0s autopkgtest [15:59:10]: starting date and time: 2025-03-15 15:59:10+0000 0s autopkgtest [15:59:10]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:59:10]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o8swgbjd/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-19.secgroup --name adt-plucky-arm64-r-cran-survey-20250315-155910-juju-7f2275-prod-proposed-migration-environment-15-abd818f3-07ad-4a60-93af-2ce6c4ce393e --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -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/ 195s autopkgtest [16:02:25]: testbed dpkg architecture: arm64 195s autopkgtest [16:02:25]: testbed apt version: 2.9.33 196s autopkgtest [16:02:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 196s autopkgtest [16:02:26]: testbed release detected to be: None 197s autopkgtest [16:02:27]: updating testbed package index (apt update) 197s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 198s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 198s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 198s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 198s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 198s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 198s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 198s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 199s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 199s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 199s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 199s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 199s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 199s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 199s Fetched 1078 kB in 2s (622 kB/s) 200s Reading package lists... 201s + lsb_release --codename --short 201s + RELEASE=plucky 201s + cat 201s + [ plucky != trusty ] 201s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Calculating upgrade... 202s Calculating upgrade... 202s The following packages will be upgraded: 202s pinentry-curses python3-jinja2 strace 202s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s Need to get 647 kB of archives. 202s After this operation, 11.3 kB of additional disk space will be used. 202s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 204s Fetched 647 kB in 1s (604 kB/s) 204s (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 ... 117701 files and directories currently installed.) 204s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 204s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 204s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 204s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 204s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 204s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 204s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 204s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 205s Setting up strace (6.13+ds-1ubuntu1) ... 205s Processing triggers for man-db (2.13.0-1) ... 205s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 205s + /usr/lib/apt/apt-helper analyze-pattern ?true 205s + uname -r 205s + sed s/\./\\./g 205s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 205s + apt list ?obsolete 205s + tail -n+2 205s + cut -d/+ -f1grep -v ^linux-.*6\.14\.0-10-generic.* 205s 206s + obsolete_pkgs=linux-headers-6.11.0-8-generic 206s linux-headers-6.11.0-8 206s linux-image-6.11.0-8-generic 206s linux-modules-6.11.0-8-generic 206s linux-tools-6.11.0-8-generic 206s linux-tools-6.11.0-8 206s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s Solving dependencies... 207s The following packages will be REMOVED: 207s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 207s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 207s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 207s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 207s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 207s After this operation, 267 MB disk space will be freed. 207s (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 ... 117701 files and directories currently installed.) 207s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 207s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 207s Removing libpython3.12t64:arm64 (3.12.9-1) ... 207s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 207s Removing libnsl2:arm64 (1.3.0-3build3) ... 207s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 207s Removing libunwind8:arm64 (1.6.2-3.1) ... 207s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 208s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 209s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 209s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 209s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 209s /etc/kernel/postrm.d/initramfs-tools: 209s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 210s /etc/kernel/postrm.d/zz-flash-kernel: 210s flash-kernel: Kernel 6.11.0-8-generic has been removed. 210s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 210s /etc/kernel/postrm.d/zz-update-grub: 210s Sourcing file `/etc/default/grub' 210s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 210s Generating grub configuration file ... 210s Found linux image: /boot/vmlinuz-6.14.0-10-generic 210s Found initrd image: /boot/initrd.img-6.14.0-10-generic 210s Warning: os-prober will not be executed to detect other bootable partitions. 210s Systems on them will not be added to the GRUB boot configuration. 210s Check GRUB_DISABLE_OS_PROBER documentation entry. 210s Adding boot menu entry for UEFI Firmware Settings ... 210s done 211s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 211s Processing triggers for libc-bin (2.41-1ubuntu1) ... 211s (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 ... 81650 files and directories currently installed.) 211s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 211s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 211s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 211s + grep -q trusty /etc/lsb-release 211s + [ ! -d /usr/share/doc/unattended-upgrades ] 211s + [ ! -d /usr/share/doc/lxd ] 211s + [ ! -d /usr/share/doc/lxd-client ] 211s + [ ! -d /usr/share/doc/snapd ] 211s + type iptables 211s + cat 211s + chmod 755 /etc/rc.local 211s + . /etc/rc.local 211s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 211s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 211s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 211s + uname -m 211s + [ aarch64 = ppc64le ] 211s + [ -d /run/systemd/system ] 211s + systemd-detect-virt --quiet --vm 211s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 211s + cat 211s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 211s + echo COMPRESS=lz4 211s autopkgtest [16:02:41]: upgrading testbed (apt dist-upgrade and autopurge) 211s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 212s Starting 2 pkgProblemResolver with broken count: 0 212s Done 213s Entering ResolveByKeep 213s 213s Calculating upgrade... 214s The following packages will be upgraded: 214s libc-bin libc-dev-bin libc6 libc6-dev locales 214s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 214s Need to get 9530 kB of archives. 214s After this operation, 0 B of additional disk space will be used. 214s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 216s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 216s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 219s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 220s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 225s Preconfiguring packages ... 225s Fetched 9530 kB in 11s (868 kB/s) 225s (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 ... 81647 files and directories currently installed.) 225s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 225s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 226s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 226s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Setting up libc6:arm64 (2.41-1ubuntu2) ... 226s (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 ... 81647 files and directories currently installed.) 226s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 226s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 226s Setting up libc-bin (2.41-1ubuntu2) ... 226s (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 ... 81647 files and directories currently installed.) 226s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 226s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 227s Setting up locales (2.41-1ubuntu2) ... 227s Generating locales (this might take a while)... 229s en_US.UTF-8... done 229s Generation complete. 229s Setting up libc-dev-bin (2.41-1ubuntu2) ... 229s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 229s Processing triggers for man-db (2.13.0-1) ... 230s Processing triggers for systemd (257.3-1ubuntu3) ... 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 232s Starting pkgProblemResolver with broken count: 0 232s Starting 2 pkgProblemResolver with broken count: 0 232s Done 232s Solving dependencies... 233s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 233s autopkgtest [16:03:03]: rebooting testbed after setup commands that affected boot 257s autopkgtest [16:03:27]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 260s autopkgtest [16:03:30]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 265s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (dsc) [2340 B] 265s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (tar) [2341 kB] 265s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (diff) [4580 B] 265s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC 265s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 265s gpgv: issuer "plessy@debian.org" 265s gpgv: Can't check signature: No public key 265s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found 266s autopkgtest [16:03:36]: testing package r-cran-survey version 4.4-2-2 266s autopkgtest [16:03:36]: build not needed 270s autopkgtest [16:03:40]: test run-unit-test: preparing testbed 271s Reading package lists... 