
530s > rei<-read.table(tmp<-textConnection(
530s + "  id   N n.a h n.ah n.h   sub  y
530s + 1   1 300  20 1   12   5  TRUE  1
530s + 2   2 300  20 1   12   5  TRUE  2
530s + 3   3 300  20 1   12   5  TRUE  3
530s + 4   4 300  20 1   12   5  TRUE  4
530s + 5   5 300  20 1   12   5  TRUE  5
530s + 6   6 300  20 1   12   5 FALSE NA
530s + 7   7 300  20 1   12   5 FALSE NA
530s + 8   8 300  20 1   12   5 FALSE NA
530s + 9   9 300  20 1   12   5 FALSE NA
530s + 10 10 300  20 1   12   5 FALSE NA
530s + 11 11 300  20 1   12   5 FALSE NA
530s + 12 12 300  20 1   12   5 FALSE NA
530s + 13 13 300  20 2    8   3  TRUE  6
530s + 14 14 300  20 2    8   3  TRUE  7
530s + 15 15 300  20 2    8   3  TRUE  8
530s + 16 16 300  20 2    8   3 FALSE NA
530s + 17 17 300  20 2    8   3 FALSE NA
530s + 18 18 300  20 2    8   3 FALSE NA
530s + 19 19 300  20 2    8   3 FALSE NA
530s + 20 20 300  20 2    8   3 FALSE NA
530s + "), header=TRUE)
530s > close(tmp)
530s > 
530s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h),
530s +                     fpc=list(~N,NULL), subset=~sub, data=rei, method="approx")
530s > tot<- svytotal(~y, des.rei)
530s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h),
530s +                     fpc=list(~N,NULL), subset=~sub, data=rei)
530s > tot2<- svytotal(~y, des.rei2)
530s > 
530s > ## based on Sarndal et al (9.4.14)
530s > rei$w.ah <- rei$n.ah / rei$n.a
530s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE)
530s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE)
530s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y)
530s > 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))
530s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1)))
530s > 
530s > a.rei$f.h<-with(a.rei, n.h/n.ah)
530s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh))
530s > 
530s > a.rei$f<-with(a.rei, n.a/N)
530s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1))
530s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2)))
530s > 
530s > V
530s [1] 36522.63
530s > Vphase1
530s [1] 24072.63
530s > Vphase2
530s [1] 12450
530s > vcov(tot)
530s          y
530s y 35911.05
530s attr(,"phases")
530s attr(,"phases")$phase1
530s          [,1]
530s [1,] 23461.05
530s 
530s attr(,"phases")$phase2
530s       y
530s y 12450
530s 
530s > vcov(tot2)
530s          [,1]
530s [1,] 36522.63
530s attr(,"phases")
530s attr(,"phases")$phase1
530s          [,1]
530s [1,] 24072.63
530s 
530s attr(,"phases")$phase2
530s       [,1]
530s [1,] 12450
530s 
530s > ## phase 2 identical
530s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2))
530s [1] TRUE
530s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2))
530s [1] TRUE
530s > ## phase 1 differs by 2.6% for old twophase estimator
530s > Vphase1/attr(vcov(tot),"phases")$phase1
530s          [,1]
530s [1,] 1.026068
530s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1))
530s [1] TRUE
530s > 
530s > 
531s autopkgtest [23:30:03]: test run-unit-test: -----------------------]
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705s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ...
705s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ...
705s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ...
705s Setting up wget (1.25.0-2ubuntu4) ...
705s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ...
705s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ...
705s Setting up dracut-install (109-11ubuntu1) ...
705s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ...
705s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
705s Setting up iptables (1.8.11-2ubuntu3) ...
705s Setting up iproute2 (6.18.0-1ubuntu1) ...
705s Processing triggers for man-db (2.13.1-1build1) ...
707s Processing triggers for install-info (7.2-5) ...
707s Processing triggers for libc-bin (2.42-2ubuntu4) ...
707s autopkgtest [23:32:59]: upgrading testbed (apt dist-upgrade and autopurge)
708s Reading package lists...
708s Building dependency tree...
708s Reading state information...
708s Calculating upgrade...
708s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
708s Reading package lists...
708s Building dependency tree...
708s Reading state information...
708s Solving dependencies...
708s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
710s Reading package lists...
710s Building dependency tree...
710s Reading state information...
710s Solving dependencies...
711s The following NEW packages will be installed:
711s   build-essential cpp cpp-15 cpp-15-powerpc64le-linux-gnu
711s   cpp-powerpc64le-linux-gnu dctrl-tools fontconfig fontconfig-config
711s   fonts-dejavu-core fonts-dejavu-mono fonts-glyphicons-halflings fonts-mathjax
711s   g++ g++-15 g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15
711s   gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-15
711s   gfortran-15-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu
711s   icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev
711s   libcairo2 libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0
711s   libfontconfig1 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1
711s   libgraphite2-3 libharfbuzz0b libice6 libicu-dev libisl23 libitm1 libjbig0
711s   libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev
711s   libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables
711s   libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
711s   libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0
711s   libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0
711s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev
711s   libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6
711s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1
711s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
711s   libzstd-dev linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf
711s   pkgconf-bin r-base-core r-base-dev r-cran-abind r-cran-aer r-cran-backports
711s   r-cran-bit r-cran-bit64 r-cran-blob r-cran-boot r-cran-broom r-cran-cachem
711s   r-cran-car r-cran-cardata r-cran-caret r-cran-class r-cran-cli r-cran-clock
711s   r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cowplot
711s   r-cran-cpp11 r-cran-curl r-cran-data.table r-cran-dbi r-cran-deriv
711s   r-cran-diagram r-cran-digest r-cran-doby r-cran-dplyr r-cran-e1071
711s   r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-foreach
711s   r-cran-forecast r-cran-foreign r-cran-formula r-cran-fracdiff r-cran-future
711s   r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-globals
711s   r-cran-glue r-cran-gower r-cran-gtable r-cran-hardhat r-cran-hexbin
711s   r-cran-highr r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jsonlite
711s   r-cran-kernsmooth r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava
711s   r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest
711s   r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix
711s   r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv
711s   r-cran-microbenchmark r-cran-minqa r-cran-mitools r-cran-modelmetrics
711s   r-cran-modelr r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv
711s   r-cran-parallelly r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig
711s   r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-proc r-cran-prodlim
711s   r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quadprog r-cran-quantmod
711s   r-cran-quantreg r-cran-r6 r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp
711s   r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rdpack r-cran-recipes
711s   r-cran-reformulas r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-rsqlite
711s   r-cran-sandwich r-cran-scales r-cran-shape r-cran-sparsem r-cran-sparsevctrs
711s   r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey
711s   r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect
711s   r-cran-timechange r-cran-timedate r-cran-tseries r-cran-ttr r-cran-tzdb
711s   r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr
711s   r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo rpcsvc-proto unzip x11-common
711s   xdg-utils zip zlib1g-dev
711s 0 upgraded, 249 newly installed, 0 to remove and 0 not upgraded.
711s Need to get 274 MB of archives.
711s After this operation, 740 MB of additional disk space will be used.
