0s autopkgtest [12:39:32]: starting date and time: 2025-03-15 12:39:32+0000
  0s autopkgtest [12:39:32]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [12:39:32]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3o_rr8hz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-survey --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-11.secgroup --name adt-plucky-s390x-r-cran-survey-20250315-123932-juju-7f2275-prod-proposed-migration-environment-20-41dbf533-ed9c-4119-b4e9-28d6be547f5f --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
127s autopkgtest [12:41:39]: testbed dpkg architecture: s390x
127s autopkgtest [12:41:39]: testbed apt version: 2.9.33
127s autopkgtest [12:41:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup
127s autopkgtest [12:41:39]: testbed release detected to be: None
128s autopkgtest [12:41:40]: updating testbed package index (apt update)
128s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
129s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
129s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
129s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
129s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB]
129s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
129s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB]
129s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.7 kB]
130s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1852 B]
130s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
130s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [335 kB]
130s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB]
130s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B]
130s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B]
130s Fetched 1034 kB in 2s (579 kB/s)
131s Reading package lists...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
131s Calculating upgrade...
132s Calculating upgrade...
132s The following packages were automatically installed and are no longer required:
132s   libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
132s   linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
132s   linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
132s   linux-tools-6.11.0-8-generic
132s Use 'sudo apt autoremove' to remove them.
132s The following packages will be upgraded:
132s   python3-jinja2 strace
132s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
132s Need to get 609 kB of archives.
132s After this operation, 27.6 kB of additional disk space will be used.
132s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
133s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
133s Fetched 609 kB in 1s (603 kB/s)
133s (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 ... 81428 files and directories currently installed.)
133s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
133s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
133s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
133s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
133s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
133s Setting up strace (6.13+ds-1ubuntu1) ...
133s Processing triggers for man-db (2.13.0-1) ...
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s Solving dependencies...
134s The following packages will be REMOVED:
134s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
134s   linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
134s   linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
134s   linux-tools-6.11.0-8-generic*
134s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
134s After this operation, 167 MB disk space will be freed.
134s (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 ... 81428 files and directories currently installed.)
134s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
134s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
134s Removing libpython3.12t64:s390x (3.12.9-1) ...
134s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
134s Removing libnsl2:s390x (1.3.0-3build3) ...
134s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
135s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
135s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
136s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
136s Processing triggers for libc-bin (2.41-1ubuntu1) ...
136s (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 ... 56328 files and directories currently installed.)
136s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
136s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
136s autopkgtest [12:41:48]: upgrading testbed (apt dist-upgrade and autopurge)
136s Reading package lists...
136s Building dependency tree...
136s Reading state information...
136s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
136s Starting 2 pkgProblemResolver with broken count: 0
136s Done
137s Entering ResolveByKeep
137s 
137s Calculating upgrade...
137s The following packages will be upgraded:
137s   libc-bin libc-dev-bin libc6 libc6-dev locales
137s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
137s Need to get 9512 kB of archives.
137s After this operation, 8192 B of additional disk space will be used.
137s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
139s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
139s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
142s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
143s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
147s Preconfiguring packages ...
147s Fetched 9512 kB in 10s (954 kB/s)
147s (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 ... 56326 files and directories currently installed.)
147s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
147s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
147s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
147s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
147s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
147s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
147s Setting up libc6:s390x (2.41-1ubuntu2) ...
147s (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 ... 56326 files and directories currently installed.)
147s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
147s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
147s Setting up libc-bin (2.41-1ubuntu2) ...
148s (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 ... 56326 files and directories currently installed.)
148s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
148s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
148s Setting up locales (2.41-1ubuntu2) ...
148s Generating locales (this might take a while)...
149s   en_US.UTF-8... done
149s Generation complete.
149s Setting up libc-dev-bin (2.41-1ubuntu2) ...
149s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
149s Processing triggers for man-db (2.13.0-1) ...
150s Processing triggers for systemd (257.3-1ubuntu3) ...
150s Reading package lists...
151s Building dependency tree...
151s Reading state information...
151s Starting pkgProblemResolver with broken count: 0
151s Starting 2 pkgProblemResolver with broken count: 0
151s Done
151s Solving dependencies...
151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
151s autopkgtest [12:42:03]: rebooting testbed after setup commands that affected boot
171s autopkgtest [12:42:23]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025
173s autopkgtest [12:42:25]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey
177s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (dsc) [2340 B]
177s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (tar) [2341 kB]
177s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (diff) [4580 B]
177s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC
177s gpgv:                using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
177s gpgv:                issuer "plessy@debian.org"
177s gpgv: Can't check signature: No public key
177s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found
177s autopkgtest [12:42:29]: testing package r-cran-survey version 4.4-2-2
177s autopkgtest [12:42:29]: build not needed
181s autopkgtest [12:42:33]: test run-unit-test: preparing testbed
181s Reading package lists...
181s Building dependency tree...
181s Reading state information...
181s Starting pkgProblemResolver with broken count: 0
181s Starting 2 pkgProblemResolver with broken count: 0
181s Done
182s The following NEW packages will be installed:
182s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
182s   fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1
182s   libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3
182s   libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap
182s   libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
182s   liblapack3 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
182s   libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
182s   libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
182s   libxft2 libxrender1 libxss1 libxt6t64 littler node-normalize.css r-base-core
182s   r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 r-cran-blob
182s   r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata
182s   r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr
182s   r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer
182s   r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table
182s   r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby
182s   r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi
182s   r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign
182s   r-cran-formula r-cran-future r-cran-future.apply r-cran-generics
182s   r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable
182s   r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms
182s   r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr
182s   r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv
182s   r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr
182s   r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats
182s   r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools
182s   r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr
182s   r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly
182s   r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr
182s   r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress
182s   r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.cache
182s   r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6
182s   r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo
182s   r-cran-rcppeigen r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes
182s   r-cran-reformulas r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang
182s   r-cran-rpart r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape
182s   r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr
182s   r-cran-survey r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect
182s   r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs
182s   r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun
182s   r-cran-yaml r-cran-zip r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip
182s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded.
182s Need to get 171 MB of archives.
182s After this operation, 341 MB of additional disk space will be used.
182s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB]
182s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
183s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
184s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB]
184s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB]
184s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB]
184s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
184s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
187s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB]
187s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB]
187s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB]
187s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B]
187s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB]
187s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB]
188s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB]
188s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB]
188s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB]
188s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB]
188s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB]
189s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB]
189s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB]
189s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB]
189s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB]
189s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
189s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
190s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
190s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
190s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
191s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB]
194s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB]
194s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB]
194s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.1-1 [253 kB]
194s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.1-1 [50.3 kB]
194s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.1-1 [28.3 kB]
194s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB]
194s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB]
194s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB]
194s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB]
194s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB]
195s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB]
195s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB]
196s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB]
196s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB]
196s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B]
196s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB]
197s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB]
198s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB]
198s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB]
198s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
198s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB]
228s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-littler s390x 0.3.20-2 [95.0 kB]
228s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x littler all 0.3.20-2 [2554 B]
228s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x node-normalize.css all 8.0.1-5 [10.8 kB]
228s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-abind all 1.4-8-1 [66.9 kB]
228s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cardata all 3.0.5-1 [1819 kB]
230s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-formula all 1.2-5-1 [158 kB]
230s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB]
232s Get:58 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB]
233s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB]
235s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-3-1 [4449 kB]
240s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB]
243s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nnet s390x 7.3-20-1 [116 kB]
243s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-boot all 1.3-31-1 [635 kB]
244s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
244s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcpp s390x 1.0.14-1 [2003 kB]
246s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-minqa s390x 1.2.8-1 [139 kB]
246s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x libnlopt0 s390x 2.7.1-6ubuntu3 [227 kB]
246s Get:68 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nloptr s390x 2.1.1-1 [252 kB]
246s Get:69 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rbibutils s390x 2.3-1 [1041 kB]
247s Get:70 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rdpack all 2.6.2-1syncable1 [756 kB]
248s Get:71 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-reformulas all 0.4.0-1 [91.5 kB]
248s Get:72 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcppeigen s390x 0.3.4.0.2-1 [1429 kB]
250s Get:73 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-statmod s390x 1.5.0-1 [294 kB]
250s Get:74 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lme4 s390x 1.1-36-1 [4141 kB]
254s Get:75 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-backports s390x 1.5.0-2 [121 kB]
254s Get:76 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cli s390x 3.6.4-1 [1379 kB]
255s Get:77 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-generics all 0.1.3-1 [81.3 kB]
256s Get:78 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-glue s390x 1.8.0-1 [164 kB]
256s Get:79 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rlang s390x 1.1.5-1 [1713 kB]
257s Get:80 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
257s Get:81 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-magrittr s390x 2.0.3-1 [154 kB]
258s Get:82 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-utf8 s390x 1.2.4-1 [143 kB]
258s Get:83 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vctrs s390x 0.6.5-1 [1448 kB]
259s Get:84 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
260s Get:85 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r6 all 2.6.1-1 [101 kB]
260s Get:86 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fansi s390x 1.0.5-1 [615 kB]
260s Get:87 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
260s Get:88 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tibble s390x 3.2.1+dfsg-3 [420 kB]
261s Get:89 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-withr all 3.0.2+dfsg-1 [214 kB]
261s Get:90 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tidyselect s390x 1.2.1+dfsg-1 [222 kB]
261s Get:91 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-dplyr s390x 1.1.4-4 [1537 kB]
263s Get:92 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-purrr s390x 1.0.4-1 [553 kB]
264s Get:93 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-stringi s390x 1.8.4-1build1 [917 kB]
264s Get:94 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-stringr all 1.5.1-1 [290 kB]
265s Get:95 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cpp11 all 0.5.2-1 [233 kB]
265s Get:96 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tidyr s390x 1.3.1-1 [1157 kB]
266s Get:97 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-broom all 1.0.7+dfsg-1 [1802 kB]
268s Get:98 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-numderiv all 2016.8-1.1-3 [115 kB]
268s Get:99 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
268s Get:100 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-isoband s390x 0.2.7-1 [1481 kB]
270s Get:101 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-farver s390x 2.1.2-1 [1353 kB]
272s Get:102 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-labeling all 0.4.3-1 [62.1 kB]
272s Get:103 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-colorspace s390x 2.1-1+dfsg-1 [1567 kB]
274s Get:104 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-munsell all 0.5.1-1 [213 kB]
274s Get:105 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
274s Get:106 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-viridislite all 0.4.2-2 [1088 kB]
275s Get:107 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-scales all 1.3.0-1 [603 kB]
276s Get:108 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
280s Get:109 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cowplot all 1.1.3+dfsg-1 [614 kB]
281s Get:110 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-deriv all 4.1.6-1 [151 kB]
281s Get:111 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-modelr all 0.1.11-1 [195 kB]
281s Get:112 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-microbenchmark s390x 1.5.0-1 [67.2 kB]
281s Get:113 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-doby all 4.6.25-1 [4772 kB]
286s Get:114 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-evaluate all 1.0.3-1 [114 kB]
286s Get:115 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-xfun s390x 0.51+dfsg-1 [574 kB]
287s Get:116 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-highr all 0.11+dfsg-1 [38.5 kB]
287s Get:117 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-yaml s390x 2.3.10-1 [113 kB]
287s Get:118 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
294s Get:119 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-knitr all 1.49+dfsg-1 [859 kB]
294s Get:120 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pbkrtest all 0.5.3-1 [178 kB]
295s Get:121 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-sparsem s390x 1.84-2-1 [826 kB]
295s Get:122 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrixmodels all 0.5-3-1 [361 kB]
296s Get:123 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-survival s390x 3.8-3-1 [8250 kB]
305s Get:124 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrixstats s390x 1.5.0-1 [539 kB]
306s Get:125 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcpparmadillo s390x 14.2.3-1-1 [851 kB]
307s Get:126 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-class s390x 7.3-23-1 [92.0 kB]
307s Get:127 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-proxy s390x 0.4-27-1 [182 kB]
307s Get:128 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-e1071 s390x 1.7-16-1 [572 kB]
308s Get:129 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-codetools all 0.2-20-1 [90.5 kB]
308s Get:130 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-iterators all 1.0.14-1 [336 kB]
308s Get:131 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-foreach all 1.5.2-1 [124 kB]
308s Get:132 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-data.table s390x 1.17.0+dfsg-1 [2167 kB]
311s Get:133 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-modelmetrics s390x 1.2.2.2-1build1 [122 kB]
311s Get:134 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-plyr s390x 1.8.9-1 [835 kB]
312s Get:135 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-proc s390x 1.18.5-1 [968 kB]
313s Get:136 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tzdb s390x 0.4.0-2 [514 kB]
314s Get:137 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-clock s390x 0.7.2-1 [1881 kB]
316s Get:138 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gower s390x 1.0.2-1 [209 kB]
316s Get:139 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-hardhat all 1.4.0+dfsg-1 [565 kB]
316s Get:140 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rpart s390x 4.1.24-1 [672 kB]
317s Get:141 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-shape all 1.4.6.1-1 [749 kB]
319s Get:142 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-diagram all 1.6.5-2 [656 kB]
319s Get:143 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-kernsmooth s390x 2.23-26-1 [94.7 kB]
319s Get:144 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-digest s390x 0.6.37-1 [205 kB]
319s Get:145 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-globals all 0.16.3-1 [120 kB]
319s Get:146 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-listenv all 0.9.1+dfsg-1 [112 kB]
319s Get:147 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-parallelly s390x 1.42.0-1 [540 kB]
320s Get:148 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-future all 1.34.0+dfsg-1 [646 kB]
321s Get:149 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-future.apply all 1.11.3+dfsg-1 [175 kB]
321s Get:150 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-progressr all 0.15.1-1 [353 kB]
321s Get:151 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-squarem all 2021.1-1 [179 kB]
322s Get:152 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lava all 1.8.1+dfsg-1 [2191 kB]
324s Get:153 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-prodlim s390x 2024.06.25-1 [419 kB]
324s Get:154 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ipred s390x 0.9-15-1 [386 kB]
325s Get:155 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-timechange s390x 0.3.0-1 [185 kB]
325s Get:156 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lubridate s390x 1.9.4+dfsg-1 [1010 kB]
326s Get:157 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-timedate s390x 4041.110-1 [1209 kB]
327s Get:158 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-recipes all 1.1.0+dfsg-1 [2035 kB]
330s Get:159 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-reshape2 s390x 1.4.4-2build1 [111 kB]
330s Get:160 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-caret s390x 7.0-1+dfsg-1 [3461 kB]
334s Get:161 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-conquer s390x 1.3.3-1 [459 kB]
334s Get:162 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-quantreg s390x 6.00-1 [1457 kB]
336s Get:163 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-foreign s390x 0.8.88-1 [249 kB]
336s Get:164 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ellipsis s390x 0.3.2-2 [35.4 kB]
336s Get:165 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-forcats all 1.0.0-1 [369 kB]
336s Get:166 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-hms all 1.1.3-1 [96.5 kB]
336s Get:167 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-clipr all 0.8.0-1 [53.5 kB]
336s Get:168 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-crayon all 1.5.3-1 [165 kB]
336s Get:169 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-bit s390x 4.6.0+dfsg-1 [471 kB]
337s Get:170 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-bit64 s390x 4.6.0-1-1ubuntu2 [503 kB]
337s Get:171 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-prettyunits all 1.2.0-1 [162 kB]
338s Get:172 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-progress all 1.2.3-1 [91.9 kB]
338s Get:173 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vroom s390x 1.6.5-1 [865 kB]
338s Get:174 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-readr s390x 2.1.5-1 [778 kB]
339s Get:175 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-haven s390x 2.5.4-1 [355 kB]
340s Get:176 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-curl s390x 6.2.1+dfsg-1ubuntu1 [196 kB]
340s Get:177 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rematch all 2.0.0-1 [18.3 kB]
340s Get:178 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cellranger all 1.1.0-3 [102 kB]
340s Get:179 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-readxl s390x 1.4.4-1 [360 kB]
340s Get:180 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-writexl s390x 1.5.1-1 [158 kB]
341s Get:181 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.methodss3 all 1.8.2-1 [84.0 kB]
341s Get:182 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.oo all 1.27.0-1 [979 kB]
342s Get:183 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.utils all 2.13.0-1 [1423 kB]
343s Get:184 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-zip s390x 2.3.2-1 [151 kB]
343s Get:185 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-openxlsx s390x 4.2.8-1 [2045 kB]
345s Get:186 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rio all 1.2.3-1 [546 kB]
346s Get:187 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-car all 3.1-3-1 [1525 kB]
347s Get:188 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-zoo s390x 1.8-13-1 [998 kB]
348s Get:189 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lmtest s390x 0.9.40-1 [396 kB]
348s Get:190 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-sandwich all 3.1-1-1 [1483 kB]
350s Get:191 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-aer all 1.2-14-1 [2597 kB]
353s Get:192 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-blob all 1.2.4-1 [49.8 kB]
353s Get:193 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fastmap s390x 1.2.0-1 [72.4 kB]
353s Get:194 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cachem s390x 1.1.0-1 [74.0 kB]
353s Get:195 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-dbi all 1.2.3-1 [853 kB]
354s Get:196 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-hexbin s390x 1.28.5-1 [1583 kB]
355s Get:197 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-memoise all 2.0.1-1 [53.9 kB]
355s Get:198 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mitools all 2.4-2build1 [265 kB]
355s Get:199 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-plogr all 0.2.0-3build1 [15.1 kB]
355s Get:200 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.cache all 0.16.0-1 [113 kB]
355s Get:201 http://ftpmaster.internal/ubuntu plucky/main s390x tcl8.6 s390x 8.6.16+dfsg-1 [14.8 kB]
356s Get:202 http://ftpmaster.internal/ubuntu plucky/main s390x tcl s390x 8.6.14build1 [4124 B]
356s Get:203 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.rsp all 0.46.0+ds-1 [1412 kB]
357s Get:204 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rsqlite s390x 2.3.9-1 [1331 kB]
359s Get:205 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-survey s390x 4.4-2-2 [3459 kB]
363s Preconfiguring packages ...
363s Fetched 171 MB in 3min 1s (944 kB/s)
363s Selecting previously unselected package libfreetype6:s390x.
363s (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 ... 56326 files and directories currently installed.)
363s Preparing to unpack .../000-libfreetype6_2.13.3+dfsg-1_s390x.deb ...
363s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ...
363s Selecting previously unselected package fonts-dejavu-mono.
363s Preparing to unpack .../001-fonts-dejavu-mono_2.37-8_all.deb ...
363s Unpacking fonts-dejavu-mono (2.37-8) ...
363s Selecting previously unselected package fonts-dejavu-core.
363s Preparing to unpack .../002-fonts-dejavu-core_2.37-8_all.deb ...
363s Unpacking fonts-dejavu-core (2.37-8) ...
363s Selecting previously unselected package fontconfig-config.
363s Preparing to unpack .../003-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ...
363s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
363s Selecting previously unselected package libfontconfig1:s390x.
363s Preparing to unpack .../004-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ...
363s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ...
363s Selecting previously unselected package fontconfig.
363s Preparing to unpack .../005-fontconfig_2.15.0-2ubuntu1_s390x.deb ...
363s Unpacking fontconfig (2.15.0-2ubuntu1) ...
363s Selecting previously unselected package fonts-glyphicons-halflings.
363s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
363s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
363s Selecting previously unselected package fonts-mathjax.
363s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
363s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
364s Selecting previously unselected package libblas3:s390x.
364s Preparing to unpack .../008-libblas3_3.12.1-2_s390x.deb ...
364s Unpacking libblas3:s390x (3.12.1-2) ...
364s Selecting previously unselected package libpixman-1-0:s390x.
364s Preparing to unpack .../009-libpixman-1-0_0.44.0-3_s390x.deb ...
364s Unpacking libpixman-1-0:s390x (0.44.0-3) ...
364s Selecting previously unselected package libxcb-render0:s390x.
364s Preparing to unpack .../010-libxcb-render0_1.17.0-2_s390x.deb ...
364s Unpacking libxcb-render0:s390x (1.17.0-2) ...
364s Selecting previously unselected package libxcb-shm0:s390x.
364s Preparing to unpack .../011-libxcb-shm0_1.17.0-2_s390x.deb ...
364s Unpacking libxcb-shm0:s390x (1.17.0-2) ...
364s Selecting previously unselected package libxrender1:s390x.
364s Preparing to unpack .../012-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ...
364s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ...
364s Selecting previously unselected package libcairo2:s390x.
364s Preparing to unpack .../013-libcairo2_1.18.2-2_s390x.deb ...
364s Unpacking libcairo2:s390x (1.18.2-2) ...
364s Selecting previously unselected package libdatrie1:s390x.
364s Preparing to unpack .../014-libdatrie1_0.2.13-3build1_s390x.deb ...
364s Unpacking libdatrie1:s390x (0.2.13-3build1) ...
364s Selecting previously unselected package libdeflate0:s390x.
364s Preparing to unpack .../015-libdeflate0_1.23-1_s390x.deb ...
364s Unpacking libdeflate0:s390x (1.23-1) ...
364s Selecting previously unselected package libgfortran5:s390x.
364s Preparing to unpack .../016-libgfortran5_15-20250222-0ubuntu1_s390x.deb ...
364s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ...
364s Selecting previously unselected package libgomp1:s390x.
364s Preparing to unpack .../017-libgomp1_15-20250222-0ubuntu1_s390x.deb ...
364s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ...
364s Selecting previously unselected package libgraphite2-3:s390x.
364s Preparing to unpack .../018-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ...
364s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ...
364s Selecting previously unselected package libharfbuzz0b:s390x.
364s Preparing to unpack .../019-libharfbuzz0b_10.2.0-1_s390x.deb ...
364s Unpacking libharfbuzz0b:s390x (10.2.0-1) ...
364s Selecting previously unselected package x11-common.
364s Preparing to unpack .../020-x11-common_1%3a7.7+23ubuntu3_all.deb ...
364s Unpacking x11-common (1:7.7+23ubuntu3) ...
364s Selecting previously unselected package libice6:s390x.
364s Preparing to unpack .../021-libice6_2%3a1.1.1-1_s390x.deb ...
364s Unpacking libice6:s390x (2:1.1.1-1) ...
364s Selecting previously unselected package libjpeg-turbo8:s390x.
364s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ...
364s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ...
364s Selecting previously unselected package libjpeg8:s390x.
364s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_s390x.deb ...
364s Unpacking libjpeg8:s390x (8c-2ubuntu11) ...
364s Selecting previously unselected package libjs-bootstrap.
364s Preparing to unpack .../024-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
364s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
364s Selecting previously unselected package libjs-highlight.js.
364s Preparing to unpack .../025-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
364s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ...
364s Selecting previously unselected package libjs-jquery.
364s Preparing to unpack .../026-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
364s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
364s Selecting previously unselected package libjs-jquery-datatables.
364s Preparing to unpack .../027-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
364s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ...
364s Selecting previously unselected package liblapack3:s390x.
364s Preparing to unpack .../028-liblapack3_3.12.1-2_s390x.deb ...
364s Unpacking liblapack3:s390x (3.12.1-2) ...
364s Selecting previously unselected package libthai-data.
364s Preparing to unpack .../029-libthai-data_0.1.29-2build1_all.deb ...
364s Unpacking libthai-data (0.1.29-2build1) ...
364s Selecting previously unselected package libthai0:s390x.
364s Preparing to unpack .../030-libthai0_0.1.29-2build1_s390x.deb ...
364s Unpacking libthai0:s390x (0.1.29-2build1) ...
364s Selecting previously unselected package libpango-1.0-0:s390x.
364s Preparing to unpack .../031-libpango-1.0-0_1.56.1-1_s390x.deb ...
364s Unpacking libpango-1.0-0:s390x (1.56.1-1) ...
364s Selecting previously unselected package libpangoft2-1.0-0:s390x.
364s Preparing to unpack .../032-libpangoft2-1.0-0_1.56.1-1_s390x.deb ...
364s Unpacking libpangoft2-1.0-0:s390x (1.56.1-1) ...
364s Selecting previously unselected package libpangocairo-1.0-0:s390x.
364s Preparing to unpack .../033-libpangocairo-1.0-0_1.56.1-1_s390x.deb ...
364s Unpacking libpangocairo-1.0-0:s390x (1.56.1-1) ...
364s Selecting previously unselected package libpaper2:s390x.
364s Preparing to unpack .../034-libpaper2_2.2.5-0.3_s390x.deb ...
364s Unpacking libpaper2:s390x (2.2.5-0.3) ...
364s Selecting previously unselected package libpaper-utils.
364s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3_s390x.deb ...
364s Unpacking libpaper-utils (2.2.5-0.3) ...
364s Selecting previously unselected package libsharpyuv0:s390x.
364s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1_s390x.deb ...
364s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ...
364s Selecting previously unselected package libsm6:s390x.
364s Preparing to unpack .../037-libsm6_2%3a1.2.4-1_s390x.deb ...
364s Unpacking libsm6:s390x (2:1.2.4-1) ...
364s Selecting previously unselected package libtcl8.6:s390x.
364s Preparing to unpack .../038-libtcl8.6_8.6.16+dfsg-1_s390x.deb ...
364s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ...
364s Selecting previously unselected package libjbig0:s390x.
364s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu2_s390x.deb ...
364s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ...
364s Selecting previously unselected package libwebp7:s390x.
364s Preparing to unpack .../040-libwebp7_1.5.0-0.1_s390x.deb ...
364s Unpacking libwebp7:s390x (1.5.0-0.1) ...
364s Selecting previously unselected package libtiff6:s390x.
364s Preparing to unpack .../041-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ...
364s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ...
364s Selecting previously unselected package libxft2:s390x.
364s Preparing to unpack .../042-libxft2_2.3.6-1build1_s390x.deb ...
364s Unpacking libxft2:s390x (2.3.6-1build1) ...
364s Selecting previously unselected package libxss1:s390x.
364s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build3_s390x.deb ...
364s Unpacking libxss1:s390x (1:1.2.3-1build3) ...
364s Selecting previously unselected package libtk8.6:s390x.
364s Preparing to unpack .../044-libtk8.6_8.6.16-1_s390x.deb ...
364s Unpacking libtk8.6:s390x (8.6.16-1) ...
364s Selecting previously unselected package libxt6t64:s390x.
364s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ...
364s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ...
364s Selecting previously unselected package zip.
364s Preparing to unpack .../046-zip_3.0-14ubuntu2_s390x.deb ...
364s Unpacking zip (3.0-14ubuntu2) ...
364s Selecting previously unselected package unzip.
364s Preparing to unpack .../047-unzip_6.0-28ubuntu6_s390x.deb ...
364s Unpacking unzip (6.0-28ubuntu6) ...
364s Selecting previously unselected package xdg-utils.
364s Preparing to unpack .../048-xdg-utils_1.2.1-2ubuntu1_all.deb ...
364s Unpacking xdg-utils (1.2.1-2ubuntu1) ...
364s Selecting previously unselected package r-base-core.
364s Preparing to unpack .../049-r-base-core_4.4.3-1_s390x.deb ...
364s Unpacking r-base-core (4.4.3-1) ...
364s Selecting previously unselected package r-cran-littler.
364s Preparing to unpack .../050-r-cran-littler_0.3.20-2_s390x.deb ...
364s Unpacking r-cran-littler (0.3.20-2) ...
364s Selecting previously unselected package littler.
364s Preparing to unpack .../051-littler_0.3.20-2_all.deb ...
364s Unpacking littler (0.3.20-2) ...
364s Selecting previously unselected package node-normalize.css.
364s Preparing to unpack .../052-node-normalize.css_8.0.1-5_all.deb ...
364s Unpacking node-normalize.css (8.0.1-5) ...
364s Selecting previously unselected package r-cran-abind.
364s Preparing to unpack .../053-r-cran-abind_1.4-8-1_all.deb ...
364s Unpacking r-cran-abind (1.4-8-1) ...
364s Selecting previously unselected package r-cran-cardata.
364s Preparing to unpack .../054-r-cran-cardata_3.0.5-1_all.deb ...
364s Unpacking r-cran-cardata (3.0.5-1) ...
364s Selecting previously unselected package r-cran-formula.
364s Preparing to unpack .../055-r-cran-formula_1.2-5-1_all.deb ...
364s Unpacking r-cran-formula (1.2-5-1) ...
364s Selecting previously unselected package r-cran-mass.
364s Preparing to unpack .../056-r-cran-mass_7.3-64-1_s390x.deb ...
364s Unpacking r-cran-mass (7.3-64-1) ...
364s Selecting previously unselected package r-cran-lattice.
364s Preparing to unpack .../057-r-cran-lattice_0.22-6-1_s390x.deb ...
364s Unpacking r-cran-lattice (0.22-6-1) ...
364s Selecting previously unselected package r-cran-nlme.
364s Preparing to unpack .../058-r-cran-nlme_3.1.167-1_s390x.deb ...
364s Unpacking r-cran-nlme (3.1.167-1) ...
364s Selecting previously unselected package r-cran-matrix.
364s Preparing to unpack .../059-r-cran-matrix_1.7-3-1_s390x.deb ...
364s Unpacking r-cran-matrix (1.7-3-1) ...
364s Selecting previously unselected package r-cran-mgcv.
364s Preparing to unpack .../060-r-cran-mgcv_1.9-1-1_s390x.deb ...
364s Unpacking r-cran-mgcv (1.9-1-1) ...
365s Selecting previously unselected package r-cran-nnet.
365s Preparing to unpack .../061-r-cran-nnet_7.3-20-1_s390x.deb ...
365s Unpacking r-cran-nnet (7.3-20-1) ...
365s Selecting previously unselected package r-cran-boot.
365s Preparing to unpack .../062-r-cran-boot_1.3-31-1_all.deb ...
365s Unpacking r-cran-boot (1.3-31-1) ...
365s Selecting previously unselected package r-cran-pkgkitten.
365s Preparing to unpack .../063-r-cran-pkgkitten_0.2.4-1_all.deb ...
365s Unpacking r-cran-pkgkitten (0.2.4-1) ...
365s Selecting previously unselected package r-cran-rcpp.
365s Preparing to unpack .../064-r-cran-rcpp_1.0.14-1_s390x.deb ...
365s Unpacking r-cran-rcpp (1.0.14-1) ...
365s Selecting previously unselected package r-cran-minqa.
365s Preparing to unpack .../065-r-cran-minqa_1.2.8-1_s390x.deb ...
365s Unpacking r-cran-minqa (1.2.8-1) ...
365s Selecting previously unselected package libnlopt0:s390x.
365s Preparing to unpack .../066-libnlopt0_2.7.1-6ubuntu3_s390x.deb ...
365s Unpacking libnlopt0:s390x (2.7.1-6ubuntu3) ...
365s Selecting previously unselected package r-cran-nloptr.
365s Preparing to unpack .../067-r-cran-nloptr_2.1.1-1_s390x.deb ...
365s Unpacking r-cran-nloptr (2.1.1-1) ...
365s Selecting previously unselected package r-cran-rbibutils.
365s Preparing to unpack .../068-r-cran-rbibutils_2.3-1_s390x.deb ...
365s Unpacking r-cran-rbibutils (2.3-1) ...
365s Selecting previously unselected package r-cran-rdpack.
365s Preparing to unpack .../069-r-cran-rdpack_2.6.2-1syncable1_all.deb ...
365s Unpacking r-cran-rdpack (2.6.2-1syncable1) ...
365s Selecting previously unselected package r-cran-reformulas.
365s Preparing to unpack .../070-r-cran-reformulas_0.4.0-1_all.deb ...
365s Unpacking r-cran-reformulas (0.4.0-1) ...
365s Selecting previously unselected package r-cran-rcppeigen.
365s Preparing to unpack .../071-r-cran-rcppeigen_0.3.4.0.2-1_s390x.deb ...
365s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ...
365s Selecting previously unselected package r-cran-statmod.
365s Preparing to unpack .../072-r-cran-statmod_1.5.0-1_s390x.deb ...
365s Unpacking r-cran-statmod (1.5.0-1) ...
365s Selecting previously unselected package r-cran-lme4.
365s Preparing to unpack .../073-r-cran-lme4_1.1-36-1_s390x.deb ...
365s Unpacking r-cran-lme4 (1.1-36-1) ...
365s Selecting previously unselected package r-cran-backports.
365s Preparing to unpack .../074-r-cran-backports_1.5.0-2_s390x.deb ...
365s Unpacking r-cran-backports (1.5.0-2) ...
365s Selecting previously unselected package r-cran-cli.
365s Preparing to unpack .../075-r-cran-cli_3.6.4-1_s390x.deb ...
365s Unpacking r-cran-cli (3.6.4-1) ...
365s Selecting previously unselected package r-cran-generics.
365s Preparing to unpack .../076-r-cran-generics_0.1.3-1_all.deb ...
365s Unpacking r-cran-generics (0.1.3-1) ...
365s Selecting previously unselected package r-cran-glue.
365s Preparing to unpack .../077-r-cran-glue_1.8.0-1_s390x.deb ...
365s Unpacking r-cran-glue (1.8.0-1) ...
365s Selecting previously unselected package r-cran-rlang.
365s Preparing to unpack .../078-r-cran-rlang_1.1.5-1_s390x.deb ...
365s Unpacking r-cran-rlang (1.1.5-1) ...
365s Selecting previously unselected package r-cran-lifecycle.
365s Preparing to unpack .../079-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
365s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
365s Selecting previously unselected package r-cran-magrittr.
365s Preparing to unpack .../080-r-cran-magrittr_2.0.3-1_s390x.deb ...
365s Unpacking r-cran-magrittr (2.0.3-1) ...
365s Selecting previously unselected package r-cran-utf8.
365s Preparing to unpack .../081-r-cran-utf8_1.2.4-1_s390x.deb ...
365s Unpacking r-cran-utf8 (1.2.4-1) ...
365s Selecting previously unselected package r-cran-vctrs.
365s Preparing to unpack .../082-r-cran-vctrs_0.6.5-1_s390x.deb ...
365s Unpacking r-cran-vctrs (0.6.5-1) ...
365s Selecting previously unselected package r-cran-pillar.
365s Preparing to unpack .../083-r-cran-pillar_1.10.1+dfsg-1_all.deb ...
365s Unpacking r-cran-pillar (1.10.1+dfsg-1) ...
365s Selecting previously unselected package r-cran-r6.
365s Preparing to unpack .../084-r-cran-r6_2.6.1-1_all.deb ...
365s Unpacking r-cran-r6 (2.6.1-1) ...
365s Selecting previously unselected package r-cran-fansi.
365s Preparing to unpack .../085-r-cran-fansi_1.0.5-1_s390x.deb ...
365s Unpacking r-cran-fansi (1.0.5-1) ...
365s Selecting previously unselected package r-cran-pkgconfig.
365s Preparing to unpack .../086-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
365s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
365s Selecting previously unselected package r-cran-tibble.
365s Preparing to unpack .../087-r-cran-tibble_3.2.1+dfsg-3_s390x.deb ...
365s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
365s Selecting previously unselected package r-cran-withr.
365s Preparing to unpack .../088-r-cran-withr_3.0.2+dfsg-1_all.deb ...
365s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
365s Selecting previously unselected package r-cran-tidyselect.
365s Preparing to unpack .../089-r-cran-tidyselect_1.2.1+dfsg-1_s390x.deb ...
365s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
365s Selecting previously unselected package r-cran-dplyr.
365s Preparing to unpack .../090-r-cran-dplyr_1.1.4-4_s390x.deb ...
365s Unpacking r-cran-dplyr (1.1.4-4) ...
365s Selecting previously unselected package r-cran-purrr.
365s Preparing to unpack .../091-r-cran-purrr_1.0.4-1_s390x.deb ...
365s Unpacking r-cran-purrr (1.0.4-1) ...
365s Selecting previously unselected package r-cran-stringi.
365s Preparing to unpack .../092-r-cran-stringi_1.8.4-1build1_s390x.deb ...
365s Unpacking r-cran-stringi (1.8.4-1build1) ...
365s Selecting previously unselected package r-cran-stringr.
365s Preparing to unpack .../093-r-cran-stringr_1.5.1-1_all.deb ...
365s Unpacking r-cran-stringr (1.5.1-1) ...
365s Selecting previously unselected package r-cran-cpp11.
365s Preparing to unpack .../094-r-cran-cpp11_0.5.2-1_all.deb ...
365s Unpacking r-cran-cpp11 (0.5.2-1) ...
365s Selecting previously unselected package r-cran-tidyr.
365s Preparing to unpack .../095-r-cran-tidyr_1.3.1-1_s390x.deb ...
365s Unpacking r-cran-tidyr (1.3.1-1) ...
365s Selecting previously unselected package r-cran-broom.
365s Preparing to unpack .../096-r-cran-broom_1.0.7+dfsg-1_all.deb ...
365s Unpacking r-cran-broom (1.0.7+dfsg-1) ...
365s Selecting previously unselected package r-cran-numderiv.
365s Preparing to unpack .../097-r-cran-numderiv_2016.8-1.1-3_all.deb ...
365s Unpacking r-cran-numderiv (2016.8-1.1-3) ...
365s Selecting previously unselected package r-cran-gtable.
365s Preparing to unpack .../098-r-cran-gtable_0.3.6+dfsg-1_all.deb ...
365s Unpacking r-cran-gtable (0.3.6+dfsg-1) ...
365s Selecting previously unselected package r-cran-isoband.
365s Preparing to unpack .../099-r-cran-isoband_0.2.7-1_s390x.deb ...
365s Unpacking r-cran-isoband (0.2.7-1) ...
365s Selecting previously unselected package r-cran-farver.
365s Preparing to unpack .../100-r-cran-farver_2.1.2-1_s390x.deb ...
365s Unpacking r-cran-farver (2.1.2-1) ...
365s Selecting previously unselected package r-cran-labeling.
365s Preparing to unpack .../101-r-cran-labeling_0.4.3-1_all.deb ...
365s Unpacking r-cran-labeling (0.4.3-1) ...
365s Selecting previously unselected package r-cran-colorspace.
365s Preparing to unpack .../102-r-cran-colorspace_2.1-1+dfsg-1_s390x.deb ...
365s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ...
365s Selecting previously unselected package r-cran-munsell.
365s Preparing to unpack .../103-r-cran-munsell_0.5.1-1_all.deb ...
365s Unpacking r-cran-munsell (0.5.1-1) ...
365s Selecting previously unselected package r-cran-rcolorbrewer.
365s Preparing to unpack .../104-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
365s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
365s Selecting previously unselected package r-cran-viridislite.
365s Preparing to unpack .../105-r-cran-viridislite_0.4.2-2_all.deb ...
365s Unpacking r-cran-viridislite (0.4.2-2) ...
365s Selecting previously unselected package r-cran-scales.
365s Preparing to unpack .../106-r-cran-scales_1.3.0-1_all.deb ...
365s Unpacking r-cran-scales (1.3.0-1) ...
365s Selecting previously unselected package r-cran-ggplot2.
365s Preparing to unpack .../107-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
365s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
365s Selecting previously unselected package r-cran-cowplot.
365s Preparing to unpack .../108-r-cran-cowplot_1.1.3+dfsg-1_all.deb ...
365s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ...
365s Selecting previously unselected package r-cran-deriv.
365s Preparing to unpack .../109-r-cran-deriv_4.1.6-1_all.deb ...
365s Unpacking r-cran-deriv (4.1.6-1) ...
365s Selecting previously unselected package r-cran-modelr.
365s Preparing to unpack .../110-r-cran-modelr_0.1.11-1_all.deb ...
365s Unpacking r-cran-modelr (0.1.11-1) ...
366s Selecting previously unselected package r-cran-microbenchmark.
366s Preparing to unpack .../111-r-cran-microbenchmark_1.5.0-1_s390x.deb ...
366s Unpacking r-cran-microbenchmark (1.5.0-1) ...
366s Selecting previously unselected package r-cran-doby.
366s Preparing to unpack .../112-r-cran-doby_4.6.25-1_all.deb ...
366s Unpacking r-cran-doby (4.6.25-1) ...
366s Selecting previously unselected package r-cran-evaluate.
366s Preparing to unpack .../113-r-cran-evaluate_1.0.3-1_all.deb ...
366s Unpacking r-cran-evaluate (1.0.3-1) ...
366s Selecting previously unselected package r-cran-xfun.
366s Preparing to unpack .../114-r-cran-xfun_0.51+dfsg-1_s390x.deb ...
366s Unpacking r-cran-xfun (0.51+dfsg-1) ...
366s Selecting previously unselected package r-cran-highr.
366s Preparing to unpack .../115-r-cran-highr_0.11+dfsg-1_all.deb ...
366s Unpacking r-cran-highr (0.11+dfsg-1) ...
366s Selecting previously unselected package r-cran-yaml.