271s Building dependency tree... 271s Reading state information... 271s Starting pkgProblemResolver with broken count: 0 271s Starting 2 pkgProblemResolver with broken count: 0 271s Done 272s The following NEW packages will be installed: 272s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 272s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 272s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 272s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 272s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 272s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 272s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 272s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 272s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler node-normalize.css 272s r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 272s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 272s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 272s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 272s r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 272s r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby 272s r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi 272s r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign 272s r-cran-formula r-cran-future r-cran-future.apply r-cran-generics 272s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable 272s r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms 272s r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr 272s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 272s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 272s r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats 272s r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools 272s r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr 272s r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly 272s r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 272s r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress 272s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.cache 272s r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6 272s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 272s r-cran-rcppeigen r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes 272s r-cran-reformulas r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang 272s r-cran-rpart r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape 272s r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr 272s r-cran-survey r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 272s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 272s r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun 272s r-cran-yaml r-cran-zip r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip 272s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded. 272s Need to get 167 MB of archives. 272s After this operation, 339 MB of additional disk space will be used. 272s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 273s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 274s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 274s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 275s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 275s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 275s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 278s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 278s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 278s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 278s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 278s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 278s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 279s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 279s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 279s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 279s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 280s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 280s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 280s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 280s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 280s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 281s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 281s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 281s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 281s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 282s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 282s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 285s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 285s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 285s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 285s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 285s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 285s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 286s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 286s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 286s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 286s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 286s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 287s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 287s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 287s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 287s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 287s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 287s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 288s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 288s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 289s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 289s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 289s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 325s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB] 326s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B] 326s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 326s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 326s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cardata all 3.0.5-1 [1819 kB] 328s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 328s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 329s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 331s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 334s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 339s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 343s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 343s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-boot all 1.3-31-1 [635 kB] 344s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 344s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB] 346s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-minqa arm64 1.2.8-1 [112 kB] 346s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnlopt0 arm64 2.7.1-6ubuntu3 [179 kB] 347s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nloptr arm64 2.1.1-1 [251 kB] 347s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rbibutils arm64 2.3-1 [1016 kB] 348s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 349s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-reformulas all 0.4.0-1 [91.5 kB] 349s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcppeigen arm64 0.3.4.0.2-1 [1422 kB] 351s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 351s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lme4 arm64 1.1-36-1 [4108 kB] 356s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 357s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 358s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 358s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 359s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB] 361s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 361s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 361s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 361s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 363s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 364s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 364s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 365s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 365s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 365s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 365s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 366s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 368s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 368s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringi arm64 1.8.4-1build1 [902 kB] 369s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 370s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB] 370s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 371s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 374s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 375s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 375s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 376s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 378s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 378s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 380s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB] 380s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 380s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 381s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 382s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 387s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 388s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-deriv all 4.1.6-1 [151 kB] 388s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 388s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-microbenchmark arm64 1.5.0-1 [67.5 kB] 388s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-doby