711s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc-dev-bin ppc64el 2.42-2ubuntu4 [23.9 kB]
711s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el linux-libc-dev ppc64el 6.19.0-3.3 [1832 kB]
714s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcrypt-dev ppc64el 1:4.5.1-1 [162 kB]
714s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el rpcsvc-proto ppc64el 1.4.3-1build1 [84.2 kB]
714s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc6-dev ppc64el 2.42-2ubuntu4 [2080 kB]
718s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB]
720s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB]
720s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [11.4 MB]
741s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-12ubuntu1 [1038 B]
741s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B]
741s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB]
741s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-12ubuntu1 [49.0 kB]
741s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB]
741s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-12ubuntu1 [32.2 kB]
741s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-12ubuntu1 [3006 kB]
747s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-12ubuntu1 [1374 kB]
750s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-12ubuntu1 [2729 kB]
754s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-12ubuntu1 [1231 kB]
756s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-12ubuntu1 [160 kB]
756s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-12ubuntu1 [1670 kB]
759s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [22.4 MB]
799s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-12ubuntu1 [530 kB]
800s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B]
800s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B]
800s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-12ubuntu1 [2747 kB]
805s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [13.0 MB]
827s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-12ubuntu1 [25.3 kB]
827s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B]
827s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B]
827s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B]
827s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el dctrl-tools ppc64el 2.24-3build4 [108 kB]
827s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB]
827s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB]
828s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB]
828s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB]
828s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB]
828s Get:37 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
828s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
833s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB]
834s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran-15-dev ppc64el 15.2.0-12ubuntu1 [651 kB]
835s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [12.3 MB]
877s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15 ppc64el 15.2.0-12ubuntu1 [18.1 kB]
877s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1020 B]
877s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran ppc64el 4:15.2.0-4ubuntu1 [1166 B]
877s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el icu-devtools ppc64el 78.2-1ubuntu1 [246 kB]
877s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB]
877s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas-dev ppc64el 3.12.1-7ubuntu1 [306 kB]
877s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbz2-dev ppc64el 1.0.8-6build2 [50.0 kB]
877s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB]
877s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB]
877s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B]
877s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB]
877s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB]
879s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB]
879s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB]
879s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate-dev ppc64el 1.23-2build1 [71.8 kB]
879s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB]
879s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB]
881s Get:59 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB]
881s Get:60 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB]
881s Get:61 http://ftpmaster.internal/ubuntu resolute/main ppc64el libicu-dev ppc64el 78.2-1ubuntu1 [13.3 MB]
907s Get:62 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB]
907s Get:63 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-4ubuntu3 [358 kB]
907s Get:64 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
907s Get:65 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B]
907s Get:66 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B]
907s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
907s Get:68 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
907s Get:69 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
907s Get:70 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
907s Get:71 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB]
913s Get:72 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack-dev ppc64el 3.12.1-7ubuntu1 [6357 kB]
925s Get:73 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB]
925s Get:74 http://ftpmaster.internal/ubuntu resolute/main ppc64el libncurses-dev ppc64el 6.6+20251231-1 [505 kB]
925s Get:75 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB]
925s Get:76 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB]
925s Get:77 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB]
925s Get:78 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB]
925s Get:79 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB]
925s Get:80 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB]
925s Get:81 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB]
925s Get:82 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-16-0 ppc64el 10.46-1 [292 kB]
925s Get:83 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-32-0 ppc64el 10.46-1 [275 kB]
925s Get:84 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-posix3 ppc64el 10.46-1 [7334 B]
925s Get:85 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-dev ppc64el 10.46-1 [937 kB]
928s Get:86 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpkgconf3 ppc64el 1.8.1-4build1 [37.9 kB]
928s Get:87 http://ftpmaster.internal/ubuntu resolute/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu2 [903 kB]
932s Get:88 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpng-dev ppc64el 1.6.54-1 [326 kB]
932s Get:89 http://ftpmaster.internal/ubuntu resolute/main ppc64el libreadline-dev ppc64el 8.3-3 [252 kB]
932s Get:90 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB]
932s Get:91 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB]
932s Get:92 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB]
935s Get:93 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB]
935s Get:94 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB]
935s Get:95 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB]
935s Get:96 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB]
935s Get:97 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B]
935s Get:98 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB]
937s Get:99 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB]
937s Get:100 http://ftpmaster.internal/ubuntu resolute/main ppc64el libzstd-dev ppc64el 1.5.7+dfsg-3 [528 kB]
939s Get:101 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-normalize.css all 8.0.1-5.1 [10.4 kB]
939s Get:102 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB]
939s Get:103 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB]
939s Get:104 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
939s Get:105 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB]
994s Get:106 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblzma-dev ppc64el 5.8.2-2 [210 kB]
994s Get:107 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf-bin ppc64el 1.8.1-4build1 [22.7 kB]
994s Get:108 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf ppc64el 1.8.1-4build1 [16.8 kB]
994s Get:109 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtirpc-dev ppc64el 1.3.6+ds-1 [223 kB]
994s Get:110 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-dev all 4.5.2-1ubuntu2 [1880 B]
994s Get:111 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pkg-r-autopkgtest all 20250812 [6158 B]
994s Get:112 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-abind all 1.4-8-1build1 [67.0 kB]
994s Get:113 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cardata all 3.0.6-1 [1687 kB]
996s Get:114 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-formula all 1.2-5-1 [158 kB]
996s Get:115 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB]
998s Get:116 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-lattice ppc64el 0.22-9-1 [1399 kB]
1000s Get:117 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB]
1004s Get:118 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB]
1012s Get:119 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mgcv ppc64el 1.9-4-1 [3694 kB]
1025s Get:120 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nnet ppc64el 7.3-20-1 [119 kB]
1025s Get:121 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-boot all 1.3-32-1 [636 kB]
1026s Get:122 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-littler ppc64el 0.3.22-1 [85.5 kB]
1026s Get:123 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
1026s Get:124 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpp ppc64el 1.1.0-1 [2037 kB]
1029s Get:125 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-minqa ppc64el 1.2.8-1 [141 kB]
1029s Get:126 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libnlopt0 ppc64el 2.7.1-7ubuntu1 [292 kB]
1029s Get:127 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nloptr ppc64el 2.2.1-2 [251 kB]
1029s Get:128 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rbibutils ppc64el 2.3-1 [1047 kB]
1031s Get:129 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rdpack all 2.6.3-1 [636 kB]
1032s Get:130 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-reformulas all 0.4.4-1 [151 kB]
1033s Get:131 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rlang ppc64el 1.1.5-3 [1738 kB]
1036s Get:132 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcppeigen ppc64el 0.3.4.0.2-1 [1477 kB]
1039s Get:133 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-statmod ppc64el 1.5.0-1 [298 kB]
1039s Get:134 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lme4 ppc64el 1.1-38-1 [4220 kB]
1046s Get:135 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-backports ppc64el 1.5.0-2 [122 kB]
1046s Get:136 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cli ppc64el 3.6.4-1 [1411 kB]
1048s Get:137 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-generics all 0.1.4-1 [84.0 kB]
1048s Get:138 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-glue ppc64el 1.8.0-1 [165 kB]