366s Preparing to unpack .../116-r-cran-yaml_2.3.10-1_s390x.deb ...
366s Unpacking r-cran-yaml (2.3.10-1) ...
366s Selecting previously unselected package libjs-mathjax.
366s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
366s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
366s Selecting previously unselected package r-cran-knitr.
366s Preparing to unpack .../118-r-cran-knitr_1.49+dfsg-1_all.deb ...
366s Unpacking r-cran-knitr (1.49+dfsg-1) ...
366s Selecting previously unselected package r-cran-pbkrtest.
366s Preparing to unpack .../119-r-cran-pbkrtest_0.5.3-1_all.deb ...
366s Unpacking r-cran-pbkrtest (0.5.3-1) ...
366s Selecting previously unselected package r-cran-sparsem.
366s Preparing to unpack .../120-r-cran-sparsem_1.84-2-1_s390x.deb ...
366s Unpacking r-cran-sparsem (1.84-2-1) ...
366s Selecting previously unselected package r-cran-matrixmodels.
366s Preparing to unpack .../121-r-cran-matrixmodels_0.5-3-1_all.deb ...
366s Unpacking r-cran-matrixmodels (0.5-3-1) ...
366s Selecting previously unselected package r-cran-survival.
366s Preparing to unpack .../122-r-cran-survival_3.8-3-1_s390x.deb ...
366s Unpacking r-cran-survival (3.8-3-1) ...
366s Selecting previously unselected package r-cran-matrixstats.
366s Preparing to unpack .../123-r-cran-matrixstats_1.5.0-1_s390x.deb ...
366s Unpacking r-cran-matrixstats (1.5.0-1) ...
366s Selecting previously unselected package r-cran-rcpparmadillo.
366s Preparing to unpack .../124-r-cran-rcpparmadillo_14.2.3-1-1_s390x.deb ...
366s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ...
366s Selecting previously unselected package r-cran-class.
366s Preparing to unpack .../125-r-cran-class_7.3-23-1_s390x.deb ...
366s Unpacking r-cran-class (7.3-23-1) ...
366s Selecting previously unselected package r-cran-proxy.
366s Preparing to unpack .../126-r-cran-proxy_0.4-27-1_s390x.deb ...
366s Unpacking r-cran-proxy (0.4-27-1) ...
366s Selecting previously unselected package r-cran-e1071.
366s Preparing to unpack .../127-r-cran-e1071_1.7-16-1_s390x.deb ...
366s Unpacking r-cran-e1071 (1.7-16-1) ...
366s Selecting previously unselected package r-cran-codetools.
366s Preparing to unpack .../128-r-cran-codetools_0.2-20-1_all.deb ...
366s Unpacking r-cran-codetools (0.2-20-1) ...
366s Selecting previously unselected package r-cran-iterators.
366s Preparing to unpack .../129-r-cran-iterators_1.0.14-1_all.deb ...
366s Unpacking r-cran-iterators (1.0.14-1) ...
366s Selecting previously unselected package r-cran-foreach.
366s Preparing to unpack .../130-r-cran-foreach_1.5.2-1_all.deb ...
366s Unpacking r-cran-foreach (1.5.2-1) ...
366s Selecting previously unselected package r-cran-data.table.
366s Preparing to unpack .../131-r-cran-data.table_1.17.0+dfsg-1_s390x.deb ...
366s Unpacking r-cran-data.table (1.17.0+dfsg-1) ...
366s Selecting previously unselected package r-cran-modelmetrics.
366s Preparing to unpack .../132-r-cran-modelmetrics_1.2.2.2-1build1_s390x.deb ...
366s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ...
366s Selecting previously unselected package r-cran-plyr.
366s Preparing to unpack .../133-r-cran-plyr_1.8.9-1_s390x.deb ...
366s Unpacking r-cran-plyr (1.8.9-1) ...
366s Selecting previously unselected package r-cran-proc.
366s Preparing to unpack .../134-r-cran-proc_1.18.5-1_s390x.deb ...
366s Unpacking r-cran-proc (1.18.5-1) ...
366s Selecting previously unselected package r-cran-tzdb.
366s Preparing to unpack .../135-r-cran-tzdb_0.4.0-2_s390x.deb ...
366s Unpacking r-cran-tzdb (0.4.0-2) ...
366s Selecting previously unselected package r-cran-clock.
366s Preparing to unpack .../136-r-cran-clock_0.7.2-1_s390x.deb ...
366s Unpacking r-cran-clock (0.7.2-1) ...
367s Selecting previously unselected package r-cran-gower.
367s Preparing to unpack .../137-r-cran-gower_1.0.2-1_s390x.deb ...
367s Unpacking r-cran-gower (1.0.2-1) ...
367s Selecting previously unselected package r-cran-hardhat.
367s Preparing to unpack .../138-r-cran-hardhat_1.4.0+dfsg-1_all.deb ...
367s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ...
367s Selecting previously unselected package r-cran-rpart.
367s Preparing to unpack .../139-r-cran-rpart_4.1.24-1_s390x.deb ...
367s Unpacking r-cran-rpart (4.1.24-1) ...
367s Selecting previously unselected package r-cran-shape.
367s Preparing to unpack .../140-r-cran-shape_1.4.6.1-1_all.deb ...
367s Unpacking r-cran-shape (1.4.6.1-1) ...
367s Selecting previously unselected package r-cran-diagram.
367s Preparing to unpack .../141-r-cran-diagram_1.6.5-2_all.deb ...
367s Unpacking r-cran-diagram (1.6.5-2) ...
367s Selecting previously unselected package r-cran-kernsmooth.
367s Preparing to unpack .../142-r-cran-kernsmooth_2.23-26-1_s390x.deb ...
367s Unpacking r-cran-kernsmooth (2.23-26-1) ...
367s Selecting previously unselected package r-cran-digest.
367s Preparing to unpack .../143-r-cran-digest_0.6.37-1_s390x.deb ...
367s Unpacking r-cran-digest (0.6.37-1) ...
367s Selecting previously unselected package r-cran-globals.
367s Preparing to unpack .../144-r-cran-globals_0.16.3-1_all.deb ...
367s Unpacking r-cran-globals (0.16.3-1) ...
367s Selecting previously unselected package r-cran-listenv.
367s Preparing to unpack .../145-r-cran-listenv_0.9.1+dfsg-1_all.deb ...
367s Unpacking r-cran-listenv (0.9.1+dfsg-1) ...
367s Selecting previously unselected package r-cran-parallelly.
367s Preparing to unpack .../146-r-cran-parallelly_1.42.0-1_s390x.deb ...
367s Unpacking r-cran-parallelly (1.42.0-1) ...
367s Selecting previously unselected package r-cran-future.
367s Preparing to unpack .../147-r-cran-future_1.34.0+dfsg-1_all.deb ...
367s Unpacking r-cran-future (1.34.0+dfsg-1) ...
367s Selecting previously unselected package r-cran-future.apply.
367s Preparing to unpack .../148-r-cran-future.apply_1.11.3+dfsg-1_all.deb ...
367s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ...
367s Selecting previously unselected package r-cran-progressr.
367s Preparing to unpack .../149-r-cran-progressr_0.15.1-1_all.deb ...
367s Unpacking r-cran-progressr (0.15.1-1) ...
367s Selecting previously unselected package r-cran-squarem.
367s Preparing to unpack .../150-r-cran-squarem_2021.1-1_all.deb ...
367s Unpacking r-cran-squarem (2021.1-1) ...
367s Selecting previously unselected package r-cran-lava.
367s Preparing to unpack .../151-r-cran-lava_1.8.1+dfsg-1_all.deb ...
367s Unpacking r-cran-lava (1.8.1+dfsg-1) ...
367s Selecting previously unselected package r-cran-prodlim.
367s Preparing to unpack .../152-r-cran-prodlim_2024.06.25-1_s390x.deb ...
367s Unpacking r-cran-prodlim (2024.06.25-1) ...
367s Selecting previously unselected package r-cran-ipred.
367s Preparing to unpack .../153-r-cran-ipred_0.9-15-1_s390x.deb ...
367s Unpacking r-cran-ipred (0.9-15-1) ...
367s Selecting previously unselected package r-cran-timechange.
367s Preparing to unpack .../154-r-cran-timechange_0.3.0-1_s390x.deb ...
367s Unpacking r-cran-timechange (0.3.0-1) ...
367s Selecting previously unselected package r-cran-lubridate.
367s Preparing to unpack .../155-r-cran-lubridate_1.9.4+dfsg-1_s390x.deb ...
367s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ...
367s Selecting previously unselected package r-cran-timedate.
367s Preparing to unpack .../156-r-cran-timedate_4041.110-1_s390x.deb ...
367s Unpacking r-cran-timedate (4041.110-1) ...
367s Selecting previously unselected package r-cran-recipes.
367s Preparing to unpack .../157-r-cran-recipes_1.1.0+dfsg-1_all.deb ...
367s Unpacking r-cran-recipes (1.1.0+dfsg-1) ...
367s Selecting previously unselected package r-cran-reshape2.
367s Preparing to unpack .../158-r-cran-reshape2_1.4.4-2build1_s390x.deb ...
367s Unpacking r-cran-reshape2 (1.4.4-2build1) ...
367s Selecting previously unselected package r-cran-caret.
367s Preparing to unpack .../159-r-cran-caret_7.0-1+dfsg-1_s390x.deb ...
367s Unpacking r-cran-caret (7.0-1+dfsg-1) ...
367s Selecting previously unselected package r-cran-conquer.
367s Preparing to unpack .../160-r-cran-conquer_1.3.3-1_s390x.deb ...
367s Unpacking r-cran-conquer (1.3.3-1) ...
367s Selecting previously unselected package r-cran-quantreg.
367s Preparing to unpack .../161-r-cran-quantreg_6.00-1_s390x.deb ...
367s Unpacking r-cran-quantreg (6.00-1) ...
367s Selecting previously unselected package r-cran-foreign.
367s Preparing to unpack .../162-r-cran-foreign_0.8.88-1_s390x.deb ...
367s Unpacking r-cran-foreign (0.8.88-1) ...
367s Selecting previously unselected package r-cran-ellipsis.
367s Preparing to unpack .../163-r-cran-ellipsis_0.3.2-2_s390x.deb ...
367s Unpacking r-cran-ellipsis (0.3.2-2) ...
367s Selecting previously unselected package r-cran-forcats.
367s Preparing to unpack .../164-r-cran-forcats_1.0.0-1_all.deb ...
367s Unpacking r-cran-forcats (1.0.0-1) ...
367s Selecting previously unselected package r-cran-hms.
367s Preparing to unpack .../165-r-cran-hms_1.1.3-1_all.deb ...
367s Unpacking r-cran-hms (1.1.3-1) ...
367s Selecting previously unselected package r-cran-clipr.
367s Preparing to unpack .../166-r-cran-clipr_0.8.0-1_all.deb ...
367s Unpacking r-cran-clipr (0.8.0-1) ...
367s Selecting previously unselected package r-cran-crayon.
367s Preparing to unpack .../167-r-cran-crayon_1.5.3-1_all.deb ...
367s Unpacking r-cran-crayon (1.5.3-1) ...
367s Selecting previously unselected package r-cran-bit.
367s Preparing to unpack .../168-r-cran-bit_4.6.0+dfsg-1_s390x.deb ...
367s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
367s Selecting previously unselected package r-cran-bit64.
367s Preparing to unpack .../169-r-cran-bit64_4.6.0-1-1ubuntu2_s390x.deb ...
367s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ...
367s Selecting previously unselected package r-cran-prettyunits.
367s Preparing to unpack .../170-r-cran-prettyunits_1.2.0-1_all.deb ...
367s Unpacking r-cran-prettyunits (1.2.0-1) ...
367s Selecting previously unselected package r-cran-progress.
367s Preparing to unpack .../171-r-cran-progress_1.2.3-1_all.deb ...
367s Unpacking r-cran-progress (1.2.3-1) ...
367s Selecting previously unselected package r-cran-vroom.
367s Preparing to unpack .../172-r-cran-vroom_1.6.5-1_s390x.deb ...
367s Unpacking r-cran-vroom (1.6.5-1) ...
367s Selecting previously unselected package r-cran-readr.
367s Preparing to unpack .../173-r-cran-readr_2.1.5-1_s390x.deb ...
367s Unpacking r-cran-readr (2.1.5-1) ...
367s Selecting previously unselected package r-cran-haven.
367s Preparing to unpack .../174-r-cran-haven_2.5.4-1_s390x.deb ...
367s Unpacking r-cran-haven (2.5.4-1) ...
367s Selecting previously unselected package r-cran-curl.
367s Preparing to unpack .../175-r-cran-curl_6.2.1+dfsg-1ubuntu1_s390x.deb ...
367s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
367s Selecting previously unselected package r-cran-rematch.
367s Preparing to unpack .../176-r-cran-rematch_2.0.0-1_all.deb ...
367s Unpacking r-cran-rematch (2.0.0-1) ...
367s Selecting previously unselected package r-cran-cellranger.
367s Preparing to unpack .../177-r-cran-cellranger_1.1.0-3_all.deb ...
367s Unpacking r-cran-cellranger (1.1.0-3) ...
367s Selecting previously unselected package r-cran-readxl.
367s Preparing to unpack .../178-r-cran-readxl_1.4.4-1_s390x.deb ...
367s Unpacking r-cran-readxl (1.4.4-1) ...
367s Selecting previously unselected package r-cran-writexl.
367s Preparing to unpack .../179-r-cran-writexl_1.5.1-1_s390x.deb ...
367s Unpacking r-cran-writexl (1.5.1-1) ...
367s Selecting previously unselected package r-cran-r.methodss3.
367s Preparing to unpack .../180-r-cran-r.methodss3_1.8.2-1_all.deb ...
367s Unpacking r-cran-r.methodss3 (1.8.2-1) ...
367s Selecting previously unselected package r-cran-r.oo.
367s Preparing to unpack .../181-r-cran-r.oo_1.27.0-1_all.deb ...
367s Unpacking r-cran-r.oo (1.27.0-1) ...
367s Selecting previously unselected package r-cran-r.utils.
367s Preparing to unpack .../182-r-cran-r.utils_2.13.0-1_all.deb ...
367s Unpacking r-cran-r.utils (2.13.0-1) ...
367s Selecting previously unselected package r-cran-zip.
367s Preparing to unpack .../183-r-cran-zip_2.3.2-1_s390x.deb ...
367s Unpacking r-cran-zip (2.3.2-1) ...
367s Selecting previously unselected package r-cran-openxlsx.
367s Preparing to unpack .../184-r-cran-openxlsx_4.2.8-1_s390x.deb ...
367s Unpacking r-cran-openxlsx (4.2.8-1) ...
367s Selecting previously unselected package r-cran-rio.
367s Preparing to unpack .../185-r-cran-rio_1.2.3-1_all.deb ...
367s Unpacking r-cran-rio (1.2.3-1) ...
367s Selecting previously unselected package r-cran-car.
367s Preparing to unpack .../186-r-cran-car_3.1-3-1_all.deb ...
367s Unpacking r-cran-car (3.1-3-1) ...
367s Selecting previously unselected package r-cran-zoo.
367s Preparing to unpack .../187-r-cran-zoo_1.8-13-1_s390x.deb ...
367s Unpacking r-cran-zoo (1.8-13-1) ...
367s Selecting previously unselected package r-cran-lmtest.
367s Preparing to unpack .../188-r-cran-lmtest_0.9.40-1_s390x.deb ...
367s Unpacking r-cran-lmtest (0.9.40-1) ...
367s Selecting previously unselected package r-cran-sandwich.
367s Preparing to unpack .../189-r-cran-sandwich_3.1-1-1_all.deb ...
367s Unpacking r-cran-sandwich (3.1-1-1) ...
367s Selecting previously unselected package r-cran-aer.
367s Preparing to unpack .../190-r-cran-aer_1.2-14-1_all.deb ...
367s Unpacking r-cran-aer (1.2-14-1) ...
367s Selecting previously unselected package r-cran-blob.
367s Preparing to unpack .../191-r-cran-blob_1.2.4-1_all.deb ...
367s Unpacking r-cran-blob (1.2.4-1) ...
368s Selecting previously unselected package r-cran-fastmap.
368s Preparing to unpack .../192-r-cran-fastmap_1.2.0-1_s390x.deb ...
368s Unpacking r-cran-fastmap (1.2.0-1) ...
368s Selecting previously unselected package r-cran-cachem.
368s Preparing to unpack .../193-r-cran-cachem_1.1.0-1_s390x.deb ...
368s Unpacking r-cran-cachem (1.1.0-1) ...
368s Selecting previously unselected package r-cran-dbi.
368s Preparing to unpack .../194-r-cran-dbi_1.2.3-1_all.deb ...
368s Unpacking r-cran-dbi (1.2.3-1) ...
368s Selecting previously unselected package r-cran-hexbin.
368s Preparing to unpack .../195-r-cran-hexbin_1.28.5-1_s390x.deb ...
368s Unpacking r-cran-hexbin (1.28.5-1) ...
368s Selecting previously unselected package r-cran-memoise.
368s Preparing to unpack .../196-r-cran-memoise_2.0.1-1_all.deb ...
368s Unpacking r-cran-memoise (2.0.1-1) ...
368s Selecting previously unselected package r-cran-mitools.
368s Preparing to unpack .../197-r-cran-mitools_2.4-2build1_all.deb ...
368s Unpacking r-cran-mitools (2.4-2build1) ...
368s Selecting previously unselected package r-cran-plogr.
368s Preparing to unpack .../198-r-cran-plogr_0.2.0-3build1_all.deb ...
368s Unpacking r-cran-plogr (0.2.0-3build1) ...
368s Selecting previously unselected package r-cran-r.cache.
368s Preparing to unpack .../199-r-cran-r.cache_0.16.0-1_all.deb ...
368s Unpacking r-cran-r.cache (0.16.0-1) ...
368s Selecting previously unselected package tcl8.6.
368s Preparing to unpack .../200-tcl8.6_8.6.16+dfsg-1_s390x.deb ...
368s Unpacking tcl8.6 (8.6.16+dfsg-1) ...
368s Selecting previously unselected package tcl.
368s Preparing to unpack .../201-tcl_8.6.14build1_s390x.deb ...
368s Unpacking tcl (8.6.14build1) ...
368s Selecting previously unselected package r-cran-r.rsp.
368s Preparing to unpack .../202-r-cran-r.rsp_0.46.0+ds-1_all.deb ...
368s Unpacking r-cran-r.rsp (0.46.0+ds-1) ...
368s Selecting previously unselected package r-cran-rsqlite.
368s Preparing to unpack .../203-r-cran-rsqlite_2.3.9-1_s390x.deb ...
368s Unpacking r-cran-rsqlite (2.3.9-1) ...
368s Selecting previously unselected package r-cran-survey.
368s Preparing to unpack .../204-r-cran-survey_4.4-2-2_s390x.deb ...
368s Unpacking r-cran-survey (4.4-2-2) ...
368s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ...
368s Setting up libpixman-1-0:s390x (0.44.0-3) ...
368s Setting up libsharpyuv0:s390x (1.5.0-0.1) ...
368s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
368s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
368s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ...
368s Setting up libdatrie1:s390x (0.2.13-3build1) ...
368s Setting up libxcb-render0:s390x (1.17.0-2) ...
368s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
368s Setting up unzip (6.0-28ubuntu6) ...
368s Setting up x11-common (1:7.7+23ubuntu3) ...
368s Setting up libdeflate0:s390x (1.23-1) ...
368s Setting up libnlopt0:s390x (2.7.1-6ubuntu3) ...
368s Setting up libxcb-shm0:s390x (1.17.0-2) ...
368s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ...
368s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ...
368s Setting up zip (3.0-14ubuntu2) ...
368s Setting up libblas3:s390x (3.12.1-2) ...
368s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
368s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ...
368s Setting up fonts-dejavu-mono (2.37-8) ...
368s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ...
368s Setting up fonts-dejavu-core (2.37-8) ...
368s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ...
368s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ...
368s Setting up libwebp7:s390x (1.5.0-0.1) ...
368s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
368s Setting up libharfbuzz0b:s390x (10.2.0-1) ...
368s Setting up libthai-data (0.1.29-2build1) ...
368s Setting up libxss1:s390x (1:1.2.3-1build3) ...
368s Setting up libpaper2:s390x (2.2.5-0.3) ...
368s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
368s Setting up node-normalize.css (8.0.1-5) ...
368s Setting up xdg-utils (1.2.1-2ubuntu1) ...
368s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
368s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
368s Setting up libjpeg8:s390x (8c-2ubuntu11) ...
368s Setting up libice6:s390x (2:1.1.1-1) ...
368s Setting up tcl8.6 (8.6.16+dfsg-1) ...
368s Setting up liblapack3:s390x (3.12.1-2) ...
368s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
368s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
368s Setting up libpaper-utils (2.2.5-0.3) ...
368s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
368s Setting up libthai0:s390x (0.1.29-2build1) ...
368s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ...
368s Setting up tcl (8.6.14build1) ...
368s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ...
368s Setting up libsm6:s390x (2:1.2.4-1) ...
368s Setting up fontconfig (2.15.0-2ubuntu1) ...
370s Regenerating fonts cache... done.
370s Setting up libxft2:s390x (2.3.6-1build1) ...
370s Setting up libtk8.6:s390x (8.6.16-1) ...
370s Setting up libpango-1.0-0:s390x (1.56.1-1) ...
370s Setting up libcairo2:s390x (1.18.2-2) ...
370s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ...
370s Setting up libpangoft2-1.0-0:s390x (1.56.1-1) ...
370s Setting up libpangocairo-1.0-0:s390x (1.56.1-1) ...
370s Setting up r-base-core (4.4.3-1) ...
370s Creating config file /etc/R/Renviron with new version
371s Setting up r-cran-crayon (1.5.3-1) ...
371s Setting up r-cran-squarem (2021.1-1) ...
371s Setting up r-cran-labeling (0.4.3-1) ...
371s Setting up r-cran-lattice (0.22-6-1) ...
371s Setting up r-cran-nlme (3.1.167-1) ...
371s Setting up r-cran-farver (2.1.2-1) ...
371s Setting up r-cran-formula (1.2-5-1) ...
371s Setting up r-cran-hexbin (1.28.5-1) ...
371s Setting up r-cran-zip (2.3.2-1) ...
371s Setting up r-cran-viridislite (0.4.2-2) ...
371s Setting up r-cran-sparsem (1.84-2-1) ...
371s Setting up r-cran-statmod (1.5.0-1) ...
371s Setting up r-cran-nnet (7.3-20-1) ...
371s Setting up r-cran-clipr (0.8.0-1) ...
371s Setting up r-cran-proxy (0.4-27-1) ...
371s Setting up r-cran-r6 (2.6.1-1) ...
371s Setting up r-cran-pkgkitten (0.2.4-1) ...
371s Setting up r-cran-numderiv (2016.8-1.1-3) ...
371s Setting up r-cran-magrittr (2.0.3-1) ...
371s Setting up r-cran-microbenchmark (1.5.0-1) ...
371s Setting up r-cran-littler (0.3.20-2) ...
371s Setting up r-cran-rcpp (1.0.14-1) ...
371s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
371s Setting up r-cran-codetools (0.2-20-1) ...
371s Setting up r-cran-nloptr (2.1.1-1) ...
371s Setting up r-cran-boot (1.3-31-1) ...
371s Setting up r-cran-rematch (2.0.0-1) ...
371s Setting up r-cran-rlang (1.1.5-1) ...
371s Setting up r-cran-matrixstats (1.5.0-1) ...
371s Setting up r-cran-listenv (0.9.1+dfsg-1) ...
371s Setting up littler (0.3.20-2) ...
371s Setting up r-cran-xfun (0.51+dfsg-1) ...
371s Setting up r-cran-plogr (0.2.0-3build1) ...
371s Setting up r-cran-withr (3.0.2+dfsg-1) ...
371s Setting up r-cran-backports (1.5.0-2) ...
371s Setting up r-cran-deriv (4.1.6-1) ...
371s Setting up r-cran-generics (0.1.3-1) ...
371s Setting up r-cran-iterators (1.0.14-1) ...
371s Setting up r-cran-abind (1.4-8-1) ...
371s Setting up r-cran-digest (0.6.37-1) ...
371s Setting up r-cran-yaml (2.3.10-1) ...
371s Setting up r-cran-gower (1.0.2-1) ...
371s Setting up r-cran-evaluate (1.0.3-1) ...
371s Setting up r-cran-dbi (1.2.3-1) ...
371s Setting up r-cran-timedate (4041.110-1) ...
371s Setting up r-cran-highr (0.11+dfsg-1) ...
371s Setting up r-cran-foreach (1.5.2-1) ...
371s Setting up r-cran-prettyunits (1.2.0-1) ...
371s Setting up r-cran-fansi (1.0.5-1) ...
371s Setting up r-cran-cardata (3.0.5-1) ...
371s Setting up r-cran-mass (7.3-64-1) ...
371s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
371s Setting up r-cran-glue (1.8.0-1) ...
371s Setting up r-cran-foreign (0.8.88-1) ...
371s Setting up r-cran-writexl (1.5.1-1) ...
371s Setting up r-cran-bit (4.6.0+dfsg-1) ...
371s Setting up r-cran-cli (3.6.4-1) ...
371s Setting up r-cran-rbibutils (2.3-1) ...
371s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
371s Setting up r-cran-bit64 (4.6.0-1-1ubuntu2) ...
371s Setting up r-cran-progressr (0.15.1-1) ...
371s Setting up r-cran-shape (1.4.6.1-1) ...
371s Setting up r-cran-fastmap (1.2.0-1) ...
371s Setting up r-cran-r.methodss3 (1.8.2-1) ...
371s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
371s Setting up r-cran-utf8 (1.2.4-1) ...
371s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
371s Setting up r-cran-parallelly (1.42.0-1) ...
371s Setting up r-cran-stringi (1.8.4-1build1) ...
371s Setting up r-cran-cpp11 (0.5.2-1) ...
371s Setting up r-cran-plyr (1.8.9-1) ...
371s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
371s Setting up r-cran-isoband (0.2.7-1) ...
371s Setting up r-cran-diagram (1.6.5-2) ...
371s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
371s Setting up r-cran-zoo (1.8-13-1) ...
371s Setting up r-cran-matrix (1.7-3-1) ...
371s Setting up r-cran-kernsmooth (2.23-26-1) ...
371s Setting up r-cran-knitr (1.49+dfsg-1) ...
371s Setting up r-cran-mgcv (1.9-1-1) ...
371s Setting up r-cran-cachem (1.1.0-1) ...
371s Setting up r-cran-lmtest (0.9.40-1) ...
371s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ...
371s Setting up r-cran-tzdb (0.4.0-2) ...
371s Setting up r-cran-globals (0.16.3-1) ...
371s Setting up r-cran-vctrs (0.6.5-1) ...
371s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ...
371s Setting up r-cran-mitools (2.4-2build1) ...
371s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
371s Setting up r-cran-ellipsis (0.3.2-2) ...
371s Setting up r-cran-minqa (1.2.8-1) ...
371s Setting up r-cran-stringr (1.5.1-1) ...
371s Setting up r-cran-class (7.3-23-1) ...
371s Setting up r-cran-modelmetrics (1.2.2.2-1build1) ...
371s Setting up r-cran-openxlsx (4.2.8-1) ...
371s Setting up r-cran-matrixmodels (0.5-3-1) ...
371s Setting up r-cran-munsell (0.5.1-1) ...
371s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
371s Setting up r-cran-clock (0.7.2-1) ...
371s Setting up r-cran-sandwich (3.1-1-1) ...
371s Setting up r-cran-proc (1.18.5-1) ...
371s Setting up r-cran-survival (3.8-3-1) ...
371s Setting up r-cran-survey (4.4-2-2) ...
371s Setting up r-cran-r.oo (1.27.0-1) ...
371s Setting up r-cran-rdpack (2.6.2-1syncable1) ...
371s Setting up r-cran-future (1.34.0+dfsg-1) ...
371s Setting up r-cran-forcats (1.0.0-1) ...
371s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
371s Setting up r-cran-reshape2 (1.4.4-2build1) ...
371s Setting up r-cran-future.apply (1.11.3+dfsg-1) ...
371s Setting up r-cran-timechange (0.3.0-1) ...
371s Setting up r-cran-hms (1.1.3-1) ...
371s Setting up r-cran-scales (1.3.0-1) ...
371s Setting up r-cran-memoise (2.0.1-1) ...
371s Setting up r-cran-lava (1.8.1+dfsg-1) ...
371s Setting up r-cran-purrr (1.0.4-1) ...
371s Setting up r-cran-e1071 (1.7-16-1) ...
371s Setting up r-cran-blob (1.2.4-1) ...
371s Setting up r-cran-hardhat (1.4.0+dfsg-1) ...
371s Setting up r-cran-dplyr (1.1.4-4) ...
371s Setting up r-cran-reformulas (0.4.0-1) ...
371s Setting up r-cran-rsqlite (2.3.9-1) ...
371s Setting up r-cran-progress (1.2.3-1) ...
371s Setting up r-cran-lubridate (1.9.4+dfsg-1) ...
371s Setting up r-cran-r.utils (2.13.0-1) ...
371s Setting up r-cran-vroom (1.6.5-1) ...
371s Setting up r-cran-prodlim (2024.06.25-1) ...
371s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
371s Setting up r-cran-cellranger (1.1.0-3) ...
371s Setting up r-cran-rpart (4.1.24-1) ...
371s Setting up r-cran-ipred (0.9-15-1) ...
371s Setting up r-cran-lme4 (1.1-36-1) ...
371s Setting up r-cran-readr (2.1.5-1) ...
371s Setting up r-cran-tidyr (1.3.1-1) ...
371s Setting up r-cran-recipes (1.1.0+dfsg-1) ...
371s Setting up r-cran-r.cache (0.16.0-1) ...
371s Setting up r-cran-cowplot (1.1.3+dfsg-1) ...
371s Setting up r-cran-readxl (1.4.4-1) ...
371s Setting up r-cran-haven (2.5.4-1) ...
371s Setting up r-cran-caret (7.0-1+dfsg-1) ...
371s Setting up r-cran-broom (1.0.7+dfsg-1) ...
371s Setting up r-cran-conquer (1.3.3-1) ...
371s Setting up r-cran-r.rsp (0.46.0+ds-1) ...
371s Setting up r-cran-rio (1.2.3-1) ...
371s Setting up r-cran-quantreg (6.00-1) ...
371s Setting up r-cran-modelr (0.1.11-1) ...
371s Setting up r-cran-doby (4.6.25-1) ...
371s Setting up r-cran-pbkrtest (0.5.3-1) ...
371s Setting up r-cran-car (3.1-3-1) ...
371s Setting up r-cran-aer (1.2-14-1) ...
371s Processing triggers for libc-bin (2.41-1ubuntu2) ...
371s Processing triggers for man-db (2.13.0-1) ...
371s Processing triggers for install-info (7.1.1-1) ...
373s autopkgtest [12:45:45]: test run-unit-test: [-----------------------
373s BEGIN TEST 3stage2phase.R
373s 
373s R version 4.4.3 (2025-02-28) -- "Trophy Case"
373s Copyright (C) 2025 The R Foundation for Statistical Computing
373s Platform: s390x-ibm-linux-gnu
373s 
373s R is free software and comes with ABSOLUTELY NO WARRANTY.
373s You are welcome to redistribute it under certain conditions.
373s Type 'license()' or 'licence()' for distribution details.
373s 
373s R is a collaborative project with many contributors.
373s Type 'contributors()' for more information and
373s 'citation()' on how to cite R or R packages in publications.
373s 
373s Type 'demo()' for some demos, 'help()' for on-line help, or
373s 'help.start()' for an HTML browser interface to help.
373s Type 'q()' to quit R.
373s 
373s > ## simulated data with three-stage sample at phase 1, SRS at phase 2
373s > ## motivated by dietary biomarker substudy in HCHS
373s > 
373s > library(survey)
373s Loading required package: grid
373s Loading required package: Matrix
374s Loading required package: survival
374s > 
374s > load("simdata1.RData")
374s > 
374s Attaching package: 'survey'
374s 
374s The following object is masked from 'package:graphics':
374s 
374s     dotchart
374s 
374s 
374s > twophase.full = twophase(id=list(~block+house+ind,~1),
374s +                          strata=list(~strat,NULL),
374s +                          probs=list(~P.block+P.house+P.ind,NULL),
374s +                          subset=~phase2,
374s +                          data=simdata1,method='full')
374s > 
374s > twophase.approx = twophase(id=list(~block+house+ind,~1),
374s +                          strata=list(~strat,NULL),
374s +                          probs=list(~P.block+P.house+P.ind,NULL),
374s +                          subset=~phase2,
374s +                          data=simdata1,method='approx')
374s > 
374s > twophase.rep = twophase(id=list(~block,~1),
374s +                          strata=list(~strat,NULL),
374s +                          probs=list(~I(P.block*P.house*P.ind),NULL),
374s +                          subset=~phase2,
374s +                          data=simdata1,method='full')
374s > 
374s > 
374s > twophase.repapprox = twophase(id=list(~block,~1),
374s +                          strata=list(~strat,NULL),
374s +                          probs=list(~I(P.block*P.house*P.ind),NULL),
374s +                          subset=~phase2,
374s +                          data=simdata1,method='approx')
374s > 
374s > 
374s > svymean(~age, twophase.full)
374s       mean     SE
374s age 41.116 0.8114
374s > svymean(~age, twophase.approx)
374s       mean     SE
374s age 41.116 0.6693
374s > svymean(~age, twophase.rep)
374s       mean    SE
374s age 41.116 0.784
374s > svymean(~age, twophase.repapprox)
374s       mean     SE
374s age 41.116 0.6592
374s > 
374s BEGIN TEST DBIcheck.R
374s 
374s R version 4.4.3 (2025-02-28) -- "Trophy Case"
374s Copyright (C) 2025 The R Foundation for Statistical Computing
374s Platform: s390x-ibm-linux-gnu
374s 
374s R is free software and comes with ABSOLUTELY NO WARRANTY.
374s You are welcome to redistribute it under certain conditions.
374s Type 'license()' or 'licence()' for distribution details.
374s 
374s R is a collaborative project with many contributors.
374s Type 'contributors()' for more information and
374s 'citation()' on how to cite R or R packages in publications.
374s 
374s Type 'demo()' for some demos, 'help()' for on-line help, or
374s 'help.start()' for an HTML browser interface to help.
374s Type 'q()' to quit R.
374s 
375s > 
375s > library(survey)
375s Loading required package: grid
375s Loading required package: Matrix
375s Loading required package: survival
375s > library(RSQLite)
375s 
375s Attaching package: 'survey'
375s 
375s The following object is masked from 'package:graphics':
375s 
375s     dotchart
375s 
376s > 
376s > data(api)
376s > apiclus1$api_stu<-apiclus1$api.stu
376s > apiclus1$comp_imp<-apiclus1$comp.imp
376s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1)
376s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,
376s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey"))
376s > 
376s > m<-svymean(~api00+stype,dclus1)
376s > m.db<-svymean(~api00+stype, dbclus1)
376s > all.equal(coef(m),coef(m.db))
376s [1] TRUE
376s > all.equal(vcov(m), vcov(m.db))
376s [1] TRUE
376s > 
376s > r<-svyratio(~api_stu, ~enroll, design=dclus1)
376s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1)
376s > all.equal(coef(r), coef(r.db))
376s [1] TRUE
376s > all.equal(SE(r), SE(r.db))
376s [1] TRUE
376s > 
376s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE)
376s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE)
376s > all.equal(coef(b), coef(b.db))
376s [1] TRUE
376s > all.equal(SE(b), SE(b.db))
376s [1] TRUE
376s > all.equal(deff(b), deff(b.db))
376s [1] TRUE
376s > 
376s > l<-svyglm(api00~api99+mobility, design=dclus1)
376s > l.db<-svyglm(api00~api99+mobility, design=dbclus1)
376s > all.equal(coef(l),coef(l.db))
376s [1] TRUE
376s > all.equal(vcov(l), vcov(l.db))
376s [1] TRUE
376s > 
376s > dclus1<-update(dclus1, apidiff=api00-api99)
376s > dclus1<-update(dclus1, apipct= apidiff/api99)
376s > dbclus1<-update(dbclus1, apidiff=api00-api99)
376s > dbclus1<-update(dbclus1, apipct= apidiff/api99)
376s > 
376s > u<-svymean(~api00+apidiff+apipct, dclus1)
376s > u.db<-svymean(~api00+apidiff+apipct, dbclus1)
376s > all.equal(u, u.db)
376s [1] TRUE
376s > 
376s > all.equal(nrow(dclus1),nrow(dbclus1))
376s [1] TRUE
376s > all.equal(nrow(subset(dclus1,stype=="E")),
376s +           nrow(subset(dbclus1,stype=="E")))
376s [1] "Mean relative difference: 0.2708333"
376s > 
376s > ## replicate weights
376s > rclus1<-as.svrepdesign(dclus1)
376s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15,
376s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE)
376s > m<-svymean(~api00+api99,rclus1)
376s > m.db<-svymean(~api00+api99,db_rclus1)
376s > all.equal(m,m.db)
376s [1] TRUE
376s > 
376s > summary(db_rclus1)
376s DB-backed replicate weight design
376s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 
376s     scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 
376s     dbname = system.file("api.db", package = "survey"), combined.weights = FALSE)
376s Unstratified cluster jacknife (JK1) with 15 replicates.
376s Variables: 
376s  [1] "row_names"   "cds"         "stype"       "name"        "sname"      
376s  [6] "snum"        "dname"       "dnum"        "cname"       "cnum"       
376s [11] "flag"        "pcttest"     "api00"       "api99"       "target"     
376s [16] "growth"      "sch_wide"    "comp_imp"    "both"        "awards"     
376s [21] "meals"       "ell"         "yr_rnd"      "mobility"    "acs_k3"     
376s [26] "acs_46"      "acs_core"    "pct_resp"    "not_hsg"     "hsg"        
376s [31] "some_col"    "col_grad"    "grad_sch"    "avg_ed"      "full__1"    
376s [36] "emer"        "enroll"      "api_stu"     "fpc"         "pw"         
376s [41] "row_names:1" "wt1"         "wt2"         "wt3"         "wt4"        
376s [46] "wt5"         "wt6"         "wt7"         "wt8"         "wt9"        
376s [51] "wt10"        "wt11"        "wt12"        "wt13"        "wt14"       
376s [56] "wt15"       
376s > 
376s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes"))
376s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes"))
376s > all.equal(s,s.db)
376s [1] TRUE
376s > 
376s BEGIN TEST anova-svycoxph.R
376s 
376s R version 4.4.3 (2025-02-28) -- "Trophy Case"
376s Copyright (C) 2025 The R Foundation for Statistical Computing
376s Platform: s390x-ibm-linux-gnu
376s 
376s R is free software and comes with ABSOLUTELY NO WARRANTY.
376s You are welcome to redistribute it under certain conditions.
376s Type 'license()' or 'licence()' for distribution details.
376s 
376s R is a collaborative project with many contributors.
376s Type 'contributors()' for more information and
376s 'citation()' on how to cite R or R packages in publications.
376s 
376s Type 'demo()' for some demos, 'help()' for on-line help, or
376s 'help.start()' for an HTML browser interface to help.
376s Type 'q()' to quit R.
376s 
376s > 
376s >  library(survey)
376s Loading required package: grid
376s Loading required package: Matrix
377s Loading required package: survival
377s 
377s Attaching package: 'survey'
377s 
377s The following object is masked from 'package:graphics':
377s 
377s     dotchart
377s 
377s > example(svycoxph, ask=FALSE)
377s 
377s svycxp> ## Somewhat unrealistic example of nonresponse bias.