all 4.6.25-1 [4772 kB] 394s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB] 395s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.51+dfsg-1 [573 kB] 395s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 395s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 395s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 403s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 405s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pbkrtest all 0.5.3-1 [178 kB] 405s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sparsem arm64 1.84-2-1 [812 kB] 406s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrixmodels all 0.5-3-1 [361 kB] 407s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 421s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB] 422s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpparmadillo arm64 14.2.3-1-1 [843 kB] 423s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-class arm64 7.3-23-1 [90.5 kB] 423s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-proxy arm64 0.4-27-1 [181 kB] 423s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-e1071 arm64 1.7-16-1 [563 kB] 424s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-codetools all 0.2-20-1 [90.5 kB] 424s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 424s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 425s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 427s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-modelmetrics arm64 1.2.2.2-1build1 [121 kB] 427s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 428s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-proc arm64 1.18.5-1 [963 kB] 429s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tzdb arm64 0.4.0-2 [512 kB] 430s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-clock arm64 0.7.2-1 [1829 kB] 432s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gower arm64 1.0.2-1 [208 kB] 433s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hardhat all 1.4.0+dfsg-1 [565 kB] 433s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 434s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-shape all 1.4.6.1-1 [749 kB] 435s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-diagram all 1.6.5-2 [656 kB] 436s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-kernsmooth arm64 2.23-26-1 [93.3 kB] 436s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB] 436s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-globals all 0.16.3-1 [120 kB] 436s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 436s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-parallelly arm64 1.42.0-1 [540 kB] 437s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 438s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 438s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-progressr all 0.15.1-1 [353 kB] 438s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-squarem all 2021.1-1 [179 kB] 439s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lava all 1.8.1+dfsg-1 [2191 kB] 441s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-prodlim arm64 2024.06.25-1 [415 kB] 442s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ipred arm64 0.9-15-1 [386 kB] 442s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-timechange arm64 0.3.0-1 [172 kB] 442s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lubridate arm64 1.9.4+dfsg-1 [1009 kB] 444s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-timedate arm64 4041.110-1 [1210 kB] 445s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 448s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-reshape2 arm64 1.4.4-2build1 [110 kB] 448s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-caret arm64 7.0-1+dfsg-1 [3461 kB] 452s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-conquer arm64 1.3.3-1 [440 kB] 452s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-quantreg arm64 6.00-1 [1436 kB] 454s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-foreign arm64 0.8.88-1 [243 kB] 455s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 455s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-forcats all 1.0.0-1 [369 kB] 455s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hms all 1.1.3-1 [96.5 kB] 455s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-clipr all 0.8.0-1 [53.5 kB] 455s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB] 455s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bit arm64 4.6.0+dfsg-1 [450 kB] 456s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bit64 arm64 4.6.0-1-1ubuntu2 [497 kB] 457s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-prettyunits all 1.2.0-1 [162 kB] 457s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-progress all 1.2.3-1 [91.9 kB] 457s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vroom arm64 1.6.5-1 [832 kB] 458s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-readr arm64 2.1.5-1 [756 kB] 459s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-haven arm64 2.5.4-1 [338 kB] 459s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB] 459s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rematch all 2.0.0-1 [18.3 kB] 459s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cellranger all 1.1.0-3 [102 kB] 459s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-readxl arm64 1.4.4-1 [341 kB] 460s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-writexl arm64 1.5.1-1 [159 kB] 460s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 460s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.oo all 1.27.0-1 [979 kB] 461s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.utils all 2.13.0-1 [1423 kB] 463s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-zip arm64 2.3.2-1 [147 kB] 463s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openxlsx arm64 4.2.8-1 [2018 kB] 466s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rio all 1.2.3-1 [546 kB] 466s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-car all 3.1-3-1 [1525 kB] 468s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-zoo arm64 1.8-13-1 [996 kB] 469s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lmtest arm64 0.9.40-1 [396 kB] 469s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sandwich all 3.1-1-1 [1483 kB] 471s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-aer all 1.2-14-1 [2597 kB] 474s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-blob all 1.2.4-1 [49.8 kB] 474s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB] 475s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB] 475s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dbi all 1.2.3-1 [853 kB] 476s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hexbin arm64 1.28.5-1 [1580 kB] 477s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 477s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mitools all 2.4-2build1 [265 kB] 478s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 478s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.cache all 0.16.0-1 [113 kB] 478s Get:201 http://ftpmaster.internal/ubuntu plucky/main arm64 tcl8.6 arm64 8.6.16+dfsg-1 [14.8 kB] 478s Get:202 http://ftpmaster.internal/ubuntu plucky/main arm64 tcl arm64 8.6.14build1 [4124 B] 478s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.rsp all 0.46.0+ds-1 [1412 kB] 480s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rsqlite arm64 2.3.9-1 [1247 kB] 481s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survey arm64 4.4-2-2 [3448 kB] 486s Preconfiguring packages ... 486s Fetched 167 MB in 3min 33s (785 kB/s) 487s Selecting previously unselected package fonts-dejavu-mono. 487s (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 ... 81647 files and directories currently installed.) 487s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8_all.deb ... 487s Unpacking fonts-dejavu-mono (2.37-8) ... 487s Selecting previously unselected package fonts-dejavu-core. 487s Preparing to unpack .../001-fonts-dejavu-core_2.37-8_all.deb ... 487s Unpacking fonts-dejavu-core (2.37-8) ... 487s Selecting previously unselected package fontconfig-config. 487s Preparing to unpack .../002-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 487s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 487s Selecting previously unselected package libfontconfig1:arm64. 487s Preparing to unpack .../003-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 487s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 487s Selecting previously unselected package fontconfig. 487s Preparing to unpack .../004-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 487s Unpacking fontconfig (2.15.0-2ubuntu1) ... 487s Selecting previously unselected package fonts-glyphicons-halflings. 487s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 487s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 487s Selecting previously unselected package fonts-mathjax. 487s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 487s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 487s Selecting previously unselected package libblas3:arm64. 487s Preparing to unpack .../007-libblas3_3.12.1-2_arm64.deb ... 487s Unpacking libblas3:arm64 (3.12.1-2) ... 487s Selecting previously unselected package libpixman-1-0:arm64. 487s Preparing to unpack .../008-libpixman-1-0_0.44.0-3_arm64.deb ... 487s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 487s Selecting previously unselected package libxcb-render0:arm64. 488s Preparing to unpack .../009-libxcb-render0_1.17.0-2_arm64.deb ... 488s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 488s Selecting previously unselected package libxcb-shm0:arm64. 488s Preparing to unpack .../010-libxcb-shm0_1.17.0-2_arm64.deb ... 488s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 488s Selecting previously unselected package libxrender1:arm64. 488s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 488s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 488s Selecting previously unselected package libcairo2:arm64. 