1048s Get:139 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
1048s Get:140 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB]
1048s Get:141 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB]
1048s Get:142 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB]
1050s Get:143 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pillar all 1.11.1+dfsg-1 [456 kB]
1050s Get:144 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-r6 all 2.6.1-1 [101 kB]
1051s Get:145 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fansi ppc64el 1.0.6-2 [637 kB]
1052s Get:146 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
1052s Get:147 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-3 [420 kB]
1052s Get:148 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-withr all 3.0.2+dfsg-1 [214 kB]
1052s Get:149 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyselect ppc64el 1.2.1+dfsg-1 [222 kB]
1052s Get:150 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dplyr ppc64el 1.1.4-4 [1542 kB]
1054s Get:151 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-purrr ppc64el 1.0.4-1 [555 kB]
1055s Get:152 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringi ppc64el 1.8.4-1build2 [947 kB]
1057s Get:153 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB]
1057s Get:154 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cpp11 all 0.5.3-1 [242 kB]
1057s Get:155 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB]
1059s Get:156 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-broom all 1.0.12+dfsg-1 [1708 kB]
1062s Get:157 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-numderiv all 2016.8-1.1-3build1 [116 kB]
1062s Get:158 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
1062s Get:159 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB]
1064s Get:160 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-farver ppc64el 2.1.2-1 [1389 kB]
1067s Get:161 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB]
1067s Get:162 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
1067s Get:163 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-viridislite all 0.4.3-1 [1088 kB]
1069s Get:164 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-scales all 1.4.0-1 [725 kB]
1071s Get:165 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
1079s Get:166 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cowplot all 1.1.3+dfsg-1 [614 kB]
1080s Get:167 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-deriv all 4.2.0-1 [154 kB]
1080s Get:168 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-colorspace ppc64el 2.1-1+dfsg-1 [1570 kB]
1082s Get:169 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fracdiff ppc64el 1.5-3-1 [118 kB]
1082s Get:170 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-zoo ppc64el 1.8-15-1 [1028 kB]
1084s Get:171 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lmtest ppc64el 0.9.40-1build1 [401 kB]
1084s Get:172 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-timedate ppc64el 4052.112-1 [1299 kB]
1086s Get:173 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quadprog ppc64el 1.5-8-1build2 [38.8 kB]
1086s Get:174 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xts ppc64el 0.14.1-1 [1209 kB]
1088s Get:175 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-curl ppc64el 7.0.0+dfsg-1 [205 kB]
1088s Get:176 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ttr ppc64el 0.24.4-1 [516 kB]
1088s Get:177 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-jsonlite ppc64el 1.9.1+dfsg-1 [452 kB]
1088s Get:178 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quantmod all 0.4.28-1 [1037 kB]
1090s Get:179 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tseries ppc64el 0.10-59-3 [390 kB]
1090s Get:180 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-urca ppc64el 1.3-4-1build1 [1056 kB]
1092s Get:181 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rcpparmadillo ppc64el 15.2.3-1-1 [935 kB]
1094s Get:182 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-forecast ppc64el 8.23.0-1 [1598 kB]
1096s Get:183 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-modelr all 0.1.11-1 [195 kB]
1096s Get:184 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-microbenchmark ppc64el 1.5.0-1 [67.9 kB]
1096s Get:185 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-doby all 4.7.1-3 [4741 kB]
1105s Get:186 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-evaluate all 1.0.5-1 [117 kB]
1105s Get:187 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xfun ppc64el 0.55+dfsg-1 [589 kB]
1106s Get:188 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB]
1106s Get:189 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB]
1106s Get:190 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
1118s Get:191 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-knitr all 1.51+dfsg-1 [847 kB]
1120s Get:192 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-pbkrtest all 0.5.5-1 [217 kB]
1120s Get:193 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sparsem ppc64el 1.84-2-1 [832 kB]
1123s Get:194 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrixmodels all 0.5-4-1 [351 kB]
1123s Get:195 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-survival ppc64el 3.8-6-1 [8312 kB]
1148s Get:196 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrixstats ppc64el 1.5.0-1 [578 kB]
1149s Get:197 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-class ppc64el 7.3-23-1 [94.5 kB]
1149s Get:198 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-proxy ppc64el 0.4-27-1 [185 kB]
1149s Get:199 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-e1071 ppc64el 1.7-17-1 [595 kB]
1150s Get:200 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-codetools all 0.2-20-1build1 [91.1 kB]
1150s Get:201 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-iterators all 1.0.14-1build1 [336 kB]
1150s Get:202 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-foreach all 1.5.2-1build1 [124 kB]
1150s Get:203 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-data.table ppc64el 1.17.0+dfsg-1 [2197 kB]
1154s Get:204 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-modelmetrics ppc64el 1.2.2.2-1build2 [147 kB]
1154s Get:205 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-plyr ppc64el 1.8.9-1 [834 kB]
1155s Get:206 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-proc ppc64el 1.18.5-1 [965 kB]
1157s Get:207 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-tzdb ppc64el 0.5.0-1 [540 kB]
1158s Get:208 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-clock ppc64el 0.7.2-1 [1910 kB]
1161s Get:209 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-gower ppc64el 1.0.2-1 [211 kB]
1161s Get:210 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sparsevctrs ppc64el 0.2.0-2 [172 kB]
1161s Get:211 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-hardhat all 1.4.2+dfsg-1 [596 kB]
1162s Get:212 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rpart ppc64el 4.1.24-1build1 [678 kB]
1163s Get:213 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-shape all 1.4.6.1-1 [749 kB]
1165s Get:214 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-diagram all 1.6.5-2 [656 kB]
1166s Get:215 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-kernsmooth ppc64el 2.23-26-1build1 [96.8 kB]
1166s Get:216 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-digest ppc64el 0.6.39-1 [238 kB]
1166s Get:217 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-globals all 0.19.0-1 [160 kB]
1166s Get:218 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-listenv all 0.10.0+dfsg-1 [113 kB]
1166s Get:219 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-parallelly ppc64el 1.42.0-1 [540 kB]
1167s Get:220 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-future all 1.34.0+dfsg-1 [646 kB]
1169s Get:221 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-future.apply all 1.11.3+dfsg-1 [175 kB]
1169s Get:222 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-progressr all 0.15.1-1 [353 kB]
1169s Get:223 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-squarem all 2021.1-1build1 [180 kB]
1169s Get:224 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lava all 1.8.2+dfsg-1 [2210 kB]
1173s Get:225 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-prodlim ppc64el 2024.06.25-1 [420 kB]
1173s Get:226 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-ipred ppc64el 0.9-15-1 [386 kB]
1174s Get:227 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-timechange ppc64el 0.3.0-2 [211 kB]
1174s Get:228 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-lubridate ppc64el 1.9.4+dfsg-1 [1011 kB]
1175s Get:229 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-recipes all 1.1.0+dfsg-1 [2035 kB]
1179s Get:230 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-reshape2 ppc64el 1.4.4-2build2 [124 kB]
1179s Get:231 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-caret ppc64el 7.0-1+dfsg-1 [3461 kB]
1185s Get:232 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-conquer ppc64el 1.3.3-1 [468 kB]
1185s Get:233 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-quantreg ppc64el 6.1-1 [1463 kB]
1188s Get:234 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-car all 3.1-5-1 [1526 kB]
1191s Get:235 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-sandwich all 3.1-1-1build1 [1483 kB]
1194s Get:236 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-aer all 1.2-15-1 [2607 kB]
1198s Get:237 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bit ppc64el 4.6.0+dfsg-1 [475 kB]
1198s Get:238 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-bit64 ppc64el 4.6.0-1-4 [507 kB]
1198s Get:239 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-blob all 1.3.0-1 [54.1 kB]
1198s Get:240 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-fastmap ppc64el 1.2.0-1 [75.0 kB]
1198s Get:241 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cachem ppc64el 1.1.0-1 [74.1 kB]
1198s Get:242 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-dbi all 1.2.3-1build1 [855 kB]
1200s Get:243 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-foreign ppc64el 0.8.91-1 [255 kB]
1200s Get:244 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-hexbin ppc64el 1.28.5-1 [1583 kB]
1203s Get:245 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-memoise all 2.0.1-1build1 [54.5 kB]
1203s Get:246 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mitools all 2.4-2build2 [266 kB]
1203s Get:247 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-plogr all 0.2.0-3build2 [15.8 kB]
1203s Get:248 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-rsqlite ppc64el 2.3.9-1 [1572 kB]
1205s Get:249 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-survey ppc64el 4.4-2-2 [3458 kB]
1214s Preconfiguring packages ...
1214s Fetched 274 MB in 8min 22s (546 kB/s)
1214s Selecting previously unselected package libc-dev-bin.
1214s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 122006 files and directories currently installed.)
1214s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_ppc64el.deb ...