377s svycxp> data(pbc, package="survival")
377s 
377s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
377s 
377s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
377s 
377s svycxp> pbc$randprob<-fitted(biasmodel)
377s 
377s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0
377s 
377s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))
377s 
377s svycxp> rpbc<-as.svrepdesign(dpbc)
377s 
377s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc))
377s Call:
377s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 
377s     albumin, design = dpbc)
377s 
377s               coef exp(coef) se(coef) robust se      z        p
377s log(bili)  0.88592   2.42522  0.09140   0.09048  9.791  < 2e-16
377s protime    0.24487   1.27745  0.07825   0.08122  3.015  0.00257
377s albumin   -1.04298   0.35240  0.21211   0.20454 -5.099 3.41e-07
377s 
377s Likelihood ratio test=  on 3 df, p=
377s n= 312, number of events= 144 
377s 
377s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc)
377s Call:
377s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 
377s     protime + albumin, design = rpbc)
377s 
377s               coef exp(coef) se(coef)      z        p
377s log(bili)  0.88592   2.42522  0.09838  9.005  < 2e-16
377s protime    0.24487   1.27745  0.09373  2.612  0.00899
377s albumin   -1.04298   0.35240  0.21966 -4.748 2.05e-06
377s 
377s Likelihood ratio test=NA  on 3 df, p=NA
377s n= 312, number of events= 144 
377s 
377s svycxp> s<-predict(model,se=TRUE, type="curve",
377s svycxp+      newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5)))
377s 
377s svycxp> plot(s[[1]],ci=TRUE,col="sienna")
377s 
377s svycxp> lines(s[[2]], ci=TRUE,col="royalblue")
377s 
377s svycxp> quantile(s[[1]], ci=TRUE)
377s 0.75  0.5 0.25 
377s 1435 2503 3574 
377s attr(,"ci")
377s      0.025 0.975
377s 0.75  1217  1786
377s 0.5   2256  3170
377s 0.25  3222   Inf
377s 
377s svycxp> confint(s[[2]], parm=365*(1:5))
377s          0.025     0.975
377s 365  0.8375139 0.9453781
377s 730  0.7382750 0.8999016
377s 1095 0.4784105 0.7478460
377s 1460 0.3192009 0.6206764
377s 1825 0.2149475 0.5292978
377s > m<-update(model, .~.+I(protime^2))
377s > a<-anova(m,model)
378s > b<-anova(m, model,force=TRUE)
378s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)])))
378s > 
378s BEGIN TEST api.R
378s 
378s R version 4.4.3 (2025-02-28) -- "Trophy Case"
378s Copyright (C) 2025 The R Foundation for Statistical Computing
378s Platform: s390x-ibm-linux-gnu
378s 
378s R is free software and comes with ABSOLUTELY NO WARRANTY.
378s You are welcome to redistribute it under certain conditions.
378s Type 'license()' or 'licence()' for distribution details.
378s 
378s R is a collaborative project with many contributors.
378s Type 'contributors()' for more information and
378s 'citation()' on how to cite R or R packages in publications.
378s 
378s Type 'demo()' for some demos, 'help()' for on-line help, or
378s 'help.start()' for an HTML browser interface to help.
378s Type 'q()' to quit R.
378s 
378s > library(survey)
378s Loading required package: grid
378s Loading required package: Matrix
378s Loading required package: survival
379s 
379s Attaching package: 'survey'
379s 
379s The following object is masked from 'package:graphics':
379s 
379s     dotchart
379s 
379s > options(survey.replicates.mse=TRUE)
379s > example(api)
379s 
379s api> library(survey)
379s 
379s api> data(api)
379s 
379s api> mean(apipop$api00)
379s [1] 664.7126
379s 
379s api> sum(apipop$enroll, na.rm=TRUE)
379s [1] 3811472
379s 
379s api> #stratified sample
379s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
379s 
379s api> summary(dstrat)
379s Stratified Independent Sampling design
379s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
379s Probabilities:
379s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
379s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 
379s Stratum Sizes: 
379s              E  H  M
379s obs        100 50 50
379s design.PSU 100 50 50
379s actual.PSU 100 50 50
379s Population stratum sizes (PSUs): 
379s    E    H    M 
379s 4421  755 1018 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "pw"       "fpc"     
379s 
379s api> svymean(~api00, dstrat)
379s         mean     SE
379s api00 662.29 9.4089
379s 
379s api> svytotal(~enroll, dstrat, na.rm=TRUE)
379s          total     SE
379s enroll 3687178 114642
379s 
379s api> # one-stage cluster sample
379s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
379s 
379s api> summary(dclus1)
379s 1 - level Cluster Sampling design
379s With (15) clusters.
379s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
379s Probabilities:
379s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
379s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
379s Population size (PSUs): 757 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> svymean(~api00, dclus1)
379s         mean     SE
379s api00 644.17 23.542
379s 
379s api> svytotal(~enroll, dclus1, na.rm=TRUE)
379s          total     SE
379s enroll 3404940 932235
379s 
379s api> # two-stage cluster sample
379s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
379s 
379s api> summary(dclus2)
379s 2 - level Cluster Sampling design
379s With (40, 126) clusters.
379s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
379s Probabilities:
379s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
379s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
379s Population size (PSUs): 757 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
379s 
379s api> svymean(~api00, dclus2)
379s         mean     SE
379s api00 670.81 30.099
379s 
379s api> svytotal(~enroll, dclus2, na.rm=TRUE)
379s          total     SE
379s enroll 2639273 799638
379s 
379s api> # two-stage `with replacement'
379s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
379s 
379s api> summary(dclus2wr)
379s 2 - level Cluster Sampling design (with replacement)
379s With (40, 126) clusters.
379s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
379s Probabilities:
379s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
379s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
379s 
379s api> svymean(~api00, dclus2wr)
379s         mean     SE
379s api00 670.81 30.712
379s 
379s api> svytotal(~enroll, dclus2wr, na.rm=TRUE)
379s          total     SE
379s enroll 2639273 820261
379s 
379s api> # convert to replicate weights
379s api> rclus1<-as.svrepdesign(dclus1)
379s 
379s api> summary(rclus1)
379s Call: as.svrepdesign.default(dclus1)
379s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances.
379s Variables: 
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> svymean(~api00, rclus1)
379s         mean     SE
379s api00 644.17 26.335
379s 
379s api> svytotal(~enroll, rclus1, na.rm=TRUE)
379s          total     SE
379s enroll 3404940 932235
379s 
379s api> # post-stratify on school type
379s api> pop.types<-xtabs(~stype, data=apipop)
379s 
379s api> rclus1p<-postStratify(rclus1, ~stype, pop.types)
379s 
379s api> dclus1p<-postStratify(dclus1, ~stype, pop.types)
379s 
379s api> summary(dclus1p)
379s 1 - level Cluster Sampling design
379s With (15) clusters.
379s dclus1p<-postStratify(dclus1, ~stype, pop.types)
379s Probabilities:
379s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
379s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 
379s Population size (PSUs): 757 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> summary(rclus1p)
379s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types)
379s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances.
379s Variables: 
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> svymean(~api00, dclus1p)
379s         mean     SE
379s api00 642.31 23.921
379s 
379s api> svytotal(~enroll, dclus1p, na.rm=TRUE)
379s          total     SE
379s enroll 3680893 406293
379s 
379s api> svymean(~api00, rclus1p)
379s         mean     SE
379s api00 642.31 26.936
379s 
379s api> svytotal(~enroll, rclus1p, na.rm=TRUE)
379s          total     SE
379s enroll 3680893 473434
379s > 
379s > options(survey.replicates.mse=FALSE)
379s > example(api)
379s 
379s api> library(survey)
379s 
379s api> data(api)
379s 
379s api> mean(apipop$api00)
379s [1] 664.7126
379s 
379s api> sum(apipop$enroll, na.rm=TRUE)
379s [1] 3811472
379s 
379s api> #stratified sample
379s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
379s 
379s api> summary(dstrat)
379s Stratified Independent Sampling design
379s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
379s Probabilities:
379s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
379s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 
379s Stratum Sizes: 
379s              E  H  M
379s obs        100 50 50
379s design.PSU 100 50 50
379s actual.PSU 100 50 50
379s Population stratum sizes (PSUs): 
379s    E    H    M 
379s 4421  755 1018 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "pw"       "fpc"     
379s 
379s api> svymean(~api00, dstrat)
379s         mean     SE
379s api00 662.29 9.4089
379s 
379s api> svytotal(~enroll, dstrat, na.rm=TRUE)
379s          total     SE
379s enroll 3687178 114642
379s 
379s api> # one-stage cluster sample
379s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
379s 
379s api> summary(dclus1)
379s 1 - level Cluster Sampling design
379s With (15) clusters.
379s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
379s Probabilities:
379s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
379s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
379s Population size (PSUs): 757 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> svymean(~api00, dclus1)
379s         mean     SE
379s api00 644.17 23.542
379s 
379s api> svytotal(~enroll, dclus1, na.rm=TRUE)
379s          total     SE
379s enroll 3404940 932235
379s 
379s api> # two-stage cluster sample
379s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
379s 
379s api> summary(dclus2)
379s 2 - level Cluster Sampling design
379s With (40, 126) clusters.
379s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
379s Probabilities:
379s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
379s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
379s Population size (PSUs): 757 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
379s 
379s api> svymean(~api00, dclus2)
379s         mean     SE
379s api00 670.81 30.099
379s 
379s api> svytotal(~enroll, dclus2, na.rm=TRUE)
379s          total     SE
379s enroll 2639273 799638
379s 
379s api> # two-stage `with replacement'
379s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
379s 
379s api> summary(dclus2wr)
379s 2 - level Cluster Sampling design (with replacement)
379s With (40, 126) clusters.
379s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
379s Probabilities:
379s     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
379s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "pw"       "fpc1"     "fpc2"    
379s 
379s api> svymean(~api00, dclus2wr)
379s         mean     SE
379s api00 670.81 30.712
379s 
379s api> svytotal(~enroll, dclus2wr, na.rm=TRUE)
379s          total     SE
379s enroll 2639273 820261
379s 
379s api> # convert to replicate weights
379s api> rclus1<-as.svrepdesign(dclus1)
379s 
379s api> summary(rclus1)
379s Call: as.svrepdesign.default(dclus1)
379s Unstratified cluster jacknife (JK1) with 15 replicates.
379s Variables: 
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> svymean(~api00, rclus1)
379s         mean     SE
379s api00 644.17 26.329
379s 
379s api> svytotal(~enroll, rclus1, na.rm=TRUE)
379s          total     SE
379s enroll 3404940 932235
379s 
379s api> # post-stratify on school type
379s api> pop.types<-xtabs(~stype, data=apipop)
379s 
379s api> rclus1p<-postStratify(rclus1, ~stype, pop.types)
379s 
379s api> dclus1p<-postStratify(dclus1, ~stype, pop.types)
379s 
379s api> summary(dclus1p)
379s 1 - level Cluster Sampling design
379s With (15) clusters.
379s dclus1p<-postStratify(dclus1, ~stype, pop.types)
379s Probabilities:
379s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
379s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 
379s Population size (PSUs): 757 
379s Data variables:
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> summary(rclus1p)
379s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types)
379s Unstratified cluster jacknife (JK1) with 15 replicates.
379s Variables: 
379s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
379s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
379s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
379s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
379s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
379s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
379s [37] "api.stu"  "fpc"      "pw"      
379s 
379s api> svymean(~api00, dclus1p)
379s         mean     SE
379s api00 642.31 23.921
379s 
379s api> svytotal(~enroll, dclus1p, na.rm=TRUE)
379s          total     SE
379s enroll 3680893 406293
379s 
379s api> svymean(~api00, rclus1p)
379s         mean     SE
379s api00 642.31 26.934
379s 
379s api> svytotal(~enroll, rclus1p, na.rm=TRUE)
379s          total     SE
379s enroll 3680893 473431
379s > 
379s BEGIN TEST badcal.R
379s 
379s R version 4.4.3 (2025-02-28) -- "Trophy Case"
379s Copyright (C) 2025 The R Foundation for Statistical Computing
379s Platform: s390x-ibm-linux-gnu
379s 
379s R is free software and comes with ABSOLUTELY NO WARRANTY.
379s You are welcome to redistribute it under certain conditions.
379s Type 'license()' or 'licence()' for distribution details.
379s 
379s R is a collaborative project with many contributors.
379s Type 'contributors()' for more information and
379s 'citation()' on how to cite R or R packages in publications.
379s 
379s Type 'demo()' for some demos, 'help()' for on-line help, or
379s 'help.start()' for an HTML browser interface to help.
379s Type 'q()' to quit R.
379s 
379s > ##
379s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya)
379s > ##
379s > library(survey)
379s Loading required package: grid
379s Loading required package: Matrix
380s Loading required package: survival
380s 
380s Attaching package: 'survey'
380s 
380s The following object is masked from 'package:graphics':
380s 
380s     dotchart
380s 
380s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10))
380s > des <- svydesign(ids=~1, weights=~w, data=data)
380s > des.c <- calibrate(des, ~factor(x), c(10000, 5000))
380s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking')
380s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r)))
380s > 
380s BEGIN TEST brewer_cpp.R
380s 
380s R version 4.4.3 (2025-02-28) -- "Trophy Case"
380s Copyright (C) 2025 The R Foundation for Statistical Computing
380s Platform: s390x-ibm-linux-gnu
380s 
380s R is free software and comes with ABSOLUTELY NO WARRANTY.
380s You are welcome to redistribute it under certain conditions.
380s Type 'license()' or 'licence()' for distribution details.
380s 
380s R is a collaborative project with many contributors.
380s Type 'contributors()' for more information and
380s 'citation()' on how to cite R or R packages in publications.
380s 
380s Type 'demo()' for some demos, 'help()' for on-line help, or
380s 'help.start()' for an HTML browser interface to help.
380s Type 'q()' to quit R.
380s 
380s > ## pps="brewer" can't use rcpp
380s > ## this checks that it doesn't
380s > library(survey)
380s Loading required package: grid
380s Loading required package: Matrix
381s Loading required package: survival
381s 
381s Attaching package: 'survey'
381s 
381s The following object is masked from 'package:graphics':
381s 
381s     dotchart
381s 
381s > data(election)
381s > 
381s > dpps_br<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="brewer")
381s > options(survey.use_rcpp=TRUE)
381s > a<-svytotal(~Bush+Kerry+Nader, dpps_br)
381s > options(survey.use_rcpp=FALSE)
381s > b<-svytotal(~Bush+Kerry+Nader, dpps_br)
381s > 
381s > stopifnot(identical(a,b))
381s > 
381s BEGIN TEST bycovmat.R
381s 
381s R version 4.4.3 (2025-02-28) -- "Trophy Case"
381s Copyright (C) 2025 The R Foundation for Statistical Computing
381s Platform: s390x-ibm-linux-gnu
381s 
381s R is free software and comes with ABSOLUTELY NO WARRANTY.
381s You are welcome to redistribute it under certain conditions.
381s Type 'license()' or 'licence()' for distribution details.
381s 
381s R is a collaborative project with many contributors.
381s Type 'contributors()' for more information and
381s 'citation()' on how to cite R or R packages in publications.
381s 
381s Type 'demo()' for some demos, 'help()' for on-line help, or
381s 'help.start()' for an HTML browser interface to help.
381s Type 'q()' to quit R.
381s 
382s > 
382s > library(survey)
382s Loading required package: grid
382s Loading required package: Matrix
382s Loading required package: survival
383s 
383s Attaching package: 'survey'
383s 
383s > data(api)
383s The following object is masked from 'package:graphics':
383s 
383s     dotchart
383s 
383s > options(survey.replicates.mse=TRUE)
383s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
383s > rclus1<-as.svrepdesign(dclus1)
383s > 
383s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
383s +          covmat=TRUE,drop.empty.groups=FALSE)
383s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
383s +          covmat=TRUE,drop.empty.groups=TRUE)
383s > 
383s > stopifnot(all.equal(
383s +               as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a))))
383s + ))
383s > stopifnot(all.equal(
383s +               as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b))))
383s +               ))
383s > 
383s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE)
383s > all <- svytotal(~ell+mobility+meals, dclus1)
383s > 
383s > stopifnot(all(abs(vcov(svycontrast(all,
383s +                                    list(quote(ell/mobility),
383s +                                         quote(mobility/mobility),
383s +                                         quote(ell/meals),quote(mobility/meals))))
383s +                   -vcov(rat))<1e-10))
383s > 
383s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10))
383s > 
383s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE)
383s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE)
383s > 
383s > con<-svycontrast(all,
383s +                  list(quote(ell/mobility),
383s +                       quote(mobility/mobility),
383s +                       quote(ell/meals),quote(mobility/meals)))
383s > 
383s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10))
383s > 
383s > options(survey.replicates.mse=FALSE)
383s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
383s > rclus1<-as.svrepdesign(dclus1)
383s > 
383s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
383s +          covmat=TRUE,drop.empty.groups=FALSE)
383s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean,
383s +          covmat=TRUE,drop.empty.groups=TRUE)
383s > 
383s > stopifnot(all.equal(
383s +               as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a))))
383s + ))
383s > stopifnot(all.equal(
383s +               as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b))))
383s +               ))
383s > 
383s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE)
383s > all <- svytotal(~ell+mobility+meals, dclus1)
383s > 
383s > stopifnot(all(abs(vcov(svycontrast(all,
383s +                                    list(quote(ell/mobility),
383s +                                         quote(mobility/mobility),
383s +                                         quote(ell/meals),quote(mobility/meals))))
383s +                   -vcov(rat))<1e-10))
383s > 
383s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10))
383s > 
383s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE)
383s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE)
383s > 
383s > con<-svycontrast(all,
383s +                  list(quote(ell/mobility),
383s +                       quote(mobility/mobility),
383s +                       quote(ell/meals),quote(mobility/meals)))
383s > 
383s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10))
383s > 
383s > 
383s > 
383s BEGIN TEST caleg.R
383s 
383s R version 4.4.3 (2025-02-28) -- "Trophy Case"
383s Copyright (C) 2025 The R Foundation for Statistical Computing
383s Platform: s390x-ibm-linux-gnu
383s 
383s R is free software and comes with ABSOLUTELY NO WARRANTY.
383s You are welcome to redistribute it under certain conditions.
383s Type 'license()' or 'licence()' for distribution details.
383s 
383s R is a collaborative project with many contributors.
383s Type 'contributors()' for more information and
383s 'citation()' on how to cite R or R packages in publications.
383s 
383s Type 'demo()' for some demos, 'help()' for on-line help, or
383s 'help.start()' for an HTML browser interface to help.
383s Type 'q()' to quit R.
383s 
383s > ##
383s > ## Calibration examples
383s > ##
383s > 
383s > 
383s > ## Example of calibration to first-stage clusters
383s > library(survey)
383s Loading required package: grid
383s Loading required package: Matrix
384s Loading required package: survival
384s 
384s Attaching package: 'survey'
384s 
384s > data(api)
384s The following object is masked from 'package:graphics':
384s 
384s     dotchart
384s 
384s > 
384s > clusters<-table(apiclus2$dnum)
384s > clusters<-clusters[clusters>1 & names(clusters)!="639"]
384s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters)))
384s > 
384s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a)
384s > 
384s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters)))
384s > 
384s > pop<-lapply(as.numeric(names(clusters)), function(cluster) {
384s +   colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))})
384s > 
384s > names(pop)<-names(clusters)
384s > 
384s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1)
384s > 
384s > svymean(~api99, dclus2)
384s         mean     SE
384s api99 642.14 31.434
384s > svymean(~api99, dclus2g)
384s         mean    SE
384s api99 654.49 29.82
384s > 
384s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4)
384s     dnum    api99      se
384s 83    83 694.3333  0.0000
384s 132  132 505.0000  0.0000
384s 152  152 574.0000  0.0000
384s 173  173 894.7500  0.0000
384s 198  198 533.7500  0.0000
384s 200  200 589.8000  6.8335
384s 228  228 477.0000  0.0000
384s 295  295 646.4000  0.0000
384s 302  302 903.5000  0.0000
384s 403  403 852.4000  0.0000
384s 452  452 533.0000  0.0000
384s 480  480 614.2000  0.0000
384s 523  523 580.5000  0.0000
384s 534  534 564.6000  0.0000
384s 549  549 896.2000  0.0000
384s 552  552 730.0000  0.0000
384s 570  570 518.4000  7.5478
384s 575  575 800.8000  4.2513
384s 596  596 785.6000  2.4155
384s 620  620 591.6000 10.5869
384s 638  638 560.2000  4.0954
384s 674  674 760.0000  0.0000
384s 679  679 610.2500  0.0000
384s 687  687 718.6667  0.0000
384s 701  701 651.5000  0.0000
384s 711  711 690.5000  0.0000
384s 731  731 702.0000  2.1744
384s 768  768 562.5000  0.0000
384s 781  781 854.4000  0.7456
384s > 
384s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4)
385s     dnum    api99 se
385s 83    83 694.3333  0
385s 132  132 505.0000  0
385s 152  152 574.0000  0
385s 173  173 894.7500  0
385s 198  198 533.7500  0
385s 200  200 567.5455  0
385s 228  228 477.0000  0
385s 295  295 646.4000  0
385s 302  302 903.5000  0
385s 403  403 852.4000  0
385s 452  452 533.0000  0
385s 480  480 614.2000  0
385s 523  523 580.5000  0
385s 534  534 564.6000  0
385s 549  549 896.2000  0
385s 552  552 730.0000  0
385s 570  570 548.9444  0
385s 575  575 824.5357  0
385s 596  596 787.5714  0
385s 620  620 609.3750  0
385s 638  638 585.6429  0
385s 674  674 760.0000  0
385s 679  679 610.2500  0
385s 687  687 718.6667  0
385s 701  701 651.5000  0
385s 711  711 690.5000  0
385s 731  731 700.6667  0
385s 768  768 562.5000  0
385s 781  781 851.0000  0
385s > 
385s > ## Averaging to first stage
385s > 
385s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
385s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE)
385s > 
385s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1)
385s > 
385s > svytotal(~enroll,dclus1g)
385s          total SE
385s enroll 3811472  0
385s > svytotal(~api.stu,dclus1g)
385s           total    SE
385s api.stu 3242857 38967
385s > 
385s > #variation within clusters should be zero
385s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE))
385s [1] TRUE
385s > 
385s > ##bounded weights
385s >  dclus1g<-calibrate(dclus1, ~enroll, pop)
385s >  range(weights(dclus1g)/weights(dclus1))
385s [1] 0.7906782 1.7891164
385s >  dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5))
385s >  range(weights(dclus1gb)/weights(dclus1))
385s [1] 0.7198751 1.5000000
385s > 
385s > ## Ratio estimators
385s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
385s > svytotal(~api.stu,dstrat)
385s           total    SE
385s api.stu 3086009 99477
385s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE)
385s > total.enroll<-sum(apipop$enroll,na.rm=TRUE)
385s > predict(common, total=total.enroll)
385s $total
385s          enroll
385s api.stu 3190038
385s 
385s $se
385s           enroll
385s api.stu 29565.98
385s 
385s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1)
385s > svytotal(~api.stu, dstratg)
385s           total    SE
385s api.stu 3190038 29566
385s > 
385s > ## postStratify vs calibrate in stratified sample (Ben French)
385s > set.seed(17)
385s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100),
385s +                 z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100))
385s > dat$w<-ifelse(dat$y,dat$z,1-dat$z)
385s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000))
385s >  des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y)
385s > postStratify(des,~w,popw)->dps
385s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000))
385s > 
385s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps)))
385s [1] TRUE
385s > 
385s > ## missing data in calibrated design
385s > dps$variables$z[1]<-NA
385s > summary(svyglm(y~z+x,design=dps,family=quasibinomial))
385s 
385s Call:
385s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial)
385s 
385s Survey design:
385s postStratify(des, ~w, popw)
385s 
385s Coefficients:
385s             Estimate Std. Error t value Pr(>|t|)    
385s (Intercept)  -0.1203     0.3380  -0.356    0.722    
385s z             6.2118     0.6451   9.630   <2e-16 ***
385s x             2.2602     0.2514   8.992   <2e-16 ***
385s ---
385s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
385s 
385s (Dispersion parameter for quasibinomial family taken to be 1.919987)
385s 
385s Number of Fisher Scoring iterations: 9
385s 
385s > 
385s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm)
385s > # should match the ratio estmate above
385s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll)
385s > svytotal(~api.stu, dstratgh)
385s           total    SE
385s api.stu 3190038 29566
385s > 
385s > ## individual boundary constraints as multiplicative values (Daniel Oehm)
385s > bnds <- list(
385s +   lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 
385s +   upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move
385s > lapply(bnds, head)
385s $lower
385s [1]    1    1 -Inf -Inf -Inf -Inf
385s 
385s $upper
385s [1]   1   1 Inf Inf Inf Inf
385s 
385s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll)
385s > svytotal(~api.stu, dstratg1)
385s           total    SE
385s api.stu 3190133 29561
385s > head(weights(dstrat))
385s     1     2     3     4     5     6 
385s 44.21 44.21 44.21 44.21 44.21 44.21 
385s > head(weights(dstratg1))
385s        1        2        3        4        5        6 
385s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 
385s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2])
385s [1] TRUE
385s > 
385s > ## individual boundary constraints as constant values (Daniel Oehm)
385s > bnds <- list(
385s +   lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 
385s +   upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged
385s > lapply(bnds, head)
385s $lower
385s [1] 44.21 44.21  -Inf  -Inf  -Inf  -Inf
385s 
385s $upper
385s [1] 44.21 44.21   Inf   Inf   Inf   Inf
385s 
385s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll)
385s > svytotal(~api.stu, dstratg2)
385s           total    SE
385s api.stu 3190133 29561
385s > head(weights(dstrat))
385s     1     2     3     4     5     6 
385s 44.21 44.21 44.21 44.21 44.21 44.21 
385s > head(weights(dstratg2))
385s        1        2        3        4        5        6 
385s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 
385s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good
385s [1] TRUE
385s > 
385s > # sparse matrix support (Daniel Oehm)
385s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
385s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
385s > dclus1g<-calibrate(dclus1, ~stype, pop.totals)
385s > svymean(~api00, dclus1g)
385s         mean     SE
385s api00 642.31 23.921
385s > svytotal(~enroll, dclus1g)
385s          total     SE
385s enroll 3680893 406293
385s > 
385s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
385s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE)
385s > svymean(~api00, dclus1g)
385s         mean     SE
385s api00 642.31 23.921
385s > svytotal(~enroll, dclus1g)
385s          total     SE
385s enroll 3680893 406293
385s > 
385s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
385s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking")
385s > svymean(~api00, dclus1g)
385s         mean     SE
385s api00 642.31 23.921
385s > svytotal(~enroll, dclus1g)
385s          total     SE
385s enroll 3680893 406293
385s > 
385s BEGIN TEST check.R
385s 
385s R version 4.4.3 (2025-02-28) -- "Trophy Case"
385s Copyright (C) 2025 The R Foundation for Statistical Computing
385s Platform: s390x-ibm-linux-gnu
385s 
385s R is free software and comes with ABSOLUTELY NO WARRANTY.
385s You are welcome to redistribute it under certain conditions.
385s Type 'license()' or 'licence()' for distribution details.
385s 
385s R is a collaborative project with many contributors.
385s Type 'contributors()' for more information and
385s 'citation()' on how to cite R or R packages in publications.
385s 
385s Type 'demo()' for some demos, 'help()' for on-line help, or
385s 'help.start()' for an HTML browser interface to help.
385s Type 'q()' to quit R.
385s 
385s > library(survey)
385s Loading required package: grid
385s Loading required package: Matrix
386s Loading required package: survival
386s > data(fpc)
386s 
386s Attaching package: 'survey'
386s 
386s The following object is masked from 'package:graphics':
386s 
386s     dotchart
386s 
386s > ## test various possibilities for svydesign
386s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 
386s     variables = ~x, data = fpc, nest = TRUE)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7413
386s > Warning message:
386s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x,  :
386s   No weights or probabilities supplied, assuming equal probability
386s Warning message:
386s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x,  :
386s   No weights or probabilities supplied, assuming equal probability
386s Warning message:
386s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) :
386s   No weights or probabilities supplied, assuming equal probability
386s a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 
386s     data = fpc, nest = TRUE)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7413
386s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 
386s     data = fpc, nest = TRUE)
386s > svymean(~x,a)
386s   mean    SE
386s x 44.2 6.237
386s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 
386s     nest = TRUE)
386s > svymean(~x,a)
386s    mean     SE
386s x 5.525 0.7796
386s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 
386s     data = fpc, nest = TRUE)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7413
386s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 
386s     nest = TRUE)
386s > svymean(~x,a)
386s    mean     SE
386s x 5.525 0.7796
386s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE)
386s > a
386s 1 - level Cluster Sampling design (with replacement)
386s With (5) clusters.
386s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE)
386s > svymean(~x,a)
386s    mean    SE
386s x 5.525 0.838
386s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE)
386s > a
386s 1 - level Cluster Sampling design (with replacement)
386s With (5) clusters.
386s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 
386s     nest = TRUE)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7938
386s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc)
386s > a
386s 2 - level Cluster Sampling design (with replacement)
386s Warning message:
386s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) :
386s   No weights or probabilities supplied, assuming equal probability
386s With (2, 8) clusters.
386s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 
386s     data = fpc)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.5465
386s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc)
386s > a
386s 2 - level Cluster Sampling design (with replacement)
386s With (2, 8) clusters.
386s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc)
386s > svymean(~x,a)
386s    mean     SE
386s x 5.525 0.5188
386s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE],  nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
386s     variables = fpc[, "x", drop = FALSE], nest = TRUE)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7413
386s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6],  nest=TRUE)
386s > a
386s Stratified Independent Sampling design (with replacement)
386s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
386s     variables = fpc[, 4:6], nest = TRUE)
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7413
386s > 
386s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid,  variables=fpc[,4:6], fpc=rep(27,8))
386s > a
386s 1 - level Cluster Sampling design
386s With (5) clusters.
386s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 
386s     4:6], fpc = rep(27, 8))
386s > svymean(~x,a)
386s     mean     SE
386s x 5.4481 0.7165
386s > 
386s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid,  strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh)
386s > a
386s Stratified Independent Sampling design
386s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 
386s     nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh)
386s > svymean(~x,a)
386s     mean    SE
386s x 5.4481 0.616
386s > 
386s BEGIN TEST confintrep.R
386s 
386s R version 4.4.3 (2025-02-28) -- "Trophy Case"
386s Copyright (C) 2025 The R Foundation for Statistical Computing
386s Platform: s390x-ibm-linux-gnu
386s 
386s R is free software and comes with ABSOLUTELY NO WARRANTY.
386s You are welcome to redistribute it under certain conditions.
386s Type 'license()' or 'licence()' for distribution details.
386s 
386s R is a collaborative project with many contributors.
386s Type 'contributors()' for more information and
386s 'citation()' on how to cite R or R packages in publications.
386s 
386s Type 'demo()' for some demos, 'help()' for on-line help, or
386s 'help.start()' for an HTML browser interface to help.
386s Type 'q()' to quit R.
386s 
386s > library(survey)
386s Loading required package: grid
386s Loading required package: Matrix
387s Loading required package: survival
388s 
388s Attaching package: 'survey'
388s 
388s The following object is masked from 'package:graphics':
388s 
388s     dotchart
388s 
388s > data(api)
388s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2)
388s > rclus2<-as.svrepdesign(dclus2)
388s Warning message:
388s In as.svrepdesign.default(dclus2) :
388s   Finite population corrections after first stage have been dropped
388s > 
388s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial)
388s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint")
388s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial)
388s > if(anyNA(confint(mrep))) stop("NA in confint")
388s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint")
388s > 
388s BEGIN TEST contrast-replicates.R
388s 
388s R version 4.4.3 (2025-02-28) -- "Trophy Case"
388s Copyright (C) 2025 The R Foundation for Statistical Computing
388s Platform: s390x-ibm-linux-gnu
388s 
388s R is free software and comes with ABSOLUTELY NO WARRANTY.
388s You are welcome to redistribute it under certain conditions.
388s Type 'license()' or 'licence()' for distribution details.
388s 
388s R is a collaborative project with many contributors.
388s Type 'contributors()' for more information and
388s 'citation()' on how to cite R or R packages in publications.
388s 
388s Type 'demo()' for some demos, 'help()' for on-line help, or
388s 'help.start()' for an HTML browser interface to help.
388s Type 'q()' to quit R.
388s 
388s > ## test use of replicates in svyby, svycontrast
388s > library(survey)
388s Loading required package: grid
388s Loading required package: Matrix
389s Loading required package: survival
389s > 
389s > data(api)
389s 
389s Attaching package: 'survey'
389s 
389s The following object is masked from 'package:graphics':
389s 
389s     dotchart
389s 
389s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
389s > rclus1<-as.svrepdesign(dclus1)
389s > 
389s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE)
389s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H)))
389s > vcov(c_without)
389s            contrast
389s contrast 0.06862947
389s > 
389s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE)
389s > 
389s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H)))
389s > 
389s > v_with<- vcov(rclus1, c_with$replicates)
389s > 
389s > r<- attr(meanlogs_with, "replicates")
389s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2]))
389s > 
389s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with)))
389s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with))))
389s > 
389s BEGIN TEST coxph-termtest.R
389s 
389s R version 4.4.3 (2025-02-28) -- "Trophy Case"
389s Copyright (C) 2025 The R Foundation for Statistical Computing
389s Platform: s390x-ibm-linux-gnu
389s 
389s R is free software and comes with ABSOLUTELY NO WARRANTY.
389s You are welcome to redistribute it under certain conditions.
389s Type 'license()' or 'licence()' for distribution details.
389s 
389s R is a collaborative project with many contributors.
389s Type 'contributors()' for more information and
389s 'citation()' on how to cite R or R packages in publications.
389s 
389s Type 'demo()' for some demos, 'help()' for on-line help, or
389s 'help.start()' for an HTML browser interface to help.
389s Type 'q()' to quit R.
389s 
389s > library(survey)
389s Loading required package: grid
389s Loading required package: Matrix
390s Loading required package: survival
390s 
390s Attaching package: 'survey'
390s 
390s > library(survival)
390s The following object is masked from 'package:graphics':
390s 
390s     dotchart
390s 
390s > set.seed(2021-6-25)
390s > test1 <- list(time=c(4,3,1,1,2,2,3),
390s +               status=c(1,1,1,0,1,1,0),
390s +               x1=as.factor(rbinom(7, 2, 0.5)),
390s +               x=c(0,2,1,1,1,0,0))
390s > # Fit a stratified model
390s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1)
390s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1)
390s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")],
390s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")]))
390s > 
390s > data(pbc, package="survival")
390s > 
390s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
390s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
390s > pbc$randprob<-fitted(biasmodel)
390s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0
390s > 
390s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))
390s > library(splines)
390s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc)
390s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT")
390s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4))
390s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4))
390s > 
390s BEGIN TEST deff.R
390s 
390s R version 4.4.3 (2025-02-28) -- "Trophy Case"
390s Copyright (C) 2025 The R Foundation for Statistical Computing
390s Platform: s390x-ibm-linux-gnu
390s 
390s R is free software and comes with ABSOLUTELY NO WARRANTY.
390s You are welcome to redistribute it under certain conditions.
390s Type 'license()' or 'licence()' for distribution details.
390s 
390s R is a collaborative project with many contributors.
390s Type 'contributors()' for more information and
390s 'citation()' on how to cite R or R packages in publications.
390s 
390s Type 'demo()' for some demos, 'help()' for on-line help, or
390s 'help.start()' for an HTML browser interface to help.
390s Type 'q()' to quit R.
390s 
391s > ## from Takahiro Tsuchiya
391s > library(survey)
391s Loading required package: grid
391s Loading required package: Matrix
391s Loading required package: survival
391s > kigyo<-read.table(tmp<-textConnection("  obs uriage srs.w pps.w
391s + 1    1     15   100    20
391s + 2    2    143   100   200
391s + 3    3     21   100    11
391s + 4    4     51   100    25
391s 
391s Attaching package: 'survey'
391s 
391s The following object is masked from 'package:graphics':
391s 
391s     dotchart
391s 
392s + 5    5    337   100   550
392s + 6    6     50   100    30
392s + 7    7    274   100   250
392s + 8    8    145   100   100
392s + 9    9     15   100    10
392s + 10  10     86   100    55
392s + ",open="r"),header=TRUE)
392s > close(tmp)
392s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo)
392s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE))
392s           mean      SE   DEff
392s uriage 113.700  35.626 1.0101
392s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10)
392s          uriage
392s uriage 1.010101
392s > 
392s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE))
392s         total     SE   DEff
392s uriage 113700  35626 1.0101
392s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10)
392s          uriage
392s uriage 1.010101
392s > 
392s > 
392s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo)
392s > (res.pps <- svymean(~uriage, des.pps, deff='replace'))
392s           mean      SE   DEff
392s uriage 243.914  48.752 1.9741
392s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10)
392s          uriage
392s uriage 1.974067
392s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace'))
392s         total     SE   DEff
392s uriage 305136 184965 18.157
392s > (N.hat <- sum(weights(des.pps)))
392s [1] 1251
392s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10)
392s          uriage
392s uriage 18.15669
392s > 
392s BEGIN TEST defftest.R
392s 
392s R version 4.4.3 (2025-02-28) -- "Trophy Case"
392s Copyright (C) 2025 The R Foundation for Statistical Computing
392s Platform: s390x-ibm-linux-gnu
392s 
392s R is free software and comes with ABSOLUTELY NO WARRANTY.
392s You are welcome to redistribute it under certain conditions.
392s Type 'license()' or 'licence()' for distribution details.
392s 
392s R is a collaborative project with many contributors.
392s Type 'contributors()' for more information and
392s 'citation()' on how to cite R or R packages in publications.
392s 
392s Type 'demo()' for some demos, 'help()' for on-line help, or
392s 'help.start()' for an HTML browser interface to help.
392s Type 'q()' to quit R.
392s 
392s > library(survey)
392s Loading required package: grid
392s Loading required package: Matrix
392s Loading required package: survival
393s > 
393s > data(api)
393s 
393s Attaching package: 'survey'
393s 
393s The following object is masked from 'package:graphics':
393s 
393s     dotchart
393s 
393s > 
393s > ## one-stage cluster sample
393s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
393s > 
393s > # svyglm model
393s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE)
393s > 
393s > #deffs returned from svyglm model - implausibly high
393s > deff(mod)
393s (Intercept)      enroll     api.stu 
393s    1.919945    2.500983    2.686102 
393s > #> (Intercept)      enroll     api.stu 
393s > #>    351.3500    457.6799    491.5567
393s > 
393s > # run mod with same data and glm()
393s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1)
393s > 
393s > # manually calculate deffs
393s > 
393s > clust_se <- summary(mod)$coefficients[,2]
393s > srs_se <- summary(srs_mod)$coefficients[,2]
393s > 
393s > deffs <- clust_se^2 / srs_se^2
393s > stopifnot(all.equal(deffs, deff(mod)))
393s > 
393s > 
393s BEGIN TEST degf-svrepdesign.R
393s 
393s R version 4.4.3 (2025-02-28) -- "Trophy Case"
393s Copyright (C) 2025 The R Foundation for Statistical Computing
393s Platform: s390x-ibm-linux-gnu
393s 
393s R is free software and comes with ABSOLUTELY NO WARRANTY.
393s You are welcome to redistribute it under certain conditions.
393s Type 'license()' or 'licence()' for distribution details.
393s 
393s R is a collaborative project with many contributors.
393s Type 'contributors()' for more information and
393s 'citation()' on how to cite R or R packages in publications.
393s 
393s Type 'demo()' for some demos, 'help()' for on-line help, or
393s 'help.start()' for an HTML browser interface to help.
393s Type 'q()' to quit R.
393s 
393s > library(survey)
393s Loading required package: grid
393s Loading required package: Matrix
394s Loading required package: survival
394s 
394s Attaching package: 'survey'
394s 
394s The following object is masked from 'package:graphics':
394s 
394s     dotchart
394s 
394s > data(scd)
394s > 
394s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1),
394s + c(0,1,0,1,1,0))
394s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights)
394s Warning message:
394s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) :
394s   No sampling weights provided: equal probability assumed
394s > 
394s > stopifnot(degf(scdrep)==3)
394s > 
394s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4)
394s > stopifnot(degf(scdrep)==4)
394s > 
394s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2)
394s > stopifnot(degf(scdrep)==2)
394s > 
394s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 
394s +    warning=function(w) w)
394s > 
394s > stopifnot(inherits(msg,"warning"))
394s > 
394s > 
394s > 
394s > 
394s BEGIN TEST domain.R
394s Warning message:
394s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights,  :
394s   No sampling weights provided: equal probability assumed
394s Warning message:
394s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights,  :
394s   No sampling weights provided: equal probability assumed
394s 
394s R version 4.4.3 (2025-02-28) -- "Trophy Case"
394s Copyright (C) 2025 The R Foundation for Statistical Computing
394s Platform: s390x-ibm-linux-gnu
394s 
394s R is free software and comes with ABSOLUTELY NO WARRANTY.
394s You are welcome to redistribute it under certain conditions.
394s Type 'license()' or 'licence()' for distribution details.
394s 
394s R is a collaborative project with many contributors.
394s Type 'contributors()' for more information and
394s 'citation()' on how to cite R or R packages in publications.
394s 
394s Type 'demo()' for some demos, 'help()' for on-line help, or
394s 'help.start()' for an HTML browser interface to help.
394s Type 'q()' to quit R.
394s 
394s > ##
394s > ## Domain means can be written as ratio estimators or as regression coefficients
394s > ##
394s > ## This code checks that subsetting the design object gives the same results as
394s > ## these approaches.