488s Preparing to unpack .../012-libcairo2_1.18.2-2_arm64.deb ... 488s Unpacking libcairo2:arm64 (1.18.2-2) ... 488s Selecting previously unselected package libdatrie1:arm64. 488s Preparing to unpack .../013-libdatrie1_0.2.13-3build1_arm64.deb ... 488s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 488s Selecting previously unselected package libdeflate0:arm64. 488s Preparing to unpack .../014-libdeflate0_1.23-1_arm64.deb ... 488s Unpacking libdeflate0:arm64 (1.23-1) ... 488s Selecting previously unselected package libgfortran5:arm64. 488s Preparing to unpack .../015-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 488s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 488s Selecting previously unselected package libgomp1:arm64. 488s Preparing to unpack .../016-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 488s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 488s Selecting previously unselected package libgraphite2-3:arm64. 488s Preparing to unpack .../017-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 488s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 488s Selecting previously unselected package libharfbuzz0b:arm64. 488s Preparing to unpack .../018-libharfbuzz0b_10.2.0-1_arm64.deb ... 488s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 488s Selecting previously unselected package x11-common. 488s Preparing to unpack .../019-x11-common_1%3a7.7+23ubuntu3_all.deb ... 488s Unpacking x11-common (1:7.7+23ubuntu3) ... 488s Selecting previously unselected package libice6:arm64. 488s Preparing to unpack .../020-libice6_2%3a1.1.1-1_arm64.deb ... 488s Unpacking libice6:arm64 (2:1.1.1-1) ... 488s Selecting previously unselected package libjpeg-turbo8:arm64. 488s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 488s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 488s Selecting previously unselected package libjpeg8:arm64. 488s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_arm64.deb ... 488s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 488s Selecting previously unselected package libjs-bootstrap. 488s Preparing to unpack .../023-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 488s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 488s Selecting previously unselected package libjs-highlight.js. 488s Preparing to unpack .../024-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 488s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 488s Selecting previously unselected package libjs-jquery. 488s Preparing to unpack .../025-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 488s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 488s Selecting previously unselected package libjs-jquery-datatables. 488s Preparing to unpack .../026-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 488s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 488s Selecting previously unselected package liblapack3:arm64. 488s Preparing to unpack .../027-liblapack3_3.12.1-2_arm64.deb ... 488s Unpacking liblapack3:arm64 (3.12.1-2) ... 488s Selecting previously unselected package liblerc4:arm64. 488s Preparing to unpack .../028-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 488s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 488s Selecting previously unselected package libthai-data. 488s Preparing to unpack .../029-libthai-data_0.1.29-2build1_all.deb ... 488s Unpacking libthai-data (0.1.29-2build1) ... 488s Selecting previously unselected package libthai0:arm64. 488s Preparing to unpack .../030-libthai0_0.1.29-2build1_arm64.deb ... 488s Unpacking libthai0:arm64 (0.1.29-2build1) ... 488s Selecting previously unselected package libpango-1.0-0:arm64. 488s Preparing to unpack .../031-libpango-1.0-0_1.56.2-1_arm64.deb ... 488s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ... 488s Selecting previously unselected package libpangoft2-1.0-0:arm64. 488s Preparing to unpack .../032-libpangoft2-1.0-0_1.56.2-1_arm64.deb ... 488s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ... 488s Selecting previously unselected package libpangocairo-1.0-0:arm64. 488s Preparing to unpack .../033-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 488s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 489s Selecting previously unselected package libpaper2:arm64. 489s Preparing to unpack .../034-libpaper2_2.2.5-0.3_arm64.deb ... 489s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 489s Selecting previously unselected package libpaper-utils. 489s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3_arm64.deb ... 489s Unpacking libpaper-utils (2.2.5-0.3) ... 489s Selecting previously unselected package libsharpyuv0:arm64. 489s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1_arm64.deb ... 489s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 489s Selecting previously unselected package libsm6:arm64. 489s Preparing to unpack .../037-libsm6_2%3a1.2.4-1_arm64.deb ... 489s Unpacking libsm6:arm64 (2:1.2.4-1) ... 489s Selecting previously unselected package libtcl8.6:arm64. 489s Preparing to unpack .../038-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 489s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 489s Selecting previously unselected package libjbig0:arm64. 489s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 489s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 489s Selecting previously unselected package libwebp7:arm64. 489s Preparing to unpack .../040-libwebp7_1.5.0-0.1_arm64.deb ... 489s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 489s Selecting previously unselected package libtiff6:arm64. 489s Preparing to unpack .../041-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 489s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 489s Selecting previously unselected package libxft2:arm64. 489s Preparing to unpack .../042-libxft2_2.3.6-1build1_arm64.deb ... 489s Unpacking libxft2:arm64 (2.3.6-1build1) ... 489s Selecting previously unselected package libxss1:arm64. 489s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build3_arm64.deb ... 489s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 489s Selecting previously unselected package libtk8.6:arm64. 489s Preparing to unpack .../044-libtk8.6_8.6.16-1_arm64.deb ... 489s Unpacking libtk8.6:arm64 (8.6.16-1) ... 489s Selecting previously unselected package libxt6t64:arm64. 489s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 489s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 489s Selecting previously unselected package zip. 489s Preparing to unpack .../046-zip_3.0-14ubuntu2_arm64.deb ... 489s Unpacking zip (3.0-14ubuntu2) ... 489s Selecting previously unselected package unzip. 489s Preparing to unpack .../047-unzip_6.0-28ubuntu6_arm64.deb ... 489s Unpacking unzip (6.0-28ubuntu6) ... 489s Selecting previously unselected package xdg-utils. 489s Preparing to unpack .../048-xdg-utils_1.2.1-2ubuntu1_all.deb ... 489s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 489s Selecting previously unselected package r-base-core. 489s Preparing to unpack .../049-r-base-core_4.4.3-1_arm64.deb ... 489s Unpacking r-base-core (4.4.3-1) ... 489s Selecting previously unselected package r-cran-littler. 489s Preparing to unpack .../050-r-cran-littler_0.3.20-2_arm64.deb ... 489s Unpacking r-cran-littler (0.3.20-2) ... 490s Selecting previously unselected package littler. 490s Preparing to unpack .../051-littler_0.3.20-2_all.deb ... 490s Unpacking littler (0.3.20-2) ... 490s Selecting previously unselected package node-normalize.css. 490s Preparing to unpack .../052-node-normalize.css_8.0.1-5_all.deb ... 490s Unpacking node-normalize.css (8.0.1-5) ... 490s Selecting previously unselected package r-cran-abind. 490s Preparing to unpack .../053-r-cran-abind_1.4-8-1_all.deb ... 490s Unpacking r-cran-abind (1.4-8-1) ... 490s Selecting previously unselected package r-cran-cardata. 490s Preparing to unpack .../054-r-cran-cardata_3.0.5-1_all.deb ... 490s Unpacking r-cran-cardata (3.0.5-1) ... 490s Selecting previously unselected package r-cran-formula. 490s Preparing to unpack .../055-r-cran-formula_1.2-5-1_all.deb ... 490s Unpacking r-cran-formula (1.2-5-1) ... 490s Selecting previously unselected package r-cran-mass. 490s Preparing to unpack .../056-r-cran-mass_7.3-64-1_arm64.deb ... 490s Unpacking r-cran-mass (7.3-64-1) ... 490s Selecting previously unselected package r-cran-lattice. 490s Preparing to unpack .../057-r-cran-lattice_0.22-6-1_arm64.deb ... 490s Unpacking r-cran-lattice (0.22-6-1) ... 490s Selecting previously unselected package r-cran-nlme. 490s Preparing to unpack .../058-r-cran-nlme_3.1.167-1_arm64.deb ... 490s Unpacking r-cran-nlme (3.1.167-1) ... 490s Selecting previously unselected package r-cran-matrix. 490s Preparing to unpack .../059-r-cran-matrix_1.7-3-1_arm64.deb ... 490s Unpacking r-cran-matrix (1.7-3-1) ... 490s Selecting previously unselected package r-cran-mgcv. 490s Preparing to unpack .../060-r-cran-mgcv_1.9-1-1_arm64.deb ... 490s Unpacking r-cran-mgcv (1.9-1-1) ... 490s Selecting previously unselected package r-cran-nnet. 490s Preparing to unpack .../061-r-cran-nnet_7.3-20-1_arm64.deb ... 490s Unpacking r-cran-nnet (7.3-20-1) ... 490s Selecting previously unselected package r-cran-boot. 490s Preparing to unpack .../062-r-cran-boot_1.3-31-1_all.deb ... 490s Unpacking r-cran-boot (1.3-31-1) ... 490s Selecting previously unselected package r-cran-pkgkitten. 490s Preparing to unpack .../063-r-cran-pkgkitten_0.2.4-1_all.deb ... 490s Unpacking r-cran-pkgkitten (0.2.4-1) ... 490s Selecting previously unselected package r-cran-rcpp. 490s Preparing to unpack .../064-r-cran-rcpp_1.0.14-1_arm64.deb ... 490s Unpacking r-cran-rcpp (1.0.14-1) ... 490s Selecting previously unselected package r-cran-minqa. 490s Preparing to unpack .../065-r-cran-minqa_1.2.8-1_arm64.deb ... 490s Unpacking r-cran-minqa (1.2.8-1) ... 490s Selecting previously unselected package libnlopt0:arm64. 490s Preparing to unpack .../066-libnlopt0_2.7.1-6ubuntu3_arm64.deb ... 