1214s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
1214s Selecting previously unselected package linux-libc-dev:ppc64el.
1214s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_ppc64el.deb ...
1214s Unpacking linux-libc-dev:ppc64el (6.19.0-3.3) ...
1214s Selecting previously unselected package libcrypt-dev:ppc64el.
1214s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_ppc64el.deb ...
1214s Unpacking libcrypt-dev:ppc64el (1:4.5.1-1) ...
1214s Selecting previously unselected package rpcsvc-proto.
1214s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_ppc64el.deb ...
1214s Unpacking rpcsvc-proto (1.4.3-1build1) ...
1214s Selecting previously unselected package libc6-dev:ppc64el.
1214s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_ppc64el.deb ...
1214s Unpacking libc6-dev:ppc64el (2.42-2ubuntu4) ...
1214s Selecting previously unselected package libisl23:ppc64el.
1214s Preparing to unpack .../005-libisl23_0.27-1build1_ppc64el.deb ...
1214s Unpacking libisl23:ppc64el (0.27-1build1) ...
1214s Selecting previously unselected package libmpc3:ppc64el.
1214s Preparing to unpack .../006-libmpc3_1.3.1-2_ppc64el.deb ...
1214s Unpacking libmpc3:ppc64el (1.3.1-2) ...
1214s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu.
1214s Preparing to unpack .../007-cpp-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package cpp-15.
1214s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package cpp-powerpc64le-linux-gnu.
1214s Preparing to unpack .../009-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ...
1214s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ...
1214s Selecting previously unselected package cpp.
1214s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ...
1214s Unpacking cpp (4:15.2.0-4ubuntu1) ...
1214s Selecting previously unselected package libcc1-0:ppc64el.
1214s Preparing to unpack .../011-libcc1-0_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking libcc1-0:ppc64el (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package libgomp1:ppc64el.
1214s Preparing to unpack .../012-libgomp1_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking libgomp1:ppc64el (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package libitm1:ppc64el.
1214s Preparing to unpack .../013-libitm1_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking libitm1:ppc64el (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package libasan8:ppc64el.
1214s Preparing to unpack .../014-libasan8_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking libasan8:ppc64el (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package liblsan0:ppc64el.
1214s Preparing to unpack .../015-liblsan0_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking liblsan0:ppc64el (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package libtsan2:ppc64el.
1214s Preparing to unpack .../016-libtsan2_15.2.0-12ubuntu1_ppc64el.deb ...
1214s Unpacking libtsan2:ppc64el (15.2.0-12ubuntu1) ...
1214s Selecting previously unselected package libubsan1:ppc64el.
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1214s Selecting previously unselected package libquadmath0:ppc64el.
1214s Preparing to unpack .../018-libquadmath0_15.2.0-12ubuntu1_ppc64el.deb ...
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1214s Selecting previously unselected package libgcc-15-dev:ppc64el.
1214s Preparing to unpack .../019-libgcc-15-dev_15.2.0-12ubuntu1_ppc64el.deb ...
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1214s Selecting previously unselected package gcc-15-powerpc64le-linux-gnu.
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1214s Unpacking gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ...
1215s Selecting previously unselected package gcc-15.
1215s Preparing to unpack .../021-gcc-15_15.2.0-12ubuntu1_ppc64el.deb ...
1215s Unpacking gcc-15 (15.2.0-12ubuntu1) ...
1215s Selecting previously unselected package gcc-powerpc64le-linux-gnu.
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1215s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ...
1215s Selecting previously unselected package gcc.
1215s Preparing to unpack .../023-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ...
1215s Unpacking gcc (4:15.2.0-4ubuntu1) ...
1215s Selecting previously unselected package libstdc++-15-dev:ppc64el.
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1215s Selecting previously unselected package g++-15-powerpc64le-linux-gnu.
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1215s Preparing to unpack .../026-g++-15_15.2.0-12ubuntu1_ppc64el.deb ...
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1215s Selecting previously unselected package g++-powerpc64le-linux-gnu.
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1215s Selecting previously unselected package g++.
1215s Preparing to unpack .../028-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ...
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1215s Selecting previously unselected package build-essential.
1215s Preparing to unpack .../029-build-essential_12.12ubuntu2_ppc64el.deb ...
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1215s Selecting previously unselected package dctrl-tools.
1215s Preparing to unpack .../030-dctrl-tools_2.24-3build4_ppc64el.deb ...
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1215s Selecting previously unselected package fonts-dejavu-mono.
1215s Preparing to unpack .../031-fonts-dejavu-mono_2.37-8build1_all.deb ...
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1215s Selecting previously unselected package fonts-dejavu-core.
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1215s Selecting previously unselected package fontconfig-config.
1215s Preparing to unpack .../033-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ...
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1216s Selecting previously unselected package fonts-glyphicons-halflings.
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1216s Selecting previously unselected package fonts-mathjax.
1216s Preparing to unpack .../037-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ...
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1216s Selecting previously unselected package libgfortran5:ppc64el.
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1216s Selecting previously unselected package libgfortran-15-dev:ppc64el.
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1216s Selecting previously unselected package gfortran-15-powerpc64le-linux-gnu.
1216s Preparing to unpack .../040-gfortran-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ...
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1216s Selecting previously unselected package gfortran-15.
1216s Preparing to unpack .../041-gfortran-15_15.2.0-12ubuntu1_ppc64el.deb ...
1216s Unpacking gfortran-15 (15.2.0-12ubuntu1) ...
1216s Selecting previously unselected package gfortran-powerpc64le-linux-gnu.
1216s Preparing to unpack .../042-gfortran-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ...
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1216s Selecting previously unselected package gfortran.
1216s Preparing to unpack .../043-gfortran_4%3a15.2.0-4ubuntu1_ppc64el.deb ...
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1216s Selecting previously unselected package icu-devtools.
1216s Preparing to unpack .../044-icu-devtools_78.2-1ubuntu1_ppc64el.deb ...
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1216s Selecting previously unselected package libblas3:ppc64el.
1216s Preparing to unpack .../045-libblas3_3.12.1-7ubuntu1_ppc64el.deb ...
1216s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ...
1216s Selecting previously unselected package libblas-dev:ppc64el.
1216s Preparing to unpack .../046-libblas-dev_3.12.1-7ubuntu1_ppc64el.deb ...
1216s Unpacking libblas-dev:ppc64el (3.12.1-7ubuntu1) ...
1216s Selecting previously unselected package libbz2-dev:ppc64el.
1216s Preparing to unpack .../047-libbz2-dev_1.0.8-6build2_ppc64el.deb ...
1216s Unpacking libbz2-dev:ppc64el (1.0.8-6build2) ...
1216s Selecting previously unselected package libpixman-1-0:ppc64el.
1216s Preparing to unpack .../048-libpixman-1-0_0.46.4-1_ppc64el.deb ...
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1216s Selecting previously unselected package libxcb-render0:ppc64el.
1216s Preparing to unpack .../049-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ...
1216s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ...
1216s Selecting previously unselected package libxcb-shm0:ppc64el.
1216s Preparing to unpack .../050-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ...
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1216s Selecting previously unselected package libxrender1:ppc64el.
1216s Preparing to unpack .../051-libxrender1_1%3a0.9.12-1_ppc64el.deb ...
1216s Unpacking libxrender1:ppc64el (1:0.9.12-1) ...
1216s Selecting previously unselected package libcairo2:ppc64el.
1216s Preparing to unpack .../052-libcairo2_1.18.4-3_ppc64el.deb ...
1216s Unpacking libcairo2:ppc64el (1.18.4-3) ...
1216s Selecting previously unselected package libdatrie1:ppc64el.
1216s Preparing to unpack .../053-libdatrie1_0.2.14-1_ppc64el.deb ...
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1216s Selecting previously unselected package libdeflate0:ppc64el.