394s > ##
394s > 
394s > 
394s > library(survey)
394s Loading required package: grid
394s Loading required package: Matrix
395s Loading required package: survival
395s 
395s Attaching package: 'survey'
395s 
395s The following object is masked from 'package:graphics':
395s 
395s     dotchart
395s 
395s > data(fpc)
395s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE)
395s > dsub<-subset(dfpc,x>4)
395s > (m1<-svymean(~x,design=dsub))
395s    mean     SE
395s x 6.195 0.7555
395s > 
395s > ## These should give the same domain estimates and standard errors
395s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE))
395s       I(x > 4)        x        se
395s FALSE    FALSE 3.314286 0.3117042
395s TRUE      TRUE 6.195000 0.7555129
395s > m3<-svyglm(x~I(x>4)+0,design=dfpc)
395s > summary(m3)
395s 
395s Call:
395s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc)
395s 
395s Survey design:
395s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 
395s     nest = TRUE)
395s 
395s Coefficients:
395s               Estimate Std. Error t value Pr(>|t|)    
395s I(x > 4)FALSE   3.3143     0.3117   10.63 0.000127 ***
395s I(x > 4)TRUE    6.1950     0.7555    8.20 0.000439 ***
395s ---
395s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
395s 
395s (Dispersion parameter for gaussian family taken to be 2.557379)
395s 
395s Number of Fisher Scoring iterations: 2
395s 
395s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc))
395s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 
395s     dfpc)
395s Ratios=
395s                as.numeric(x > 4)
395s I(x * (x > 4))             6.195
395s SEs=
395s                as.numeric(x > 4)
395s I(x * (x > 4))         0.7555129
395s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3)))))
395s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4)))))
395s > 
395s > ## with strata
395s > data(api)
395s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
395s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes"))
395s > m2<-svyglm(enroll~comp.imp-1, dstrat)
395s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat)
395s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
395s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
395s > 
395s > ## with calibration
395s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
395s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018)
395s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069)))
395s 1 - level Cluster Sampling design
395s With (15) clusters.
395s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069))
395s > 
395s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes"))
395s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3)
395s > m2<-svyglm(api00~comp.imp-1, dclus1g3)
395s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
395s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
395s > 
395s > ## with raking
395s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
395s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
395s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
395s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes"))
395s > m2<-svyglm(api00~comp.imp-1, dclus1r)
395s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r)
395s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1)))))
395s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3))))))
395s > 
395s > 
395s > 
395s > ##
395s > ## based on bug report from Takahiro Tsuchiya for version 3.4
395s > ## 
395s > rei<-read.table(tmp<-textConnection(
395s + "  id   N n.a h n.ah n.h   sub  y
395s + 1   1 300  20 1   12   5  TRUE  1
395s + 2   2 300  20 1   12   5  TRUE  2
395s + 3   3 300  20 1   12   5  TRUE  3
395s + 4   4 300  20 1   12   5  TRUE  4
395s + 5   5 300  20 1   12   5  TRUE  5
395s + 6   6 300  20 1   12   5 FALSE NA
395s + 7   7 300  20 1   12   5 FALSE NA
395s + 8   8 300  20 1   12   5 FALSE NA
395s + 9   9 300  20 1   12   5 FALSE NA
395s + 10 10 300  20 1   12   5 FALSE NA
395s + 11 11 300  20 1   12   5 FALSE NA
395s + 12 12 300  20 1   12   5 FALSE NA
395s + 13 13 300  20 2    8   3  TRUE  6
395s + 14 14 300  20 2    8   3  TRUE  7
395s + 15 15 300  20 2    8   3  TRUE  8
395s + 16 16 300  20 2    8   3 FALSE NA
395s + 17 17 300  20 2    8   3 FALSE NA
395s + 18 18 300  20 2    8   3 FALSE NA
395s + 19 19 300  20 2    8   3 FALSE NA
395s + 20 20 300  20 2    8   3 FALSE NA
395s + "), header=TRUE)
395s > close(tmp)
395s > 
395s > 
395s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h),
395s +                     fpc=list(~N,NULL), subset=~sub, data=rei, method="full")
395s > tot2<- svytotal(~y, subset(des.rei2, y>3))
395s > 
395s > rei$y<-rei$y*(rei$y>3)
395s > ## based on Sarndal et al (9.4.14)
395s > rei$w.ah <- rei$n.ah / rei$n.a
395s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE)
395s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE)
395s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y)
395s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h))
395s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1)))
395s > 
395s > a.rei$f.h<-with(a.rei, n.h/n.ah)
395s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh))
395s > 
395s > a.rei$f<-with(a.rei, n.a/N)
395s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1))
395s > 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)))
395s > 
395s > V
395s [1] 70761.47
395s > Vphase1
395s [1] 44325.47
395s > Vphase2
395s [1] 26436
395s > vcov(tot2)
395s          [,1]
395s [1,] 70761.47
395s attr(,"phases")
395s attr(,"phases")$phase1
395s          [,1]
395s [1,] 44325.47
395s 
395s attr(,"phases")$phase2
395s       [,1]
395s [1,] 26436
395s 
395s > 
395s > ## comparing to regression
395s > reg<-svyglm(y~I(y<4), design=des.rei2)
395s > mn<-svymean(~y, subset(des.rei2,y>3))
395s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn)))
395s [1] TRUE
395s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn)))
395s [1] TRUE
395s > vcov(mn)
395s           [,1]
395s [1,] 0.3292258
395s attr(,"phases")
395s attr(,"phases")$phase1
395s           [,1]
395s [1,] 0.1599264
395s 
395s attr(,"phases")$phase2
395s           [,1]
395s [1,] 0.1692994
395s 
395s > vcov(reg)
395s              (Intercept) I(y < 4)TRUE
395s (Intercept)    0.3292258   -0.3292258
395s I(y < 4)TRUE  -0.3292258    0.5901907
395s attr(,"phases")
395s attr(,"phases")$phase1
395s              (Intercept) I(y < 4)TRUE
395s (Intercept)    0.1599264   -0.1599264
395s I(y < 4)TRUE  -0.1599264    0.2588542
395s 
395s attr(,"phases")$phase2
395s              (Intercept) I(y < 4)TRUE
395s (Intercept)    0.1692994   -0.1692994
395s I(y < 4)TRUE  -0.1692994    0.3313365
395s 
395s > 
395s > 
395s BEGIN TEST fpc.R
395s 
395s R version 4.4.3 (2025-02-28) -- "Trophy Case"
395s Copyright (C) 2025 The R Foundation for Statistical Computing
395s Platform: s390x-ibm-linux-gnu
395s 
395s R is free software and comes with ABSOLUTELY NO WARRANTY.
395s You are welcome to redistribute it under certain conditions.
395s Type 'license()' or 'licence()' for distribution details.
395s 
395s R is a collaborative project with many contributors.
395s Type 'contributors()' for more information and
395s 'citation()' on how to cite R or R packages in publications.
395s 
395s Type 'demo()' for some demos, 'help()' for on-line help, or
395s 'help.start()' for an HTML browser interface to help.
395s Type 'q()' to quit R.
395s 
395s > library(survey)
395s Loading required package: grid
396s Loading required package: Matrix
396s Loading required package: survival
396s 
396s Attaching package: 'survey'
396s 
396s The following object is masked from 'package:graphics':
396s 
396s     dotchart
396s 
396s > ## check many permutations of fpc specification
396s > example(fpc)
396s 
396s fpc> data(fpc)
396s 
396s fpc> fpc
396s   stratid psuid weight nh Nh   x
396s 1       1     1      3  5 15 2.8
396s 2       1     2      3  5 15 4.1
396s 3       1     3      3  5 15 6.8
396s 4       1     4      3  5 15 6.8
396s 5       1     5      3  5 15 9.2
396s 6       2     1      4  3 12 3.7
396s 7       2     2      4  3 12 6.6
396s 8       2     3      4  3 12 4.2
396s 
396s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 
396s fpc+    data=fpc, nest=TRUE)
396s 
396s fpc> withoutfpc
396s Stratified Independent Sampling design (with replacement)
396s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 
396s    data=fpc, nest=TRUE)
396s 
396s fpc> svymean(~x, withoutfpc)
396s     mean     SE
396s x 5.4481 0.7413
396s 
396s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
396s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
396s 
396s fpc> withfpc
396s Stratified Independent Sampling design
396s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
396s fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
396s 
396s fpc> svymean(~x, withfpc)
396s     mean    SE
396s x 5.4481 0.616
396s 
396s fpc> ## Other equivalent forms 
396s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid,
396s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE)
396s 
396s fpc> svymean(~x, withfpc)
396s     mean    SE
396s x 5.4481 0.616
396s 
396s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid,
396s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE)
396s 
396s fpc> svymean(~x, withfpc)
396s     mean    SE
396s x 5.4481 0.616
396s 
396s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid),
396s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc)
396s 
396s fpc> svymean(~x, withfpc)
396s     mean    SE
396s x 5.4481 0.616
396s 
396s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh,
396s fpc+  variables=~x,data=fpc,nest=TRUE)
396s 
396s fpc> svymean(~x, withfpc)
396s     mean    SE
396s x 5.4481 0.616
396s 
396s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid,
396s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE)
396s 
396s fpc> svymean(~x, withfpc)
396s     mean    SE
396s x 5.4481 0.616
396s > 
396s > 
396s BEGIN TEST glm-scoping.R
397s 
397s R version 4.4.3 (2025-02-28) -- "Trophy Case"
397s Copyright (C) 2025 The R Foundation for Statistical Computing
397s Platform: s390x-ibm-linux-gnu
397s 
397s R is free software and comes with ABSOLUTELY NO WARRANTY.
397s You are welcome to redistribute it under certain conditions.
397s Type 'license()' or 'licence()' for distribution details.
397s 
397s R is a collaborative project with many contributors.
397s Type 'contributors()' for more information and
397s 'citation()' on how to cite R or R packages in publications.
397s 
397s Type 'demo()' for some demos, 'help()' for on-line help, or
397s 'help.start()' for an HTML browser interface to help.
397s Type 'q()' to quit R.
397s 
397s > ## bug report from Thomas Leeper, fixed in version 3.32-3
397s > 
397s > library("survey")
397s Loading required package: grid
397s Loading required package: Matrix
397s Loading required package: survival
398s 
398s Attaching package: 'survey'
398s 
398s > The following object is masked from 'package:graphics':
398s 
398s     dotchart
398s 
398s data(api)
398s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
398s > 
398s > # pass `family` directly (WORKS!)
398s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian())
398s Stratified Independent Sampling design
398s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
398s     fpc = ~fpc)
398s 
398s Call:  svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 
398s     family = gaussian())
398s 
398s Coefficients:
398s (Intercept)          ell        meals     mobility  
398s    820.8873      -0.4806      -3.1415       0.2257  
398s 
398s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
398s Null Deviance:	    3023000 
398s Residual Deviance: 1029000 	AIC: 2308
398s > 
398s > # passing `family` via ... (WORKS!)
398s > myfun1 <- function(formula, design, ...) {
398s +     svyglm(formula, design = design, ...)
398s + }
398s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian())
398s Stratified Independent Sampling design
398s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
398s     fpc = ~fpc)
398s 
398s Call:  svyglm(formula = formula, design = design, family = ..1)
398s 
398s Coefficients:
398s (Intercept)          ell        meals     mobility  
398s    820.8873      -0.4806      -3.1415       0.2257  
398s 
398s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
398s Null Deviance:	    3023000 
398s Residual Deviance: 1029000 	AIC: 2308
398s > 
398s > # passing `family` via default argument (DOES NOT WORK!)
398s > myfun2 <- function(formula, design, family = gaussian()) {
398s +     svyglm(formula, design = design, family = family)
398s + }
398s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian())
398s Stratified Independent Sampling design
398s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
398s     fpc = ~fpc)
398s 
398s Call:  svyglm(formula = formula, design = design, family = family)
398s 
398s Coefficients:
398s (Intercept)          ell        meals     mobility  
398s    820.8873      -0.4806      -3.1415       0.2257  
398s 
398s Degrees of Freedom: 199 Total (i.e. Null);  194 Residual
398s Null Deviance:	    3023000 
398s Residual Deviance: 1029000 	AIC: 2308
398s > 
398s BEGIN TEST kalton.R
398s 
398s R version 4.4.3 (2025-02-28) -- "Trophy Case"
398s Copyright (C) 2025 The R Foundation for Statistical Computing
398s Platform: s390x-ibm-linux-gnu
398s 
398s R is free software and comes with ABSOLUTELY NO WARRANTY.
398s You are welcome to redistribute it under certain conditions.
398s Type 'license()' or 'licence()' for distribution details.
398s 
398s R is a collaborative project with many contributors.
398s Type 'contributors()' for more information and
398s 'citation()' on how to cite R or R packages in publications.
398s 
398s Type 'demo()' for some demos, 'help()' for on-line help, or
398s 'help.start()' for an HTML browser interface to help.
398s Type 'q()' to quit R.
398s 
398s > library(survey)
398s Loading required package: grid
398s Loading required package: Matrix
398s Loading required package: survival
399s 
399s Attaching package: 'survey'
399s 
399s > 
399s The following object is masked from 'package:graphics':
399s 
399s     dotchart
399s 
399s > ab<-expand.grid(a=factor(1:4),b=factor(1:3))
399s > 
399s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),]
399s > 
399s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),]
399s > 
399s > jointpop<-colSums(model.matrix(~a*b,kaltonpop))
399s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop))
399s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop))
399s > 
399s > dkalton<-svydesign(id=~1,data=kaltonsample)
399s > 
399s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop))
399s > 
399s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001))
399s > 
399s > dcalps<-calibrate(dkalton, ~a*b, jointpop)
399s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking")
399s > dlinear<-calibrate(dkalton, ~a+b, marginalpop)
399s > 
399s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2))
399s > 
399s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit")
399s > 
399s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop)
399s Warning message:
399s In svydesign.default(id = ~1, data = kaltonsample) :
399s   No weights or probabilities supplied, assuming equal probability
399s > 
399s > 
399s > #table A
399s >  round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 4.00 1.00 1.38
399s   2 1.20 1.07 1.10
399s   3 1.70 1.20 4.00
399s   4 1.83 1.65 1.79
399s >  round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 4.00 1.00 1.37
399s   2 1.20 1.07 1.10
399s   3 1.70 1.20 4.00
399s   4 1.83 1.65 1.79
399s > 
399s > #table B
399s >  round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 1.81 1.45 2.02
399s   2 1.08 0.87 1.21
399s   3 2.20 1.76 2.45
399s   4 1.83 1.47 2.04
399s >  round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 1.81 1.45 2.02
399s   2 1.08 0.87 1.21
399s   3 2.20 1.76 2.45
399s   4 1.83 1.47 2.04
399s > 
399s > #table C
399s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 1.82 1.50 1.97
399s   2 1.09 0.78 1.24
399s   3 2.19 1.88 2.34
399s   4 1.83 1.52 1.98
399s > 
399s > #table D
399s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 1.21 1.17 1.14
399s   2 1.43 1.40 1.36
399s   3 1.66 1.62 1.59
399s   4 1.88 1.85 1.81
399s > 
399s > #table G
399s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 1.87 1.46 1.98
399s   2 1.08 0.74 1.27
399s   3 2.17 2.09 2.18
399s   4 1.89 1.49 1.99
399s > 
399s > #table G
399s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2)
399s    b
399s a      1    2    3
399s   1 1.81 1.48 1.99
399s   2 1.08 0.75 1.26
399s   3 2.20 2.00 2.20
399s   4 1.83 1.50 2.00
399s > 
399s BEGIN TEST logranktest.R
399s 
399s R version 4.4.3 (2025-02-28) -- "Trophy Case"
399s Copyright (C) 2025 The R Foundation for Statistical Computing
399s Platform: s390x-ibm-linux-gnu
399s 
399s R is free software and comes with ABSOLUTELY NO WARRANTY.
399s You are welcome to redistribute it under certain conditions.
399s Type 'license()' or 'licence()' for distribution details.
399s 
399s R is a collaborative project with many contributors.
399s Type 'contributors()' for more information and
399s 'citation()' on how to cite R or R packages in publications.
399s 
399s Type 'demo()' for some demos, 'help()' for on-line help, or
399s 'help.start()' for an HTML browser interface to help.
399s Type 'q()' to quit R.
399s 
399s > ## StackOverflow 63333282
399s > 
399s > library(survey)
399s Loading required package: grid
399s Loading required package: Matrix
400s Loading required package: survival
400s 
400s Attaching package: 'survey'
400s 
400s The following object is masked from 'package:graphics':
400s 
400s     dotchart
400s 
400s > D = data.frame(unique_id = 1:135,
400s +                
400s +                weights = rep(1,135),
400s +                
400s +                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 ,
400s +                               
400s +                               6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522,
400s +                               
400s +                               15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263,
400s +                               
400s +                               23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409,
400s +                               
400s +                               9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009,
400s +                               
400s +                               2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540,
400s +                               
400s +                               1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679,
400s +                               
400s +                               0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630,
400s +                               
400s +                               2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901,
400s +                               
400s +                               2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354,
400s +                               
400s +                               11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594,
400s +                               
400s +                               2.35699896, 2.94956000, 8.85381736),
400s +                
400s +                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,
400s +                               
400s +                               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,
400s +                               
400s +                               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),
400s +                
400s +                group = c(rep("group1", 40), rep("group2", 95)))
400s > 
400s > 
400s > 
400s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group")
400s > 
400s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D )
400s > 
400s > a<-svylogrank(formula = svykm_formula, design = svy_design)
400s > 
400s > ii<-with(D, order(event_time, event_flag))
400s > 
400s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] )
400s > 
400s > b<-svylogrank(formula = svykm_formula, design = svy_design2)
400s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large")
400s > 
400s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score")
400s > 
400s > 
400s > stopifnot(all.equal(a[[2]],b[[2]]))
400s > 
400s > stopifnot(all.equal(a[[2]],d[[2]]))
400s > 
400s > stopifnot(all.equal(a[[2]],f[-1]))
400s > 
400s > 
400s BEGIN TEST lonely.psu.R
400s 
400s R version 4.4.3 (2025-02-28) -- "Trophy Case"
400s Copyright (C) 2025 The R Foundation for Statistical Computing
400s Platform: s390x-ibm-linux-gnu
400s 
400s R is free software and comes with ABSOLUTELY NO WARRANTY.
400s You are welcome to redistribute it under certain conditions.
400s Type 'license()' or 'licence()' for distribution details.
400s 
400s R is a collaborative project with many contributors.
400s Type 'contributors()' for more information and
400s 'citation()' on how to cite R or R packages in publications.
400s 
400s Type 'demo()' for some demos, 'help()' for on-line help, or
400s 'help.start()' for an HTML browser interface to help.
400s Type 'q()' to quit R.
400s 
400s > 
400s > ## lonely PSUs by design
400s > library(survey)
400s Loading required package: grid
400s Loading required package: Matrix
401s Loading required package: survival
401s 
401s Attaching package: 'survey'
401s 
401s > data(api)
401s The following object is masked from 'package:graphics':
401s 
401s     dotchart
401s 
401s > ## not certainty PSUs by fpc
401s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1)
401s > summary(ds)
401s Stratified Independent Sampling design (with replacement)
401s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1)
401s Probabilities:
401s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
401s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
401s Stratum Sizes: 
401s            61 135 178 197 255 406 413 437 448 510 568 637 716 778 815
401s obs        13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
401s design.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
401s actual.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
401s Data variables:
401s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
401s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
401s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
401s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
401s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
401s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
401s [37] "api.stu"  "fpc"      "pw"      
401s > 
401s > options(survey.lonely.psu="fail")
401s > try(svymean(~api00,ds))
401s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  : 
401s   Stratum (413) has only one PSU at stage 1
401s > try(svymean(~api00, as.svrepdesign(ds)))
401s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc,  : 
401s   Stratum413has only one PSU
401s > options(survey.lonely.psu="remove")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.8058
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.8058
401s > options(survey.lonely.psu="certainty")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.8058
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.8058
401s > options(survey.lonely.psu="adjust")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.8281
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.8267
401s > options(survey.lonely.psu="average")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 6.0096
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.8217
401s > 
401s > ## fpc specified
401s > fpc<-ifelse(apiclus1$dnum==413, 1,1000)
401s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc)
401s > summary(ds)
401s Stratified Independent Sampling design
401s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 
401s     fpc = fpc)
401s Probabilities:
401s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
401s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
401s Stratum Sizes: 
401s            61 135 178 197 255 406 413 437 448 510 568 637 716 778 815
401s obs        13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
401s design.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
401s actual.PSU 13  34   4  13  16   2   1   4  12  21   9  11  37   2   4
401s Population stratum sizes (PSUs): 
401s  135  178  197  255  406  413  437  448  510  568   61  637  716  778  815 
401s 1000 1000 1000 1000 1000    1 1000 1000 1000 1000 1000 1000 1000 1000 1000 
401s Data variables:
401s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
401s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
401s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
401s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
401s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
401s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
401s [37] "api.stu"  "fpc"      "pw"      
401s > 
401s > options(survey.lonely.psu="fail")
401s > try(svymean(~api00,ds))
401s         mean     SE
401s api00 644.17 5.7344
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.7344
401s > options(survey.lonely.psu="remove")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.7344
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.7344
401s > options(survey.lonely.psu="certainty")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.7344
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.7344
401s > options(survey.lonely.psu="adjust")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.7344
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.7344
401s > options(survey.lonely.psu="average")
401s > svymean(~api00,ds)
401s         mean     SE
401s api00 644.17 5.7344
401s > svymean(~api00, as.svrepdesign(ds))
401s         mean     SE
401s api00 644.17 5.7501
401s > 
401s > rs<-as.svrepdesign(ds)
401s > svytotal(~api00,rs)
401s         total    SE
401s api00 3989986 35616
401s > SE(svytotal(~api00,subset(rs, dnum==413)))==0
401s [1] TRUE
401s > 
401s > ## lonely PSUs after subsetting
401s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413))
401s > ds1<-ds[-31,]
401s > summary(ds1)
401s Stratified Independent Sampling design (with replacement)
401s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 
401s     dnum != 413))
401s Probabilities:
401s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
401s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
401s Stratum Sizes: 
401s            61 135 178 197 255 406 437 448 510 568 637 716 778 815
401s obs        13  34   4  13  16   1   4  12  21   9  11  37   2   4
401s design.PSU 13  34   4  13  16   2   4  12  21   9  11  37   2   4
401s actual.PSU 13  34   4  13  16   1   4  12  21   9  11  37   2   4
401s Data variables:
401s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
401s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
401s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
401s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
401s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
401s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
401s [37] "api.stu"  "fpc"      "pw"      
401s > 
401s > options(survey.lonely.psu="fail")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.8909
401s > options(survey.lonely.psu="remove")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.8909
401s > options(survey.lonely.psu="certainty")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.8909
401s > options(survey.lonely.psu="adjust")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.8909
401s > options(survey.lonely.psu="average")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.8909
401s > 
401s > ## with adjustment
401s > options(survey.adjust.domain.lonely=TRUE)
401s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413))
401s > ds1<-ds[-31,]
401s > summary(ds1)
401s Stratified Independent Sampling design (with replacement)
401s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 
401s     dnum != 413))
401s Probabilities:
401s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
401s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 
401s Stratum Sizes: 
401s            61 135 178 197 255 406 437 448 510 568 637 716 778 815
401s obs        13  34   4  13  16   1   4  12  21   9  11  37   2   4
401s design.PSU 13  34   4  13  16   2   4  12  21   9  11  37   2   4
401s actual.PSU 13  34   4  13  16   1   4  12  21   9  11  37   2   4
401s Data variables:
401s  [1] "cds"      "stype"    "name"     "sname"    "snum"     "dname"   
401s  [7] "dnum"     "cname"    "cnum"     "flag"     "pcttest"  "api00"   
401s [13] "api99"    "target"   "growth"   "sch.wide" "comp.imp" "both"    
401s [19] "awards"   "meals"    "ell"      "yr.rnd"   "mobility" "acs.k3"  
401s [25] "acs.46"   "acs.core" "pct.resp" "not.hsg"  "hsg"      "some.col"
401s [31] "col.grad" "grad.sch" "avg.ed"   "full"     "emer"     "enroll"  
401s [37] "api.stu"  "fpc"      "pw"      
401s > 
401s > options(survey.lonely.psu="fail")
401s > try(svymean(~api00,ds1))
401s         mean     SE
401s api00 645.14 5.8909
401s > options(survey.lonely.psu="remove")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.8909
401s > options(survey.lonely.psu="certainty")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14Warning message:
401s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
401s   Stratum (406) has only one PSU at stage 1
401s Warning message:
401s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
401s   Stratum (406) has only one PSU at stage 1
401s Warning message:
401s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
401s   Stratum (406) has only one PSU at stage 1
401s Warning message:
401s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
401s   Stratum (406) has only one PSU at stage 1
401s Warning message:
401s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering),  :
401s   Stratum (406) has only one PSU at stage 1
401s  5.8909
401s > options(survey.lonely.psu="adjust")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 5.9119
401s > options(survey.lonely.psu="average")
401s > svymean(~api00,ds1)
401s         mean     SE
401s api00 645.14 6.0914
401s > 
401s > ## checks for `svytotal()`
401s > 
401s > df_w_singleton <- data.frame(
401s +   Stratum = c(1, 1, 2, 2, 3),
401s +   PSU = c(1, 2, 3, 4, 5),
401s +   Design_Weight = c(10.5, 10.5, 20, 20, 15),
401s +   Sex = c("M", "F", "F", "M",  "M"),
401s +   Age = c(30.5, 40.5, 35, 52, 44),
401s +   Height = c(6.2, 5.0, 5.3, 5.7, 5.5)
401s + )
401s > 
401s > design_w_singleton <- survey::svydesign(
401s +   data = df_w_singleton,
401s +   ids = ~ PSU, strata = ~ Stratum,
401s +   weights = ~ Design_Weight
401s + )
401s > 
401s > options("survey.lonely.psu" = "remove")
401s > 
401s > stopifnot(all.equal(
401s +   target = 126625,
401s +   current = as.numeric(
401s +     vcov(svytotal(x = ~ Age, design = design_w_singleton))
401s +   )
401s + ))
401s > 
401s > options("survey.lonely.psu" = "certainty")
401s > 
401s > stopifnot(all.equal(
401s +   target = 126625,
401s +   current = as.numeric(
401s +     vcov(svytotal(x = ~ Age, design = design_w_singleton))
401s +   )
401s + ))
401s > 
401s > options("survey.lonely.psu" = "adjust")
401s > 
401s > stopifnot(all.equal(
401s +   target = 127579.8,
401s +   current = as.numeric(
401s +     vcov(svytotal(x = ~ Age, design = design_w_singleton))
401s +   ),
401s +   scale = 127579.8, tolerance = 0.000001
401s + ))
401s > 
401s BEGIN TEST mtcars-var.R
401s 
401s R version 4.4.3 (2025-02-28) -- "Trophy Case"
401s Copyright (C) 2025 The R Foundation for Statistical Computing
401s Platform: s390x-ibm-linux-gnu
401s 
401s R is free software and comes with ABSOLUTELY NO WARRANTY.
401s You are welcome to redistribute it under certain conditions.
401s Type 'license()' or 'licence()' for distribution details.
401s 
401s R is a collaborative project with many contributors.
401s Type 'contributors()' for more information and
401s 'citation()' on how to cite R or R packages in publications.
401s 
401s Type 'demo()' for some demos, 'help()' for on-line help, or
401s 'help.start()' for an HTML browser interface to help.
401s Type 'q()' to quit R.
401s 
401s > library(survey)
401s Loading required package: grid
401s Loading required package: Matrix
402s Loading required package: survival
402s 
402s Attaching package: 'survey'
402s 
402s The following object is masked from 'package:graphics':
402s 
402s     dotchart
402s 
402s > 
402s > # don't throw an error on domains of size 1, just return NA
402s > input <- mtcars
402s > input$carb <- factor(input$carb)
402s > design <- svydesign(ids = ~0, weights = NULL, data = input)
402s > svyby(
402s +   ~mpg,
402s +   ~carb,
402s +   design,
402s +   svyvar
402s + )
402s   carb      mpg         se
402s 1    1 36.01619 11.2823286
402s 2    2 29.94444  9.0030898
402s 3    3  1.11000  0.4604066
402s 4    4 15.29656  4.3174617
402s 6    6       NA         NA
402s 8    8       NA         NA
402s > 
402s > 
402s > ## same n with na.rm=TRUE as subset(, !is.na)
402s > input$mpg[1]<-NA
402s > design <- svydesign(ids = ~0, weights = NULL, data = input)
402s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE),
402s +           svyvar(~mpg, subset(design, !is.na(mpg)))))
402s > 
402s BEGIN TEST multistage-rcpp.R
403s 
403s R version 4.4.3 (2025-02-28) -- "Trophy Case"
403s Copyright (C) 2025 The R Foundation for Statistical Computing
403s Platform: s390x-ibm-linux-gnu
403s 
403s R is free software and comes with ABSOLUTELY NO WARRANTY.
403s You are welcome to redistribute it under certain conditions.
403s Type 'license()' or 'licence()' for distribution details.
403s 
403s R is a collaborative project with many contributors.
403s Type 'contributors()' for more information and
403s 'citation()' on how to cite R or R packages in publications.
403s 
403s Type 'demo()' for some demos, 'help()' for on-line help, or
403s 'help.start()' for an HTML browser interface to help.
403s Type 'q()' to quit R.
403s 
403s > ## temporarily disable while it's being fixed
403s > ## q("no")
403s > 
403s > ## 
403s > ## Check that multistage() and multistage_rcpp() give same results
403s > ## for different options.
403s > ##
403s > library(survey)
403s Loading required package: grid
403s Loading required package: Matrix
403s Loading required package: survival
404s 
404s Attaching package: 'survey'
404s 
404s The following object is masked from 'package:graphics':
404s 
404s     dotchart
404s 
404s > 
404s > # Check for a simple random sample ----
404s > 
404s >   data('api', package = 'survey')
404s >   api_srs_design <- svydesign(
404s +     data = apisrs,
404s +     ids = ~ 1,
404s +     weights = ~ 1
404s +   )
404s >   
404s >   x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob)
404s >   
404s >   base_r_result <- survey:::multistage(x = x,
404s +                                        clusters = api_srs_design$cluster,
404s +                                        stratas = api_srs_design$strata,
404s +                                        nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize,
404s +                                        lonely.psu=getOption("survey.lonely.psu"),
404s +                                        one.stage=TRUE, stage = 1, cal = NULL)
404s >   
404s >   rcpp_result <- survey:::multistage_rcpp(x = x,
404s +                                           clusters = api_srs_design$cluster,
404s +                                           stratas = api_srs_design$strata,
404s +                                           nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize,
404s +                                           lonely.psu=getOption("survey.lonely.psu"),
404s +                                           one.stage=TRUE, stage = 1, cal = NULL)
404s >   
404s >   if (!isTRUE(all.equal(base_r_result, rcpp_result))) {
404s +     stop("Differences between `multistage()` and `multistage_rcpp()` for SRS")
404s +   }
404s >   
404s > # Check for a stratified simple random sample ----
404s >   
404s >   apistrat_design <- svydesign(
404s +     data = apistrat,
404s +     id =~ 1,
404s +     strata =~ stype,
404s +     weights =~ pw,
404s +     fpc =~ fpc
404s +   )
404s >   
404s >   x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob)
404s >   
404s >   base_r_result <- survey:::multistage(x = x,
404s +                                        clusters = apistrat_design$cluster,
404s +                                        stratas = apistrat_design$strata,
404s +                                        nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
404s +                                        lonely.psu=getOption("survey.lonely.psu"),
404s +                                        one.stage=TRUE, stage = 1, cal = NULL)
404s >   
404s >   rcpp_result <- survey:::multistage_rcpp(x = x,
404s +                                           clusters = apistrat_design$cluster,
404s +                                           stratas = apistrat_design$strata,
404s +                                           nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
404s +                                           lonely.psu=getOption("survey.lonely.psu"),
404s +                                           one.stage=TRUE, stage = 1, cal = NULL)
404s >   
404s >   if (!isTRUE(all.equal(base_r_result, rcpp_result))) {
404s +     stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample")
404s +   }
404s >   
404s >   ##_ Check whether expected true zeroes are actually computed as zeroes ----
404s >   
404s >   x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob))
404s >   
404s >   base_r_result <- survey:::multistage(x = x,
404s +                                        clusters = apistrat_design$cluster,
404s +                                        stratas = apistrat_design$strata,
404s +                                        nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
404s +                                        lonely.psu=getOption("survey.lonely.psu"),
404s +                                        one.stage=TRUE, stage = 1, cal = NULL)
404s >   
404s >   rcpp_result <- survey:::multistage_rcpp(x = x,
404s +                                           clusters = apistrat_design$cluster,
404s +                                           stratas = apistrat_design$strata,
404s +                                           nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize,
404s +                                           lonely.psu=getOption("survey.lonely.psu"),
404s +                                           one.stage=TRUE, stage = 1, cal = NULL)
404s >   
404s >   if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) {
404s +     stop("Computations which should equal zero do not.")
404s +   }
404s > 
404s > # Create a stratified, multistage design ----
404s >   
404s >   data(mu284)
404s >   
404s >   ## Create three strata, the third of which has only one PSU
404s >   mu284_stratified <- rbind(
404s +     transform(mu284, stratum = 1,
404s +               y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)),
404s +     transform(mu284, stratum = 2,
404s +               y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)),
404s +     transform(mu284[1,], stratum = 3,
404s +               y2 = y1 + 2)
404s +   )
404s >   
404s >   ## Create domain variables which yield a lonely PSU or a lonely SSU
404s >   mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19)
404s >   mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1)
404s >   
404s >   ## Create a survey design object with no lonely PSUs
404s >   dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3),
404s +                             strata = ~ stratum, nest = TRUE,
404s +                             id = ~ id1 + id2, fpc = ~ n1 + n2)
404s >   ## Create a survey design with one lonely PSU
404s >   dmu284_strat_w_lonely <- svydesign(data = mu284_stratified,
404s +                                      strata = ~ stratum, nest = TRUE,
404s +                                      id = ~ id1 + id2, fpc = ~ n1 + n2)
404s >   ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU
404s >   dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU)
404s >   dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU)
404s >   
404s >   
404s > # Check same results for different values of 'lonely PSU' options ----
404s >   
404s >   lonely_psu_options <- c(certainty = 'certainty',
404s +                           remove    = 'remove',
404s +                           average   = 'average',
404s +                           adjust    = 'adjust')
404s >   one_stage_options <- c(TRUE, FALSE)
404s >   
404s >   design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options,
404s +                                                'one.stage' = one_stage_options,
404s +                                                stringsAsFactors = FALSE)
404s >   design_lonely_psu_comparisons[['results_match']] <- NA
404s >   
404s >   ##_ Check for lonely PSUs caused by design ----
404s >   for (i in seq_len(nrow(design_lonely_psu_comparisons))) {
404s +     survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i]
404s +     one.stage <- design_lonely_psu_comparisons[['one.stage']][i]
404s +     options('survey.lonely.psu' = survey.lonely.psu)
404s +     
404s +     x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob)
404s +     
404s +     base_r_result <- survey:::multistage(x = x,
404s +                                          clusters = dmu284_strat_w_lonely$cluster,
404s +                                          stratas = dmu284_strat_w_lonely$strata,
404s +                                          nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize,
404s +                                          lonely.psu=getOption("survey.lonely.psu"),
404s +                                          one.stage=one.stage, stage = 1, cal = NULL)
404s +     
404s +     rcpp_result <- survey:::multistage_rcpp(x = x,
404s +                                             clusters = dmu284_strat_w_lonely$cluster,
404s +                                             stratas = dmu284_strat_w_lonely$strata,
404s +                                             nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize,
404s +                                             lonely.psu=getOption("survey.lonely.psu"),
404s +                                             one.stage=one.stage, stage = 1, cal = NULL)
404s +     
404s +       design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result))
404s +   }
404s >   
404s >   print(design_lonely_psu_comparisons)
404s   survey.lonely.psu one.stage results_match
404s 1         certainty      TRUE          TRUE
404s 2            remove      TRUE          TRUE
404s 3           average      TRUE          TRUE
404s 4            adjust      TRUE          TRUE
404s 5         certainty     FALSE          TRUE
404s 6            remove     FALSE          TRUE
404s 7           average     FALSE          TRUE
404s 8            adjust     FALSE          TRUE
404s >   if (!all(design_lonely_psu_comparisons$results_match)) {
404s +     stop("Results for design lonely PSUs differ between base R and Rcpp implementations.")
404s +   }
404s > 
404s >   ##_ Check for domain lonely PSUs caused by subsetting ----
404s >   
404s >   domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options,
404s +                                                'survey.adjust.domain.lonely' = c(FALSE, TRUE),
404s +                                                'one.stage' = one_stage_options,
404s +                                                stringsAsFactors = FALSE)
404s >   domain_lonely_psu_comparisons[['results_match']] <- NA
404s >   
404s >   for (i in seq_len(nrow(domain_lonely_psu_comparisons))) {
404s +       
404s +     options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i])
404s +     options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i])
404s +     one.stage <- domain_lonely_psu_comparisons[['one.stage']][i]
404s +     
404s +     
404s +     x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob)
404s +     suppressWarnings({
404s +       base_r_result <- survey:::multistage(x = x,
404s +                                            clusters = dmu284_strat_domain_lonely_psu$cluster,
404s +                                            stratas = dmu284_strat_domain_lonely_psu$strata,
404s +                                            nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize,
404s +                                            fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize,
404s +                                            lonely.psu=getOption("survey.lonely.psu"),
404s +                                            one.stage=one.stage, stage = 1, cal = NULL)
404s +     })
404s +     
404s +     rcpp_result <- survey:::multistage_rcpp(x = x,
404s +                                             clusters = dmu284_strat_domain_lonely_psu$cluster,
404s +                                             stratas = dmu284_strat_domain_lonely_psu$strata,
404s +                                             nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize,
404s +                                             fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize,
404s +                                             lonely.psu=getOption("survey.lonely.psu"),
404s +                                             one.stage=one.stage, stage = 1, cal = NULL)
404s +     
404s +     domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result))
404s +   }
404s Warning messages:
404s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas,  :
404s   At least one stratum contains only one PSU at stage 1
404s >   
404s >   print(domain_lonely_psu_comparisons)
404s    survey.lonely.psu survey.adjust.domain.lonely one.stage results_match
404s 1          certainty                       FALSE      TRUE          TRUE
404s 2             remove                       FALSE      TRUE          TRUE
404s 3            average                       FALSE      TRUE          TRUE
404s 4             adjust                       FALSE      TRUE          TRUE
404s 5          certainty                        TRUE      TRUE          TRUE
404s 6             remove                        TRUE      TRUE          TRUE
404s 7            average                        TRUE      TRUE          TRUE
404s 8             adjust                        TRUE      TRUE          TRUE
404s 9          certainty                       FALSE     FALSE          TRUE
404s 10            remove                       FALSE     FALSE          TRUE
404s 11           average                       FALSE     FALSE          TRUE
404s 12            adjust                       FALSE     FALSE          TRUE
404s 13         certainty                        TRUE     FALSE          TRUE
404s 14            remove                        TRUE     FALSE          TRUE
404s 15           average                        TRUE     FALSE          TRUE
404s 16            adjust                        TRUE     FALSE          TRUE
404s >   if (!all(domain_lonely_psu_comparisons$results_match)) {
404s +     stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.")
404s +   }
404s >   
404s > # Checks for edge cases ----
404s >   
404s >   ## Zero records ----
404s >   
404s >   zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent")
404s >   
404s >   zero_row_result <- survey:::multistage_rcpp(
404s +     x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]),
404s +     clusters = zero_row_design$cluster,
404s +     stratas = zero_row_design$strata,
404s +     nPSUs = zero_row_design$fpc$sampsize, 
404s +     fpcs = zero_row_design$fpc$popsize,
404s +     lonely.psu=getOption("survey.lonely.psu"),
404s +     one.stage=one.stage, stage = 1, cal = NULL
404s +   )
404s >   
404s >   if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) {
404s +     stop("`multistage_rcpp()` should return zeros for zero-row inputs.")
404s +   }
404s >   
404s > 
404s BEGIN TEST multistage.R
404s 
404s R version 4.4.3 (2025-02-28) -- "Trophy Case"
404s Copyright (C) 2025 The R Foundation for Statistical Computing
404s Platform: s390x-ibm-linux-gnu
404s 
404s R is free software and comes with ABSOLUTELY NO WARRANTY.