490s Unpacking libnlopt0:arm64 (2.7.1-6ubuntu3) ... 490s Selecting previously unselected package r-cran-nloptr. 490s Preparing to unpack .../067-r-cran-nloptr_2.1.1-1_arm64.deb ... 490s Unpacking r-cran-nloptr (2.1.1-1) ... 490s Selecting previously unselected package r-cran-rbibutils. 490s Preparing to unpack .../068-r-cran-rbibutils_2.3-1_arm64.deb ... 490s Unpacking r-cran-rbibutils (2.3-1) ... 490s Selecting previously unselected package r-cran-rdpack. 490s Preparing to unpack .../069-r-cran-rdpack_2.6.2-1syncable1_all.deb ... 490s Unpacking r-cran-rdpack (2.6.2-1syncable1) ... 490s Selecting previously unselected package r-cran-reformulas. 490s Preparing to unpack .../070-r-cran-reformulas_0.4.0-1_all.deb ... 490s Unpacking r-cran-reformulas (0.4.0-1) ... 490s Selecting previously unselected package r-cran-rcppeigen. 490s Preparing to unpack .../071-r-cran-rcppeigen_0.3.4.0.2-1_arm64.deb ... 490s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 491s Selecting previously unselected package r-cran-statmod. 491s Preparing to unpack .../072-r-cran-statmod_1.5.0-1_arm64.deb ... 491s Unpacking r-cran-statmod (1.5.0-1) ... 491s Selecting previously unselected package r-cran-lme4. 491s Preparing to unpack .../073-r-cran-lme4_1.1-36-1_arm64.deb ... 491s Unpacking r-cran-lme4 (1.1-36-1) ... 491s Selecting previously unselected package r-cran-backports. 491s Preparing to unpack .../074-r-cran-backports_1.5.0-2_arm64.deb ... 491s Unpacking r-cran-backports (1.5.0-2) ... 491s Selecting previously unselected package r-cran-cli. 491s Preparing to unpack .../075-r-cran-cli_3.6.4-1_arm64.deb ... 491s Unpacking r-cran-cli (3.6.4-1) ... 491s Selecting previously unselected package r-cran-generics. 491s Preparing to unpack .../076-r-cran-generics_0.1.3-1_all.deb ... 491s Unpacking r-cran-generics (0.1.3-1) ... 491s Selecting previously unselected package r-cran-glue. 491s Preparing to unpack .../077-r-cran-glue_1.8.0-1_arm64.deb ... 491s Unpacking r-cran-glue (1.8.0-1) ... 491s Selecting previously unselected package r-cran-rlang. 491s Preparing to unpack .../078-r-cran-rlang_1.1.5-1_arm64.deb ... 491s Unpacking r-cran-rlang (1.1.5-1) ... 491s Selecting previously unselected package r-cran-lifecycle. 491s Preparing to unpack .../079-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 491s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 491s Selecting previously unselected package r-cran-magrittr. 491s Preparing to unpack .../080-r-cran-magrittr_2.0.3-1_arm64.deb ... 491s Unpacking r-cran-magrittr (2.0.3-1) ... 491s Selecting previously unselected package r-cran-utf8. 491s Preparing to unpack .../081-r-cran-utf8_1.2.4-1_arm64.deb ... 491s Unpacking r-cran-utf8 (1.2.4-1) ... 491s Selecting previously unselected package r-cran-vctrs. 491s Preparing to unpack .../082-r-cran-vctrs_0.6.5-1_arm64.deb ... 491s Unpacking r-cran-vctrs (0.6.5-1) ... 491s Selecting previously unselected package r-cran-pillar. 491s Preparing to unpack .../083-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 491s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 491s Selecting previously unselected package r-cran-r6. 491s Preparing to unpack .../084-r-cran-r6_2.6.1-1_all.deb ... 491s Unpacking r-cran-r6 (2.6.1-1) ... 491s Selecting previously unselected package r-cran-fansi. 491s Preparing to unpack .../085-r-cran-fansi_1.0.5-1_arm64.deb ... 491s Unpacking r-cran-fansi (1.0.5-1) ... 491s Selecting previously unselected package r-cran-pkgconfig. 491s Preparing to unpack .../086-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 491s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 491s Selecting previously unselected package r-cran-tibble. 491s Preparing to unpack .../087-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 491s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 491s Selecting previously unselected package r-cran-withr. 491s Preparing to unpack .../088-r-cran-withr_3.0.2+dfsg-1_all.deb ... 491s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 491s Selecting previously unselected package r-cran-tidyselect. 491s Preparing to unpack .../089-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 491s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 491s Selecting previously unselected package r-cran-dplyr. 491s Preparing to unpack .../090-r-cran-dplyr_1.1.4-4_arm64.deb ... 491s Unpacking r-cran-dplyr (1.1.4-4) ... 491s Selecting previously unselected package r-cran-purrr. 492s Preparing to unpack .../091-r-cran-purrr_1.0.4-1_arm64.deb ... 492s Unpacking r-cran-purrr (1.0.4-1) ... 492s Selecting previously unselected package r-cran-stringi. 492s Preparing to unpack .../092-r-cran-stringi_1.8.4-1build1_arm64.deb ... 492s Unpacking r-cran-stringi (1.8.4-1build1) ... 492s Selecting previously unselected package r-cran-stringr. 492s Preparing to unpack .../093-r-cran-stringr_1.5.1-1_all.deb ... 492s Unpacking r-cran-stringr (1.5.1-1) ... 492s Selecting previously unselected package r-cran-cpp11. 492s Preparing to unpack .../094-r-cran-cpp11_0.5.2-1_all.deb ... 492s Unpacking r-cran-cpp11 (0.5.2-1) ... 492s Selecting previously unselected package r-cran-tidyr. 492s Preparing to unpack .../095-r-cran-tidyr_1.3.1-1_arm64.deb ... 492s Unpacking r-cran-tidyr (1.3.1-1) ... 492s Selecting previously unselected package r-cran-broom. 492s Preparing to unpack .../096-r-cran-broom_1.0.7+dfsg-1_all.deb ... 492s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 492s Selecting previously unselected package r-cran-numderiv. 492s Preparing to unpack .../097-r-cran-numderiv_2016.8-1.1-3_all.deb ... 492s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 492s Selecting previously unselected package r-cran-gtable. 492s Preparing to unpack .../098-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 492s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 492s Selecting previously unselected package r-cran-isoband. 492s Preparing to unpack .../099-r-cran-isoband_0.2.7-1_arm64.deb ... 492s Unpacking r-cran-isoband (0.2.7-1) ... 492s Selecting previously unselected package r-cran-farver. 492s Preparing to unpack .../100-r-cran-farver_2.1.2-1_arm64.deb ... 492s Unpacking r-cran-farver (2.1.2-1) ... 492s Selecting previously unselected package r-cran-labeling. 492s Preparing to unpack .../101-r-cran-labeling_0.4.3-1_all.deb ... 492s Unpacking r-cran-labeling (0.4.3-1) ... 492s Selecting previously unselected package r-cran-colorspace. 492s Preparing to unpack .../102-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 492s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 492s Selecting previously unselected package r-cran-munsell. 492s Preparing to unpack .../103-r-cran-munsell_0.5.1-1_all.deb ... 492s Unpacking r-cran-munsell (0.5.1-1) ... 492s Selecting previously unselected package r-cran-rcolorbrewer. 492s Preparing to unpack .../104-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 492s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 492s Selecting previously unselected package r-cran-viridislite. 492s Preparing to unpack .../105-r-cran-viridislite_0.4.2-2_all.deb ... 492s Unpacking r-cran-viridislite (0.4.2-2) ... 492s Selecting previously unselected package r-cran-scales. 492s Preparing to unpack .../106-r-cran-scales_1.3.0-1_all.deb ... 492s Unpacking r-cran-scales (1.3.0-1) ... 492s Selecting previously unselected package r-cran-ggplot2. 492s Preparing to unpack .../107-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 492s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 492s Selecting previously unselected package r-cran-cowplot. 492s Preparing to unpack .../108-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 492s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 492s Selecting previously unselected package r-cran-deriv. 492s Preparing to unpack .../109-r-cran-deriv_4.1.6-1_all.deb ... 492s Unpacking r-cran-deriv (4.1.6-1) ... 492s Selecting previously unselected package r-cran-modelr. 492s Preparing to unpack .../110-r-cran-modelr_0.1.11-1_all.deb ... 492s Unpacking r-cran-modelr (0.1.11-1) ... 492s Selecting previously unselected package r-cran-microbenchmark. 492s Preparing to unpack .../111-r-cran-microbenchmark_1.5.0-1_arm64.deb ... 492s Unpacking r-cran-microbenchmark (1.5.0-1) ... 493s Selecting previously unselected package r-cran-doby. 493s Preparing to unpack .../112-r-cran-doby_4.6.25-1_all.deb ... 493s Unpacking r-cran-doby (4.6.25-1) ... 493s Selecting previously unselected package r-cran-evaluate. 493s Preparing to unpack .../113-r-cran-evaluate_1.0.3-1_all.deb ... 493s Unpacking r-cran-evaluate (1.0.3-1) ... 493s Selecting previously unselected package r-cran-xfun. 493s Preparing to unpack .../114-r-cran-xfun_0.51+dfsg-1_arm64.deb ... 493s Unpacking r-cran-xfun (0.51+dfsg-1) ... 493s Selecting previously unselected package r-cran-highr. 493s Preparing to unpack .../115-r-cran-highr_0.11+dfsg-1_all.deb ... 493s Unpacking r-cran-highr (0.11+dfsg-1) ... 493s Selecting previously unselected package r-cran-yaml. 493s Preparing to unpack .../116-r-cran-yaml_2.3.10-1_arm64.deb ... 493s Unpacking r-cran-yaml (2.3.10-1) ... 493s Selecting previously unselected package libjs-mathjax. 493s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 493s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 493s Selecting previously unselected package r-cran-knitr. 493s Preparing to unpack .../118-r-cran-knitr_1.49+dfsg-1_all.deb ... 493s Unpacking r-cran-knitr (1.49+dfsg-1) ... 493s Selecting previously unselected package r-cran-pbkrtest. 493s Preparing to unpack .../119-r-cran-pbkrtest_0.5.3-1_all.deb ... 493s Unpacking r-cran-pbkrtest (0.5.3-1) ... 493s Selecting previously unselected package r-cran-sparsem. 493s Preparing to unpack .../120-r-cran-sparsem_1.84-2-1_arm64.deb ... 493s Unpacking r-cran-sparsem (1.84-2-1) ... 493s Selecting previously unselected package r-cran-matrixmodels. 494s Preparing to unpack .../121-r-cran-matrixmodels_0.5-3-1_all.deb ... 