1216s Preparing to unpack .../054-libdeflate0_1.23-2build1_ppc64el.deb ...
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1216s Selecting previously unselected package libdeflate-dev:ppc64el.
1216s Preparing to unpack .../055-libdeflate-dev_1.23-2build1_ppc64el.deb ...
1216s Unpacking libdeflate-dev:ppc64el (1.23-2build1) ...
1216s Selecting previously unselected package libgraphite2-3:ppc64el.
1216s Preparing to unpack .../056-libgraphite2-3_1.3.14-11ubuntu1_ppc64el.deb ...
1216s Unpacking libgraphite2-3:ppc64el (1.3.14-11ubuntu1) ...
1216s Selecting previously unselected package libharfbuzz0b:ppc64el.
1216s Preparing to unpack .../057-libharfbuzz0b_12.3.2-1_ppc64el.deb ...
1216s Unpacking libharfbuzz0b:ppc64el (12.3.2-1) ...
1216s Selecting previously unselected package x11-common.
1216s Preparing to unpack .../058-x11-common_1%3a7.7+24ubuntu1_all.deb ...
1216s Unpacking x11-common (1:7.7+24ubuntu1) ...
1216s Selecting previously unselected package libice6:ppc64el.
1216s Preparing to unpack .../059-libice6_2%3a1.1.1-1build1_ppc64el.deb ...
1216s Unpacking libice6:ppc64el (2:1.1.1-1build1) ...
1216s Selecting previously unselected package libicu-dev:ppc64el.
1216s Preparing to unpack .../060-libicu-dev_78.2-1ubuntu1_ppc64el.deb ...
1216s Unpacking libicu-dev:ppc64el (78.2-1ubuntu1) ...
1216s Selecting previously unselected package libjpeg-turbo8:ppc64el.
1216s Preparing to unpack .../061-libjpeg-turbo8_2.1.5-4ubuntu3_ppc64el.deb ...
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1217s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el.
1217s Preparing to unpack .../062-libjpeg-turbo8-dev_2.1.5-4ubuntu3_ppc64el.deb ...
1217s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ...
1217s Selecting previously unselected package libjpeg8:ppc64el.
1217s Preparing to unpack .../063-libjpeg8_8c-2ubuntu11_ppc64el.deb ...
1217s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ...
1217s Selecting previously unselected package libjpeg8-dev:ppc64el.
1217s Preparing to unpack .../064-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ...
1217s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ...
1217s Selecting previously unselected package libjpeg-dev:ppc64el.
1217s Preparing to unpack .../065-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ...
1217s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ...
1217s Selecting previously unselected package libjs-bootstrap.
1217s Preparing to unpack .../066-libjs-bootstrap_3.4.1+dfsg-6_all.deb ...
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1217s Selecting previously unselected package libjs-highlight.js.
1217s Preparing to unpack .../067-libjs-highlight.js_10.7.3+dfsg-2_all.deb ...
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1217s Selecting previously unselected package libjs-jquery.
1217s Preparing to unpack .../068-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ...
1217s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ...
1217s Selecting previously unselected package libjs-jquery-datatables.
1217s Preparing to unpack .../069-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ...
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1217s Selecting previously unselected package liblapack3:ppc64el.
1217s Preparing to unpack .../070-liblapack3_3.12.1-7ubuntu1_ppc64el.deb ...
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1217s Selecting previously unselected package liblapack-dev:ppc64el.
1217s Preparing to unpack .../071-liblapack-dev_3.12.1-7ubuntu1_ppc64el.deb ...
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1217s Selecting previously unselected package liblerc4:ppc64el.
1217s Preparing to unpack .../072-liblerc4_4.0.0+ds-5ubuntu2_ppc64el.deb ...
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1217s Selecting previously unselected package libncurses-dev:ppc64el.
1217s Preparing to unpack .../073-libncurses-dev_6.6+20251231-1_ppc64el.deb ...
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1217s Selecting previously unselected package libthai-data.
1217s Preparing to unpack .../074-libthai-data_0.1.30-1_all.deb ...
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1217s Selecting previously unselected package libthai0:ppc64el.
1217s Preparing to unpack .../075-libthai0_0.1.30-1_ppc64el.deb ...
1217s Unpacking libthai0:ppc64el (0.1.30-1) ...
1217s Selecting previously unselected package libpango-1.0-0:ppc64el.
1217s Preparing to unpack .../076-libpango-1.0-0_1.57.0-1_ppc64el.deb ...
1217s Unpacking libpango-1.0-0:ppc64el (1.57.0-1) ...
1217s Selecting previously unselected package libpangoft2-1.0-0:ppc64el.
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1217s Unpacking libpangoft2-1.0-0:ppc64el (1.57.0-1) ...
1217s Selecting previously unselected package libpangocairo-1.0-0:ppc64el.
1217s Preparing to unpack .../078-libpangocairo-1.0-0_1.57.0-1_ppc64el.deb ...
1217s Unpacking libpangocairo-1.0-0:ppc64el (1.57.0-1) ...
1217s Selecting previously unselected package libpaper2:ppc64el.
1217s Preparing to unpack .../079-libpaper2_2.2.5-0.3build1_ppc64el.deb ...
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1217s Selecting previously unselected package libpaper-utils.
1217s Preparing to unpack .../080-libpaper-utils_2.2.5-0.3build1_ppc64el.deb ...
1217s Unpacking libpaper-utils (2.2.5-0.3build1) ...
1217s Selecting previously unselected package libpcre2-16-0:ppc64el.
1217s Preparing to unpack .../081-libpcre2-16-0_10.46-1_ppc64el.deb ...
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1217s Selecting previously unselected package libpcre2-32-0:ppc64el.
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1217s Selecting previously unselected package libpcre2-posix3:ppc64el.
1217s Preparing to unpack .../083-libpcre2-posix3_10.46-1_ppc64el.deb ...
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1217s Selecting previously unselected package libpcre2-dev:ppc64el.
1217s Preparing to unpack .../084-libpcre2-dev_10.46-1_ppc64el.deb ...
1217s Unpacking libpcre2-dev:ppc64el (10.46-1) ...
1217s Selecting previously unselected package libpkgconf3:ppc64el.
1217s Preparing to unpack .../085-libpkgconf3_1.8.1-4build1_ppc64el.deb ...
1217s Unpacking libpkgconf3:ppc64el (1.8.1-4build1) ...
1217s Selecting previously unselected package zlib1g-dev:ppc64el.
1217s Preparing to unpack .../086-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_ppc64el.deb ...
1217s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ...
1217s Selecting previously unselected package libpng-dev:ppc64el.
1217s Preparing to unpack .../087-libpng-dev_1.6.54-1_ppc64el.deb ...
1217s Unpacking libpng-dev:ppc64el (1.6.54-1) ...
1217s Selecting previously unselected package libreadline-dev:ppc64el.
1217s Preparing to unpack .../088-libreadline-dev_8.3-3_ppc64el.deb ...
1217s Unpacking libreadline-dev:ppc64el (8.3-3) ...
1217s Selecting previously unselected package libsharpyuv0:ppc64el.
1217s Preparing to unpack .../089-libsharpyuv0_1.5.0-0.1build1_ppc64el.deb ...
1217s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1build1) ...
1217s Selecting previously unselected package libsm6:ppc64el.
1217s Preparing to unpack .../090-libsm6_2%3a1.2.6-1build1_ppc64el.deb ...
1217s Unpacking libsm6:ppc64el (2:1.2.6-1build1) ...
1217s Selecting previously unselected package libtcl8.6:ppc64el.
1217s Preparing to unpack .../091-libtcl8.6_8.6.17+dfsg-1build1_ppc64el.deb ...
