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 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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: - 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(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 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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 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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 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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 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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.