494s Unpacking r-cran-matrixmodels (0.5-3-1) ... 494s Selecting previously unselected package r-cran-survival. 494s Preparing to unpack .../122-r-cran-survival_3.8-3-1_arm64.deb ... 494s Unpacking r-cran-survival (3.8-3-1) ... 494s Selecting previously unselected package r-cran-matrixstats. 494s Preparing to unpack .../123-r-cran-matrixstats_1.5.0-1_arm64.deb ... 494s Unpacking r-cran-matrixstats (1.5.0-1) ... 494s Selecting previously unselected package r-cran-rcpparmadillo. 494s Preparing to unpack .../124-r-cran-rcpparmadillo_14.2.3-1-1_arm64.deb ... 494s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 494s Selecting previously unselected package r-cran-class. 494s Preparing to unpack .../125-r-cran-class_7.3-23-1_arm64.deb ... 494s Unpacking r-cran-class (7.3-23-1) ... 494s Selecting previously unselected package r-cran-proxy. 494s Preparing to unpack .../126-r-cran-proxy_0.4-27-1_arm64.deb ... 494s Unpacking r-cran-proxy (0.4-27-1) ... 494s Selecting previously unselected package r-cran-e1071. 494s Preparing to unpack .../127-r-cran-e1071_1.7-16-1_arm64.deb ... 494s Unpacking r-cran-e1071 (1.7-16-1) ... 494s Selecting previously unselected package r-cran-codetools. 494s Preparing to unpack .../128-r-cran-codetools_0.2-20-1_all.deb ... 494s Unpacking r-cran-codetools (0.2-20-1) ... 494s Selecting previously unselected package r-cran-iterators. 494s Preparing to unpack .../129-r-cran-iterators_1.0.14-1_all.deb ... 494s Unpacking r-cran-iterators (1.0.14-1) ... 494s Selecting previously unselected package r-cran-foreach. 494s Preparing to unpack .../130-r-cran-foreach_1.5.2-1_all.deb ... 494s Unpacking r-cran-foreach (1.5.2-1) ... 494s Selecting previously unselected package r-cran-data.table. 494s Preparing to unpack .../131-r-cran-data.table_1.17.0+dfsg-1_arm64.deb ... 494s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 494s Selecting previously unselected package r-cran-modelmetrics. 494s Preparing to unpack .../132-r-cran-modelmetrics_1.2.2.2-1build1_arm64.deb ... 494s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 494s Selecting previously unselected package r-cran-plyr. 494s Preparing to unpack .../133-r-cran-plyr_1.8.9-1_arm64.deb ... 494s Unpacking r-cran-plyr (1.8.9-1) ... 494s Selecting previously unselected package r-cran-proc. 494s Preparing to unpack .../134-r-cran-proc_1.18.5-1_arm64.deb ... 494s Unpacking r-cran-proc (1.18.5-1) ... 494s Selecting previously unselected package r-cran-tzdb. 494s Preparing to unpack .../135-r-cran-tzdb_0.4.0-2_arm64.deb ... 494s Unpacking r-cran-tzdb (0.4.0-2) ... 494s Selecting previously unselected package r-cran-clock. 494s Preparing to unpack .../136-r-cran-clock_0.7.2-1_arm64.deb ... 494s Unpacking r-cran-clock (0.7.2-1) ... 494s Selecting previously unselected package r-cran-gower. 494s Preparing to unpack .../137-r-cran-gower_1.0.2-1_arm64.deb ... 494s Unpacking r-cran-gower (1.0.2-1) ... 494s Selecting previously unselected package r-cran-hardhat. 494s Preparing to unpack .../138-r-cran-hardhat_1.4.0+dfsg-1_all.deb ... 494s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ... 494s Selecting previously unselected package r-cran-rpart. 494s Preparing to unpack .../139-r-cran-rpart_4.1.24-1_arm64.deb ... 494s Unpacking r-cran-rpart (4.1.24-1) ... 495s Selecting previously unselected package r-cran-shape. 495s Preparing to unpack .../140-r-cran-shape_1.4.6.1-1_all.deb ... 495s Unpacking r-cran-shape (1.4.6.1-1) ... 495s Selecting previously unselected package r-cran-diagram. 495s Preparing to unpack .../141-r-cran-diagram_1.6.5-2_all.deb ... 495s Unpacking r-cran-diagram (1.6.5-2) ... 495s Selecting previously unselected package r-cran-kernsmooth. 495s Preparing to unpack .../142-r-cran-kernsmooth_2.23-26-1_arm64.deb ... 495s Unpacking r-cran-kernsmooth (2.23-26-1) ... 495s Selecting previously unselected package r-cran-digest. 495s Preparing to unpack .../143-r-cran-digest_0.6.37-1_arm64.deb ... 495s Unpacking r-cran-digest (0.6.37-1) ... 495s Selecting previously unselected package r-cran-globals. 495s Preparing to unpack .../144-r-cran-globals_0.16.3-1_all.deb ... 495s Unpacking r-cran-globals (0.16.3-1) ... 495s Selecting previously unselected package r-cran-listenv. 495s Preparing to unpack .../145-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 495s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 495s Selecting previously unselected package r-cran-parallelly. 495s Preparing to unpack .../146-r-cran-parallelly_1.42.0-1_arm64.deb ... 495s Unpacking r-cran-parallelly (1.42.0-1) ... 495s Selecting previously unselected package r-cran-future. 495s Preparing to unpack .../147-r-cran-future_1.34.0+dfsg-1_all.deb ... 495s Unpacking r-cran-future (1.34.0+dfsg-1) ... 495s Selecting previously unselected package r-cran-future.apply. 495s Preparing to unpack .../148-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 495s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 495s Selecting previously unselected package r-cran-progressr. 495s Preparing to unpack .../149-r-cran-progressr_0.15.1-1_all.deb ... 495s Unpacking r-cran-progressr (0.15.1-1) ... 495s Selecting previously unselected package r-cran-squarem. 495s Preparing to unpack .../150-r-cran-squarem_2021.1-1_all.deb ... 495s Unpacking r-cran-squarem (2021.1-1) ... 495s Selecting previously unselected package r-cran-lava. 495s Preparing to unpack .../151-r-cran-lava_1.8.1+dfsg-1_all.deb ... 495s Unpacking r-cran-lava (1.8.1+dfsg-1) ... 495s Selecting previously unselected package r-cran-prodlim. 495s Preparing to unpack .../152-r-cran-prodlim_2024.06.25-1_arm64.deb ... 495s Unpacking r-cran-prodlim (2024.06.25-1) ... 495s Selecting previously unselected package r-cran-ipred. 495s Preparing to unpack .../153-r-cran-ipred_0.9-15-1_arm64.deb ... 495s Unpacking r-cran-ipred (0.9-15-1) ... 495s Selecting previously unselected package r-cran-timechange. 495s Preparing to unpack .../154-r-cran-timechange_0.3.0-1_arm64.deb ... 495s Unpacking r-cran-timechange (0.3.0-1) ... 495s Selecting previously unselected package r-cran-lubridate. 495s Preparing to unpack .../155-r-cran-lubridate_1.9.4+dfsg-1_arm64.deb ... 495s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 495s Selecting previously unselected package r-cran-timedate. 495s Preparing to unpack .../156-r-cran-timedate_4041.110-1_arm64.deb ... 495s Unpacking r-cran-timedate (4041.110-1) ... 495s Selecting previously unselected package r-cran-recipes. 495s Preparing to unpack .../157-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 495s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 495s Selecting previously unselected package r-cran-reshape2. 495s Preparing to unpack .../158-r-cran-reshape2_1.4.4-2build1_arm64.deb ... 495s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 495s Selecting previously unselected package r-cran-caret. 495s Preparing to unpack .../159-r-cran-caret_7.0-1+dfsg-1_arm64.deb ... 495s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 495s Selecting previously unselected package r-cran-conquer. 495s Preparing to unpack .../160-r-cran-conquer_1.3.3-1_arm64.deb ... 495s Unpacking r-cran-conquer (1.3.3-1) ... 496s Selecting previously unselected package r-cran-quantreg. 496s Preparing to unpack .../161-r-cran-quantreg_6.00-1_arm64.deb ... 496s Unpacking r-cran-quantreg (6.00-1) ... 496s Selecting previously unselected package r-cran-foreign. 496s Preparing to unpack .../162-r-cran-foreign_0.8.88-1_arm64.deb ... 496s Unpacking r-cran-foreign (0.8.88-1) ... 496s Selecting previously unselected package r-cran-ellipsis. 496s Preparing to unpack .../163-r-cran-ellipsis_0.3.2-2_arm64.deb ... 496s Unpacking r-cran-ellipsis (0.3.2-2) ... 496s Selecting previously unselected package r-cran-forcats. 496s Preparing to unpack .../164-r-cran-forcats_1.0.0-1_all.deb ... 496s Unpacking r-cran-forcats (1.0.0-1) ... 496s Selecting previously unselected package r-cran-hms. 496s Preparing to unpack .../165-r-cran-hms_1.1.3-1_all.deb ... 496s Unpacking r-cran-hms (1.1.3-1) ... 496s Selecting previously unselected package r-cran-clipr. 496s Preparing to unpack .../166-r-cran-clipr_0.8.0-1_all.deb ... 496s Unpacking r-cran-clipr (0.8.0-1) ... 496s Selecting previously unselected package r-cran-crayon. 496s Preparing to unpack .../167-r-cran-crayon_1.5.3-1_all.deb ... 496s Unpacking r-cran-crayon (1.5.3-1) ... 496s Selecting previously unselected package r-cran-bit. 496s Preparing to unpack .../168-r-cran-bit_4.6.0+dfsg-1_arm64.deb ... 496s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 496s Selecting previously unselected package r-cran-bit64. 496s Preparing to unpack .../169-r-cran-bit64_4.6.0-1-1ubuntu2_arm64.deb ... 496s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ... 496s Selecting previously unselected package r-cran-prettyunits. 496s Preparing to unpack .../170-r-cran-prettyunits_1.2.0-1_all.deb ... 496s Unpacking r-cran-prettyunits (1.2.0-1) ... 496s Selecting previously unselected package r-cran-progress. 496s Preparing to unpack .../171-r-cran-progress_1.2.3-1_all.deb ... 496s Unpacking r-cran-progress (1.2.3-1) ... 496s Selecting previously unselected package r-cran-vroom. 496s Preparing to unpack .../172-r-cran-vroom_1.6.5-1_arm64.deb ... 496s Unpacking r-cran-vroom (1.6.5-1) ... 496s Selecting previously unselected package r-cran-readr. 496s Preparing to unpack .../173-r-cran-readr_2.1.5-1_arm64.deb ... 496s Unpacking r-cran-readr (2.1.5-1) ... 496s Selecting previously unselected package r-cran-haven. 496s Preparing to unpack .../174-r-cran-haven_2.5.4-1_arm64.deb ... 496s Unpacking r-cran-haven (2.5.4-1) ... 496s Selecting previously unselected package r-cran-curl. 496s Preparing to unpack .../175-r-cran-curl_6.2.1+dfsg-1ubuntu1_arm64.deb ... 496s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 496s Selecting previously unselected package r-cran-rematch. 496s Preparing to unpack .../176-r-cran-rematch_2.0.0-1_all.deb ... 496s Unpacking r-cran-rematch (2.0.0-1) ... 