1217s Unpacking libtcl8.6:ppc64el (8.6.17+dfsg-1build1) ...
1217s Selecting previously unselected package libjbig0:ppc64el.
1217s Preparing to unpack .../092-libjbig0_2.1-6.1ubuntu3_ppc64el.deb ...
1217s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu3) ...
1217s Selecting previously unselected package libwebp7:ppc64el.
1217s Preparing to unpack .../093-libwebp7_1.5.0-0.1build1_ppc64el.deb ...
1217s Unpacking libwebp7:ppc64el (1.5.0-0.1build1) ...
1217s Selecting previously unselected package libtiff6:ppc64el.
1217s Preparing to unpack .../094-libtiff6_4.7.0-3ubuntu3_ppc64el.deb ...
1217s Unpacking libtiff6:ppc64el (4.7.0-3ubuntu3) ...
1217s Selecting previously unselected package libxft2:ppc64el.
1217s Preparing to unpack .../095-libxft2_2.3.6-1build2_ppc64el.deb ...
1217s Unpacking libxft2:ppc64el (2.3.6-1build2) ...
1217s Selecting previously unselected package libxss1:ppc64el.
1217s Preparing to unpack .../096-libxss1_1%3a1.2.3-1build4_ppc64el.deb ...
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1217s Selecting previously unselected package libtk8.6:ppc64el.
1217s Preparing to unpack .../097-libtk8.6_8.6.17-1_ppc64el.deb ...
1217s Unpacking libtk8.6:ppc64el (8.6.17-1) ...
1218s Selecting previously unselected package libxt6t64:ppc64el.
1218s Preparing to unpack .../098-libxt6t64_1%3a1.2.1-1.3_ppc64el.deb ...
1218s Unpacking libxt6t64:ppc64el (1:1.2.1-1.3) ...
1218s Selecting previously unselected package libzstd-dev:ppc64el.
1218s Preparing to unpack .../099-libzstd-dev_1.5.7+dfsg-3_ppc64el.deb ...
1218s Unpacking libzstd-dev:ppc64el (1.5.7+dfsg-3) ...
1218s Selecting previously unselected package node-normalize.css.
1218s Preparing to unpack .../100-node-normalize.css_8.0.1-5.1_all.deb ...
1218s Unpacking node-normalize.css (8.0.1-5.1) ...
1218s Selecting previously unselected package zip.
1218s Preparing to unpack .../101-zip_3.0-15ubuntu3_ppc64el.deb ...
1218s Unpacking zip (3.0-15ubuntu3) ...
1218s Selecting previously unselected package unzip.
1218s Preparing to unpack .../102-unzip_6.0-29ubuntu1_ppc64el.deb ...
1218s Unpacking unzip (6.0-29ubuntu1) ...
1218s Selecting previously unselected package xdg-utils.
1218s Preparing to unpack .../103-xdg-utils_1.2.1-2ubuntu2_all.deb ...
1218s Unpacking xdg-utils (1.2.1-2ubuntu2) ...
1218s Selecting previously unselected package r-base-core.
1218s Preparing to unpack .../104-r-base-core_4.5.2-1ubuntu2_ppc64el.deb ...
1218s Unpacking r-base-core (4.5.2-1ubuntu2) ...
1218s Selecting previously unselected package liblzma-dev:ppc64el.
1218s Preparing to unpack .../105-liblzma-dev_5.8.2-2_ppc64el.deb ...
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1218s Selecting previously unselected package pkgconf-bin.
1218s Preparing to unpack .../106-pkgconf-bin_1.8.1-4build1_ppc64el.deb ...
1218s Unpacking pkgconf-bin (1.8.1-4build1) ...
1218s Selecting previously unselected package pkgconf:ppc64el.
1218s Preparing to unpack .../107-pkgconf_1.8.1-4build1_ppc64el.deb ...
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1218s Selecting previously unselected package libtirpc-dev:ppc64el.
1218s Preparing to unpack .../108-libtirpc-dev_1.3.6+ds-1_ppc64el.deb ...
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1218s Selecting previously unselected package r-base-dev.
1218s Preparing to unpack .../109-r-base-dev_4.5.2-1ubuntu2_all.deb ...
1218s Unpacking r-base-dev (4.5.2-1ubuntu2) ...
1218s Selecting previously unselected package pkg-r-autopkgtest.
1218s Preparing to unpack .../110-pkg-r-autopkgtest_20250812_all.deb ...
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1218s Selecting previously unselected package r-cran-abind.
1218s Preparing to unpack .../111-r-cran-abind_1.4-8-1build1_all.deb ...
1218s Unpacking r-cran-abind (1.4-8-1build1) ...
1218s Selecting previously unselected package r-cran-cardata.
1218s Preparing to unpack .../112-r-cran-cardata_3.0.6-1_all.deb ...
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1218s Selecting previously unselected package r-cran-formula.
1218s Preparing to unpack .../113-r-cran-formula_1.2-5-1_all.deb ...
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1218s Selecting previously unselected package r-cran-mass.
1218s Preparing to unpack .../114-r-cran-mass_7.3-65-1_ppc64el.deb ...
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1218s Selecting previously unselected package r-cran-lattice.
1218s Preparing to unpack .../115-r-cran-lattice_0.22-9-1_ppc64el.deb ...
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1218s Selecting previously unselected package r-cran-nlme.
1218s Preparing to unpack .../116-r-cran-nlme_3.1.168-1_ppc64el.deb ...
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1218s Selecting previously unselected package r-cran-matrix.
1218s Preparing to unpack .../117-r-cran-matrix_1.7-4-1_ppc64el.deb ...
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1218s Selecting previously unselected package r-cran-mgcv.
1218s Preparing to unpack .../118-r-cran-mgcv_1.9-4-1_ppc64el.deb ...
1218s Unpacking r-cran-mgcv (1.9-4-1) ...
1218s Selecting previously unselected package r-cran-nnet.
1218s Preparing to unpack .../119-r-cran-nnet_7.3-20-1_ppc64el.deb ...
1218s Unpacking r-cran-nnet (7.3-20-1) ...
1219s Selecting previously unselected package r-cran-boot.
1219s Preparing to unpack .../120-r-cran-boot_1.3-32-1_all.deb ...
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1219s Selecting previously unselected package r-cran-littler.
1219s Preparing to unpack .../121-r-cran-littler_0.3.22-1_ppc64el.deb ...
1219s Unpacking r-cran-littler (0.3.22-1) ...
1219s Selecting previously unselected package r-cran-pkgkitten.
1219s Preparing to unpack .../122-r-cran-pkgkitten_0.2.4-1_all.deb ...
1219s Unpacking r-cran-pkgkitten (0.2.4-1) ...
1219s Selecting previously unselected package r-cran-rcpp.
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1219s Selecting previously unselected package r-cran-minqa.
1219s Preparing to unpack .../124-r-cran-minqa_1.2.8-1_ppc64el.deb ...
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1219s Selecting previously unselected package libnlopt0:ppc64el.
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1219s Selecting previously unselected package r-cran-nloptr.
1219s Preparing to unpack .../126-r-cran-nloptr_2.2.1-2_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-rbibutils.
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1219s Selecting previously unselected package r-cran-rdpack.
1219s Preparing to unpack .../128-r-cran-rdpack_2.6.3-1_all.deb ...
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1219s Selecting previously unselected package r-cran-reformulas.
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1219s Selecting previously unselected package r-cran-rlang.
1219s Preparing to unpack .../130-r-cran-rlang_1.1.5-3_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-rcppeigen.
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1219s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ...
1219s Selecting previously unselected package r-cran-statmod.
1219s Preparing to unpack .../132-r-cran-statmod_1.5.0-1_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-lme4.
1219s Preparing to unpack .../133-r-cran-lme4_1.1-38-1_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-backports.