404s You are welcome to redistribute it under certain conditions.
404s Type 'license()' or 'licence()' for distribution details.
404s 
404s R is a collaborative project with many contributors.
404s Type 'contributors()' for more information and
404s 'citation()' on how to cite R or R packages in publications.
404s 
404s Type 'demo()' for some demos, 'help()' for on-line help, or
404s 'help.start()' for an HTML browser interface to help.
404s Type 'q()' to quit R.
404s 
404s > ## 
404s > ## Check that multistage samples still work
404s > ##
404s > library(survey)
404s Loading required package: grid
404s Loading required package: Matrix
405s Loading required package: survival
405s 
405s Attaching package: 'survey'
405s 
405s The following object is masked from 'package:graphics':
405s 
405s     dotchart
405s 
405s > example(mu284)
405s 
405s mu284> data(mu284)
405s 
405s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284))
405s 2 - level Cluster Sampling design
405s With (5, 15) clusters.
405s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284))
405s 
405s mu284> (ytotal<-svytotal(~y1, dmu284))
405s    total     SE
405s y1 15080 2274.3
405s 
405s mu284> vcov(ytotal)
405s         y1
405s y1 5172234
405s > 
405s > 
405s BEGIN TEST na_action.R
405s 
405s R version 4.4.3 (2025-02-28) -- "Trophy Case"
405s Copyright (C) 2025 The R Foundation for Statistical Computing
405s Platform: s390x-ibm-linux-gnu
405s 
405s R is free software and comes with ABSOLUTELY NO WARRANTY.
405s You are welcome to redistribute it under certain conditions.
405s Type 'license()' or 'licence()' for distribution details.
405s 
405s R is a collaborative project with many contributors.
405s Type 'contributors()' for more information and
405s 'citation()' on how to cite R or R packages in publications.
405s 
405s Type 'demo()' for some demos, 'help()' for on-line help, or
405s 'help.start()' for an HTML browser interface to help.
405s Type 'q()' to quit R.
405s 
405s > ## from Terry Therneau
405s > library(survey)
405s Loading required package: grid
405s Loading required package: Matrix
406s Loading required package: survival
406s 
406s Attaching package: 'survey'
406s 
406s The following object is masked from 'package:graphics':
406s 
406s     dotchart
406s 
406s > load("naa.rda")
406s > 
406s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times),  design= adata.s,na.action=na.exclude)
406s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times),  design= adata.s)
406s > all.equal(coef(fit1e),coef(fit1o))
406s [1] TRUE
406s > all.equal(vcov(fit1e),vcov(fit1o))
406s [1] TRUE
406s > 
406s BEGIN TEST newquantile.R
406s 
406s R version 4.4.3 (2025-02-28) -- "Trophy Case"
406s Copyright (C) 2025 The R Foundation for Statistical Computing
406s Platform: s390x-ibm-linux-gnu
406s 
406s R is free software and comes with ABSOLUTELY NO WARRANTY.
406s You are welcome to redistribute it under certain conditions.
406s Type 'license()' or 'licence()' for distribution details.
406s 
406s R is a collaborative project with many contributors.
406s Type 'contributors()' for more information and
406s 'citation()' on how to cite R or R packages in publications.
406s 
406s Type 'demo()' for some demos, 'help()' for on-line help, or
406s 'help.start()' for an HTML browser interface to help.
406s Type 'q()' to quit R.
406s 
406s > ## quantiles with equal weights
406s > 
406s > library(survey)
406s Loading required package: grid
406s Loading required package: Matrix
407s Loading required package: survival
407s 
407s Attaching package: 'survey'
407s 
407s > The following object is masked from 'package:graphics':
407s 
407s     dotchart
407s 
407s data(api)
407s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
407s > 
407s > 
407s > for(i in 1:9){
407s +     print(i)
407s +     all.equal(
407s +         as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))),
407s +         as.vector(quantile(apiclus1$ell,  c(0.2,0.5,0.9), type=i))
407s +     )
407s +     
407s + }
407s [1] 1
407s [1] 2
407s [1] 3
407s [1] 4
407s [1] 5
407s [1] 6
407s [1] 7
407s [1] 8
407s [1] 9
407s > 
407s BEGIN TEST nwts-cch.R
407s 
407s R version 4.4.3 (2025-02-28) -- "Trophy Case"
407s Copyright (C) 2025 The R Foundation for Statistical Computing
407s Platform: s390x-ibm-linux-gnu
407s 
407s R is free software and comes with ABSOLUTELY NO WARRANTY.
407s You are welcome to redistribute it under certain conditions.
407s Type 'license()' or 'licence()' for distribution details.
407s 
407s R is a collaborative project with many contributors.
407s Type 'contributors()' for more information and
407s 'citation()' on how to cite R or R packages in publications.
407s 
407s Type 'demo()' for some demos, 'help()' for on-line help, or
407s 'help.start()' for an HTML browser interface to help.
407s Type 'q()' to quit R.
407s 
407s > library(survey)
407s Loading required package: grid
407s Loading required package: Matrix
408s Loading required package: survival
408s 
408s Attaching package: 'survey'
408s 
408s > library(survival)
408s > data(nwtco)
408s The following object is masked from 'package:graphics':
408s 
408s     dotchart
408s 
408s > 
408s > ntwco<-subset(nwtco, !is.na(edrel))
408s > 
408s > load("nwtco-subcohort.rda")
408s > nwtco$subcohort<-subcohort
408s > 
408s > d_BorganII <- twophase(id=list(~seqno,~seqno),
408s +                        strata=list(NULL,~interaction(instit,rel)),
408s +                        data=nwtco, subset=~I(rel |subcohort))
409s > 
409s > ##Coefficient results same as Splus with code from
409s > ## http://faculty.washington.edu/norm/software.html
409s > ## SE slightly larger due to using sandwich variance.
409s > 
409s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII)
409s Call:
409s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 
409s     I(age/12), design = d_BorganII)
409s 
409s                    coef exp(coef) se(coef) robust se      z        p
409s factor(stage)2  0.46286   1.58861  0.23762   0.18087  2.559  0.01049
409s factor(stage)3  0.58309   1.79156  0.23965   0.17848  3.267  0.00109
409s factor(stage)4  1.05967   2.88541  0.26182   0.20524  5.163 2.43e-07
409s factor(histol)2 1.59744   4.94035  0.17688   0.13342 11.973  < 2e-16
409s I(age/12)       0.02994   1.03039  0.02942   0.03337  0.897  0.36972
409s 
409s Likelihood ratio test=  on 5 df, p=
409s n= 1062, number of events= 571 
409s > 
409s > ##
409s > ## This gives higher standard errors. calibrate() does not recompute the
409s > ## finite population correction if a calibration variable happens to predict
409s > ## sampling perfectly. It probably should.
409s > ##
409s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno),
409s +                            strata=list(NULL,~rel),
409s +                            data=nwtco, subset=~I(rel |subcohort)), 
409s +                         phase=2, formula=~interaction(instit,rel),
409s +                         epsilon=1e-10)
409s > 
409s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps)
409s Call:
409s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 
409s     I(age/12), design = d_BorganIIps)
409s 
409s                    coef exp(coef) se(coef) robust se      z        p
409s factor(stage)2  0.46286   1.58861  0.23762   0.18076  2.561  0.01045
409s factor(stage)3  0.58309   1.79156  0.23965   0.17838  3.269  0.00108
409s factor(stage)4  1.05967   2.88541  0.26182   0.20513  5.166 2.39e-07
409s factor(histol)2 1.59744   4.94035  0.17688   0.13044 12.246  < 2e-16
409s I(age/12)       0.02994   1.03039  0.02942   0.03331  0.899  0.36876
409s 
409s Likelihood ratio test=  on 5 df, p=
409s n= 1062, number of events= 571 
409s > 
409s BEGIN TEST nwts.R
409s 
409s R version 4.4.3 (2025-02-28) -- "Trophy Case"
409s Copyright (C) 2025 The R Foundation for Statistical Computing
409s Platform: s390x-ibm-linux-gnu
409s 
409s R is free software and comes with ABSOLUTELY NO WARRANTY.
409s You are welcome to redistribute it under certain conditions.
409s Type 'license()' or 'licence()' for distribution details.
409s 
409s R is a collaborative project with many contributors.
409s Type 'contributors()' for more information and
409s 'citation()' on how to cite R or R packages in publications.
409s 
409s Type 'demo()' for some demos, 'help()' for on-line help, or
409s 'help.start()' for an HTML browser interface to help.
409s Type 'q()' to quit R.
409s 
409s > 
409s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458
409s > ## data from Norman Breslow's web page.
409s > library(survey)
409s Loading required package: grid
409s Loading required package: Matrix
410s Loading required package: survival
410s 
410s Attaching package: 'survey'
410s 
410s The following object is masked from 'package:graphics':
410s 
410s     dotchart
410s 
410s > load("nwts.rda")
410s > nwtsnb<-nwts
410s > nwtsnb$case<-nwts$case-nwtsb$case
410s > nwtsnb$control<-nwts$control-nwtsb$control
410s > 
410s > a<-rbind(nwtsb,nwtsnb)
410s > a$in.ccs<-rep(c(TRUE,FALSE),each=16)
410s > 
410s > b<-rbind(a,a)
410s > b$rel<-rep(c(1,0),each=32)
410s > b$n<-ifelse(b$rel,b$case,b$control)
410s > 
410s > index<-rep(1:64,b$n)
410s > 
410s > nwt.exp<-b[index,c(1:3,6,7)]
410s > nwt.exp$id<-1:4088
410s > 
410s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs,
410s +                 strata=list(NULL,~interaction(instit,rel)),data=nwt.exp)
411s > 
411s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs,
411s +                 strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp)
411s > 
411s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel))
411s > 
411s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2))
411s 
411s Call:
411s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 
411s     family = quasibinomial)
411s 
411s Survey design:
411s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
411s     subset = subset, data = data, pps = pps)
411s 
411s Coefficients:
411s                                Estimate Std. Error t value Pr(>|t|)    
411s (Intercept)                     -2.5701     0.1288 -19.955  < 2e-16 ***
411s factor(stage)2                   0.5482     0.1979   2.769 0.005708 ** 
411s factor(stage)3                   0.4791     0.2032   2.359 0.018515 *  
411s factor(stage)4                   1.0037     0.2592   3.872 0.000114 ***
411s factor(histol)2                  1.3505     0.3107   4.346 1.51e-05 ***
411s factor(stage)2:factor(histol)2   0.1152     0.4410   0.261 0.793876    
411s factor(stage)3:factor(histol)2   0.5066     0.4241   1.194 0.232548    
411s factor(stage)4:factor(histol)2   0.9785     0.6214   1.575 0.115615    
411s ---
411s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
411s 
411s (Dispersion parameter for quasibinomial family taken to be 1.000876)
411s 
411s Number of Fisher Scoring iterations: 4
411s 
411s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8))
411s 
411s Call:
411s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 
411s     family = quasibinomial)
411s 
411s Survey design:
411s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
411s     subset = subset, data = data, pps = pps)
411s 
411s Coefficients:
411s                                Estimate Std. Error t value Pr(>|t|)    
411s (Intercept)                    -2.71604    0.10827 -25.085  < 2e-16 ***
411s factor(stage)2                  0.78141    0.14726   5.306 1.35e-07 ***
411s factor(stage)3                  0.80093    0.15250   5.252 1.80e-07 ***
411s factor(stage)4                  1.07293    0.17817   6.022 2.33e-09 ***
411s factor(histol)2                 1.45836    0.31780   4.589 4.96e-06 ***
411s factor(stage)2:factor(histol)2 -0.04743    0.43495  -0.109    0.913    
411s factor(stage)3:factor(histol)2  0.28064    0.41298   0.680    0.497    
411s factor(stage)4:factor(histol)2  0.90983    0.63774   1.427    0.154    
411s ---
411s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
411s 
411s (Dispersion parameter for quasibinomial family taken to be 1.000876)
411s 
411s Number of Fisher Scoring iterations: 4
411s 
411s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8))
411s 
411s Call:
411s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 
411s     family = quasibinomial)
411s 
411s Survey design:
411s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 
411s     rel))
411s 
411s Coefficients:
411s                                Estimate Std. Error t value Pr(>|t|)    
411s (Intercept)                    -2.71604    0.10878 -24.968  < 2e-16 ***
411s factor(stage)2                  0.78141    0.14729   5.305 1.35e-07 ***
411s factor(stage)3                  0.80093    0.15212   5.265 1.68e-07 ***
411s factor(stage)4                  1.07293    0.17905   5.993 2.77e-09 ***
411s factor(histol)2                 1.45836    0.31757   4.592 4.88e-06 ***
411s factor(stage)2:factor(histol)2 -0.04743    0.43432  -0.109    0.913    
411s factor(stage)3:factor(histol)2  0.28064    0.41231   0.681    0.496    
411s factor(stage)4:factor(histol)2  0.90983    0.63187   1.440    0.150    
411s ---
411s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
411s 
411s (Dispersion parameter for quasibinomial family taken to be 1.000876)
411s 
411s Number of Fisher Scoring iterations: 4
411s 
411s > 
411s > ## check subsets of calibrated designs.
411s > summary(svyglm(rel~factor(stage),
411s +                family=quasibinomial,design=subset(dccs8,histol==1)))
411s 
411s Call:
411s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 
411s     histol == 1), family = quasibinomial)
411s 
411s Survey design:
411s subset(dccs8, histol == 1)
411s 
411s Coefficients:
411s                Estimate Std. Error t value Pr(>|t|)    
411s (Intercept)     -2.7160     0.1083 -25.085  < 2e-16 ***
411s factor(stage)2   0.7814     0.1473   5.306 1.48e-07 ***
411s factor(stage)3   0.8009     0.1525   5.252 1.97e-07 ***
411s factor(stage)4   1.0729     0.1782   6.022 2.73e-09 ***
411s ---
411s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
411s 
411s (Dispersion parameter for quasibinomial family taken to be 1.001333)
411s 
411s Number of Fisher Scoring iterations: 4
411s 
411s > summary(svyglm(rel~factor(stage),
411s +                family=quasibinomial,design=subset(gccs8,histol==1)))
411s Warning messages:
411s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset.
411s 2: In summary.glm(g) :
411s   observations with zero weight not used for calculating dispersion
411s 3: In summary.glm(glm.object) :
411s   observations with zero weight not used for calculating dispersion
411s 4: In `[.twophase2`(design, nas == 0, ) :
411s   1 strata have only one PSU in this subset.
411s 5: In `[.twophase2`(design, nas == 0, ) :
411s   1 strata have only one PSU in this subset.
411s 
411s Call:
411s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 
411s     histol == 1), family = quasibinomial)
411s 
411s Survey design:
411s subset(gccs8, histol == 1)
411s 
411s Coefficients:
411s                Estimate Std. Error t value Pr(>|t|)    
411s (Intercept)     -2.7160     0.1082 -25.105  < 2e-16 ***
411s factor(stage)2   0.7814     0.1457   5.363 1.10e-07 ***
411s factor(stage)3   0.8009     0.1504   5.324 1.34e-07 ***
411s factor(stage)4   1.0729     0.1759   6.101 1.70e-09 ***
411s ---
411s Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
411s Warning messages:
411s 1: In summary.glm(g) :
411s   observations with zero weight not used for calculating dispersion
411s 2: In summary.glm(glm.object) :
411s   observations with zero weight not used for calculating dispersion
411s 
411s (Dispersion parameter for quasibinomial family taken to be 1.001333)
411s 
411s Number of Fisher Scoring iterations: 4
411s 
411s > 
411s > 
411s BEGIN TEST poisson.R
411s 
411s R version 4.4.3 (2025-02-28) -- "Trophy Case"
411s Copyright (C) 2025 The R Foundation for Statistical Computing
411s Platform: s390x-ibm-linux-gnu
411s 
411s R is free software and comes with ABSOLUTELY NO WARRANTY.
411s You are welcome to redistribute it under certain conditions.
411s Type 'license()' or 'licence()' for distribution details.
411s 
411s R is a collaborative project with many contributors.
411s Type 'contributors()' for more information and
411s 'citation()' on how to cite R or R packages in publications.
411s 
411s Type 'demo()' for some demos, 'help()' for on-line help, or
411s 'help.start()' for an HTML browser interface to help.
411s Type 'q()' to quit R.
411s 
411s > ## check poisson sampling
411s > library(survey)
411s Loading required package: grid
411s Loading required package: Matrix
412s Loading required package: survival
412s 
412s Attaching package: 'survey'
412s 
412s > data(api)
412s The following object is masked from 'package:graphics':
412s 
412s     dotchart
412s 
412s > set.seed(2021-7-15)
412s > apipop$prob<-apipop$api00/1000
412s > insample<-rbinom(nrow(apipop),1,apipop$prob)
412s > apipois<-apipop[insample,]
412s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois)
412s > 
412s > stopifnot(isTRUE(all.equal(
412s +  as.vector(SE(svytotal(~api00,design=des))),
412s +  as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob))))
412s +  )))
412s >  
412s > 
412s BEGIN TEST pps.R
412s 
412s R version 4.4.3 (2025-02-28) -- "Trophy Case"
412s Copyright (C) 2025 The R Foundation for Statistical Computing
412s Platform: s390x-ibm-linux-gnu
412s 
412s R is free software and comes with ABSOLUTELY NO WARRANTY.
412s You are welcome to redistribute it under certain conditions.
412s Type 'license()' or 'licence()' for distribution details.
412s 
412s R is a collaborative project with many contributors.
412s Type 'contributors()' for more information and
412s 'citation()' on how to cite R or R packages in publications.
412s 
412s Type 'demo()' for some demos, 'help()' for on-line help, or
412s 'help.start()' for an HTML browser interface to help.
412s Type 'q()' to quit R.
412s 
412s > library(survey)
412s Loading required package: grid
412s Loading required package: Matrix
413s Loading required package: survival
413s 
413s Attaching package: 'survey'
413s 
413s The following object is masked from 'package:graphics':
413s 
413s     dotchart
413s 
413s > data(election)
413s > 
413s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer")
413s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps)
413s > svytotal(~Bush+Kerry+Nader, dpps)
413s          total      SE
413s Bush  64518472 2447629
413s Kerry 51202102 2450787
413s Nader   478530  102420
413s > svytotal(~Bush+Kerry+Nader, dppswr)
413s          total      SE
413s Bush  64518472 2671455
413s Kerry 51202102 2679433
413s Nader   478530  105303
413s > 
413s > ##subsets
413s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0))
413s          total      SE
413s Bush  34944285 5399833
413s Kerry 25581714 4028434
413s Nader   478530  102420
413s > 
413s > ##multistage: should agree with STRS analysis
413s > data(api)
413s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2)
413s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2)
413s > 
413s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps))
413s [1] TRUE
413s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps))
414s [1] TRUE
414s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps))
414s [1] TRUE
414s > 
414s > ## the new without-replacement methods
414s > data(election)
414s > dpps_br<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="brewer")
414s > dpps_ov<- svydesign(id=~1,  fpc=~p, data=election_pps, pps="overton")
414s > dpps_hr<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40))
414s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR())
414s > dpps_ht<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=ppsmat(election_jointprob))
414s > ## Yates-Grundy type
414s > dpps_yg<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG")
414s > dpps_hryg<- svydesign(id=~1,  fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG")
414s > 
414s > ## The with-replacement approximation
414s > svytotal(~Bush+Kerry+Nader, dpps_ht)
414s          total      SE
414s Bush  64518472 2604404
414s Kerry 51202102 2523712
414s Nader   478530  102326
414s > svytotal(~Bush+Kerry+Nader, dpps_yg)
414s          total      SE
414s Bush  64518472 2406526
414s Kerry 51202102 2408091
414s Nader   478530  101664
414s > svytotal(~Bush+Kerry+Nader, dpps_hr)
414s          total      SE
414s Bush  64518472 2624662
414s Kerry 51202102 2525222
414s Nader   478530  102793
414s > svytotal(~Bush+Kerry+Nader, dpps_hryg)
414s          total      SE
414s Bush  64518472 2436738
414s Kerry 51202102 2439845
414s Nader   478530  102016
414s > svytotal(~Bush+Kerry+Nader, dpps_hr1)
414s          total      SE
414s Bush  64518472 2472753
414s Kerry 51202102 2426842
414s Nader   478530  102595
414s > svytotal(~Bush+Kerry+Nader, dpps_br)
414s          total      SE
414s Bush  64518472 2447629
414s Kerry 51202102 2450787
414s Nader   478530  102420
414s > svytotal(~Bush+Kerry+Nader, dpps_ov)
414s          total      SE
414s Bush  64518472 2939608
414s Kerry 51202102 1964632
414s Nader   478530  104373
414s > 
414s > ## subsets
414s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0))
414s          total      SE
414s Bush  34944285 5406348
414s Kerry 25581714 4047741
414s Nader   478530  102326
414s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0))
414s          total      SE
414s Bush  34944285 5377659
414s Kerry 25581714 4010908
414s Nader   478530  102016
414s > 
414s > ## counts
414s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht)
414s       I(Nader > 0) counts se
414s FALSE        FALSE     19  0
414s TRUE          TRUE     21  0
414s > 
414s BEGIN TEST qrule-swiss.R
414s 
414s R version 4.4.3 (2025-02-28) -- "Trophy Case"
414s Copyright (C) 2025 The R Foundation for Statistical Computing
414s Platform: s390x-ibm-linux-gnu
414s 
414s R is free software and comes with ABSOLUTELY NO WARRANTY.
414s You are welcome to redistribute it under certain conditions.
414s Type 'license()' or 'licence()' for distribution details.
414s 
414s R is a collaborative project with many contributors.
414s Type 'contributors()' for more information and
414s 'citation()' on how to cite R or R packages in publications.
414s 
414s Type 'demo()' for some demos, 'help()' for on-line help, or
414s 'help.start()' for an HTML browser interface to help.
414s Type 'q()' to quit R.
414s 
414s > library(survey)
414s Loading required package: grid
414s Loading required package: Matrix
415s Loading required package: survival
415s 
415s Attaching package: 'survey'
415s 
415s The following object is masked from 'package:graphics':
415s 
415s     dotchart
415s 
415s > 
415s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1)
415s > 
415s > design_no_strat <- svydesign(id = ~id, 
415s +                              probs = ~probs, 
415s +                              data = data_no_strat, 
415s +                              fpc = ~fpc)
415s > 
415s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99)
415s > 
415s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE,
415s +             interval.type = "mean", qrule = "hf1")
415s > 
415s > stopifnot(all(diff(res$x[,"quantile"])>=0))
415s > 
415s > 
415s > 
415s BEGIN TEST quantile.R
415s 
415s R version 4.4.3 (2025-02-28) -- "Trophy Case"
415s Copyright (C) 2025 The R Foundation for Statistical Computing
415s Platform: s390x-ibm-linux-gnu
415s 
415s R is free software and comes with ABSOLUTELY NO WARRANTY.
415s You are welcome to redistribute it under certain conditions.
415s Type 'license()' or 'licence()' for distribution details.
415s 
415s R is a collaborative project with many contributors.
415s Type 'contributors()' for more information and
415s 'citation()' on how to cite R or R packages in publications.
415s 
415s Type 'demo()' for some demos, 'help()' for on-line help, or
415s 'help.start()' for an HTML browser interface to help.
415s Type 'q()' to quit R.
415s 
415s > Loading required package: grid
415s library(survey)
415s Loading required package: Matrix
416s Loading required package: survival
416s 
416s Attaching package: 'survey'
416s 
416s The following object is masked from 'package:graphics':
416s 
416s     dotchart
416s 
416s > set.seed(42)
416s > 
416s > df<-data.frame(x=exp(rnorm(1000)))
416s > df$y<-round(df$x,1)
416s > ddf<-svydesign(id=~1,data=df)
416s > rdf<-as.svrepdesign(ddf)
416s Warning message:
416s In svydesign.default(id = ~1, data = df) :
416s   No weights or probabilities supplied, assuming equal probability
417s > 
417s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
417s       0.01        0.1        0.5        0.9       0.99 
417s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 
417s > 
417s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
417s                x
417s q0.01 0.01554946
417s q0.1  0.01425828
417s q0.5  0.03428012
417s q0.9  0.16457488
417s q0.99 1.88672412
417s > 
417s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
417s       0.01        0.1        0.5        0.9       0.99 
417s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 
417s > 
417s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
417s                x
417s q0.01 0.01556240
417s q0.1  0.01420086
417s q0.5  0.03430175
417s q0.9  0.16461019
417s q0.99 1.88818131
417s > 
417s > 
417s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald")
417s $quantiles
417s         0.01       0.1       0.5  0.9 0.99
417s y 0.02352941 0.2230769 0.9340909 3.55  9.4
417s 
417s $CIs
417s , , y
417s 
417s              0.01       0.1       0.5      0.9      0.99
417s (lower 0.01594200 0.2020115 0.8578143 3.207543  7.568142
417s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632
417s 
417s 
417s > 
417s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)
417s Statistic:
417s         y
417s q0.01 0.1
417s q0.1  0.3
417s q0.5  1.0
417s q0.9  3.6
417s q0.99 9.4
417s SE:
417s                y
417s q0.01 0.02547977
417s q0.1  0.02547977
417s q0.5  0.02547977
417s q0.9  0.15287859
417s q0.99 1.88302540
417s > 
417s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf)
417s $quantiles
417s         0.01       0.1       0.5  0.9 0.99
417s y 0.02352941 0.2230769 0.9340909 3.55  9.4
417s 
417s $CIs
417s , , y
417s 
417s              0.01       0.1       0.5      0.9      0.99
417s (lower 0.01594200 0.2020115 0.8578143 3.207543  7.568142
417s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632
417s 
417s 
417s > 
417s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf)
417s Statistic:
417s         y
417s q0.01 0.1
417s q0.1  0.3
417s q0.5  1.0
417s q0.9  3.6
417s q0.99 9.4
417s SE:
417s                y
417s q0.01 0.02551067
417s q0.1  0.02551067
417s q0.5  0.02551067
417s q0.9  0.15306404
417s q0.99 1.88450896
417s > 
417s > 
417s > 
417s > df<-data.frame(x=exp(rnorm(20)))
417s > df$y<-round(df$x,1)
417s > ddf<-svydesign(id=~1,data=df)
417s > rdf<-as.svrepdesign(ddf)
417s Warning message:
417s In svydesign.default(id = ~1, data = df) :
417s   No weights or probabilities supplied, assuming equal probability
417s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
417s       0.01        0.1        0.5        0.9       0.99 
417s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 
417s > 
417s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE))
417s                x
417s q0.01 0.00000000
417s q0.1  0.04598541
417s q0.5  0.25943731
417s q0.9  2.12343073
417s q0.99 1.91998924
417s > 
417s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
417s       0.01        0.1        0.5        0.9       0.99 
417s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 
417s > 
417s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf))
417s                x
417s q0.01 0.00000000
417s q0.1  0.04732818
417s q0.5  0.24957966
417s q0.9  2.25211815
417s q0.99 2.04043154
417s > 
417s > 
417s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald")
417s $quantiles
417s   0.01  0.1  0.5 0.9 0.99
417s y  0.1 0.15 0.75 2.4 8.68
417s 
417s $CIs
417s , , y
417s 
417s            0.01       0.1       0.5      0.9       0.99
417s (lower 0.100000 0.1000000 0.3674054 1.352279  0.5674674
417s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000
417s 
417s 
417s > 
417s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)
417s Statistic:
417s          y
417s q0.01 0.10
417s q0.1  0.20
417s q0.5  0.80
417s q0.9  2.40
417s q0.99 8.68
417s SE:
417s                y
417s q0.01 0.00000000
417s q0.1  0.02611112
417s q0.5  0.26542051
417s q0.9  2.10908603
417s q0.99 1.91777710
417s > 
417s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf)
417s $quantiles
417s   0.01  0.1  0.5 0.9 0.99
417s y  0.1 0.15 0.75 2.4 8.68
417s 
417s $CIs
417s , , y
417s 
417s            0.01       0.1       0.5      0.9       0.99
417s (lower 0.100000 0.1000000 0.3674054 1.352279  0.5674674
417s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000
417s 
417s 
417s > 
417s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf)
417s Statistic:
417s          y
417s q0.01 0.10
417s q0.1  0.20
417s q0.5  0.80
417s q0.9  2.40
417s q0.99 8.68
417s SE:
417s                y
417s q0.01 0.00000000
417s q0.1  0.02551067
417s q0.5  0.25244616
417s q0.9  2.23558589
417s q0.99 2.03881114
417s > 
417s BEGIN TEST quantiles-chile.R
417s 
417s R version 4.4.3 (2025-02-28) -- "Trophy Case"
417s Copyright (C) 2025 The R Foundation for Statistical Computing
417s Platform: s390x-ibm-linux-gnu
417s 
417s R is free software and comes with ABSOLUTELY NO WARRANTY.
417s You are welcome to redistribute it under certain conditions.
417s Type 'license()' or 'licence()' for distribution details.
417s 
417s R is a collaborative project with many contributors.
417s Type 'contributors()' for more information and
417s 'citation()' on how to cite R or R packages in publications.
417s 
417s Type 'demo()' for some demos, 'help()' for on-line help, or
417s 'help.start()' for an HTML browser interface to help.
417s Type 'q()' to quit R.
417s 
418s > library(survey)
418s Loading required package: grid
418s Loading required package: Matrix
418s Loading required package: survival
418s 
418s Attaching package: 'survey'
418s 
418s The following object is masked from 'package:graphics':
418s 
418s     dotchart
418s 
418s > datos <- readRDS("datos_ejemplo.rds")
418s > 
418s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos)
418s > set.seed(234262762)
418s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20)
418s > options(survey.lonely.psu="remove")
418s > 
418s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"]
418s > 
418s > suppressWarnings({
418s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math"))
418s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school"))
418s + })
419s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5)))
419s [1] TRUE
419s > 
419s > suppressWarnings({
419s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math"))
419s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school"))
419s + })
419s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5)))
419s [1] TRUE
419s > 
419s BEGIN TEST rakecheck.R
419s 
419s R version 4.4.3 (2025-02-28) -- "Trophy Case"
419s Copyright (C) 2025 The R Foundation for Statistical Computing
419s Platform: s390x-ibm-linux-gnu
419s 
419s R is free software and comes with ABSOLUTELY NO WARRANTY.
419s You are welcome to redistribute it under certain conditions.
419s Type 'license()' or 'licence()' for distribution details.
419s 
419s R is a collaborative project with many contributors.
419s Type 'contributors()' for more information and
419s 'citation()' on how to cite R or R packages in publications.
419s 
419s Type 'demo()' for some demos, 'help()' for on-line help, or
419s 'help.start()' for an HTML browser interface to help.
419s Type 'q()' to quit R.
419s 
419s > library(survey)
419s Loading required package: grid
419s Loading required package: Matrix
419s Loading required package: survival
420s 
420s Attaching package: 'survey'
420s 
420s The following object is masked from 'package:graphics':
420s 
420s     dotchart
420s 
420s > 
420s > data(api)
420s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
420s > rclus1 <- as.svrepdesign(dclus1)
420s > 
420s > ## population marginal totals for each stratum
420s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
420s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
420s > 
420s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
420s > 
420s > svymean(~api00, rclus1r)
420s         mean     SE
420s api00 641.23 26.873
420s > svytotal(~enroll, rclus1r)
420s          total     SE
420s enroll 3647300 463511
420s > 
420s > ff<-~stype+sch.wide
420s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop)))
420s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking")
420s > 
420s > svymean(~api00,rclus1g)
420s         mean     SE
420s api00 641.23 26.874
420s > svytotal(~enroll,rclus1g)
420s          total     SE
420s enroll 3647280 463582
420s > 
420s > summary(weights(rclus1g)/weights(rclus1r))
420s        V1           V2          V3          V4           V5          V6   
420s  Min.   :1    Min.   :1   Min.   :1   Min.   :1    Min.   :1   Min.   :1  
420s  1st Qu.:1    1st Qu.:1   1st Qu.:1   1st Qu.:1    1st Qu.:1   1st Qu.:1  
420s  Median :1    Median :1   Median :1   Median :1    Median :1   Median :1  
420s  Mean   :1    Mean   :1   Mean   :1   Mean   :1    Mean   :1   Mean   :1  
420s  3rd Qu.:1    3rd Qu.:1   3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1  
420s  Max.   :1    Max.   :1   Max.   :1   Max.   :1    Max.   :1   Max.   :1  
420s  NA's   :11   NA's   :4   NA's   :2   NA's   :13   NA's   :2   NA's   :4  
420s        V7          V8           V9         V10          V11    
420s  Min.   :1   Min.   :1    Min.   :1   Min.   :1    Min.   :1   
420s  1st Qu.:1   1st Qu.:1    1st Qu.:1   1st Qu.:1    1st Qu.:1   
420s  Median :1   Median :1    Median :1   Median :1    Median :1   
420s  Mean   :1   Mean   :1    Mean   :1   Mean   :1    Mean   :1   
420s  3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1    3rd Qu.:1   
420s  Max.   :1   Max.   :1    Max.   :1   Max.   :1    Max.   :1   
420s  NA's   :4   NA's   :16   NA's   :9   NA's   :34   NA's   :21  
420s       V12              V13          V14         V15    
420s  Min.   :0.9997   Min.   :1    Min.   :1   Min.   :1   
420s  1st Qu.:1.0001   1st Qu.:1    1st Qu.:1   1st Qu.:1   
420s  Median :1.0001   Median :1    Median :1   Median :1   
420s  Mean   :1.0000   Mean   :1    Mean   :1   Mean   :1   
420s  3rd Qu.:1.0001   3rd Qu.:1    3rd Qu.:1   3rd Qu.:1   
420s  Max.   :1.0002   Max.   :1    Max.   :1   Max.   :1   
420s  NA's   :37       NA's   :13   NA's   :1   NA's   :12  
420s > 
420s > 
420s > ## Do it for a design without replicate weights
420s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
420s > 
420s > svymean(~api00, dclus1r)
420s         mean     SE
420s api00 641.23 23.704
420s > svytotal(~enroll, dclus1r)
420s          total     SE
420s enroll 3647300 400603
420s > 
420s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking")
420s > 
420s > svymean(~api00,dclus1g)
420s         mean     SE
420s api00 641.23 23.704
420s > svytotal(~enroll,dclus1g)
420s          total     SE
420s enroll 3647280 400603
420s > 
420s > summary(weights(dclus1g)/weights(dclus1r))
420s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
420s       1       1       1       1       1       1 
420s > 
420s > 
420s > 
420s > ## Example of raking with partial joint distributions
420s > pop.table <- xtabs(~stype+sch.wide,apipop)
420s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482))
420s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp),
420s +                list(pop.table, pop.imp))
420s > svymean(~api00, dclus1r2)
420s         mean     SE
420s api00 642.62 22.732
420s > 
420s > ff1 <-~stype*sch.wide+comp.imp
420s > 
420s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop)))
420s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking")
420s > 
420s > svymean(~api00, dclus1g2)
420s         mean     SE
420s api00 642.61 22.731
420s > 
420s > summary(weights(dclus1r2)/weights(dclus1g2))
420s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
420s   0.999   1.000   1.000   1.000   1.000   1.002 
420s > 
420s BEGIN TEST raowuboot.R
420s 
420s R version 4.4.3 (2025-02-28) -- "Trophy Case"
420s Copyright (C) 2025 The R Foundation for Statistical Computing
420s Platform: s390x-ibm-linux-gnu
420s 
420s R is free software and comes with ABSOLUTELY NO WARRANTY.
420s You are welcome to redistribute it under certain conditions.
420s Type 'license()' or 'licence()' for distribution details.
420s 
420s R is a collaborative project with many contributors.
420s Type 'contributors()' for more information and
420s 'citation()' on how to cite R or R packages in publications.
420s 
420s Type 'demo()' for some demos, 'help()' for on-line help, or
420s 'help.start()' for an HTML browser interface to help.
420s Type 'q()' to quit R.
420s 
420s Loading required package: grid
420s > ## regression test for bug reported by Richard Valliant
420s > library(survey)
420s Loading required package: Matrix
421s Loading required package: survival
421s 
421s Attaching package: 'survey'
421s 
421s The following object is masked from 'package:graphics':
421s 
421s     dotchart
421s 
421s > s<-subbootweights(c(1,1),1:2, 50)
421s > stopifnot(all(s$repweights$weights %in% c(0,2)))
421s > 
421s BEGIN TEST regTermTest-missing.R
421s 
421s R version 4.4.3 (2025-02-28) -- "Trophy Case"
421s Copyright (C) 2025 The R Foundation for Statistical Computing
421s Platform: s390x-ibm-linux-gnu
421s 
421s R is free software and comes with ABSOLUTELY NO WARRANTY.
421s You are welcome to redistribute it under certain conditions.
421s Type 'license()' or 'licence()' for distribution details.
421s 
421s R is a collaborative project with many contributors.
421s Type 'contributors()' for more information and
421s 'citation()' on how to cite R or R packages in publications.
421s 
421s Type 'demo()' for some demos, 'help()' for on-line help, or
421s 'help.start()' for an HTML browser interface to help.
421s Type 'q()' to quit R.
421s 
421s Loading required package: grid
421s > library(survey)
421s Loading required package: Matrix
422s Loading required package: survival
422s 
422s Attaching package: 'survey'
422s 
422s The following object is masked from 'package:graphics':
422s 
422s     dotchart
422s 
422s > data(nhanes)
422s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes)
422s > 
422s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR,  design = subset(design,!is.na(HI_CHOL)), family=quasibinomial)
422s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR,  design =design , family=quasibinomial)
422s > 
422s > ta<-regTermTest(a, ~HI_CHOL)
422s > tb<-regTermTest(b, ~HI_CHOL)
422s > 
422s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq)))
422s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda)))
422s > 
422s BEGIN TEST regpredict.R
422s 
422s R version 4.4.3 (2025-02-28) -- "Trophy Case"
422s Copyright (C) 2025 The R Foundation for Statistical Computing
422s Platform: s390x-ibm-linux-gnu
422s 
422s R is free software and comes with ABSOLUTELY NO WARRANTY.
422s You are welcome to redistribute it under certain conditions.
422s Type 'license()' or 'licence()' for distribution details.
422s 
422s R is a collaborative project with many contributors.
422s Type 'contributors()' for more information and
422s 'citation()' on how to cite R or R packages in publications.
422s 
422s Type 'demo()' for some demos, 'help()' for on-line help, or
422s 'help.start()' for an HTML browser interface to help.
422s Type 'q()' to quit R.
422s 
422s > library(survey)
422s Loading required package: grid
422s Loading required package: Matrix
423s Loading required package: survival
423s 
423s Attaching package: 'survey'
423s 
423s > data(api)
423s The following object is masked from 'package:graphics':
423s 
423s     dotchart
423s 
423s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
423s > 
423s > 
423s > ## regression estimator of total, three ways
423s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE))
423s > npop <- sum(!is.na(apipop$enroll))
423s > 
423s > api.reg <- svyglm(api.stu~enroll, design=dstrat)
423s > a <- predict(api.reg, newdata=pop, total=npop)
423s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll)))
423s > 
423s > all.equal(as.vector(coef(a)),as.vector(coef(b)))
423s [1] TRUE
423s > all.equal(as.vector(SE(a)), as.vector(SE(b)))
423s [1] TRUE
423s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix
423s +     d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE]))
423s +     all.equal(as.vector(coef(a)), as.vector(sum(coef(d))))
423s +     all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d)))))
423s + }
423s > 
423s > ## classical ratio estimator, four ways.
423s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat,
423s +                    family=quasi(link="identity", var="mu"))
423s > 
423s > a <- predict(api.reg2, newdata=pop, total=npop)
423s > b <- svytotal(~api.stu,
423s +               calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2))
423s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll)
423s > 
423s > all.equal(as.vector(coef(a)),as.vector(coef(b)))
423s [1] TRUE
423s > all.equal(as.vector(SE(a)), as.vector(SE(b)))
423s [1] TRUE
423s > all.equal(as.vector(coef(a)),as.vector(e$total))
423s [1] TRUE
423s > all.equal(as.vector(SE(a)), as.vector(e$se))
423s [1] TRUE
423s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix
423s +     d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE]))
423s +     all.equal(as.vector(coef(a)), as.vector(sum(coef(d))))
423s +     all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d)))))
423s + }
423s > 
423s BEGIN TEST rss_scores.R
423s 
423s R version 4.4.3 (2025-02-28) -- "Trophy Case"
423s Copyright (C) 2025 The R Foundation for Statistical Computing
423s Platform: s390x-ibm-linux-gnu
423s 
423s R is free software and comes with ABSOLUTELY NO WARRANTY.