496s Selecting previously unselected package r-cran-cellranger. 496s Preparing to unpack .../177-r-cran-cellranger_1.1.0-3_all.deb ... 496s Unpacking r-cran-cellranger (1.1.0-3) ... 496s Selecting previously unselected package r-cran-readxl. 496s Preparing to unpack .../178-r-cran-readxl_1.4.4-1_arm64.deb ... 496s Unpacking r-cran-readxl (1.4.4-1) ... 496s Selecting previously unselected package r-cran-writexl. 496s Preparing to unpack .../179-r-cran-writexl_1.5.1-1_arm64.deb ... 496s Unpacking r-cran-writexl (1.5.1-1) ... 496s Selecting previously unselected package r-cran-r.methodss3. 496s Preparing to unpack .../180-r-cran-r.methodss3_1.8.2-1_all.deb ... 496s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 496s Selecting previously unselected package r-cran-r.oo. 496s Preparing to unpack .../181-r-cran-r.oo_1.27.0-1_all.deb ... 496s Unpacking r-cran-r.oo (1.27.0-1) ... 497s Selecting previously unselected package r-cran-r.utils. 497s Preparing to unpack .../182-r-cran-r.utils_2.13.0-1_all.deb ... 497s Unpacking r-cran-r.utils (2.13.0-1) ... 497s Selecting previously unselected package r-cran-zip. 497s Preparing to unpack .../183-r-cran-zip_2.3.2-1_arm64.deb ... 497s Unpacking r-cran-zip (2.3.2-1) ... 497s Selecting previously unselected package r-cran-openxlsx. 497s Preparing to unpack .../184-r-cran-openxlsx_4.2.8-1_arm64.deb ... 497s Unpacking r-cran-openxlsx (4.2.8-1) ... 497s Selecting previously unselected package r-cran-rio. 497s Preparing to unpack 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501s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 501s Setting up r-cran-readxl (1.4.4-1) ... 501s Setting up r-cran-haven (2.5.4-1) ... 501s Setting up r-cran-caret (7.0-1+dfsg-1) ... 501s Setting up r-cran-broom (1.0.7+dfsg-1) ... 501s Setting up r-cran-conquer (1.3.3-1) ... 501s Setting up r-cran-r.rsp (0.46.0+ds-1) ... 501s Setting up r-cran-rio (1.2.3-1) ... 501s Setting up r-cran-quantreg (6.00-1) ... 501s Setting up r-cran-modelr (0.1.11-1) ... 501s Setting up r-cran-doby (4.6.25-1) ... 501s Setting up r-cran-pbkrtest (0.5.3-1) ... 501s Setting up r-cran-car (3.1-3-1) ... 501s Setting up r-cran-aer (1.2-14-1) ... 501s Processing triggers for libc-bin (2.41-1ubuntu2) ... 501s Processing triggers for man-db (2.13.0-1) ... 502s Processing triggers for install-info (7.1.1-1) ... 504s autopkgtest [16:07:34]: test run-unit-test: [----------------------- 504s BEGIN TEST 3stage2phase.R 505s 505s R version 4.4.3 (2025-02-28) -- "Trophy Case" 505s Copyright (C) 2025 The R Foundation for Statistical Computing 505s Platform: aarch64-unknown-linux-gnu 505s 505s R is free software and comes with ABSOLUTELY NO WARRANTY. 505s You are welcome to redistribute it under certain conditions. 505s Type 'license()' or 'licence()' for distribution details. 505s 505s R is a collaborative project with many contributors. 505s Type 'contributors()' for more information and 505s 'citation()' on how to cite R or R packages in publications. 505s 505s Type 'demo()' for some demos, 'help()' for on-line help, or 505s 'help.start()' for an HTML browser interface to help. 505s Type 'q()' to quit R. 505s 505s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 505s > ## motivated by dietary biomarker substudy in HCHS 505s > 505s > library(survey) 505s Loading required package: grid 505s Loading required package: Matrix 506s Loading required package: survival 506s 506s Attaching package: 'survey' 506s 506s > 506s > load("simdata1.RData") 506s The following object is masked from 'package:graphics': 506s 506s dotchart 506s 506s > 506s > twophase.full = twophase(id=list(~block+house+ind,~1), 506s + strata=list(~strat,NULL), 506s + probs=list(~P.block+P.house+P.ind,NULL), 506s + subset=~phase2, 506s + data=simdata1,method='full') 506s > 506s > twophase.approx = twophase(id=list(~block+house+ind,~1), 506s + strata=list(~strat,NULL), 506s + probs=list(~P.block+P.house+P.ind,NULL), 506s + subset=~phase2, 506s + data=simdata1,method='approx') 506s > 506s > twophase.rep = twophase(id=list(~block,~1), 506s + strata=list(~strat,NULL), 506s + probs=list(~I(P.block*P.house*P.ind),NULL), 506s + subset=~phase2, 506s + data=simdata1,method='full') 506s > 506s > 506s > twophase.repapprox = twophase(id=list(~block,~1), 506s + strata=list(~strat,NULL), 506s + probs=list(~I(P.block*P.house*P.ind),NULL), 506s + subset=~phase2, 506s + data=simdata1,method='approx') 506s > 506s > 506s > svymean(~age, twophase.full) 506s mean SE 506s age 41.116 0.8114 506s > svymean(~age, twophase.approx) 506s mean SE 506s age 41.116 0.6693 506s > svymean(~age, twophase.rep) 506s mean SE 506s age 41.116 0.784 506s > svymean(~age, twophase.repapprox) 506s mean SE 506s age 41.116 0.6592 506s > 506s BEGIN TEST DBIcheck.R 507s 507s R version 4.4.3 (2025-02-28) -- "Trophy Case" 507s Copyright (C) 2025 The R Foundation for Statistical Computing 507s Platform: aarch64-unknown-linux-gnu 507s 507s R is free software and comes with ABSOLUTELY NO WARRANTY. 507s You are welcome to redistribute it under certain conditions. 507s Type 'license()' or 'licence()' for distribution details. 507s 507s R is a collaborative project with many contributors. 507s Type 'contributors()' for more information and 507s 'citation()' on how to cite R or R packages in publications. 507s 507s Type 'demo()' for some demos, 'help()' for on-line help, or 507s 'help.start()' for an HTML browser interface to help. 507s Type 'q()' to quit R. 507s 507s > 507s > library(survey) 507s Loading required package: grid 507s Loading required package: Matrix 508s Loading required package: survival 508s 508s Attaching package: 'survey' 508s 508s The following object is masked from 'package:graphics': 508s 508s dotchart 508s 508s > library(RSQLite) 508s > 508s > data(api) 508s > apiclus1$api_stu<-apiclus1$api.stu 508s > apiclus1$comp_imp<-apiclus1$comp.imp 508s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 508s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 508s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 508s > 508s > m<-svymean(~api00+stype,dclus1) 508s > m.db<-svymean(~api00+stype, dbclus1) 508s > all.equal(coef(m),coef(m.db)) 508s [1] TRUE 508s > all.equal(vcov(m), vcov(m.db)) 508s [1] TRUE 508s > 508s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 508s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 508s > all.equal(coef(r), coef(r.db)) 508s [1] TRUE 508s > all.equal(SE(r), SE(r.db)) 508s [1] TRUE 508s > 508s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 508s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 508s > all.equal(coef(b), coef(b.db)) 508s [1] TRUE 508s > all.equal(SE(b), SE(b.db)) 508s [1] TRUE 508s > all.equal(deff(b), deff(b.db)) 508s [1] TRUE 508s > 508s > l<-svyglm(api00~api99+mobility, design=dclus1) 508s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 508s > all.equal(coef(l),coef(l.db)) 508s [1] TRUE 508s > all.equal(vcov(l), vcov(l.db)) 508s [1] TRUE 508s > 508s > dclus1<-update(dclus1, apidiff=api00-api99) 508s > dclus1<-update(dclus1, apipct= apidiff/api99) 508s > dbclus1<-update(dbclus1, apidiff=api00-api99) 508s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 508s > 508s > u<-svymean(~api00+apidiff+apipct, dclus1) 508s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 508s > all.equal(u, u.db) 508s [1] TRUE 508s > 508s > all.equal(nrow(dclus1),nrow(dbclus1)) 508s [1] TRUE 508s > all.equal(nrow(subset(dclus1,stype=="E")), 508s + nrow(subset(dbclus1,stype=="E"))) 508s [1] "Mean relative difference: 0.2708333" 508s > 508s > ## replicate weights 508s > rclus1<-as.svrepdesign(dclus1) 508s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 508s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 508s > m<-svymean(~api00+api99,rclus1) 508s > m.db<-svymean(~api00+api99,db_rclus1) 508s > all.equal(m,m.db) 508s [1] TRUE 508s > 508s > summary(db_rclus1) 508s DB-backed replicate weight design 508s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 508s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 508s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 508s Unstratified cluster jacknife (JK1) with 15 replicates. 508s Variables: 508s [1] "row_names" "cds" "stype" "name" "sname" 508s [6] "snum" "dname" "dnum" "cname" "cnum" 508s [11] "flag" "pcttest" "api00" "api99" "target" 508s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 508s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 508s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 508s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 508s [36] "emer" "enroll" "api_stu" "fpc" "pw" 508s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 508s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 508s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 508s [56] "wt15" 508s > 508s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 508s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 508s > all.equal(s,s.db) 508s [1] TRUE 508s > 508s BEGIN TEST anova-svycoxph.R 508s 508s R version 4.4.3 (2025-02-28) -- "Trophy Case" 508s Copyright (C) 2025 The R Foundation for Statistical Computing 508s Platform: aarch64-unknown-linux-gnu 508s 508s R is free software and comes with ABSOLUTELY NO WARRANTY. 508s You are welcome to redistribute it under certain conditions. 508s Type 'license()' or 'licence()' for distribution details. 508s 508s R is a collaborative project with many contributors. 508s Type 'contributors()' for more information and 508s 'citation()' on how to cite R or R packages in publications. 