1219s Preparing to unpack .../134-r-cran-backports_1.5.0-2_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-cli.
1219s Preparing to unpack .../135-r-cran-cli_3.6.4-1_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-generics.
1219s Preparing to unpack .../136-r-cran-generics_0.1.4-1_all.deb ...
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1219s Selecting previously unselected package r-cran-glue.
1219s Preparing to unpack .../137-r-cran-glue_1.8.0-1_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-lifecycle.
1219s Preparing to unpack .../138-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ...
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1219s Selecting previously unselected package r-cran-magrittr.
1219s Preparing to unpack .../139-r-cran-magrittr_2.0.3-1_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-utf8.
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1219s Selecting previously unselected package r-cran-vctrs.
1219s Preparing to unpack .../141-r-cran-vctrs_0.6.5-1_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-pillar.
1219s Preparing to unpack .../142-r-cran-pillar_1.11.1+dfsg-1_all.deb ...
1219s Unpacking r-cran-pillar (1.11.1+dfsg-1) ...
1219s Selecting previously unselected package r-cran-r6.
1219s Preparing to unpack .../143-r-cran-r6_2.6.1-1_all.deb ...
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1219s Selecting previously unselected package r-cran-fansi.
1219s Preparing to unpack .../144-r-cran-fansi_1.0.6-2_ppc64el.deb ...
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1219s Selecting previously unselected package r-cran-pkgconfig.
1219s Preparing to unpack .../145-r-cran-pkgconfig_2.0.3-2build2_all.deb ...
1219s Unpacking r-cran-pkgconfig (2.0.3-2build2) ...
1219s Selecting previously unselected package r-cran-tibble.
1219s Preparing to unpack .../146-r-cran-tibble_3.2.1+dfsg-3_ppc64el.deb ...
1219s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
1219s Selecting previously unselected package r-cran-withr.
1219s Preparing to unpack .../147-r-cran-withr_3.0.2+dfsg-1_all.deb ...
1219s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
1219s Selecting previously unselected package r-cran-tidyselect.
1219s Preparing to unpack .../148-r-cran-tidyselect_1.2.1+dfsg-1_ppc64el.deb ...
1219s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
1219s Selecting previously unselected package r-cran-dplyr.
1219s Preparing to unpack .../149-r-cran-dplyr_1.1.4-4_ppc64el.deb ...
1219s Unpacking r-cran-dplyr (1.1.4-4) ...
1220s Selecting previously unselected package r-cran-purrr.
1220s Preparing to unpack .../150-r-cran-purrr_1.0.4-1_ppc64el.deb ...
1220s Unpacking r-cran-purrr (1.0.4-1) ...
1220s Selecting previously unselected package r-cran-stringi.
1220s Preparing to unpack .../151-r-cran-stringi_1.8.4-1build2_ppc64el.deb ...
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1220s Selecting previously unselected package r-cran-stringr.
1220s Preparing to unpack .../152-r-cran-stringr_1.5.1-1_all.deb ...
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1220s Selecting previously unselected package r-cran-cpp11.
1220s Preparing to unpack .../153-r-cran-cpp11_0.5.3-1_all.deb ...
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1220s Selecting previously unselected package r-cran-tidyr.
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1220s Selecting previously unselected package r-cran-broom.
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1220s Selecting previously unselected package r-cran-numderiv.
1220s Preparing to unpack .../156-r-cran-numderiv_2016.8-1.1-3build1_all.deb ...
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1220s Selecting previously unselected package r-cran-gtable.
1220s Preparing to unpack .../157-r-cran-gtable_0.3.6+dfsg-1_all.deb ...
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1220s Selecting previously unselected package r-cran-isoband.
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1220s Selecting previously unselected package r-cran-farver.
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1220s Selecting previously unselected package r-cran-labeling.
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1220s Selecting previously unselected package r-cran-rcolorbrewer.
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1220s Selecting previously unselected package r-cran-viridislite.
1220s Preparing to unpack .../162-r-cran-viridislite_0.4.3-1_all.deb ...
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1220s Selecting previously unselected package r-cran-scales.
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1220s Selecting previously unselected package r-cran-ggplot2.
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1220s Selecting previously unselected package r-cran-cowplot.
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1220s Selecting previously unselected package r-cran-deriv.
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1220s Selecting previously unselected package r-cran-colorspace.
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1220s Selecting previously unselected package r-cran-fracdiff.
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1220s Selecting previously unselected package r-cran-zoo.
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1220s Selecting previously unselected package r-cran-lmtest.
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1220s Selecting previously unselected package r-cran-timedate.
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1220s Selecting previously unselected package r-cran-quadprog.
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1220s Selecting previously unselected package r-cran-xts.
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1220s Selecting previously unselected package r-cran-curl.
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1220s Selecting previously unselected package r-cran-ttr.
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1220s Selecting previously unselected package r-cran-jsonlite.
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1220s Selecting previously unselected package r-cran-quantmod.
1220s Preparing to unpack .../177-r-cran-quantmod_0.4.28-1_all.deb ...
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1220s Selecting previously unselected package r-cran-tseries.
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1220s Selecting previously unselected package r-cran-urca.
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1220s Selecting previously unselected package r-cran-rcpparmadillo.
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1221s Selecting previously unselected package r-cran-forecast.
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1221s Unpacking r-cran-forecast (8.23.0-1) ...
1221s Selecting previously unselected package r-cran-modelr.
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1221s Selecting previously unselected package r-cran-microbenchmark.
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1221s Unpacking r-cran-microbenchmark (1.5.0-1) ...
1221s Selecting previously unselected package r-cran-doby.
1221s Preparing to unpack .../184-r-cran-doby_4.7.1-3_all.deb ...
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1221s Selecting previously unselected package r-cran-evaluate.
1221s Preparing to unpack .../185-r-cran-evaluate_1.0.5-1_all.deb ...
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1221s Selecting previously unselected package r-cran-xfun.
1221s Preparing to unpack .../186-r-cran-xfun_0.55+dfsg-1_ppc64el.deb ...
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1221s Selecting previously unselected package r-cran-highr.
1221s Preparing to unpack .../187-r-cran-highr_0.11+dfsg-1_all.deb ...
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1221s Selecting previously unselected package r-cran-yaml.
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1221s Selecting previously unselected package libjs-mathjax.
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1221s Selecting previously unselected package r-cran-knitr.
1221s Preparing to unpack .../190-r-cran-knitr_1.51+dfsg-1_all.deb ...
1221s Unpacking r-cran-knitr (1.51+dfsg-1) ...
1221s Selecting previously unselected package r-cran-pbkrtest.
1221s Preparing to unpack .../191-r-cran-pbkrtest_0.5.5-1_all.deb ...
1221s Unpacking r-cran-pbkrtest (0.5.5-1) ...
1221s Selecting previously unselected package r-cran-sparsem.
1221s Preparing to unpack .../192-r-cran-sparsem_1.84-2-1_ppc64el.deb ...
1221s Unpacking r-cran-sparsem (1.84-2-1) ...
1221s Selecting previously unselected package r-cran-matrixmodels.
1221s Preparing to unpack .../193-r-cran-matrixmodels_0.5-4-1_all.deb ...
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1221s Selecting previously unselected package r-cran-survival.
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1221s Unpacking r-cran-survival (3.8-6-1) ...
1221s Selecting previously unselected package r-cran-matrixstats.
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1221s Selecting previously unselected package r-cran-class.
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1221s Selecting previously unselected package r-cran-proxy.
1221s Preparing to unpack .../197-r-cran-proxy_0.4-27-1_ppc64el.deb ...
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1221s Selecting previously unselected package r-cran-e1071.
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1222s Selecting previously unselected package r-cran-codetools.