423s You are welcome to redistribute it under certain conditions.
423s Type 'license()' or 'licence()' for distribution details.
423s 
423s R is a collaborative project with many contributors.
423s Type 'contributors()' for more information and
423s 'citation()' on how to cite R or R packages in publications.
423s 
423s Type 'demo()' for some demos, 'help()' for on-line help, or
423s 'help.start()' for an HTML browser interface to help.
423s Type 'q()' to quit R.
423s 
424s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica
424s > library(survey)
424s Loading required package: grid
424s Loading required package: Matrix
424s Loading required package: survival
425s 
425s Attaching package: 'survey'
425s 
425s The following object is masked from 'package:graphics':
425s 
425s     dotchart
425s 
425s > data(myco)
425s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco)
425s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco)
425s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco)
425s > 
425s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2)))
425s > 
425s > s<-svyscoretest(m_full, ~Scar)
425s > stopifnot(abs(s[1]-10.73)<0.05)
425s > 
425s > t<-svyscoretest(m_full,~Scar,method="individual")
425s > stopifnot(abs(coef(t)- -32.61)<0.1)
425s > stopifnot(abs(vcov(t)-99.1)<0.1)
425s >  
425s > 
425s BEGIN TEST scoping.R
425s 
425s R version 4.4.3 (2025-02-28) -- "Trophy Case"
425s Copyright (C) 2025 The R Foundation for Statistical Computing
425s Platform: s390x-ibm-linux-gnu
425s 
425s R is free software and comes with ABSOLUTELY NO WARRANTY.
425s You are welcome to redistribute it under certain conditions.
425s Type 'license()' or 'licence()' for distribution details.
425s 
425s R is a collaborative project with many contributors.
425s Type 'contributors()' for more information and
425s 'citation()' on how to cite R or R packages in publications.
425s 
425s Type 'demo()' for some demos, 'help()' for on-line help, or
425s 'help.start()' for an HTML browser interface to help.
425s Type 'q()' to quit R.
425s 
425s > 
425s > ## regression test for testing regression
425s > 
425s > library(survey)
425s Loading required package: grid
425s Loading required package: Matrix
426s Loading required package: survival
426s 
426s Attaching package: 'survey'
426s 
426s The following object is masked from 'package:graphics':
426s 
426s     dotchart
426s 
426s > data(api)
426s > 
426s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
426s > 
426s > 
426s > f<-function(){
426s +   form<-acs.46~stype
426s +   svyglm(formula=form, design = dstrat)  
426s + }
426s > 
426s > g<-function(form){
426s +   svyglm(formula=form, design = dstrat)  
426s + }
426s > f()
426s Stratified Independent Sampling design
426s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
426s     fpc = ~fpc)
426s 
426s Call:  svyglm(formula = form, design = dstrat)
426s 
426s Coefficients:
426s (Intercept)       stypeH       stypeM  
426s     28.7449       0.7551       0.4022  
426s 
426s Degrees of Freedom: 133 Total (i.e. Null);  129 Residual
426s   (66 observations deleted due to missingness)
426s Null Deviance:	    1838 
426s Residual Deviance: 1835 	AIC: 719.8
426s > g(acs.46~stype)
426s Stratified Independent Sampling design
426s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 
426s     fpc = ~fpc)
426s 
426s Call:  svyglm(formula = form, design = dstrat)
426s 
426s Coefficients:
426s (Intercept)       stypeH       stypeM  
426s     28.7449       0.7551       0.4022  
426s 
426s Degrees of Freedom: 133 Total (i.e. Null);  129 Residual
426s   (66 observations deleted due to missingness)
426s Null Deviance:	    1838 
426s Residual Deviance: 1835 	AIC: 719.8
426s > 
426s > f<-function(){
426s +   form<-Surv(acs.46)~stype
426s +   svycoxph(formula=form, design = dstrat)  
426s + }
426s > 
426s > g<-function(form){
426s +   svycoxph(formula=form, design = dstrat)  
426s + }
426s > 
426s > f()
426s Call:
426s svycoxph(formula = form, design = dstrat)
426s 
426s           coef exp(coef) se(coef) robust se      z     p
426s stypeH -0.6766    0.5083   1.0208    0.6652 -1.017 0.309
426s stypeM -0.2509    0.7781   0.2308    0.2089 -1.201 0.230
426s 
426s Likelihood ratio test=  on 2 df, p=
426s n= 134, number of events= 134 
426s    (66 observations deleted due to missingness)
426s > g(Surv(acs.46)~stype)
426s Call:
426s svycoxph(formula = form, design = dstrat)
426s 
426s           coef exp(coef) se(coef) robust se      z     p
426s stypeH -0.6766    0.5083   1.0208    0.6652 -1.017 0.309
426s stypeM -0.2509    0.7781   0.2308    0.2089 -1.201 0.230
426s 
426s Likelihood ratio test=  on 2 df, p=
426s n= 134, number of events= 134 
426s    (66 observations deleted due to missingness)
426s > 
426s > ## check coxph for a single predictor
426s > svycoxph(Surv(acs.46)~api00,design=dstrat)
426s Call:
426s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat)
426s 
426s            coef exp(coef)  se(coef) robust se     z     p
426s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994
426s 
426s Likelihood ratio test=  on 1 df, p=
426s n= 134, number of events= 134 
426s    (66 observations deleted due to missingness)
426s > 
426s BEGIN TEST survcurve.R
426s 
426s R version 4.4.3 (2025-02-28) -- "Trophy Case"
426s Copyright (C) 2025 The R Foundation for Statistical Computing
426s Platform: s390x-ibm-linux-gnu
426s 
426s R is free software and comes with ABSOLUTELY NO WARRANTY.
426s You are welcome to redistribute it under certain conditions.
426s Type 'license()' or 'licence()' for distribution details.
426s 
426s R is a collaborative project with many contributors.
426s Type 'contributors()' for more information and
426s 'citation()' on how to cite R or R packages in publications.
426s 
426s Type 'demo()' for some demos, 'help()' for on-line help, or
426s 'help.start()' for an HTML browser interface to help.
426s Type 'q()' to quit R.
426s 
426s > library(survey)
426s Loading required package: grid
426s Loading required package: Matrix
427s Loading required package: survival
428s 
428s Attaching package: 'survey'
428s 
428s > library(survival)
428s > 
428s > pbc2<-rbind(pbc,pbc)
428s The following object is masked from 'package:graphics':
428s 
428s     dotchart
428s 
428s > pbc2$id<-rep(1:418,2)
428s > 
428s > dpbc1<-svydesign(id=~1, data=pbc)
428s Warning message:
428s In svydesign.default(id = ~1, data = pbc) :
428s   No weights or probabilities supplied, assuming equal probability
428s > dpbc2<-svydesign(id=~id, data=pbc2)
428s > 
428s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE)
428s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE)
428s Warning message:
428s In svydesign.default(id = ~id, data = pbc2) :
428s   No weights or probabilities supplied, assuming equal probability
428s > 
428s > (c1<-confint(s1,(1:5)*365))
428s          0.025     0.975
428s 365  0.6446215 0.8594153
428s 730  0.5410938 0.7766848
428s 1095 0.2683127 0.5103356
428s 1460 0.1444731 0.3722001
428s 1825 0.1009672 0.3204713
428s > (c2<-confint(s2,(1:5)*365))
428s          0.025     0.975
428s 365  0.6446215 0.8594153
428s 730  0.5410938 0.7766848
428s 1095 0.2683127 0.5103356
428s 1460 0.1444731 0.3722001
428s 1825 0.1009672 0.3204713
428s > all.equal(c1, c2)
428s [1] TRUE
428s > 
428s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1)
428s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2)
428s > 
428s > d<-data.frame(bili=c(5,10))
428s > p1<-predict(m1, se=TRUE, newdata=d,type="curve")
428s > p2<-predict(m2, se=TRUE, newdata=d,type="curve")
430s > 
430s > (pc1<-confint(p1[[1]],(1:5)*365))
430s          0.025     0.975
430s 365  0.8410027 0.9266263
430s 730  0.7371114 0.8548312
430s 1095 0.5517779 0.7018583
430s 1460 0.4335073 0.5992819
430s 1825 0.3260899 0.5046241
430s > (pc2<-confint(p2[[1]],(1:5)*365))
430s          0.025     0.975
430s 365  0.8409490 0.9267054
430s 730  0.7370152 0.8549432
430s 1095 0.5515848 0.7019513
430s 1460 0.4332252 0.5992968
430s 1825 0.3257172 0.5045795
430s > all.equal(pc1, pc2)
430s [1] "Mean relative difference: 0.0002070722"
430s > 
430s > (q1<-quantile(p1[[2]]))
430s 0.75  0.5 0.25 
430s  489  930 1492 
430s > (q2<-quantile(p2[[2]]))
430s 0.75  0.5 0.25 
430s  489  930 1492 
430s > all.equal(q1,q2)
430s [1] TRUE
430s > 
430s BEGIN TEST svyby-strings.R
430s 
430s R version 4.4.3 (2025-02-28) -- "Trophy Case"
430s Copyright (C) 2025 The R Foundation for Statistical Computing
430s Platform: s390x-ibm-linux-gnu
430s 
430s R is free software and comes with ABSOLUTELY NO WARRANTY.
430s You are welcome to redistribute it under certain conditions.
430s Type 'license()' or 'licence()' for distribution details.
430s 
430s R is a collaborative project with many contributors.
430s Type 'contributors()' for more information and
430s 'citation()' on how to cite R or R packages in publications.
430s 
430s Type 'demo()' for some demos, 'help()' for on-line help, or
430s 'help.start()' for an HTML browser interface to help.
430s Type 'q()' to quit R.
430s 
430s > 
430s > ## check that stringsAsFactors fixes the string levels problem
430s > data(api, package = "survey")
430s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
431s > est0 <-
431s +   survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 
431s > 
431s > stopifnot(isTRUE(all(dim(est0)==c(2,23))))
431s > 
431s BEGIN TEST svyby_bug.R
431s 
431s R version 4.4.3 (2025-02-28) -- "Trophy Case"
431s Copyright (C) 2025 The R Foundation for Statistical Computing
431s Platform: s390x-ibm-linux-gnu
431s 
431s R is free software and comes with ABSOLUTELY NO WARRANTY.
431s You are welcome to redistribute it under certain conditions.
431s Type 'license()' or 'licence()' for distribution details.
431s 
431s R is a collaborative project with many contributors.
431s Type 'contributors()' for more information and
431s 'citation()' on how to cite R or R packages in publications.
431s 
431s Type 'demo()' for some demos, 'help()' for on-line help, or
431s 'help.start()' for an HTML browser interface to help.
431s Type 'q()' to quit R.
431s 
431s > library(survey)
431s Loading required package: grid
431s Loading required package: Matrix
432s Loading required package: survival
432s 
432s Attaching package: 'survey'
432s 
432s The following object is masked from 'package:graphics':
432s 
432s     dotchart
432s 
432s > options(warn=2)
432s > 
432s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob)
432s > data(api)
432s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
432s > svyby(~api99, ~stype, dclus1, svymean )
432s   stype    api99       se
432s E     E 607.7917 22.81660
432s H     H 595.7143 41.76400
432s M     M 608.6000 32.56064
432s > 
432s > set.seed(123)
432s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA
432s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
432s > 
432s > # subsetting w/ na.rm = FALSE...
432s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE )
432s       mean SE
432s api99   NA NA
432s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE )
432s         mean     SE
432s api99 595.71 41.764
432s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE )
432s       mean SE
432s api99   NA NA
432s > 
432s > # ... looks like this:
432s > svyby(~api99, ~stype, dclus1.na , svymean )
432s   stype    api99     se
432s E     E       NA     NA
432s H     H 595.7143 41.764
432s M     M       NA     NA
432s > 
432s > # subsetting w/ na.rm = TRUE...
432s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE )
432s         mean     SE
432s api99 606.53 22.901
432s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE )
432s         mean     SE
432s api99 595.71 41.764
432s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE )
432s         mean     SE
432s api99 613.39 33.224
432s > 
432s > # ... looks like this
432s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE )
432s   stype    api99       se
432s E     E 606.5319 22.90084
432s H     H 595.7143 41.76400
432s M     M 613.3913 33.22358
432s > 
432s > # Without missing values, this works:
432s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE )
432s   stype    api99       se
432s E     E 607.7917 22.81660
432s H     H 595.7143 41.76400
432s M     M 608.6000 32.56064
432s > 
432s > # ... but this breaks!
432s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE )
432s   stype    api99       se
432s E     E 606.5319 22.90084
432s H     H 595.7143 41.76400
432s M     M 613.3913 33.22358
432s > 
432s > # ... and i don't think this is the expected behavior
432s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE )
432s   stype    api99     se
432s E     E       NA     NA
432s H     H 595.7143 41.764
432s M     M       NA     NA
432s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE )
432s   stype    api99       se
432s E     E 606.5319 22.90084
432s H     H 595.7143 41.76400
432s M     M 613.3913 33.22358
432s > 
432s > 
432s > ## <TL> Now some more as tests
432s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE )
432s   stype     api99       se
432s E     E 2894629.0 792809.8
432s H     H  282283.9 101492.9
432s M     M  477513.4 107555.5
432s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE )
432s   stype api99/api00 se.api99/api00
432s E     E   0.9367750    0.006365702
432s H     H   0.9630485    0.010520785
432s M     M   0.9682246    0.009390982
432s > 
432s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...)
432s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE )
432s   stype (Intercept) se.(Intercept)
432s E     E    606.5319       22.90084
432s H     H    595.7143       41.76400
432s M     M    613.3913       33.22358
432s > 
432s BEGIN TEST svyby_se.R
432s 
432s R version 4.4.3 (2025-02-28) -- "Trophy Case"
432s Copyright (C) 2025 The R Foundation for Statistical Computing
432s Platform: s390x-ibm-linux-gnu
432s 
432s R is free software and comes with ABSOLUTELY NO WARRANTY.
432s You are welcome to redistribute it under certain conditions.
432s Type 'license()' or 'licence()' for distribution details.
432s 
432s R is a collaborative project with many contributors.
432s Type 'contributors()' for more information and
432s 'citation()' on how to cite R or R packages in publications.
432s 
432s Type 'demo()' for some demos, 'help()' for on-line help, or
432s 'help.start()' for an HTML browser interface to help.
432s Type 'q()' to quit R.
432s 
432s > library(survey)
432s Loading required package: grid
432s Loading required package: Matrix
433s Loading required package: survival
433s 
433s Attaching package: 'survey'
433s 
433s The following object is masked from 'package:graphics':
433s 
433s     dotchart
433s 
433s > data(api)
433s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
433s > 
433s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se"))
433s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci"))
433s > 
433s > 
433s > stopifnot(all.equal(SE(a),SE(b)))
433s > 
433s BEGIN TEST svycontrast.R
434s 
434s R version 4.4.3 (2025-02-28) -- "Trophy Case"
434s Copyright (C) 2025 The R Foundation for Statistical Computing
434s Platform: s390x-ibm-linux-gnu
434s 
434s R is free software and comes with ABSOLUTELY NO WARRANTY.
434s You are welcome to redistribute it under certain conditions.
434s Type 'license()' or 'licence()' for distribution details.
434s 
434s R is a collaborative project with many contributors.
434s Type 'contributors()' for more information and
434s 'citation()' on how to cite R or R packages in publications.
434s 
434s Type 'demo()' for some demos, 'help()' for on-line help, or
434s 'help.start()' for an HTML browser interface to help.
434s Type 'q()' to quit R.
434s 
434s > library(survey)
434s Loading required package: grid
434s Loading required package: Matrix
435s Loading required package: survival
435s 
435s Attaching package: 'survey'
435s 
435s The following object is masked from 'package:graphics':
435s 
435s     dotchart
435s 
435s > data(api)
435s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2)
435s > rclus2<-as.svrepdesign(dclus2)
435s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2)
435s > svycontrast(model, c(ell=1,meals=0))
435s          contrast     SE
435s contrast  -2.0592 1.6177
435s > a<-svycontrast(model, c(0,1,0,0))
435s > 
435s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE)
435s > svycontrast(model2, c(ell=1,meals=0))
435s          contrast     SE
435s contrast  -2.0592 1.6177
435s > a2<-svycontrast(model2, c(0,1,0,0))
435s > stopifnot(!is.null(a2$replicates))
435s > 
435s BEGIN TEST svyivreg-var.R
435s 
435s R version 4.4.3 (2025-02-28) -- "Trophy Case"
435s Copyright (C) 2025 The R Foundation for Statistical Computing
435s Platform: s390x-ibm-linux-gnu
435s 
435s R is free software and comes with ABSOLUTELY NO WARRANTY.
435s You are welcome to redistribute it under certain conditions.
435s Type 'license()' or 'licence()' for distribution details.
435s 
435s R is a collaborative project with many contributors.
435s Type 'contributors()' for more information and
435s 'citation()' on how to cite R or R packages in publications.
435s 
435s Type 'demo()' for some demos, 'help()' for on-line help, or
435s 'help.start()' for an HTML browser interface to help.
435s Type 'q()' to quit R.
435s 
435s > 
435s > library(survey)
435s Loading required package: grid
435s Loading required package: Matrix
436s Loading required package: survival
436s 
436s Attaching package: 'survey'
436s 
436s The following object is masked from 'package:graphics':
436s 
436s     dotchart
436s 
436s > data(api)
436s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
436s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat))
436s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat))
436s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov)))
436s > 
436s BEGIN TEST svyivreg.R
436s 
436s R version 4.4.3 (2025-02-28) -- "Trophy Case"
436s Copyright (C) 2025 The R Foundation for Statistical Computing
436s Platform: s390x-ibm-linux-gnu
436s 
436s R is free software and comes with ABSOLUTELY NO WARRANTY.
436s You are welcome to redistribute it under certain conditions.
436s Type 'license()' or 'licence()' for distribution details.
436s 
436s R is a collaborative project with many contributors.
436s Type 'contributors()' for more information and
436s 'citation()' on how to cite R or R packages in publications.
436s 
436s Type 'demo()' for some demos, 'help()' for on-line help, or
436s 'help.start()' for an HTML browser interface to help.
436s Type 'q()' to quit R.
436s 
436s > library(survey)
436s Loading required package: grid
436s Loading required package: Matrix
437s Loading required package: survival
437s 
437s Attaching package: 'survey'
437s 
437s > library(AER)
437s The following object is masked from 'package:graphics':
437s 
437s     dotchart
437s 
437s Loading required package: car
437s Loading required package: carData
437s Loading required package: lmtest
437s Loading required package: zoo
437s 
437s Attaching package: 'zoo'
437s 
437s The following objects are masked from 'package:base':
437s 
437s     as.Date, as.Date.numeric
437s 
437s Loading required package: sandwich
437s > 
437s > load("cigsw.rda")
437s > 
437s > des<-svydesign(id=~1, weights=~wt, data=cigsw)
437s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des)
437s > 
437s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6)
437s [1] TRUE
437s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232,  .3614382 ),tolerance=1e-6)
437s [1] TRUE
437s > 
437s BEGIN TEST svyolr-rake-subset.R
437s 
437s R version 4.4.3 (2025-02-28) -- "Trophy Case"
437s Copyright (C) 2025 The R Foundation for Statistical Computing
437s Platform: s390x-ibm-linux-gnu
437s 
437s R is free software and comes with ABSOLUTELY NO WARRANTY.
437s You are welcome to redistribute it under certain conditions.
437s Type 'license()' or 'licence()' for distribution details.
437s 
437s R is a collaborative project with many contributors.
437s Type 'contributors()' for more information and
437s 'citation()' on how to cite R or R packages in publications.
437s 
437s Type 'demo()' for some demos, 'help()' for on-line help, or
437s 'help.start()' for an HTML browser interface to help.
437s Type 'q()' to quit R.
437s 
438s > library(survey)
438s Loading required package: grid
438s Loading required package: Matrix
439s Loading required package: survival
439s 
439s Attaching package: 'survey'
439s 
439s The following object is masked from 'package:graphics':
439s 
439s     dotchart
439s 
439s > data(api)
439s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
439s > 
439s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
439s > 
439s > ## population marginal totals for each stratum
439s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018))
439s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122))
439s > 
439s > 
439s > ## rake with the population totals
439s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide))
439s > 
439s > # works
439s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
439s > 
439s > # fails in 4.1 (should work because svyolr's default na.action is na.omit)
439s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r)
439s > 
439s > # fails in 4.1 (should work because NA values are subsetted out)
439s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) )
439s > 
439s BEGIN TEST svyolr.R
439s 
439s R version 4.4.3 (2025-02-28) -- "Trophy Case"
439s Copyright (C) 2025 The R Foundation for Statistical Computing
439s Platform: s390x-ibm-linux-gnu
439s 
439s R is free software and comes with ABSOLUTELY NO WARRANTY.
439s You are welcome to redistribute it under certain conditions.
439s Type 'license()' or 'licence()' for distribution details.
439s 
439s R is a collaborative project with many contributors.
439s Type 'contributors()' for more information and
439s 'citation()' on how to cite R or R packages in publications.
439s 
439s Type 'demo()' for some demos, 'help()' for on-line help, or
439s 'help.start()' for an HTML browser interface to help.
439s Type 'q()' to quit R.
439s 
439s Loading required package: grid
439s > library(survey)
439s Loading required package: Matrix
440s Loading required package: survival
440s 
440s Attaching package: 'survey'
440s 
440s > 
440s > ################################################################################
440s > # Example from svyolr: runs OK
440s > data(api)
440s The following object is masked from 'package:graphics':
440s 
440s     dotchart
440s 
440s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc)
440s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
440s > 
440s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
440s > m
440s Call:
440s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1)
440s 
440s Coefficients:
440s     avg.ed   mobility     stypeH     stypeM 
440s -2.6999217  0.0325042 -1.7574715 -0.6191463 
440s 
440s Intercepts:
440s   (0,25]|(25,50]  (25,50]|(50,75] (50,75]|(75,100] 
440s        -8.857919        -6.586464        -4.924938 
441s > 
441s > ## Use regTermTest for testing multiple parameters
441s > test<-regTermTest(m, ~avg.ed+stype, method="LRT")
441s > ################################################################################
441s > 
441s > ################################################################################
441s > # If we wrap everything into a function: error b/c it looks for design variable
441s > # dclus1 in .GlobalEnv
441s > 
441s > foo <- function(x){
441s +   dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc)
441s +   dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100)))
441s + 
441s +   m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1)
441s +   ## Use regTermTest for testing multiple parameters
441s +   regTermTest(m, ~avg.ed+stype, method="LRT")
441s + }
441s > 
441s > # OK
441s > foo(apiclus1)
441s Working (Rao-Scott+F) LRT for avg.ed stype
441s  in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1)
441s Working 2logLR =  0.6580304 p= 0.73257 
441s (scale factors:  2.7 0.22 0.11 );  denominator df= 10
441s > 
441s > # Clean-up everything but apiclus1 and foo
441s > rm(list = setdiff(ls(),c('apiclus1','foo','test')))
441s > 
441s > # Error
441s > test2<-foo(apiclus1)
441s > ################################################################################
441s > all.equal(test,test2)
441s [1] TRUE
441s > 
441s > 
441s BEGIN TEST toy_example_for_postStratify.R
441s 
441s R version 4.4.3 (2025-02-28) -- "Trophy Case"
441s Copyright (C) 2025 The R Foundation for Statistical Computing
441s Platform: s390x-ibm-linux-gnu
441s 
441s R is free software and comes with ABSOLUTELY NO WARRANTY.
441s You are welcome to redistribute it under certain conditions.
441s Type 'license()' or 'licence()' for distribution details.
441s 
441s R is a collaborative project with many contributors.
441s Type 'contributors()' for more information and
441s 'citation()' on how to cite R or R packages in publications.
441s 
441s Type 'demo()' for some demos, 'help()' for on-line help, or
441s 'help.start()' for an HTML browser interface to help.
441s Type 'q()' to quit R.
441s 
441s > library(survey)
441s Loading required package: grid
441s Loading required package: Matrix
442s Loading required package: survival
442s 
442s Attaching package: 'survey'
442s 
442s The following object is masked from 'package:graphics':
442s 
442s     dotchart
442s 
442s > 
442s > # Dummy data for testing nonresponse adjustments
442s > toy <- data.frame(id = 1:10,
442s +                   dummy = 1,
442s +                   class = c(rep("A", 5), rep("B", 5)),
442s +                   responded = c(rep(TRUE, 8), FALSE, FALSE),
442s +                   weight = rep(100, 10))
442s > 
442s > # With jackknife replicate weights
442s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10)
442s > diag(toy_repweights) <- rep(0, 10)
442s > 
442s > # Scramble up which person is in which jackknife group
442s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ]
442s > 
442s > toy_design <- svrepdesign(variables = toy[, 1:4],
442s +                           weights = toy$weight,
442s +                           repweights = toy_repweights,
442s +                           type = "JK1",
442s +                           scale = 0.9)
442s > 
442s > # Get the sum of the weights for the full sample
442s > poptotals <- as.data.frame(svyby(formula = ~dummy,
442s +                                  by = ~class,
442s +                                  design = toy_design,
442s +                                  FUN = survey::svytotal))
442s > 
442s > poptotals$Freq <- poptotals$dummy
442s > poptotals$dummy <- NULL
442s > poptotals$se <- NULL
442s > 
442s > # Adjust the weights of the responding sample to match to the full sample
442s > adjusted <-  postStratify(design = subset(toy_design, responded),
442s +                           strata = ~class,
442s +                           population = poptotals)
442s > 
442s > # This works for the weights...
442s > svyby(formula = ~dummy,
442s +       by = ~class,
442s +       design = adjusted,
442s +       FUN = survey::svytotal)
442s   class dummy se
442s A     A   500  0
442s B     B   500  0
442s > 
442s > # ...and some, but not all, the replicate weights
442s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights)))
442s > 
442s > 
442s > 
442s BEGIN TEST twophase.R
442s 
442s R version 4.4.3 (2025-02-28) -- "Trophy Case"
442s Copyright (C) 2025 The R Foundation for Statistical Computing
442s Platform: s390x-ibm-linux-gnu
442s 
442s R is free software and comes with ABSOLUTELY NO WARRANTY.
442s You are welcome to redistribute it under certain conditions.
442s Type 'license()' or 'licence()' for distribution details.
442s 
442s R is a collaborative project with many contributors.
442s Type 'contributors()' for more information and
442s 'citation()' on how to cite R or R packages in publications.
442s 
442s Type 'demo()' for some demos, 'help()' for on-line help, or
442s 'help.start()' for an HTML browser interface to help.
442s Type 'q()' to quit R.
442s 
442s > library(survey)
442s Loading required package: grid
442s Loading required package: Matrix
443s Loading required package: survival
443s > 
443s > ## two-phase simple random sampling.
443s > data(pbc, package="survival")
443s 
443s Attaching package: 'survey'
443s 
443s The following object is masked from 'package:graphics':
443s 
443s     dotchart
443s 
443s > pbc$id<-1:nrow(pbc)
443s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9)
443s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized)))
443s Two-phase sparse-matrix design:
443s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
443s     subset = subset, data = data, pps = pps)
443s Phase 1:
443s Independent Sampling design (with replacement)
443s svydesign(ids = ~id)
443s Phase 2:
443s Independent Sampling design
443s svydesign(ids = ~id, fpc = `*phase1*`)
443s > m<-svymean(~bili, d2pbc)
443s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized])))
443s [1] TRUE
443s > all.equal(as.vector(SE(m)),
443s +           with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))),
443s +           tolerance=0.002)
443s [1] TRUE
443s > 
443s > ## two-stage sampling as two-phase
443s > data(mu284)
443s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3)))
443s > mu284.1<-mu284[ii,]
443s > mu284.1$id<-1:nrow(mu284.1)
443s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15))
443s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)
443s > ## first phase cluster sample, second phase stratified within cluster
443s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1),
443s +                    fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx"))
443s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 
443s     NULL), data = mu284.1, subset = ~sub, method = "approx")
443s Phase 1:
443s 1 - level Cluster Sampling design
443s With (5) clusters.
443s svydesign(ids = ~id1, fpc = ~n1)
443s Phase 2:
443s Stratified Independent Sampling design
443s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
443s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1),
443s +                    fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full"))
443s Two-phase sparse-matrix design:
443s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
443s     subset = subset, data = data, pps = pps)
443s Phase 1:
443s 1 - level Cluster Sampling design
443s With (5) clusters.
443s svydesign(ids = ~id1, fpc = ~n1)
443s Phase 2:
443s Stratified Independent Sampling design
443s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
443s > summary(d2mu284)
443s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 
443s     NULL), data = mu284.1, subset = ~sub, method = "approx")
443s Phase 1:
443s 1 - level Cluster Sampling design
443s With (5) clusters.
443s svydesign(ids = ~id1, fpc = ~n1)
443s Probabilities:
443s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
443s     0.1     0.1     0.1     0.1     0.1     0.1 
443s Population size (PSUs): 50 
443s Phase 2:
443s Stratified Independent Sampling design
443s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`)
443s Probabilities:
443s    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
443s  0.3333  0.3750  0.4286  0.4674  0.6000  0.6000 
443s Stratum Sizes: 
443s            19 31 45 47 50
443s obs         3  3  3  3  3
443s design.PSU  3  3  3  3  3
443s actual.PSU  3  3  3  3  3
443s Population stratum sizes (PSUs): 
443s 19 31 45 47 50 
443s  5  7  8  5  9 
443s Data variables:
443s [1] "id1" "n1"  "id2" "y1"  "n2"  "id"  "sub"
443s > t1<-svytotal(~y1, dmu284)
443s > t2<-svytotal(~y1, d2mu284)
443s > t22<-svytotal(~y1,d22mu284)
443s > m1<-svymean(~y1, dmu284)
443s > m2<-svymean(~y1, d2mu284)
443s > m22<-svymean(~y1, d22mu284)
443s > all.equal(coef(t1),coef(t2))
443s [1] TRUE
443s > all.equal(coef(t1),coef(t22))
443s [1] TRUE
443s > all.equal(coef(m1),coef(m2))
443s [1] TRUE
443s > all.equal(coef(m1),coef(m22))
443s [1] TRUE
443s > all.equal(as.vector(SE(m1)),as.vector(SE(m2)))
443s [1] TRUE
443s > all.equal(as.vector(SE(m1)),as.vector(SE(m22)))
443s [1] TRUE
443s > all.equal(as.vector(SE(t1)),as.vector(SE(t2)))
443s [1] TRUE
443s > all.equal(as.vector(SE(t1)),as.vector(SE(t22)))
443s [1] TRUE
443s > 
443s > ## case-cohort design
443s > ##this example requires R 2.3.1 or later for cch and data.
443s > library("survival")
443s > data(nwtco, package="survival")
443s > ## unstratified, equivalent to Lin & Ying (1993)
443s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel),
443s +                  subset=~I(in.subcohort | rel), data=nwtco))
444s Two-phase sparse-matrix design:
444s  twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 
444s     subset = subset, data = data, pps = pps)
444s Phase 1:
444s Independent Sampling design (with replacement)
444s svydesign(ids = ~seqno)
444s Phase 2:
444s Stratified Independent Sampling design
444s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`)
444s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12),
444s +                design=dcchs)
444s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel),
444s +                  subset=~I(in.subcohort | rel), data=nwtco,method="approx")
444s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12),
444s +                design=dcchs)
444s > all.equal(coef(cch1),coef(cch1.2))
444s [1] TRUE
444s > all.equal(SE(cch1),SE(cch1.2))
444s [1] TRUE
444s > ## Using survival::cch 
444s > subcoh <- nwtco$in.subcohort
444s > selccoh <- with(nwtco, rel==1|subcoh==1)
444s > ccoh.data <- nwtco[selccoh,]
444s > ccoh.data$subcohort <- subcoh[selccoh]
444s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12),
444s +           data =ccoh.data, subcoh = ~subcohort, id=~seqno,
444s +           cohort.size=4028, method="LinYing", robust=TRUE)
444s > 
444s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2))))
444s [1] TRUE
444s > ## cch has smaller variances by a factor of 1.0005 because
444s > ## there is a (n/(n-1)) in the survey phase1 varianace
444s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006))
444s [1] TRUE
444s > 
444s > 
444s > ## bug report from Takahiro Tsuchiya for version 3.4
444s > ## We used to not match Sarndal exactly, because our old phase-one
444s > ## estimator had a small bias for finite populations
444s > rei<-read.table(tmp<-textConnection(
444s + "  id   N n.a h n.ah n.h   sub  y
444s + 1   1 300  20 1   12   5  TRUE  1
444s + 2   2 300  20 1   12   5  TRUE  2
444s + 3   3 300  20 1   12   5  TRUE  3
444s + 4   4 300  20 1   12   5  TRUE  4
444s + 5   5 300  20 1   12   5  TRUE  5
444s + 6   6 300  20 1   12   5 FALSE NA
444s + 7   7 300  20 1   12   5 FALSE NA
444s + 8   8 300  20 1   12   5 FALSE NA
444s + 9   9 300  20 1   12   5 FALSE NA
444s + 10 10 300  20 1   12   5 FALSE NA
444s + 11 11 300  20 1   12   5 FALSE NA
444s + 12 12 300  20 1   12   5 FALSE NA
444s + 13 13 300  20 2    8   3  TRUE  6
444s + 14 14 300  20 2    8   3  TRUE  7
444s + 15 15 300  20 2    8   3  TRUE  8
444s + 16 16 300  20 2    8   3 FALSE NA
444s + 17 17 300  20 2    8   3 FALSE NA
444s + 18 18 300  20 2    8   3 FALSE NA
444s + 19 19 300  20 2    8   3 FALSE NA
444s + 20 20 300  20 2    8   3 FALSE NA
444s + "), header=TRUE)
444s > close(tmp)
444s > 
444s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h),
444s +                     fpc=list(~N,NULL), subset=~sub, data=rei, method="approx")
444s > tot<- svytotal(~y, des.rei)
444s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h),
444s +                     fpc=list(~N,NULL), subset=~sub, data=rei)
444s > tot2<- svytotal(~y, des.rei2)
444s > 
444s > ## based on Sarndal et al (9.4.14)
444s > rei$w.ah <- rei$n.ah / rei$n.a
444s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE)
444s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE)
444s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y)
444s > 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))
444s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1)))
444s > 
444s > a.rei$f.h<-with(a.rei, n.h/n.ah)
444s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh))
444s > 
444s > a.rei$f<-with(a.rei, n.a/N)
444s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1))
444s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2)))
444s > 
444s > V
444s [1] 36522.63
444s > Vphase1
444s [1] 24072.63
444s > Vphase2
444s [1] 12450
444s > vcov(tot)
444s          y
444s y 35911.05
444s attr(,"phases")
444s attr(,"phases")$phase1
444s          [,1]
444s [1,] 23461.05
444s 
444s attr(,"phases")$phase2
444s       y
444s y 12450
444s 
444s > vcov(tot2)
444s          [,1]
444s [1,] 36522.63
444s attr(,"phases")
444s attr(,"phases")$phase1
444s          [,1]
444s [1,] 24072.63
444s 
444s attr(,"phases")$phase2
444s       [,1]
444s [1,] 12450
444s 
444s > ## phase 2 identical
444s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2))
444s [1] TRUE
444s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2))
444s [1] TRUE
444s > ## phase 1 differs by 2.6% for old twophase estimator
444s > Vphase1/attr(vcov(tot),"phases")$phase1
444s          [,1]
444s [1,] 1.026068
444s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1))
444s [1] TRUE
444s > 
444s > 
444s autopkgtest [12:46:56]: test run-unit-test: -----------------------]
445s run-unit-test        PASS
445s autopkgtest [12:46:57]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
445s autopkgtest [12:46:57]: test pkg-r-autopkgtest: preparing testbed
566s autopkgtest [12:48:58]: testbed dpkg architecture: s390x
567s autopkgtest [12:48:59]: testbed apt version: 2.9.33
567s autopkgtest [12:48:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup
567s autopkgtest [12:48:59]: testbed release detected to be: plucky
568s autopkgtest [12:49:00]: updating testbed package index (apt update)
568s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
569s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
569s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
569s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
569s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB]
569s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB]
570s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
570s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.7 kB]
570s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1852 B]
570s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
570s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [335 kB]
570s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB]
570s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B]
570s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B]
570s Fetched 1034 kB in 2s (581 kB/s)
571s Reading package lists...
571s Reading package lists...
572s Building dependency tree...
572s Reading state information...
572s Calculating upgrade...
572s Calculating upgrade...
572s The following packages were automatically installed and are no longer required:
572s   libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
572s   linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
572s   linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
572s   linux-tools-6.11.0-8-generic
572s Use 'sudo apt autoremove' to remove them.
572s The following packages will be upgraded:
572s   python3-jinja2 strace
572s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
572s Need to get 609 kB of archives.
572s After this operation, 27.6 kB of additional disk space will be used.
572s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
573s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
573s Fetched 609 kB in 1s (618 kB/s)
573s (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 ... 81428 files and directories currently installed.)
573s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
573s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
573s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
573s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
573s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
574s Setting up strace (6.13+ds-1ubuntu1) ...
574s Processing triggers for man-db (2.13.0-1) ...
574s Reading package lists...
574s Building dependency tree...
574s Reading state information...
574s Solving dependencies...
574s The following packages will be REMOVED:
574s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
574s   linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
574s   linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
574s   linux-tools-6.11.0-8-generic*
575s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
575s After this operation, 167 MB disk space will be freed.
575s (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 ... 81428 files and directories currently installed.)
575s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
575s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
575s Removing libpython3.12t64:s390x (3.12.9-1) ...
575s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
575s Removing libnsl2:s390x (1.3.0-3build3) ...
575s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
575s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
575s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
576s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
576s Processing triggers for libc-bin (2.41-1ubuntu1) ...
576s (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 ... 56328 files and directories currently installed.)
576s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
576s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
576s autopkgtest [12:49:08]: upgrading testbed (apt dist-upgrade and autopurge)
576s Reading package lists...
577s Building dependency tree...
577s Reading state information...
577s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
577s Starting 2 pkgProblemResolver with broken count: 0
577s Done
577s Entering ResolveByKeep
577s 
577s Calculating upgrade...
577s The following packages will be upgraded:
577s   libc-bin libc-dev-bin libc6 libc6-dev locales
578s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
578s Need to get 9512 kB of archives.
578s After this operation, 8192 B of additional disk space will be used.
578s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
580s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
580s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
583s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
584s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
588s Preconfiguring packages ...
588s Fetched 9512 kB in 11s (882 kB/s)
588s (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 ... 56326 files and directories currently installed.)
588s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
588s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
589s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
589s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
589s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
589s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
589s Setting up libc6:s390x (2.41-1ubuntu2) ...
589s (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 ... 56326 files and directories currently installed.)
589s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
589s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
589s Setting up libc-bin (2.41-1ubuntu2) ...
589s (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 ... 56326 files and directories currently installed.)
589s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
589s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
589s Setting up locales (2.41-1ubuntu2) ...
589s Generating locales (this might take a while)...
590s   en_US.UTF-8... done
590s Generation complete.
590s Setting up libc-dev-bin (2.41-1ubuntu2) ...
590s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
590s Processing triggers for man-db (2.13.0-1) ...
591s Processing triggers for systemd (257.3-1ubuntu3) ...
592s Reading package lists...
592s Building dependency tree...
592s Reading state information...
592s Starting pkgProblemResolver with broken count: 0
592s Starting 2 pkgProblemResolver with broken count: 0
592s Done
592s Solving dependencies...
592s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
592s autopkgtest [12:49:24]: rebooting testbed after setup commands that affected boot
617s Reading package lists...
617s Building dependency tree...
617s Reading state information...
617s Starting pkgProblemResolver with broken count: 0
617s Starting 2 pkgProblemResolver with broken count: 0
617s Done
617s The following NEW packages will be installed:
617s   build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu
617s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
617s   fonts-glyphicons-halflings fonts-mathjax g++ g++-14 g++-14-s390x-linux-gnu
617s   g++-s390x-linux-gnu gcc gcc-14 gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu
617s   gfortran gfortran-14 gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu
617s   icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0
617s   libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 libfreetype6
617s   libgcc-14-dev libgfortran-14-dev libgfortran5 libgomp1 libgraphite2-3
617s   libharfbuzz0b libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev
617s   libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap
617s   libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
617s   liblapack-dev liblapack3 liblzma-dev libmpc3 libncurses-dev libnlopt0
617s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
617s   libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
617s   libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6
617s   libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev
617s   libtk8.6 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1
617s   libxss1 libxt6t64 littler node-normalize.css pkg-r-autopkgtest pkgconf
617s   pkgconf-bin r-base-core r-base-dev r-cran-abind r-cran-aer r-cran-backports
617s   r-cran-bit r-cran-bit64 r-cran-blob r-cran-boot r-cran-broom r-cran-cachem
617s   r-cran-car r-cran-cardata r-cran-caret r-cran-cellranger r-cran-class
617s   r-cran-cli r-cran-clipr r-cran-clock r-cran-codetools r-cran-colorspace
617s   r-cran-conquer r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl
617s   r-cran-data.table r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest
617s   r-cran-doby r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate
617s   r-cran-fansi r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach
617s   r-cran-foreign r-cran-formula r-cran-future r-cran-future.apply
617s   r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower
617s   r-cran-gtable r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr
617s   r-cran-hms r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth
617s   r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle
617s   r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate
617s   r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels
617s   r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark
617s   r-cran-minqa r-cran-mitools r-cran-modelmetrics r-cran-modelr r-cran-munsell
617s   r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-openxlsx
617s   r-cran-parallelly r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig
617s   r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-prettyunits r-cran-proc
617s   r-cran-prodlim r-cran-progress r-cran-progressr r-cran-proxy r-cran-purrr
617s   r-cran-quantreg r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6
617s   r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo
617s   r-cran-rcppeigen r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes
617s   r-cran-reformulas r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang
617s   r-cran-rpart r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape
617s   r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr
617s   r-cran-survey r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect
617s   r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs
617s   r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun
617s   r-cran-yaml r-cran-zip r-cran-zoo unzip x11-common xdg-utils zip zlib1g-dev
618s 0 upgraded, 252 newly installed, 0 to remove and 0 not upgraded.
618s Need to get 251 MB of archives.
618s After this operation, 617 MB of additional disk space will be used.
618s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB]
618s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB]
618s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB]
629s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B]
629s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B]
629s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB]
629s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB]
629s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB]
629s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB]
629s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB]
633s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250222-0ubuntu1 [1212 kB]
634s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB]
636s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB]
657s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB]
657s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B]
657s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B]
657s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB]
661s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB]
674s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB]
674s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B]
674s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B]
674s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B]
674s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB]
674s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB]
675s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
675s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
676s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB]
676s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB]
676s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB]
676s Get:30 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
677s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
679s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB]
680s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB]
681s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB]
692s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB]
692s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B]
692s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B]
692s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB]
693s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB]
693s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB]
693s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB]
693s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB]
693s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB]
693s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B]
693s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB]
693s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB]
694s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB]
694s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB]
694s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB]
694s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB]
694s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB]
695s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB]
695s Get:53 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB]
695s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB]
714s Get:55 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB]
714s Get:56 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB]
715s Get:57 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
715s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B]
715s Get:59 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B]
715s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
715s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
715s Get:62 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
716s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
716s Get:64 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB]
719s Get:65 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB]
726s Get:66 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB]
726s Get:67 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB]
726s Get:68 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB]
726s Get:69 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.1-1 [253 kB]
727s Get:70 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.1-1 [50.3 kB]
727s Get:71 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.1-1 [28.3 kB]
727s Get:72 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB]
727s Get:73 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB]
727s Get:74 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB]
727s Get:75 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB]
727s Get:76 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B]
727s Get:77 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB]
728s Get:78 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB]
728s Get:79 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB]
729s Get:80 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB]
730s Get:81 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB]
730s Get:82 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB]
730s Get:83 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB]
730s Get:84 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB]
731s Get:85 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB]
731s Get:86 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB]
732s Get:87 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB]
732s Get:88 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB]
732s Get:89 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B]
732s Get:90 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB]
733s Get:91 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB]
733s Get:92 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB]
733s Get:93 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB]
733s Get:94 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
733s Get:95 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB]
767s Get:96 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-littler s390x 0.3.20-2 [95.0 kB]
767s Get:97 http://ftpmaster.internal/ubuntu plucky/universe s390x littler all 0.3.20-2 [2554 B]
767s Get:98 http://ftpmaster.internal/ubuntu plucky/universe s390x node-normalize.css all 8.0.1-5 [10.8 kB]
767s Get:99 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB]
768s Get:100 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB]
768s Get:101 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB]
768s Get:102 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB]
768s Get:103 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B]
768s Get:104 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
768s Get:105 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-abind all 1.4-8-1 [66.9 kB]
768s Get:106 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cardata all 3.0.5-1 [1819 kB]
771s Get:107 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-formula all 1.2-5-1 [158 kB]
771s Get:108 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB]
772s Get:109 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB]
774s Get:110 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB]
777s Get:111 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-3-1 [4449 kB]
782s Get:112 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB]
786s Get:113 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nnet s390x 7.3-20-1 [116 kB]
786s Get:114 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-boot all 1.3-31-1 [635 kB]
787s Get:115 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
787s Get:116 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcpp s390x 1.0.14-1 [2003 kB]
789s Get:117 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-minqa s390x 1.2.8-1 [139 kB]
789s Get:118 http://ftpmaster.internal/ubuntu plucky/universe s390x libnlopt0 s390x 2.7.1-6ubuntu3 [227 kB]
789s Get:119 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nloptr s390x 2.1.1-1 [252 kB]
791s Get:120 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rbibutils s390x 2.3-1 [1041 kB]
791s Get:121 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rdpack all 2.6.2-1syncable1 [756 kB]
792s Get:122 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-reformulas all 0.4.0-1 [91.5 kB]
792s Get:123 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcppeigen s390x 0.3.4.0.2-1 [1429 kB]
794s Get:124 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-statmod s390x 1.5.0-1 [294 kB]
794s Get:125 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lme4 s390x 1.1-36-1 [4141 kB]
799s Get:126 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-backports s390x 1.5.0-2 [121 kB]
799s Get:127 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cli s390x 3.6.4-1 [1379 kB]
800s Get:128 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-generics all 0.1.3-1 [81.3 kB]
801s Get:129 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-glue s390x 1.8.0-1 [164 kB]
805s Get:130 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rlang s390x 1.1.5-1 [1713 kB]
805s Get:131 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
805s Get:132 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-magrittr s390x 2.0.3-1 [154 kB]
805s Get:133 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-utf8 s390x 1.2.4-1 [143 kB]
805s Get:134 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vctrs s390x 0.6.5-1 [1448 kB]
805s Get:135 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
805s Get:136 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r6 all 2.6.1-1 [101 kB]
805s Get:137 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fansi s390x 1.0.5-1 [615 kB]
806s Get:138 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
806s Get:139 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tibble s390x 3.2.1+dfsg-3 [420 kB]
807s Get:140 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-withr all 3.0.2+dfsg-1 [214 kB]
807s Get:141 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tidyselect s390x 1.2.1+dfsg-1 [222 kB]
807s Get:142 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-dplyr s390x 1.1.4-4 [1537 kB]
809s Get:143 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-purrr s390x 1.0.4-1 [553 kB]
810s Get:144 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-stringi s390x 1.8.4-1build1 [917 kB]
811s Get:145 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-stringr all 1.5.1-1 [290 kB]
811s Get:146 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cpp11 all 0.5.2-1 [233 kB]
811s Get:147 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tidyr s390x 1.3.1-1 [1157 kB]
813s Get:148 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-broom all 1.0.7+dfsg-1 [1802 kB]
815s Get:149 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-numderiv all 2016.8-1.1-3 [115 kB]
815s Get:150 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
815s Get:151 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-isoband s390x 0.2.7-1 [1481 kB]
817s Get:152 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-farver s390x 2.1.2-1 [1353 kB]
819s Get:153 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-labeling all 0.4.3-1 [62.1 kB]
819s Get:154 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-colorspace s390x 2.1-1+dfsg-1 [1567 kB]
821s Get:155 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-munsell all 0.5.1-1 [213 kB]
821s Get:156 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
821s Get:157 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-viridislite all 0.4.2-2 [1088 kB]
822s Get:158 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-scales all 1.3.0-1 [603 kB]
823s Get:159 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
827s Get:160 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cowplot all 1.1.3+dfsg-1 [614 kB]
828s Get:161 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-deriv all 4.1.6-1 [151 kB]
828s Get:162 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-modelr all 0.1.11-1 [195 kB]
828s Get:163 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-microbenchmark s390x 1.5.0-1 [67.2 kB]
828s Get:164 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-doby all 4.6.25-1 [4772 kB]
834s Get:165 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-evaluate all 1.0.3-1 [114 kB]
834s Get:166 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-xfun s390x 0.51+dfsg-1 [574 kB]
835s Get:167 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-highr all 0.11+dfsg-1 [38.5 kB]
835s Get:168 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-yaml s390x 2.3.10-1 [113 kB]
835s Get:169 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
841s Get:170 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-knitr all 1.49+dfsg-1 [859 kB]
842s Get:171 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-pbkrtest all 0.5.3-1 [178 kB]
842s Get:172 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-sparsem s390x 1.84-2-1 [826 kB]
843s Get:173 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrixmodels all 0.5-3-1 [361 kB]
843s Get:174 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-survival s390x 3.8-3-1 [8250 kB]
852s Get:175 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrixstats s390x 1.5.0-1 [539 kB]
852s Get:176 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rcpparmadillo s390x 14.2.3-1-1 [851 kB]
853s Get:177 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-class s390x 7.3-23-1 [92.0 kB]
853s Get:178 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-proxy s390x 0.4-27-1 [182 kB]
853s Get:179 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-e1071 s390x 1.7-16-1 [572 kB]
854s Get:180 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-codetools all 0.2-20-1 [90.5 kB]
854s Get:181 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-iterators all 1.0.14-1 [336 kB]
854s Get:182 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-foreach all 1.5.2-1 [124 kB]
855s Get:183 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-data.table s390x 1.17.0+dfsg-1 [2167 kB]
857s Get:184 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-modelmetrics s390x 1.2.2.2-1build1 [122 kB]
857s Get:185 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-plyr s390x 1.8.9-1 [835 kB]
858s Get:186 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-proc s390x 1.18.5-1 [968 kB]
859s Get:187 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-tzdb s390x 0.4.0-2 [514 kB]
859s Get:188 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-clock s390x 0.7.2-1 [1881 kB]
861s Get:189 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gower s390x 1.0.2-1 [209 kB]
862s Get:190 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-hardhat all 1.4.0+dfsg-1 [565 kB]
862s Get:191 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rpart s390x 4.1.24-1 [672 kB]
863s Get:192 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-shape all 1.4.6.1-1 [749 kB]
864s Get:193 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-diagram all 1.6.5-2 [656 kB]
864s Get:194 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-kernsmooth s390x 2.23-26-1 [94.7 kB]
864s Get:195 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-digest s390x 0.6.37-1 [205 kB]
865s Get:196 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-globals all 0.16.3-1 [120 kB]
865s Get:197 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-listenv all 0.9.1+dfsg-1 [112 kB]
865s Get:198 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-parallelly s390x 1.42.0-1 [540 kB]
865s Get:199 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-future all 1.34.0+dfsg-1 [646 kB]
866s Get:200 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-future.apply all 1.11.3+dfsg-1 [175 kB]
866s Get:201 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-progressr all 0.15.1-1 [353 kB]
866s Get:202 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-squarem all 2021.1-1 [179 kB]
867s Get:203 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lava all 1.8.1+dfsg-1 [2191 kB]
871s Get:204 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-prodlim s390x 2024.06.25-1 [419 kB]
871s Get:205 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ipred s390x 0.9-15-1 [386 kB]
871s Get:206 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-timechange s390x 0.3.0-1 [185 kB]
871s Get:207 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lubridate s390x 1.9.4+dfsg-1 [1010 kB]
871s Get:208 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-timedate s390x 4041.110-1 [1209 kB]
873s Get:209 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-recipes all 1.1.0+dfsg-1 [2035 kB]
875s Get:210 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-reshape2 s390x 1.4.4-2build1 [111 kB]
875s Get:211 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-caret s390x 7.0-1+dfsg-1 [3461 kB]
878s Get:212 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-conquer s390x 1.3.3-1 [459 kB]
879s Get:213 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-quantreg s390x 6.00-1 [1457 kB]
881s Get:214 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-foreign s390x 0.8.88-1 [249 kB]
881s Get:215 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-ellipsis s390x 0.3.2-2 [35.4 kB]
881s Get:216 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-forcats all 1.0.0-1 [369 kB]
881s Get:217 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-hms all 1.1.3-1 [96.5 kB]
881s Get:218 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-clipr all 0.8.0-1 [53.5 kB]
881s Get:219 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-crayon all 1.5.3-1 [165 kB]
882s Get:220 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-bit s390x 4.6.0+dfsg-1 [471 kB]
882s Get:221 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-bit64 s390x 4.6.0-1-1ubuntu2 [503 kB]
883s Get:222 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-prettyunits all 1.2.0-1 [162 kB]
883s Get:223 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-progress all 1.2.3-1 [91.9 kB]
883s Get:224 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vroom s390x 1.6.5-1 [865 kB]
884s Get:225 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-readr s390x 2.1.5-1 [778 kB]
885s Get:226 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-haven s390x 2.5.4-1 [355 kB]
885s Get:227 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-curl s390x 6.2.1+dfsg-1ubuntu1 [196 kB]
885s Get:228 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rematch all 2.0.0-1 [18.3 kB]
885s Get:229 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cellranger all 1.1.0-3 [102 kB]
885s Get:230 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-readxl s390x 1.4.4-1 [360 kB]
886s Get:231 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-writexl s390x 1.5.1-1 [158 kB]
886s Get:232 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.methodss3 all 1.8.2-1 [84.0 kB]
886s Get:233 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.oo all 1.27.0-1 [979 kB]
887s Get:234 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-r.utils all 2.13.0-1 [1423 kB]
888s Get:235 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-zip s390x 2.3.2-1 [151 kB]
888s Get:236 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-openxlsx s390x 4.2.8-1 [2045 kB]
893s Get:237 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rio all 1.2.3-1 [546 kB]
893s Get:238 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-car all 3.1-3-1 [1525 kB]
893s Get:239 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-zoo s390x 1.8-13-1 [998 kB]
894s Get:240 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lmtest s390x 0.9.40-1 [396 kB]
894s Get:241 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-sandwich all 3.1-1-1 [1483 kB]
896s Get:242 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-aer all 1.2-14-1 [2597 kB]
898s Get:243 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-blob all 1.2.4-1 [49.8 kB]
898s Get:244 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-fastmap s390x 1.2.0-1 [72.4 kB]
898s Get:245 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cachem s390x 1.1.0-1 [74.0 kB]
898s Get:246 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-dbi all 1.2.3-1 [853 kB]
899s Get:247 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-hexbin s390x 1.28.5-1 [1583 kB]
901s Get:248 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-memoise all 2.0.1-1 [53.9 kB]
901s Get:249 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mitools all 2.4-2build1 [265 kB]
901s Get:250 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-plogr all 0.2.0-3build1 [15.1 kB]
901s Get:251 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-rsqlite s390x 2.3.9-1 [1331 kB]
903s Get:252 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-survey s390x 4.4-2-2 [3459 kB]
907s Preconfiguring packages ...
907s Fetched 251 MB in 4min 49s (870 kB/s)
907s Selecting previously unselected package libisl23:s390x.
907s (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 ... 56326 files and directories currently installed.)
907s Preparing to unpack .../000-libisl23_0.27-1_s390x.deb ...
907s Unpacking libisl23:s390x (0.27-1) ...
907s Selecting previously unselected package libmpc3:s390x.
907s Preparing to unpack .../001-libmpc3_1.3.1-1build2_s390x.deb ...
907s Unpacking libmpc3:s390x (1.3.1-1build2) ...
907s Selecting previously unselected package cpp-14-s390x-linux-gnu.
907s Preparing to unpack .../002-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ...
907s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
907s Selecting previously unselected package cpp-14.
907s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_s390x.deb ...
907s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
907s Selecting previously unselected package cpp-s390x-linux-gnu.
907s Preparing to unpack .../004-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ...
907s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
907s Selecting previously unselected package cpp.
907s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ...
907s Unpacking cpp (4:14.2.0-1ubuntu1) ...
907s Selecting previously unselected package libcc1-0:s390x.
907s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_s390x.deb ...
907s Unpacking libcc1-0:s390x (15-20250222-0ubuntu1) ...
907s Selecting previously unselected package libgomp1:s390x.
907s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_s390x.deb ...
907s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ...
907s Selecting previously unselected package libitm1:s390x.
907s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_s390x.deb ...
907s Unpacking libitm1:s390x (15-20250222-0ubuntu1) ...
907s Selecting previously unselected package libasan8:s390x.
907s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_s390x.deb ...
907s Unpacking libasan8:s390x (15-20250222-0ubuntu1) ...
907s Selecting previously unselected package libubsan1:s390x.
907s Preparing to unpack .../010-libubsan1_15-20250222-0ubuntu1_s390x.deb ...
907s Unpacking libubsan1:s390x (15-20250222-0ubuntu1) ...
907s Selecting previously unselected package libgcc-14-dev:s390x.
907s Preparing to unpack .../011-libgcc-14-dev_14.2.0-17ubuntu3_s390x.deb ...
907s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu3) ...
907s Selecting previously unselected package gcc-14-s390x-linux-gnu.
907s Preparing to unpack .../012-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ...
907s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package gcc-14.
908s Preparing to unpack .../013-gcc-14_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package gcc-s390x-linux-gnu.
908s Preparing to unpack .../014-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ...
908s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
908s Selecting previously unselected package gcc.
908s Preparing to unpack .../015-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ...
908s Unpacking gcc (4:14.2.0-1ubuntu1) ...
908s Selecting previously unselected package libstdc++-14-dev:s390x.
908s Preparing to unpack .../016-libstdc++-14-dev_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package g++-14-s390x-linux-gnu.
908s Preparing to unpack .../017-g++-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package g++-14.
908s Preparing to unpack .../018-g++-14_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking g++-14 (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package g++-s390x-linux-gnu.
908s Preparing to unpack .../019-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ...
908s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
908s Selecting previously unselected package g++.
908s Preparing to unpack .../020-g++_4%3a14.2.0-1ubuntu1_s390x.deb ...
908s Unpacking g++ (4:14.2.0-1ubuntu1) ...
908s Selecting previously unselected package build-essential.
908s Preparing to unpack .../021-build-essential_12.10ubuntu1_s390x.deb ...
908s Unpacking build-essential (12.10ubuntu1) ...
908s Selecting previously unselected package dctrl-tools.
908s Preparing to unpack .../022-dctrl-tools_2.24-3build3_s390x.deb ...
908s Unpacking dctrl-tools (2.24-3build3) ...
908s Selecting previously unselected package libfreetype6:s390x.
908s Preparing to unpack .../023-libfreetype6_2.13.3+dfsg-1_s390x.deb ...
908s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ...
908s Selecting previously unselected package fonts-dejavu-mono.
908s Preparing to unpack .../024-fonts-dejavu-mono_2.37-8_all.deb ...
908s Unpacking fonts-dejavu-mono (2.37-8) ...
908s Selecting previously unselected package fonts-dejavu-core.
908s Preparing to unpack .../025-fonts-dejavu-core_2.37-8_all.deb ...
908s Unpacking fonts-dejavu-core (2.37-8) ...
908s Selecting previously unselected package fontconfig-config.
908s Preparing to unpack .../026-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ...
908s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
908s Selecting previously unselected package libfontconfig1:s390x.
908s Preparing to unpack .../027-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ...
908s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ...
908s Selecting previously unselected package fontconfig.
908s Preparing to unpack .../028-fontconfig_2.15.0-2ubuntu1_s390x.deb ...
908s Unpacking fontconfig (2.15.0-2ubuntu1) ...
908s Selecting previously unselected package fonts-glyphicons-halflings.
908s Preparing to unpack .../029-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
908s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
908s Selecting previously unselected package fonts-mathjax.
908s Preparing to unpack .../030-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
908s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
908s Selecting previously unselected package libgfortran5:s390x.
908s Preparing to unpack .../031-libgfortran5_15-20250222-0ubuntu1_s390x.deb ...
908s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ...
908s Selecting previously unselected package libgfortran-14-dev:s390x.
908s Preparing to unpack .../032-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package gfortran-14-s390x-linux-gnu.
908s Preparing to unpack .../033-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package gfortran-14.
908s Preparing to unpack .../034-gfortran-14_14.2.0-17ubuntu3_s390x.deb ...
908s Unpacking gfortran-14 (14.2.0-17ubuntu3) ...
908s Selecting previously unselected package gfortran-s390x-linux-gnu.
908s Preparing to unpack .../035-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ...
908s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
908s Selecting previously unselected package gfortran.
908s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ...
908s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
908s Selecting previously unselected package icu-devtools.
908s Preparing to unpack .../037-icu-devtools_76.1-1ubuntu2_s390x.deb ...
908s Unpacking icu-devtools (76.1-1ubuntu2) ...
908s Selecting previously unselected package libblas3:s390x.
908s Preparing to unpack .../038-libblas3_3.12.1-2_s390x.deb ...
908s Unpacking libblas3:s390x (3.12.1-2) ...
909s Selecting previously unselected package libblas-dev:s390x.
909s Preparing to unpack .../039-libblas-dev_3.12.1-2_s390x.deb ...
909s Unpacking libblas-dev:s390x (3.12.1-2) ...
909s Selecting previously unselected package libbz2-dev:s390x.
909s Preparing to unpack .../040-libbz2-dev_1.0.8-6_s390x.deb ...
909s Unpacking libbz2-dev:s390x (1.0.8-6) ...
909s Selecting previously unselected package libpixman-1-0:s390x.
909s Preparing to unpack .../041-libpixman-1-0_0.44.0-3_s390x.deb ...
909s Unpacking libpixman-1-0:s390x (0.44.0-3) ...
909s Selecting previously unselected package libxcb-render0:s390x.
909s Preparing to unpack .../042-libxcb-render0_1.17.0-2_s390x.deb ...
909s Unpacking libxcb-render0:s390x (1.17.0-2) ...
909s Selecting previously unselected package libxcb-shm0:s390x.
909s Preparing to unpack .../043-libxcb-shm0_1.17.0-2_s390x.deb ...
909s Unpacking libxcb-shm0:s390x (1.17.0-2) ...
909s Selecting previously unselected package libxrender1:s390x.
909s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ...
909s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ...
909s Selecting previously unselected package libcairo2:s390x.
909s Preparing to unpack .../045-libcairo2_1.18.2-2_s390x.deb ...
909s Unpacking libcairo2:s390x (1.18.2-2) ...
909s Selecting previously unselected package libdatrie1:s390x.
909s Preparing to unpack .../046-libdatrie1_0.2.13-3build1_s390x.deb ...
909s Unpacking libdatrie1:s390x (0.2.13-3build1) ...
909s Selecting previously unselected package libdeflate0:s390x.
909s Preparing to unpack .../047-libdeflate0_1.23-1_s390x.deb ...
909s Unpacking libdeflate0:s390x (1.23-1) ...
909s Selecting previously unselected package libdeflate-dev:s390x.
909s Preparing to unpack .../048-libdeflate-dev_1.23-1_s390x.deb ...
909s Unpacking libdeflate-dev:s390x (1.23-1) ...
909s Selecting previously unselected package libgraphite2-3:s390x.
909s Preparing to unpack .../049-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ...
909s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ...
909s Selecting previously unselected package libharfbuzz0b:s390x.
909s Preparing to unpack .../050-libharfbuzz0b_10.2.0-1_s390x.deb ...
909s Unpacking libharfbuzz0b:s390x (10.2.0-1) ...
909s Selecting previously unselected package x11-common.
909s Preparing to unpack .../051-x11-common_1%3a7.7+23ubuntu3_all.deb ...
909s Unpacking x11-common (1:7.7+23ubuntu3) ...
909s Selecting previously unselected package libice6:s390x.
909s Preparing to unpack .../052-libice6_2%3a1.1.1-1_s390x.deb ...
909s Unpacking libice6:s390x (2:1.1.1-1) ...
909s Selecting previously unselected package libicu-dev:s390x.
909s Preparing to unpack .../053-libicu-dev_76.1-1ubuntu2_s390x.deb ...
909s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ...
909s Selecting previously unselected package libjpeg-turbo8:s390x.
909s Preparing to unpack .../054-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ...
909s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ...
909s Selecting previously unselected package libjpeg-turbo8-dev:s390x.
909s Preparing to unpack .../055-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ...
909s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ...
909s Selecting previously unselected package libjpeg8:s390x.
909s Preparing to unpack .../056-libjpeg8_8c-2ubuntu11_s390x.deb ...
909s Unpacking libjpeg8:s390x (8c-2ubuntu11) ...
909s Selecting previously unselected package libjpeg8-dev:s390x.
909s Preparing to unpack .../057-libjpeg8-dev_8c-2ubuntu11_s390x.deb ...
909s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ...
909s Selecting previously unselected package libjpeg-dev:s390x.
909s Preparing to unpack .../058-libjpeg-dev_8c-2ubuntu11_s390x.deb ...
909s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ...
909s Selecting previously unselected package libjs-bootstrap.
909s Preparing to unpack .../059-libjs-bootstrap_3.4.1+dfsg-3_all.deb ...
909s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ...
909s Selecting previously unselected package libjs-highlight.js.
909s Preparing to unpack .../060-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ...
909s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ...
909s Selecting previously unselected package libjs-jquery.
909s Preparing to unpack .../061-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
909s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
909s Selecting previously unselected package libjs-jquery-datatables.
909s Preparing to unpack .../062-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ...
909s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ...
909s Selecting previously unselected package liblapack3:s390x.
909s Preparing to unpack .../063-liblapack3_3.12.1-2_s390x.deb ...
909s Unpacking liblapack3:s390x (3.12.1-2) ...
909s Selecting previously unselected package liblapack-dev:s390x.
909s Preparing to unpack .../064-liblapack-dev_3.12.1-2_s390x.deb ...
909s Unpacking liblapack-dev:s390x (3.12.1-2) ...
909s Selecting previously unselected package libncurses-dev:s390x.
909s Preparing to unpack .../065-libncurses-dev_6.5+20250216-2_s390x.deb ...
909s Unpacking libncurses-dev:s390x (6.5+20250216-2) ...
909s Selecting previously unselected package libthai-data.
909s Preparing to unpack .../066-libthai-data_0.1.29-2build1_all.deb ...
909s Unpacking libthai-data (0.1.29-2build1) ...
909s Selecting previously unselected package libthai0:s390x.
909s Preparing to unpack .../067-libthai0_0.1.29-2build1_s390x.deb ...
909s Unpacking libthai0:s390x (0.1.29-2build1) ...
909s Selecting previously unselected package libpango-1.0-0:s390x.
909s Preparing to unpack .../068-libpango-1.0-0_1.56.1-1_s390x.deb ...
909s Unpacking libpango-1.0-0:s390x (1.56.1-1) ...
909s Selecting previously unselected package libpangoft2-1.0-0:s390x.
909s Preparing to unpack .../069-libpangoft2-1.0-0_1.56.1-1_s390x.deb ...
909s Unpacking libpangoft2-1.0-0:s390x (1.56.1-1) ...
909s Selecting previously unselected package libpangocairo-1.0-0:s390x.
909s Preparing to unpack .../070-libpangocairo-1.0-0_1.56.1-1_s390x.deb ...
909s Unpacking libpangocairo-1.0-0:s390x (1.56.1-1) ...
909s Selecting previously unselected package libpaper2:s390x.
909s Preparing to unpack .../071-libpaper2_2.2.5-0.3_s390x.deb ...
909s Unpacking libpaper2:s390x (2.2.5-0.3) ...
909s Selecting previously unselected package libpaper-utils.
909s Preparing to unpack .../072-libpaper-utils_2.2.5-0.3_s390x.deb ...
909s Unpacking libpaper-utils (2.2.5-0.3) ...
909s Selecting previously unselected package libpcre2-16-0:s390x.
909s Preparing to unpack .../073-libpcre2-16-0_10.45-1_s390x.deb ...
909s Unpacking libpcre2-16-0:s390x (10.45-1) ...
909s Selecting previously unselected package libpcre2-32-0:s390x.
909s Preparing to unpack .../074-libpcre2-32-0_10.45-1_s390x.deb ...
909s Unpacking libpcre2-32-0:s390x (10.45-1) ...
909s Selecting previously unselected package libpcre2-posix3:s390x.
909s Preparing to unpack .../075-libpcre2-posix3_10.45-1_s390x.deb ...
909s Unpacking libpcre2-posix3:s390x (10.45-1) ...
909s Selecting previously unselected package libpcre2-dev:s390x.
909s Preparing to unpack .../076-libpcre2-dev_10.45-1_s390x.deb ...
909s Unpacking libpcre2-dev:s390x (10.45-1) ...
909s Selecting previously unselected package libpkgconf3:s390x.
909s Preparing to unpack .../077-libpkgconf3_1.8.1-4_s390x.deb ...
909s Unpacking libpkgconf3:s390x (1.8.1-4) ...
909s Selecting previously unselected package zlib1g-dev:s390x.
909s Preparing to unpack .../078-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ...
909s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
909s Selecting previously unselected package libpng-dev:s390x.
909s Preparing to unpack .../079-libpng-dev_1.6.47-1_s390x.deb ...
909s Unpacking libpng-dev:s390x (1.6.47-1) ...
909s Selecting previously unselected package libreadline-dev:s390x.
909s Preparing to unpack .../080-libreadline-dev_8.2-6_s390x.deb ...
909s Unpacking libreadline-dev:s390x (8.2-6) ...
909s Selecting previously unselected package libsharpyuv0:s390x.
909s Preparing to unpack .../081-libsharpyuv0_1.5.0-0.1_s390x.deb ...
909s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ...
909s Selecting previously unselected package libsm6:s390x.
909s Preparing to unpack .../082-libsm6_2%3a1.2.4-1_s390x.deb ...
909s Unpacking libsm6:s390x (2:1.2.4-1) ...
909s Selecting previously unselected package libtcl8.6:s390x.
909s Preparing to unpack .../083-libtcl8.6_8.6.16+dfsg-1_s390x.deb ...
909s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ...
909s Selecting previously unselected package libjbig0:s390x.
909s Preparing to unpack .../084-libjbig0_2.1-6.1ubuntu2_s390x.deb ...
909s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ...
909s Selecting previously unselected package libwebp7:s390x.
909s Preparing to unpack .../085-libwebp7_1.5.0-0.1_s390x.deb ...
909s Unpacking libwebp7:s390x (1.5.0-0.1) ...
909s Selecting previously unselected package libtiff6:s390x.
909s Preparing to unpack .../086-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ...
909s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ...
909s Selecting previously unselected package libxft2:s390x.
909s Preparing to unpack .../087-libxft2_2.3.6-1build1_s390x.deb ...
909s Unpacking libxft2:s390x (2.3.6-1build1) ...
909s Selecting previously unselected package libxss1:s390x.
909s Preparing to unpack .../088-libxss1_1%3a1.2.3-1build3_s390x.deb ...
909s Unpacking libxss1:s390x (1:1.2.3-1build3) ...
910s Selecting previously unselected package libtk8.6:s390x.
910s Preparing to unpack .../089-libtk8.6_8.6.16-1_s390x.deb ...
910s Unpacking libtk8.6:s390x (8.6.16-1) ...
910s Selecting previously unselected package libxt6t64:s390x.
910s Preparing to unpack .../090-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ...
910s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ...
910s Selecting previously unselected package zip.
910s Preparing to unpack .../091-zip_3.0-14ubuntu2_s390x.deb ...
910s Unpacking zip (3.0-14ubuntu2) ...
910s Selecting previously unselected package unzip.
910s Preparing to unpack .../092-unzip_6.0-28ubuntu6_s390x.deb ...
910s Unpacking unzip (6.0-28ubuntu6) ...
910s Selecting previously unselected package xdg-utils.
910s Preparing to unpack .../093-xdg-utils_1.2.1-2ubuntu1_all.deb ...
910s Unpacking xdg-utils (1.2.1-2ubuntu1) ...
910s Selecting previously unselected package r-base-core.
910s Preparing to unpack .../094-r-base-core_4.4.3-1_s390x.deb ...
910s Unpacking r-base-core (4.4.3-1) ...
910s Selecting previously unselected package r-cran-littler.
910s Preparing to unpack .../095-r-cran-littler_0.3.20-2_s390x.deb ...
910s Unpacking r-cran-littler (0.3.20-2) ...
910s Selecting previously unselected package littler.
910s Preparing to unpack .../096-littler_0.3.20-2_all.deb ...
910s Unpacking littler (0.3.20-2) ...
910s Selecting previously unselected package node-normalize.css.
910s Preparing to unpack .../097-node-normalize.css_8.0.1-5_all.deb ...
910s Unpacking node-normalize.css (8.0.1-5) ...
910s Selecting previously unselected package liblzma-dev:s390x.
910s Preparing to unpack .../098-liblzma-dev_5.6.4-1_s390x.deb ...
910s Unpacking liblzma-dev:s390x (5.6.4-1) ...
910s Selecting previously unselected package pkgconf-bin.
910s Preparing to unpack .../099-pkgconf-bin_1.8.1-4_s390x.deb ...
910s Unpacking pkgconf-bin (1.8.1-4) ...
910s Selecting previously unselected package pkgconf:s390x.
910s Preparing to unpack .../100-pkgconf_1.8.1-4_s390x.deb ...
910s Unpacking pkgconf:s390x (1.8.1-4) ...
910s Selecting previously unselected package libtirpc-dev:s390x.
910s Preparing to unpack .../101-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ...
910s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ...
910s Selecting previously unselected package r-base-dev.
910s Preparing to unpack .../102-r-base-dev_4.4.3-1_all.deb ...
910s Unpacking r-base-dev (4.4.3-1) ...
910s Selecting previously unselected package pkg-r-autopkgtest.
910s Preparing to unpack .../103-pkg-r-autopkgtest_20231212ubuntu1_all.deb ...
910s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ...
910s Selecting previously unselected package r-cran-abind.
910s Preparing to unpack .../104-r-cran-abind_1.4-8-1_all.deb ...
910s Unpacking r-cran-abind (1.4-8-1) ...
910s Selecting previously unselected package r-cran-cardata.
910s Preparing to unpack .../105-r-cran-cardata_3.0.5-1_all.deb ...
910s Unpacking r-cran-cardata (3.0.5-1) ...
910s Selecting previously unselected package r-cran-formula.
910s Preparing to unpack .../106-r-cran-formula_1.2-5-1_all.deb ...
910s Unpacking r-cran-formula (1.2-5-1) ...
910s Selecting previously unselected package r-cran-mass.
910s Preparing to unpack .../107-r-cran-mass_7.3-64-1_s390x.deb ...
910s Unpacking r-cran-mass (7.3-64-1) ...
910s Selecting previously unselected package r-cran-lattice.
910s Preparing to unpack .../108-r-cran-lattice_0.22-6-1_s390x.deb ...
910s Unpacking r-cran-lattice (0.22-6-1) ...
910s Selecting previously unselected package r-cran-nlme.
910s Preparing to unpack .../109-r-cran-nlme_3.1.167-1_s390x.deb ...
910s Unpacking r-cran-nlme (3.1.167-1) ...
910s Selecting previously unselected package r-cran-matrix.
910s Preparing to unpack .../110-r-cran-matrix_1.7-3-1_s390x.deb ...
910s Unpacking r-cran-matrix (1.7-3-1) ...
910s Selecting previously unselected package r-cran-mgcv.
910s Preparing to unpack .../111-r-cran-mgcv_1.9-1-1_s390x.deb ...
910s Unpacking r-cran-mgcv (1.9-1-1) ...
910s Selecting previously unselected package r-cran-nnet.
910s Preparing to unpack .../112-r-cran-nnet_7.3-20-1_s390x.deb ...
910s Unpacking r-cran-nnet (7.3-20-1) ...
910s Selecting previously unselected package r-cran-boot.
910s Preparing to unpack .../113-r-cran-boot_1.3-31-1_all.deb ...
910s Unpacking r-cran-boot (1.3-31-1) ...
910s Selecting previously unselected package r-cran-pkgkitten.
910s Preparing to unpack .../114-r-cran-pkgkitten_0.2.4-1_all.deb ...
910s Unpacking r-cran-pkgkitten (0.2.4-1) ...
910s Selecting previously unselected package r-cran-rcpp.
910s Preparing to unpack .../115-r-cran-rcpp_1.0.14-1_s390x.deb ...
910s Unpacking r-cran-rcpp (1.0.14-1) ...
910s Selecting previously unselected package r-cran-minqa.
910s Preparing to unpack .../116-r-cran-minqa_1.2.8-1_s390x.deb ...
910s Unpacking r-cran-minqa (1.2.8-1) ...
910s Selecting previously unselected package libnlopt0:s390x.
910s Preparing to unpack .../117-libnlopt0_2.7.1-6ubuntu3_s390x.deb ...
910s Unpacking libnlopt0:s390x (2.7.1-6ubuntu3) ...
910s Selecting previously unselected package r-cran-nloptr.
910s Preparing to unpack .../118-r-cran-nloptr_2.1.1-1_s390x.deb ...
910s Unpacking r-cran-nloptr (2.1.1-1) ...
910s Selecting previously unselected package r-cran-rbibutils.
910s Preparing to unpack .../119-r-cran-rbibutils_2.3-1_s390x.deb ...
910s Unpacking r-cran-rbibutils (2.3-1) ...
910s Selecting previously unselected package r-cran-rdpack.
910s Preparing to unpack .../120-r-cran-rdpack_2.6.2-1syncable1_all.deb ...
910s Unpacking r-cran-rdpack (2.6.2-1syncable1) ...
910s Selecting previously unselected package r-cran-reformulas.
910s Preparing to unpack .../121-r-cran-reformulas_0.4.0-1_all.deb ...
910s Unpacking r-cran-reformulas (0.4.0-1) ...
910s Selecting previously unselected package r-cran-rcppeigen.
910s Preparing to unpack .../122-r-cran-rcppeigen_0.3.4.0.2-1_s390x.deb ...
910s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ...
910s Selecting previously unselected package r-cran-statmod.
910s Preparing to unpack .../123-r-cran-statmod_1.5.0-1_s390x.deb ...
910s Unpacking r-cran-statmod (1.5.0-1) ...
910s Selecting previously unselected package r-cran-lme4.
910s Preparing to unpack .../124-r-cran-lme4_1.1-36-1_s390x.deb ...
910s Unpacking r-cran-lme4 (1.1-36-1) ...
910s Selecting previously unselected package r-cran-backports.
910s Preparing to unpack .../125-r-cran-backports_1.5.0-2_s390x.deb ...
910s Unpacking r-cran-backports (1.5.0-2) ...
910s Selecting previously unselected package r-cran-cli.
910s Preparing to unpack .../126-r-cran-cli_3.6.4-1_s390x.deb ...
910s Unpacking r-cran-cli (3.6.4-1) ...
910s Selecting previously unselected package r-cran-generics.
910s Preparing to unpack .../127-r-cran-generics_0.1.3-1_all.deb ...
910s Unpacking r-cran-generics (0.1.3-1) ...
910s Selecting previously unselected package r-cran-glue.
910s Preparing to unpack .../128-r-cran-glue_1.8.0-1_s390x.deb ...
910s Unpacking r-cran-glue (1.8.0-1) ...
910s Selecting previously unselected package r-cran-rlang.
910s Preparing to unpack .../129-r-cran-rlang_1.1.5-1_s390x.deb ...
910s Unpacking r-cran-rlang (1.1.5-1) ...
910s Selecting previously unselected package r-cran-lifecycle.
910s Preparing to unpack .../130-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ...
910s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ...
910s Selecting previously unselected package r-cran-magrittr.
910s Preparing to unpack .../131-r-cran-magrittr_2.0.3-1_s390x.deb ...
910s Unpacking r-cran-magrittr (2.0.3-1) ...
911s Selecting previously unselected package r-cran-utf8.
911s Preparing to unpack .../132-r-cran-utf8_1.2.4-1_s390x.deb ...
911s Unpacking r-cran-utf8 (1.2.4-1) ...
911s Selecting previously unselected package r-cran-vctrs.
911s Preparing to unpack .../133-r-cran-vctrs_0.6.5-1_s390x.deb ...
911s Unpacking r-cran-vctrs (0.6.5-1) ...
911s Selecting previously unselected package r-cran-pillar.
911s Preparing to unpack .../134-r-cran-pillar_1.10.1+dfsg-1_all.deb ...
911s Unpacking r-cran-pillar (1.10.1+dfsg-1) ...
911s Selecting previously unselected package r-cran-r6.
911s Preparing to unpack .../135-r-cran-r6_2.6.1-1_all.deb ...
911s Unpacking r-cran-r6 (2.6.1-1) ...
911s Selecting previously unselected package r-cran-fansi.
911s Preparing to unpack .../136-r-cran-fansi_1.0.5-1_s390x.deb ...
911s Unpacking r-cran-fansi (1.0.5-1) ...