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1222s Selecting previously unselected package r-cran-iterators.
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1222s Selecting previously unselected package r-cran-foreach.
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1222s Selecting previously unselected package r-cran-data.table.
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1222s Selecting previously unselected package r-cran-modelmetrics.
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1222s Selecting previously unselected package r-cran-plyr.
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1222s Selecting previously unselected package r-cran-proc.
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1222s Selecting previously unselected package r-cran-tzdb.
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1222s Selecting previously unselected package r-cran-clock.
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1222s Selecting previously unselected package r-cran-gower.
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1222s Selecting previously unselected package r-cran-sparsevctrs.
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1222s Selecting previously unselected package r-cran-hardhat.
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1222s Selecting previously unselected package r-cran-rpart.
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1226s Setting up r-cran-pkgconfig (2.0.3-2build2) ...
1226s Setting up r-cran-utf8 (1.2.4-1) ...
1226s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
1226s Setting up r-cran-parallelly (1.42.0-1) ...
1226s Setting up r-cran-stringi (1.8.4-1build2) ...
1226s Setting up r-cran-cpp11 (0.5.3-1) ...
1226s Setting up r-cran-plyr (1.8.9-1) ...
1226s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
1226s Setting up r-cran-isoband (0.2.7-1) ...
1226s Setting up r-cran-diagram (1.6.5-2) ...
1226s Setting up r-cran-scales (1.4.0-1) ...
1226s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
1226s Setting up r-cran-zoo (1.8-15-1) ...
1226s Setting up r-cran-matrix (1.7-4-1) ...
1226s Setting up r-cran-kernsmooth (2.23-26-1build1) ...
1226s Setting up r-cran-knitr (1.51+dfsg-1) ...
1226s Setting up r-cran-mgcv (1.9-4-1) ...
1226s Setting up g++ (4:15.2.0-4ubuntu1) ...
1226s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
1226s Setting up r-cran-cachem (1.1.0-1) ...
1226s Setting up r-cran-lmtest (0.9.40-1build1) ...
1226s Setting up build-essential (12.12ubuntu2) ...
1226s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ...
1226s Setting up r-cran-tzdb (0.5.0-1) ...
1226s Setting up r-cran-globals (0.19.0-1) ...
1226s Setting up r-cran-vctrs (0.6.5-1) ...
1226s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ...
1226s Setting up r-cran-mitools (2.4-2build2) ...
1226s Setting up r-cran-pillar (1.11.1+dfsg-1) ...
1226s Setting up r-cran-minqa (1.2.8-1) ...
1226s Setting up r-base-dev (4.5.2-1ubuntu2) ...
1226s Setting up r-cran-stringr (1.5.1-1) ...
1226s Setting up r-cran-class (7.3-23-1) ...
1226s Setting up r-cran-modelmetrics (1.2.2.2-1build2) ...
1226s Setting up r-cran-matrixmodels (0.5-4-1) ...
1226s Setting up r-cran-sparsevctrs (0.2.0-2) ...
1226s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
1226s Setting up r-cran-clock (0.7.2-1) ...
1226s Setting up r-cran-sandwich (3.1-1-1build1) ...
1226s Setting up r-cran-proc (1.18.5-1) ...
1226s Setting up r-cran-survival (3.8-6-1) ...
1226s Setting up r-cran-xts (0.14.1-1) ...
1226s Setting up r-cran-survey (4.4-2-2) ...
1226s Setting up r-cran-rdpack (2.6.3-1) ...
1226s Setting up r-cran-future (1.34.0+dfsg-1) ...
1226s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
1226s Setting up r-cran-reshape2 (1.4.4-2build2) ...
1226s Setting up r-cran-future.apply (1.11.3+dfsg-1) ...
1226s Setting up r-cran-timechange (0.3.0-2) ...
1226s Setting up r-cran-memoise (2.0.1-1build1) ...
1226s Setting up r-cran-lava (1.8.2+dfsg-1) ...
1226s Setting up r-cran-purrr (1.0.4-1) ...
1226s Setting up r-cran-e1071 (1.7-17-1) ...
1226s Setting up r-cran-blob (1.3.0-1) ...
1226s Setting up pkg-r-autopkgtest (20250812) ...
1226s Setting up r-cran-hardhat (1.4.2+dfsg-1) ...
1226s Setting up r-cran-dplyr (1.1.4-4) ...
1226s Setting up r-cran-reformulas (0.4.4-1) ...
1226s Setting up r-cran-rsqlite (2.3.9-1) ...
1226s Setting up r-cran-ttr (0.24.4-1) ...
1226s Setting up r-cran-lubridate (1.9.4+dfsg-1) ...
1226s Setting up r-cran-prodlim (2024.06.25-1) ...
1226s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
1226s Setting up r-cran-rpart (4.1.24-1build1) ...
1226s Setting up r-cran-ipred (0.9-15-1) ...
1226s Setting up r-cran-lme4 (1.1-38-1) ...
1226s Setting up r-cran-tidyr (1.3.1-1) ...
1226s Setting up r-cran-recipes (1.1.0+dfsg-1) ...
1226s Setting up r-cran-quantmod (0.4.28-1) ...
1226s Setting up r-cran-cowplot (1.1.3+dfsg-1) ...
1226s Setting up r-cran-caret (7.0-1+dfsg-1) ...
1226s Setting up r-cran-tseries (0.10-59-3) ...
1226s Setting up r-cran-broom (1.0.12+dfsg-1) ...
1226s Setting up r-cran-conquer (1.3.3-1) ...
1226s Setting up r-cran-forecast (8.23.0-1) ...
1226s Setting up r-cran-quantreg (6.1-1) ...
1226s Setting up r-cran-modelr (0.1.11-1) ...
1226s Setting up r-cran-doby (4.7.1-3) ...
1226s Setting up r-cran-pbkrtest (0.5.5-1) ...
1226s Setting up r-cran-car (3.1-5-1) ...
1226s Setting up r-cran-aer (1.2-15-1) ...
1226s Processing triggers for libc-bin (2.42-2ubuntu4) ...
1226s Processing triggers for man-db (2.13.1-1build1) ...
1227s Processing triggers for install-info (7.2-5) ...
1229s autopkgtest [23:41:41]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
1229s autopkgtest [23:41:41]: test pkg-r-autopkgtest: [-----------------------
1229s Test: Try to load the R library survey
1229s 
1229s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
1229s Copyright (C) 2025 The R Foundation for Statistical Computing
1229s Platform: powerpc64le-unknown-linux-gnu
1229s 
1229s R is free software and comes with ABSOLUTELY NO WARRANTY.
1229s You are welcome to redistribute it under certain conditions.
1229s Type 'license()' or 'licence()' for distribution details.
1229s 
1229s R is a collaborative project with many contributors.
1229s Type 'contributors()' for more information and
1229s 'citation()' on how to cite R or R packages in publications.
1229s 
1229s Type 'demo()' for some demos, 'help()' for on-line help, or
1229s 'help.start()' for an HTML browser interface to help.
1229s Type 'q()' to quit R.
1229s 
1230s > library('survey')
1230s Loading required package: grid
1230s Loading required package: Matrix
1230s Loading required package: survival
1231s 
1231s Attaching package: ‘survey’
1231s 
1231s The following object is masked from ‘package:graphics’:
1231s 
1231s     dotchart
1231s 
1231s > 
1231s autopkgtest [23:41:43]: test pkg-r-autopkgtest: -----------------------]
1231s autopkgtest [23:41:43]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
1231s pkg-r-autopkgtest    PASS
1232s autopkgtest [23:41:44]: @@@@@@@@@@@@@@@@@@@@ summary
1232s run-unit-test        PASS
1232s pkg-r-autopkgtest    PASS