911s Selecting previously unselected package r-cran-pkgconfig.
911s Preparing to unpack .../137-r-cran-pkgconfig_2.0.3-2build1_all.deb ...
911s Unpacking r-cran-pkgconfig (2.0.3-2build1) ...
911s Selecting previously unselected package r-cran-tibble.
911s Preparing to unpack .../138-r-cran-tibble_3.2.1+dfsg-3_s390x.deb ...
911s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
911s Selecting previously unselected package r-cran-withr.
911s Preparing to unpack .../139-r-cran-withr_3.0.2+dfsg-1_all.deb ...
911s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
911s Selecting previously unselected package r-cran-tidyselect.
911s Preparing to unpack .../140-r-cran-tidyselect_1.2.1+dfsg-1_s390x.deb ...
911s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
911s Selecting previously unselected package r-cran-dplyr.
911s Preparing to unpack .../141-r-cran-dplyr_1.1.4-4_s390x.deb ...
911s Unpacking r-cran-dplyr (1.1.4-4) ...
911s Selecting previously unselected package r-cran-purrr.
911s Preparing to unpack .../142-r-cran-purrr_1.0.4-1_s390x.deb ...
911s Unpacking r-cran-purrr (1.0.4-1) ...
911s Selecting previously unselected package r-cran-stringi.
911s Preparing to unpack .../143-r-cran-stringi_1.8.4-1build1_s390x.deb ...
911s Unpacking r-cran-stringi (1.8.4-1build1) ...
911s Selecting previously unselected package r-cran-stringr.
911s Preparing to unpack .../144-r-cran-stringr_1.5.1-1_all.deb ...
911s Unpacking r-cran-stringr (1.5.1-1) ...
911s Selecting previously unselected package r-cran-cpp11.
911s Preparing to unpack .../145-r-cran-cpp11_0.5.2-1_all.deb ...
911s Unpacking r-cran-cpp11 (0.5.2-1) ...
911s Selecting previously unselected package r-cran-tidyr.
911s Preparing to unpack .../146-r-cran-tidyr_1.3.1-1_s390x.deb ...
911s Unpacking r-cran-tidyr (1.3.1-1) ...
911s Selecting previously unselected package r-cran-broom.
911s Preparing to unpack .../147-r-cran-broom_1.0.7+dfsg-1_all.deb ...
911s Unpacking r-cran-broom (1.0.7+dfsg-1) ...
911s Selecting previously unselected package r-cran-numderiv.
911s Preparing to unpack .../148-r-cran-numderiv_2016.8-1.1-3_all.deb ...
911s Unpacking r-cran-numderiv (2016.8-1.1-3) ...
911s Selecting previously unselected package r-cran-gtable.
911s Preparing to unpack .../149-r-cran-gtable_0.3.6+dfsg-1_all.deb ...
911s Unpacking r-cran-gtable (0.3.6+dfsg-1) ...
911s Selecting previously unselected package r-cran-isoband.
911s Preparing to unpack .../150-r-cran-isoband_0.2.7-1_s390x.deb ...
911s Unpacking r-cran-isoband (0.2.7-1) ...
911s Selecting previously unselected package r-cran-farver.
911s Preparing to unpack .../151-r-cran-farver_2.1.2-1_s390x.deb ...
911s Unpacking r-cran-farver (2.1.2-1) ...
911s Selecting previously unselected package r-cran-labeling.
911s Preparing to unpack .../152-r-cran-labeling_0.4.3-1_all.deb ...
911s Unpacking r-cran-labeling (0.4.3-1) ...
911s Selecting previously unselected package r-cran-colorspace.
911s Preparing to unpack .../153-r-cran-colorspace_2.1-1+dfsg-1_s390x.deb ...
911s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ...
911s Selecting previously unselected package r-cran-munsell.
911s Preparing to unpack .../154-r-cran-munsell_0.5.1-1_all.deb ...
911s Unpacking r-cran-munsell (0.5.1-1) ...
911s Selecting previously unselected package r-cran-rcolorbrewer.
911s Preparing to unpack .../155-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ...
911s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ...
911s Selecting previously unselected package r-cran-viridislite.
911s Preparing to unpack .../156-r-cran-viridislite_0.4.2-2_all.deb ...
911s Unpacking r-cran-viridislite (0.4.2-2) ...
911s Selecting previously unselected package r-cran-scales.
911s Preparing to unpack .../157-r-cran-scales_1.3.0-1_all.deb ...
911s Unpacking r-cran-scales (1.3.0-1) ...
911s Selecting previously unselected package r-cran-ggplot2.
911s Preparing to unpack .../158-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ...
911s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ...
911s Selecting previously unselected package r-cran-cowplot.
911s Preparing to unpack .../159-r-cran-cowplot_1.1.3+dfsg-1_all.deb ...
911s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ...
911s Selecting previously unselected package r-cran-deriv.
911s Preparing to unpack .../160-r-cran-deriv_4.1.6-1_all.deb ...
911s Unpacking r-cran-deriv (4.1.6-1) ...
911s Selecting previously unselected package r-cran-modelr.
911s Preparing to unpack .../161-r-cran-modelr_0.1.11-1_all.deb ...
911s Unpacking r-cran-modelr (0.1.11-1) ...
911s Selecting previously unselected package r-cran-microbenchmark.
911s Preparing to unpack .../162-r-cran-microbenchmark_1.5.0-1_s390x.deb ...
911s Unpacking r-cran-microbenchmark (1.5.0-1) ...
911s Selecting previously unselected package r-cran-doby.
911s Preparing to unpack .../163-r-cran-doby_4.6.25-1_all.deb ...
911s Unpacking r-cran-doby (4.6.25-1) ...
911s Selecting previously unselected package r-cran-evaluate.
911s Preparing to unpack .../164-r-cran-evaluate_1.0.3-1_all.deb ...
911s Unpacking r-cran-evaluate (1.0.3-1) ...
911s Selecting previously unselected package r-cran-xfun.
911s Preparing to unpack .../165-r-cran-xfun_0.51+dfsg-1_s390x.deb ...
911s Unpacking r-cran-xfun (0.51+dfsg-1) ...
911s Selecting previously unselected package r-cran-highr.
911s Preparing to unpack .../166-r-cran-highr_0.11+dfsg-1_all.deb ...
911s Unpacking r-cran-highr (0.11+dfsg-1) ...
911s Selecting previously unselected package r-cran-yaml.
911s Preparing to unpack .../167-r-cran-yaml_2.3.10-1_s390x.deb ...
911s Unpacking r-cran-yaml (2.3.10-1) ...
911s Selecting previously unselected package libjs-mathjax.
911s Preparing to unpack .../168-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
911s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
912s Selecting previously unselected package r-cran-knitr.
912s Preparing to unpack .../169-r-cran-knitr_1.49+dfsg-1_all.deb ...
912s Unpacking r-cran-knitr (1.49+dfsg-1) ...
912s Selecting previously unselected package r-cran-pbkrtest.
912s Preparing to unpack .../170-r-cran-pbkrtest_0.5.3-1_all.deb ...
912s Unpacking r-cran-pbkrtest (0.5.3-1) ...
912s Selecting previously unselected package r-cran-sparsem.
912s Preparing to unpack .../171-r-cran-sparsem_1.84-2-1_s390x.deb ...
912s Unpacking r-cran-sparsem (1.84-2-1) ...
912s Selecting previously unselected package r-cran-matrixmodels.
912s Preparing to unpack .../172-r-cran-matrixmodels_0.5-3-1_all.deb ...
912s Unpacking r-cran-matrixmodels (0.5-3-1) ...
912s Selecting previously unselected package r-cran-survival.
912s Preparing to unpack .../173-r-cran-survival_3.8-3-1_s390x.deb ...
912s Unpacking r-cran-survival (3.8-3-1) ...
912s Selecting previously unselected package r-cran-matrixstats.
912s Preparing to unpack .../174-r-cran-matrixstats_1.5.0-1_s390x.deb ...
912s Unpacking r-cran-matrixstats (1.5.0-1) ...
912s Selecting previously unselected package r-cran-rcpparmadillo.
912s Preparing to unpack .../175-r-cran-rcpparmadillo_14.2.3-1-1_s390x.deb ...
912s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ...
912s Selecting previously unselected package r-cran-class.
912s Preparing to unpack .../176-r-cran-class_7.3-23-1_s390x.deb ...
912s Unpacking r-cran-class (7.3-23-1) ...
912s Selecting previously unselected package r-cran-proxy.
912s Preparing to unpack .../177-r-cran-proxy_0.4-27-1_s390x.deb ...
912s Unpacking r-cran-proxy (0.4-27-1) ...
912s Selecting previously unselected package r-cran-e1071.
912s Preparing to unpack .../178-r-cran-e1071_1.7-16-1_s390x.deb ...
912s Unpacking r-cran-e1071 (1.7-16-1) ...
912s Selecting previously unselected package r-cran-codetools.
912s Preparing to unpack .../179-r-cran-codetools_0.2-20-1_all.deb ...
912s Unpacking r-cran-codetools (0.2-20-1) ...
912s Selecting previously unselected package r-cran-iterators.
912s Preparing to unpack .../180-r-cran-iterators_1.0.14-1_all.deb ...
912s Unpacking r-cran-iterators (1.0.14-1) ...
912s Selecting previously unselected package r-cran-foreach.
912s Preparing to unpack .../181-r-cran-foreach_1.5.2-1_all.deb ...
912s Unpacking r-cran-foreach (1.5.2-1) ...
912s Selecting previously unselected package r-cran-data.table.
912s Preparing to unpack .../182-r-cran-data.table_1.17.0+dfsg-1_s390x.deb ...
912s Unpacking r-cran-data.table (1.17.0+dfsg-1) ...
912s Selecting previously unselected package r-cran-modelmetrics.
912s Preparing to unpack .../183-r-cran-modelmetrics_1.2.2.2-1build1_s390x.deb ...
912s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ...
912s Selecting previously unselected package r-cran-plyr.
912s Preparing to unpack .../184-r-cran-plyr_1.8.9-1_s390x.deb ...
912s Unpacking r-cran-plyr (1.8.9-1) ...
912s Selecting previously unselected package r-cran-proc.
912s Preparing to unpack .../185-r-cran-proc_1.18.5-1_s390x.deb ...
912s Unpacking r-cran-proc (1.18.5-1) ...
912s Selecting previously unselected package r-cran-tzdb.
912s Preparing to unpack .../186-r-cran-tzdb_0.4.0-2_s390x.deb ...
912s Unpacking r-cran-tzdb (0.4.0-2) ...
912s Selecting previously unselected package r-cran-clock.
912s Preparing to unpack .../187-r-cran-clock_0.7.2-1_s390x.deb ...
912s Unpacking r-cran-clock (0.7.2-1) ...
912s Selecting previously unselected package r-cran-gower.
912s Preparing to unpack .../188-r-cran-gower_1.0.2-1_s390x.deb ...
912s Unpacking r-cran-gower (1.0.2-1) ...
912s Selecting previously unselected package r-cran-hardhat.
912s Preparing to unpack .../189-r-cran-hardhat_1.4.0+dfsg-1_all.deb ...
912s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ...
912s Selecting previously unselected package r-cran-rpart.
912s Preparing to unpack .../190-r-cran-rpart_4.1.24-1_s390x.deb ...
912s Unpacking r-cran-rpart (4.1.24-1) ...
912s Selecting previously unselected package r-cran-shape.
912s Preparing to unpack .../191-r-cran-shape_1.4.6.1-1_all.deb ...
912s Unpacking r-cran-shape (1.4.6.1-1) ...
912s Selecting previously unselected package r-cran-diagram.
912s Preparing to unpack .../192-r-cran-diagram_1.6.5-2_all.deb ...
912s Unpacking r-cran-diagram (1.6.5-2) ...
912s Selecting previously unselected package r-cran-kernsmooth.
912s Preparing to unpack .../193-r-cran-kernsmooth_2.23-26-1_s390x.deb ...
912s Unpacking r-cran-kernsmooth (2.23-26-1) ...
912s Selecting previously unselected package r-cran-digest.
912s Preparing to unpack .../194-r-cran-digest_0.6.37-1_s390x.deb ...
912s Unpacking r-cran-digest (0.6.37-1) ...
912s Selecting previously unselected package r-cran-globals.
912s Preparing to unpack .../195-r-cran-globals_0.16.3-1_all.deb ...
912s Unpacking r-cran-globals (0.16.3-1) ...
912s Selecting previously unselected package r-cran-listenv.
912s Preparing to unpack .../196-r-cran-listenv_0.9.1+dfsg-1_all.deb ...
912s Unpacking r-cran-listenv (0.9.1+dfsg-1) ...
912s Selecting previously unselected package r-cran-parallelly.
912s Preparing to unpack .../197-r-cran-parallelly_1.42.0-1_s390x.deb ...
912s Unpacking r-cran-parallelly (1.42.0-1) ...
912s Selecting previously unselected package r-cran-future.
912s Preparing to unpack .../198-r-cran-future_1.34.0+dfsg-1_all.deb ...
912s Unpacking r-cran-future (1.34.0+dfsg-1) ...
912s Selecting previously unselected package r-cran-future.apply.
912s Preparing to unpack .../199-r-cran-future.apply_1.11.3+dfsg-1_all.deb ...
912s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ...
912s Selecting previously unselected package r-cran-progressr.
912s Preparing to unpack .../200-r-cran-progressr_0.15.1-1_all.deb ...
912s Unpacking r-cran-progressr (0.15.1-1) ...
912s Selecting previously unselected package r-cran-squarem.
912s Preparing to unpack .../201-r-cran-squarem_2021.1-1_all.deb ...
912s Unpacking r-cran-squarem (2021.1-1) ...
912s Selecting previously unselected package r-cran-lava.
912s Preparing to unpack .../202-r-cran-lava_1.8.1+dfsg-1_all.deb ...
912s Unpacking r-cran-lava (1.8.1+dfsg-1) ...
912s Selecting previously unselected package r-cran-prodlim.
912s Preparing to unpack .../203-r-cran-prodlim_2024.06.25-1_s390x.deb ...
912s Unpacking r-cran-prodlim (2024.06.25-1) ...
912s Selecting previously unselected package r-cran-ipred.
912s Preparing to unpack .../204-r-cran-ipred_0.9-15-1_s390x.deb ...
912s Unpacking r-cran-ipred (0.9-15-1) ...
912s Selecting previously unselected package r-cran-timechange.
912s Preparing to unpack .../205-r-cran-timechange_0.3.0-1_s390x.deb ...
912s Unpacking r-cran-timechange (0.3.0-1) ...
912s Selecting previously unselected package r-cran-lubridate.
912s Preparing to unpack .../206-r-cran-lubridate_1.9.4+dfsg-1_s390x.deb ...
912s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ...
912s Selecting previously unselected package r-cran-timedate.
912s Preparing to unpack .../207-r-cran-timedate_4041.110-1_s390x.deb ...
912s Unpacking r-cran-timedate (4041.110-1) ...
912s Selecting previously unselected package r-cran-recipes.
912s Preparing to unpack .../208-r-cran-recipes_1.1.0+dfsg-1_all.deb ...
912s Unpacking r-cran-recipes (1.1.0+dfsg-1) ...
912s Selecting previously unselected package r-cran-reshape2.
912s Preparing to unpack .../209-r-cran-reshape2_1.4.4-2build1_s390x.deb ...
912s Unpacking r-cran-reshape2 (1.4.4-2build1) ...
912s Selecting previously unselected package r-cran-caret.
912s Preparing to unpack .../210-r-cran-caret_7.0-1+dfsg-1_s390x.deb ...
912s Unpacking r-cran-caret (7.0-1+dfsg-1) ...
912s Selecting previously unselected package r-cran-conquer.
912s Preparing to unpack .../211-r-cran-conquer_1.3.3-1_s390x.deb ...
912s Unpacking r-cran-conquer (1.3.3-1) ...
913s Selecting previously unselected package r-cran-quantreg.
913s Preparing to unpack .../212-r-cran-quantreg_6.00-1_s390x.deb ...
913s Unpacking r-cran-quantreg (6.00-1) ...
913s Selecting previously unselected package r-cran-foreign.
913s Preparing to unpack .../213-r-cran-foreign_0.8.88-1_s390x.deb ...
913s Unpacking r-cran-foreign (0.8.88-1) ...
913s Selecting previously unselected package r-cran-ellipsis.
913s Preparing to unpack .../214-r-cran-ellipsis_0.3.2-2_s390x.deb ...
913s Unpacking r-cran-ellipsis (0.3.2-2) ...
913s Selecting previously unselected package r-cran-forcats.
913s Preparing to unpack .../215-r-cran-forcats_1.0.0-1_all.deb ...
913s Unpacking r-cran-forcats (1.0.0-1) ...
913s Selecting previously unselected package r-cran-hms.
913s Preparing to unpack .../216-r-cran-hms_1.1.3-1_all.deb ...
913s Unpacking r-cran-hms (1.1.3-1) ...
913s Selecting previously unselected package r-cran-clipr.
913s Preparing to unpack .../217-r-cran-clipr_0.8.0-1_all.deb ...
913s Unpacking r-cran-clipr (0.8.0-1) ...
913s Selecting previously unselected package r-cran-crayon.
913s Preparing to unpack .../218-r-cran-crayon_1.5.3-1_all.deb ...
913s Unpacking r-cran-crayon (1.5.3-1) ...
913s Selecting previously unselected package r-cran-bit.
913s Preparing to unpack .../219-r-cran-bit_4.6.0+dfsg-1_s390x.deb ...
913s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
913s Selecting previously unselected package r-cran-bit64.
913s Preparing to unpack .../220-r-cran-bit64_4.6.0-1-1ubuntu2_s390x.deb ...
913s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ...
913s Selecting previously unselected package r-cran-prettyunits.
913s Preparing to unpack .../221-r-cran-prettyunits_1.2.0-1_all.deb ...
913s Unpacking r-cran-prettyunits (1.2.0-1) ...
913s Selecting previously unselected package r-cran-progress.
913s Preparing to unpack .../222-r-cran-progress_1.2.3-1_all.deb ...
913s Unpacking r-cran-progress (1.2.3-1) ...
913s Selecting previously unselected package r-cran-vroom.
913s Preparing to unpack .../223-r-cran-vroom_1.6.5-1_s390x.deb ...
913s Unpacking r-cran-vroom (1.6.5-1) ...
913s Selecting previously unselected package r-cran-readr.
913s Preparing to unpack .../224-r-cran-readr_2.1.5-1_s390x.deb ...
913s Unpacking r-cran-readr (2.1.5-1) ...
913s Selecting previously unselected package r-cran-haven.
913s Preparing to unpack .../225-r-cran-haven_2.5.4-1_s390x.deb ...
913s Unpacking r-cran-haven (2.5.4-1) ...
913s Selecting previously unselected package r-cran-curl.
913s Preparing to unpack .../226-r-cran-curl_6.2.1+dfsg-1ubuntu1_s390x.deb ...
913s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
913s Selecting previously unselected package r-cran-rematch.
913s Preparing to unpack .../227-r-cran-rematch_2.0.0-1_all.deb ...
913s Unpacking r-cran-rematch (2.0.0-1) ...
913s Selecting previously unselected package r-cran-cellranger.
913s Preparing to unpack .../228-r-cran-cellranger_1.1.0-3_all.deb ...
913s Unpacking r-cran-cellranger (1.1.0-3) ...
913s Selecting previously unselected package r-cran-readxl.
913s Preparing to unpack .../229-r-cran-readxl_1.4.4-1_s390x.deb ...
913s Unpacking r-cran-readxl (1.4.4-1) ...
913s Selecting previously unselected package r-cran-writexl.
913s Preparing to unpack .../230-r-cran-writexl_1.5.1-1_s390x.deb ...
913s Unpacking r-cran-writexl (1.5.1-1) ...
913s Selecting previously unselected package r-cran-r.methodss3.
913s Preparing to unpack .../231-r-cran-r.methodss3_1.8.2-1_all.deb ...
913s Unpacking r-cran-r.methodss3 (1.8.2-1) ...
913s Selecting previously unselected package r-cran-r.oo.
913s Preparing to unpack .../232-r-cran-r.oo_1.27.0-1_all.deb ...
913s Unpacking r-cran-r.oo (1.27.0-1) ...
913s Selecting previously unselected package r-cran-r.utils.
913s Preparing to unpack .../233-r-cran-r.utils_2.13.0-1_all.deb ...
913s Unpacking r-cran-r.utils (2.13.0-1) ...
913s Selecting previously unselected package r-cran-zip.
913s Preparing to unpack .../234-r-cran-zip_2.3.2-1_s390x.deb ...
913s Unpacking r-cran-zip (2.3.2-1) ...
913s Selecting previously unselected package r-cran-openxlsx.
913s Preparing to unpack .../235-r-cran-openxlsx_4.2.8-1_s390x.deb ...
913s Unpacking r-cran-openxlsx (4.2.8-1) ...
913s Selecting previously unselected package r-cran-rio.
913s Preparing to unpack .../236-r-cran-rio_1.2.3-1_all.deb ...
913s Unpacking r-cran-rio (1.2.3-1) ...
913s Selecting previously unselected package r-cran-car.
913s Preparing to unpack .../237-r-cran-car_3.1-3-1_all.deb ...
913s Unpacking r-cran-car (3.1-3-1) ...
913s Selecting previously unselected package r-cran-zoo.
913s Preparing to unpack .../238-r-cran-zoo_1.8-13-1_s390x.deb ...
913s Unpacking r-cran-zoo (1.8-13-1) ...
913s Selecting previously unselected package r-cran-lmtest.
913s Preparing to unpack .../239-r-cran-lmtest_0.9.40-1_s390x.deb ...
913s Unpacking r-cran-lmtest (0.9.40-1) ...
913s Selecting previously unselected package r-cran-sandwich.
913s Preparing to unpack .../240-r-cran-sandwich_3.1-1-1_all.deb ...
913s Unpacking r-cran-sandwich (3.1-1-1) ...
913s Selecting previously unselected package r-cran-aer.
913s Preparing to unpack .../241-r-cran-aer_1.2-14-1_all.deb ...
913s Unpacking r-cran-aer (1.2-14-1) ...
913s Selecting previously unselected package r-cran-blob.
913s Preparing to unpack .../242-r-cran-blob_1.2.4-1_all.deb ...
913s Unpacking r-cran-blob (1.2.4-1) ...
913s Selecting previously unselected package r-cran-fastmap.
913s Preparing to unpack .../243-r-cran-fastmap_1.2.0-1_s390x.deb ...
913s Unpacking r-cran-fastmap (1.2.0-1) ...
913s Selecting previously unselected package r-cran-cachem.
913s Preparing to unpack .../244-r-cran-cachem_1.1.0-1_s390x.deb ...
913s Unpacking r-cran-cachem (1.1.0-1) ...
913s Selecting previously unselected package r-cran-dbi.
913s Preparing to unpack .../245-r-cran-dbi_1.2.3-1_all.deb ...
913s Unpacking r-cran-dbi (1.2.3-1) ...
913s Selecting previously unselected package r-cran-hexbin.
913s Preparing to unpack .../246-r-cran-hexbin_1.28.5-1_s390x.deb ...
913s Unpacking r-cran-hexbin (1.28.5-1) ...
913s Selecting previously unselected package r-cran-memoise.
913s Preparing to unpack .../247-r-cran-memoise_2.0.1-1_all.deb ...
913s Unpacking r-cran-memoise (2.0.1-1) ...
913s Selecting previously unselected package r-cran-mitools.
913s Preparing to unpack .../248-r-cran-mitools_2.4-2build1_all.deb ...
913s Unpacking r-cran-mitools (2.4-2build1) ...
913s Selecting previously unselected package r-cran-plogr.
913s Preparing to unpack .../249-r-cran-plogr_0.2.0-3build1_all.deb ...
913s Unpacking r-cran-plogr (0.2.0-3build1) ...
913s Selecting previously unselected package r-cran-rsqlite.
913s Preparing to unpack .../250-r-cran-rsqlite_2.3.9-1_s390x.deb ...
913s Unpacking r-cran-rsqlite (2.3.9-1) ...
913s Selecting previously unselected package r-cran-survey.
913s Preparing to unpack .../251-r-cran-survey_4.4-2-2_s390x.deb ...
913s Unpacking r-cran-survey (4.4-2-2) ...
913s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ...
913s Setting up libpixman-1-0:s390x (0.44.0-3) ...
913s Setting up libsharpyuv0:s390x (1.5.0-0.1) ...
913s Setting up libncurses-dev:s390x (6.5+20250216-2) ...
913s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
913s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
913s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ...
913s Setting up libdatrie1:s390x (0.2.13-3build1) ...
913s Setting up libxcb-render0:s390x (1.17.0-2) ...
913s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
913s Setting up unzip (6.0-28ubuntu6) ...
913s Setting up x11-common (1:7.7+23ubuntu3) ...
913s Setting up libdeflate0:s390x (1.23-1) ...
913s Setting up libnlopt0:s390x (2.7.1-6ubuntu3) ...
913s Setting up libxcb-shm0:s390x (1.17.0-2) ...
913s Setting up libreadline-dev:s390x (8.2-6) ...
913s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ...
913s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ...
913s Setting up libpcre2-16-0:s390x (10.45-1) ...
913s Setting up zip (3.0-14ubuntu2) ...
913s Setting up libpcre2-32-0:s390x (10.45-1) ...
913s Setting up libblas3:s390x (3.12.1-2) ...
913s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
913s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ...
913s Setting up libpkgconf3:s390x (1.8.1-4) ...
913s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ...
913s Setting up fonts-dejavu-mono (2.37-8) ...
914s Setting up libmpc3:s390x (1.3.1-1build2) ...
914s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ...
914s Setting up icu-devtools (76.1-1ubuntu2) ...
914s Setting up fonts-dejavu-core (2.37-8) ...
914s Setting up pkgconf-bin (1.8.1-4) ...
914s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ...
914s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ...
914s Setting up libwebp7:s390x (1.5.0-0.1) ...
914s Setting up liblzma-dev:s390x (5.6.4-1) ...
914s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ...
914s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
914s Setting up libpcre2-posix3:s390x (10.45-1) ...
914s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
914s Setting up libasan8:s390x (15-20250222-0ubuntu1) ...
914s Setting up libharfbuzz0b:s390x (10.2.0-1) ...
914s Setting up libthai-data (0.1.29-2build1) ...
914s Setting up libxss1:s390x (1:1.2.3-1build3) ...
914s Setting up libpaper2:s390x (2.2.5-0.3) ...
914s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
914s Setting up libisl23:s390x (0.27-1) ...
914s Setting up libdeflate-dev:s390x (1.23-1) ...
914s Setting up node-normalize.css (8.0.1-5) ...
914s Setting up libicu-dev:s390x (76.1-1ubuntu2) ...
914s Setting up xdg-utils (1.2.1-2ubuntu1) ...
914s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
914s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ...
914s Setting up libblas-dev:s390x (3.12.1-2) ...
914s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode
914s Setting up dctrl-tools (2.24-3build3) ...
914s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
914s Setting up libitm1:s390x (15-20250222-0ubuntu1) ...
914s Setting up libbz2-dev:s390x (1.0.8-6) ...
914s Setting up libjpeg8:s390x (8c-2ubuntu11) ...
914s Setting up libice6:s390x (2:1.1.1-1) ...
914s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ...
914s Setting up liblapack3:s390x (3.12.1-2) ...
914s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
914s Setting up libpcre2-dev:s390x (10.45-1) ...
914s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
914s Setting up libpng-dev:s390x (1.6.47-1) ...
914s Setting up libpaper-utils (2.2.5-0.3) ...
914s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
914s Setting up pkgconf:s390x (1.8.1-4) ...
914s Setting up libthai0:s390x (0.1.29-2build1) ...
914s Setting up liblapack-dev:s390x (3.12.1-2) ...
914s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode
914s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
914s Setting up cpp-14 (14.2.0-17ubuntu3) ...
914s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ...
914s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ...
914s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ...
914s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ...
914s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ...
914s Setting up libsm6:s390x (2:1.2.4-1) ...
914s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ...
914s Setting up fontconfig (2.15.0-2ubuntu1) ...
916s Regenerating fonts cache... done.
916s Setting up libxft2:s390x (2.3.6-1build1) ...
916s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
916s Setting up libtk8.6:s390x (8.6.16-1) ...
916s Setting up libpango-1.0-0:s390x (1.56.1-1) ...
916s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ...
916s Setting up libcairo2:s390x (1.18.2-2) ...
916s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
916s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
916s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ...
916s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
916s Setting up cpp (4:14.2.0-1ubuntu1) ...
916s Setting up libpangoft2-1.0-0:s390x (1.56.1-1) ...
916s Setting up libpangocairo-1.0-0:s390x (1.56.1-1) ...
916s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
916s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
916s Setting up gcc-14 (14.2.0-17ubuntu3) ...
916s Setting up r-base-core (4.4.3-1) ...
916s Creating config file /etc/R/Renviron with new version
916s Setting up r-cran-crayon (1.5.3-1) ...
916s Setting up r-cran-squarem (2021.1-1) ...
916s Setting up r-cran-labeling (0.4.3-1) ...
916s Setting up r-cran-lattice (0.22-6-1) ...
916s Setting up r-cran-nlme (3.1.167-1) ...
916s Setting up r-cran-farver (2.1.2-1) ...
916s Setting up r-cran-formula (1.2-5-1) ...
916s Setting up r-cran-hexbin (1.28.5-1) ...
916s Setting up r-cran-zip (2.3.2-1) ...
916s Setting up r-cran-viridislite (0.4.2-2) ...
916s Setting up r-cran-sparsem (1.84-2-1) ...
916s Setting up r-cran-statmod (1.5.0-1) ...
916s Setting up r-cran-nnet (7.3-20-1) ...
916s Setting up r-cran-clipr (0.8.0-1) ...
916s Setting up g++-14 (14.2.0-17ubuntu3) ...
916s Setting up r-cran-proxy (0.4-27-1) ...
916s Setting up r-cran-r6 (2.6.1-1) ...
916s Setting up r-cran-pkgkitten (0.2.4-1) ...
916s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
916s Setting up r-cran-numderiv (2016.8-1.1-3) ...
916s Setting up r-cran-magrittr (2.0.3-1) ...
916s Setting up r-cran-microbenchmark (1.5.0-1) ...
916s Setting up r-cran-littler (0.3.20-2) ...
916s Setting up r-cran-rcpp (1.0.14-1) ...
916s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
916s Setting up r-cran-codetools (0.2-20-1) ...
916s Setting up r-cran-nloptr (2.1.1-1) ...
916s Setting up r-cran-boot (1.3-31-1) ...
916s Setting up r-cran-rematch (2.0.0-1) ...
916s Setting up r-cran-rlang (1.1.5-1) ...
916s Setting up r-cran-matrixstats (1.5.0-1) ...
916s Setting up r-cran-listenv (0.9.1+dfsg-1) ...
916s Setting up littler (0.3.20-2) ...
916s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
916s Setting up r-cran-xfun (0.51+dfsg-1) ...
916s Setting up r-cran-plogr (0.2.0-3build1) ...
916s Setting up r-cran-withr (3.0.2+dfsg-1) ...
916s Setting up r-cran-backports (1.5.0-2) ...
916s Setting up r-cran-deriv (4.1.6-1) ...
916s Setting up r-cran-generics (0.1.3-1) ...
916s Setting up r-cran-iterators (1.0.14-1) ...
916s Setting up r-cran-abind (1.4-8-1) ...
916s Setting up r-cran-digest (0.6.37-1) ...
916s Setting up r-cran-yaml (2.3.10-1) ...
916s Setting up r-cran-gower (1.0.2-1) ...
916s Setting up r-cran-evaluate (1.0.3-1) ...
916s Setting up r-cran-dbi (1.2.3-1) ...
916s Setting up r-cran-timedate (4041.110-1) ...
916s Setting up r-cran-highr (0.11+dfsg-1) ...
916s Setting up r-cran-foreach (1.5.2-1) ...
916s Setting up r-cran-prettyunits (1.2.0-1) ...
916s Setting up r-cran-fansi (1.0.5-1) ...
916s Setting up r-cran-cardata (3.0.5-1) ...
916s Setting up r-cran-mass (7.3-64-1) ...
916s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
916s Setting up r-cran-glue (1.8.0-1) ...
916s Setting up r-cran-foreign (0.8.88-1) ...
916s Setting up r-cran-writexl (1.5.1-1) ...
916s Setting up r-cran-bit (4.6.0+dfsg-1) ...
916s Setting up r-cran-cli (3.6.4-1) ...
916s Setting up r-cran-rbibutils (2.3-1) ...
916s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
916s Setting up r-cran-bit64 (4.6.0-1-1ubuntu2) ...
916s Setting up gcc (4:14.2.0-1ubuntu1) ...
916s Setting up r-cran-progressr (0.15.1-1) ...
916s Setting up r-cran-shape (1.4.6.1-1) ...
916s Setting up r-cran-fastmap (1.2.0-1) ...
916s Setting up r-cran-r.methodss3 (1.8.2-1) ...
916s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
916s Setting up r-cran-utf8 (1.2.4-1) ...
916s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
916s Setting up r-cran-parallelly (1.42.0-1) ...
916s Setting up r-cran-stringi (1.8.4-1build1) ...
916s Setting up r-cran-cpp11 (0.5.2-1) ...
916s Setting up r-cran-plyr (1.8.9-1) ...
916s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
916s Setting up r-cran-isoband (0.2.7-1) ...
916s Setting up r-cran-diagram (1.6.5-2) ...
916s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
916s Setting up r-cran-zoo (1.8-13-1) ...
916s Setting up r-cran-matrix (1.7-3-1) ...
916s Setting up r-cran-kernsmooth (2.23-26-1) ...
916s Setting up r-cran-knitr (1.49+dfsg-1) ...
916s Setting up r-cran-mgcv (1.9-1-1) ...
916s Setting up g++ (4:14.2.0-1ubuntu1) ...
916s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
916s Setting up r-cran-cachem (1.1.0-1) ...
916s Setting up r-cran-lmtest (0.9.40-1) ...
916s Setting up build-essential (12.10ubuntu1) ...
916s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ...
916s Setting up r-cran-tzdb (0.4.0-2) ...
916s Setting up r-cran-globals (0.16.3-1) ...
916s Setting up r-cran-vctrs (0.6.5-1) ...
916s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ...
916s Setting up r-cran-mitools (2.4-2build1) ...
916s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
916s Setting up r-cran-ellipsis (0.3.2-2) ...
916s Setting up r-cran-minqa (1.2.8-1) ...
916s Setting up r-cran-stringr (1.5.1-1) ...
916s Setting up r-cran-class (7.3-23-1) ...
916s Setting up r-cran-modelmetrics (1.2.2.2-1build1) ...
916s Setting up r-cran-openxlsx (4.2.8-1) ...
916s Setting up r-cran-matrixmodels (0.5-3-1) ...
916s Setting up r-cran-munsell (0.5.1-1) ...
916s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
916s Setting up r-cran-clock (0.7.2-1) ...
916s Setting up r-cran-sandwich (3.1-1-1) ...
916s Setting up r-cran-proc (1.18.5-1) ...
916s Setting up r-cran-survival (3.8-3-1) ...
916s Setting up r-cran-survey (4.4-2-2) ...
916s Setting up r-cran-r.oo (1.27.0-1) ...
916s Setting up r-cran-rdpack (2.6.2-1syncable1) ...
916s Setting up r-cran-future (1.34.0+dfsg-1) ...
916s Setting up gfortran (4:14.2.0-1ubuntu1) ...
916s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
916s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
916s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
916s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
916s Setting up r-cran-forcats (1.0.0-1) ...
916s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
916s Setting up r-cran-reshape2 (1.4.4-2build1) ...
916s Setting up r-cran-future.apply (1.11.3+dfsg-1) ...
916s Setting up r-cran-timechange (0.3.0-1) ...
916s Setting up r-cran-hms (1.1.3-1) ...
916s Setting up r-cran-scales (1.3.0-1) ...
916s Setting up r-cran-memoise (2.0.1-1) ...
916s Setting up r-cran-lava (1.8.1+dfsg-1) ...
916s Setting up r-cran-purrr (1.0.4-1) ...
916s Setting up r-cran-e1071 (1.7-16-1) ...
916s Setting up r-cran-blob (1.2.4-1) ...
916s Setting up r-cran-hardhat (1.4.0+dfsg-1) ...
916s Setting up r-cran-dplyr (1.1.4-4) ...
916s Setting up r-cran-reformulas (0.4.0-1) ...
916s Setting up r-cran-rsqlite (2.3.9-1) ...
916s Setting up r-cran-progress (1.2.3-1) ...
916s Setting up r-cran-lubridate (1.9.4+dfsg-1) ...
916s Setting up r-cran-r.utils (2.13.0-1) ...
916s Setting up r-cran-vroom (1.6.5-1) ...
916s Setting up r-base-dev (4.4.3-1) ...
916s Setting up r-cran-prodlim (2024.06.25-1) ...
916s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
916s Setting up r-cran-cellranger (1.1.0-3) ...
916s Setting up r-cran-rpart (4.1.24-1) ...
916s Setting up r-cran-ipred (0.9-15-1) ...
916s Setting up r-cran-lme4 (1.1-36-1) ...
916s Setting up r-cran-readr (2.1.5-1) ...
916s Setting up r-cran-tidyr (1.3.1-1) ...
916s Setting up r-cran-recipes (1.1.0+dfsg-1) ...
916s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
916s Setting up r-cran-cowplot (1.1.3+dfsg-1) ...
916s Setting up r-cran-readxl (1.4.4-1) ...
916s Setting up r-cran-haven (2.5.4-1) ...
916s Setting up r-cran-caret (7.0-1+dfsg-1) ...
916s Setting up r-cran-broom (1.0.7+dfsg-1) ...
916s Setting up r-cran-conquer (1.3.3-1) ...
916s Setting up r-cran-rio (1.2.3-1) ...
916s Setting up r-cran-quantreg (6.00-1) ...
916s Setting up r-cran-modelr (0.1.11-1) ...
916s Setting up r-cran-doby (4.6.25-1) ...
916s Setting up r-cran-pbkrtest (0.5.3-1) ...
916s Setting up r-cran-car (3.1-3-1) ...
916s Setting up r-cran-aer (1.2-14-1) ...
916s Processing triggers for libc-bin (2.41-1ubuntu2) ...
916s Processing triggers for man-db (2.13.0-1) ...
917s Processing triggers for install-info (7.1.1-1) ...
920s autopkgtest [12:54:52]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
920s autopkgtest [12:54:52]: test pkg-r-autopkgtest: [-----------------------
920s Test: Try to load the R library survey
920s 
920s R version 4.4.3 (2025-02-28) -- "Trophy Case"
920s Copyright (C) 2025 The R Foundation for Statistical Computing
920s Platform: s390x-ibm-linux-gnu
920s 
920s R is free software and comes with ABSOLUTELY NO WARRANTY.
920s You are welcome to redistribute it under certain conditions.
920s Type 'license()' or 'licence()' for distribution details.
920s 
920s R is a collaborative project with many contributors.
920s Type 'contributors()' for more information and
920s 'citation()' on how to cite R or R packages in publications.
920s 
920s Type 'demo()' for some demos, 'help()' for on-line help, or
920s 'help.start()' for an HTML browser interface to help.
920s Type 'q()' to quit R.
920s 
920s > library('survey')
920s Loading required package: grid
920s Loading required package: Matrix
921s Loading required package: survival
921s 
921s Attaching package: ‘survey’
921s 
921s The following object is masked from ‘package:graphics’:
921s 
921s     dotchart
921s 
921s > 
921s > 
921s Other tests are currently unsupported!
921s They will be progressively added.
922s autopkgtest [12:54:54]: test pkg-r-autopkgtest: -----------------------]
922s autopkgtest [12:54:54]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
922s pkg-r-autopkgtest    PASS
922s autopkgtest [12:54:54]: @@@@@@@@@@@@@@@@@@@@ summary
922s run-unit-test        PASS
922s pkg-r-autopkgtest    PASS
940s nova [W] Using flock in prodstack6-s390x
940s Creating nova instance adt-plucky-s390x-r-cran-survey-20250315-123932-juju-7f2275-prod-proposed-migration-environment-20-41dbf533-ed9c-4119-b4e9-28d6be547f5f from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
940s nova [W] Timed out waiting for 6781add8-f278-4871-ace8-84e069e74670 to get deleted.
940s nova [W] Using flock in prodstack6-s390x
940s Creating nova instance adt-plucky-s390x-r-cran-survey-20250315-123932-juju-7f2275-prod-proposed-migration-environment-20-41dbf533-ed9c-4119-b4e9-28d6be547f5f from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
940s nova [W] Timed out waiting for a6984016-5502-4905-9f2a-894a499f342a to get deleted.