508s 508s Type 'demo()' for some demos, 'help()' for on-line help, or 508s 'help.start()' for an HTML browser interface to help. 508s Type 'q()' to quit R. 508s 509s > 509s > library(survey) 509s Loading required package: grid 509s Loading required package: Matrix 509s Loading required package: survival 510s > example(svycoxph, ask=FALSE) 510s 510s Attaching package: 'survey' 510s 510s The following object is masked from 'package:graphics': 510s 510s dotchart 510s 510s 510s svycxp> ## Somewhat unrealistic example of nonresponse bias. 510s svycxp> data(pbc, package="survival") 510s 510s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 510s 510s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 510s 510s svycxp> pbc$randprob<-fitted(biasmodel) 510s 510s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 510s 510s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 510s 510s svycxp> rpbc<-as.svrepdesign(dpbc) 510s 510s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 510s Call: 510s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 510s albumin, design = dpbc) 510s 510s coef exp(coef) se(coef) robust se z p 510s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 510s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 510s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 510s 510s Likelihood ratio test= on 3 df, p= 510s n= 312, number of events= 144 510s 510s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 510s Call: 510s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 510s protime + albumin, design = rpbc) 510s 510s coef exp(coef) se(coef) z p 510s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 510s protime 0.24487 1.27745 0.09373 2.612 0.00899 510s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 510s 510s Likelihood ratio test=NA on 3 df, p=NA 510s n= 312, number of events= 144 510s 510s svycxp> s<-predict(model,se=TRUE, type="curve", 510s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 510s 510s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 510s 510s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 510s 510s svycxp> quantile(s[[1]], ci=TRUE) 510s 0.75 0.5 0.25 510s 1435 2503 3574 510s attr(,"ci") 510s 0.025 0.975 510s 0.75 1217 1786 510s 0.5 2256 3170 510s 0.25 3222 Inf 510s 510s svycxp> confint(s[[2]], parm=365*(1:5)) 510s 0.025 0.975 510s 365 0.8375139 0.9453781 510s 730 0.7382750 0.8999016 510s 1095 0.4784105 0.7478460 510s 1460 0.3192009 0.6206764 510s 1825 0.2149475 0.5292978 510s > m<-update(model, .~.+I(protime^2)) 510s > a<-anova(m,model) 510s > b<-anova(m, model,force=TRUE) 510s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 510s > 510s BEGIN TEST api.R 510s 510s R version 4.4.3 (2025-02-28) -- "Trophy Case" 510s Copyright (C) 2025 The R Foundation for Statistical Computing 510s Platform: aarch64-unknown-linux-gnu 510s 510s R is free software and comes with ABSOLUTELY NO WARRANTY. 510s You are welcome to redistribute it under certain conditions. 510s Type 'license()' or 'licence()' for distribution details. 510s 510s R is a collaborative project with many contributors. 510s Type 'contributors()' for more information and 510s 'citation()' on how to cite R or R packages in publications. 510s 510s Type 'demo()' for some demos, 'help()' for on-line help, or 510s 'help.start()' for an HTML browser interface to help. 510s Type 'q()' to quit R. 510s 511s > library(survey) 511s Loading required package: grid 511s Loading required package: Matrix 511s Loading required package: survival 512s > options(survey.replicates.mse=TRUE) 512s > example(api) 512s 512s Attaching package: 'survey' 512s 512s The following object is masked from 'package:graphics': 512s 512s dotchart 512s 512s 512s api> library(survey) 512s 512s api> data(api) 512s 512s api> mean(apipop$api00) 512s [1] 664.7126 512s 512s api> sum(apipop$enroll, na.rm=TRUE) 512s [1] 3811472 512s 512s api> #stratified sample 512s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 512s 512s api> summary(dstrat) 512s Stratified Independent Sampling design 512s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 512s Stratum Sizes: 512s E H M 512s obs 100 50 50 512s design.PSU 100 50 50 512s actual.PSU 100 50 50 512s Population stratum sizes (PSUs): 512s E H M 512s 4421 755 1018 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "pw" "fpc" 512s 512s api> svymean(~api00, dstrat) 512s mean SE 512s api00 662.29 9.4089 512s 512s api> svytotal(~enroll, dstrat, na.rm=TRUE) 512s total SE 512s enroll 3687178 114642 512s 512s api> # one-stage cluster sample 512s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 512s 512s api> summary(dclus1) 512s 1 - level Cluster Sampling design 512s With (15) clusters. 512s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 512s Population size (PSUs): 757 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> svymean(~api00, dclus1) 512s mean SE 512s api00 644.17 23.542 512s 512s api> svytotal(~enroll, dclus1, na.rm=TRUE) 512s total SE 512s enroll 3404940 932235 512s 512s api> # two-stage cluster sample 512s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 512s 512s api> summary(dclus2) 512s 2 - level Cluster Sampling design 512s With (40, 126) clusters. 512s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 512s Population size (PSUs): 757 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "pw" "fpc1" "fpc2" 512s 512s api> svymean(~api00, dclus2) 512s mean SE 512s api00 670.81 30.099 512s 512s api> svytotal(~enroll, dclus2, na.rm=TRUE) 512s total SE 512s enroll 2639273 799638 512s 512s api> # two-stage `with replacement' 512s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 512s 512s api> summary(dclus2wr) 512s 2 - level Cluster Sampling design (with replacement) 512s With (40, 126) clusters. 512s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "pw" "fpc1" "fpc2" 512s 512s api> svymean(~api00, dclus2wr) 512s mean SE 512s api00 670.81 30.712 512s 512s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 512s total SE 512s enroll 2639273 820261 512s 512s api> # convert to replicate weights 512s api> rclus1<-as.svrepdesign(dclus1) 512s 512s api> summary(rclus1) 512s Call: as.svrepdesign.default(dclus1) 512s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 512s Variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> svymean(~api00, rclus1) 512s mean SE 512s api00 644.17 26.335 512s 512s api> svytotal(~enroll, rclus1, na.rm=TRUE) 512s total SE 512s enroll 3404940 932235 512s 512s api> # post-stratify on school type 512s api> pop.types<-xtabs(~stype, data=apipop) 512s 512s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 512s 512s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 512s 512s api> summary(dclus1p) 512s 1 - level Cluster Sampling design 512s With (15) clusters. 512s dclus1p<-postStratify(dclus1, ~stype, pop.types) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 512s Population size (PSUs): 757 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> summary(rclus1p) 512s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 512s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 512s Variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> svymean(~api00, dclus1p) 512s mean SE 512s api00 642.31 23.921 512s 512s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 512s total SE 512s enroll 3680893 406293 512s 512s api> svymean(~api00, rclus1p) 512s mean SE 512s api00 642.31 26.936 512s 512s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 512s total SE 512s enroll 3680893 473434 512s > 512s > options(survey.replicates.mse=FALSE) 512s > example(api) 512s 512s api> library(survey) 512s 512s api> data(api) 512s 512s api> mean(apipop$api00) 512s [1] 664.7126 512s 512s api> sum(apipop$enroll, na.rm=TRUE) 512s [1] 3811472 512s 512s api> #stratified sample 512s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 512s 512s api> summary(dstrat) 512s Stratified Independent Sampling design 512s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 512s Stratum Sizes: 512s E H M 512s obs 100 50 50 512s design.PSU 100 50 50 512s actual.PSU 100 50 50 512s Population stratum sizes (PSUs): 512s E H M 512s 4421 755 1018 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "pw" "fpc" 512s 512s api> svymean(~api00, dstrat) 512s mean SE 512s api00 662.29 9.4089 512s 512s api> svytotal(~enroll, dstrat, na.rm=TRUE) 512s total SE 512s enroll 3687178 114642 512s 512s api> # one-stage cluster sample 512s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 512s 512s api> summary(dclus1) 512s 1 - level Cluster Sampling design 512s With (15) clusters. 512s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 512s Population size (PSUs): 757 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> svymean(~api00, dclus1) 512s mean SE 512s api00 644.17 23.542 512s 512s api> svytotal(~enroll, dclus1, na.rm=TRUE) 512s total SE 512s enroll 3404940 932235 512s 512s api> # two-stage cluster sample 512s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 512s 512s api> summary(dclus2) 512s 2 - level Cluster Sampling design 512s With (40, 126) clusters. 512s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 512s Population size (PSUs): 757 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "pw" "fpc1" "fpc2" 512s 512s api> svymean(~api00, dclus2) 512s mean SE 512s api00 670.81 30.099 512s 512s api> svytotal(~enroll, dclus2, na.rm=TRUE) 512s total SE 512s enroll 2639273 799638 512s 512s api> # two-stage `with replacement' 512s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 512s 512s api> summary(dclus2wr) 512s 2 - level Cluster Sampling design (with replacement) 512s With (40, 126) clusters. 512s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "pw" "fpc1" "fpc2" 512s 512s api> svymean(~api00, dclus2wr) 512s mean SE 512s api00 670.81 30.712 512s 512s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 512s total SE 512s enroll 2639273 820261 512s 512s api> # convert to replicate weights 512s api> rclus1<-as.svrepdesign(dclus1) 512s 512s api> summary(rclus1) 512s Call: as.svrepdesign.default(dclus1) 512s Unstratified cluster jacknife (JK1) with 15 replicates. 512s Variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> svymean(~api00, rclus1) 512s mean SE 512s api00 644.17 26.329 512s 512s api> svytotal(~enroll, rclus1, na.rm=TRUE) 512s total SE 512s enroll 3404940 932235 512s 512s api> # post-stratify on school type 512s api> pop.types<-xtabs(~stype, data=apipop) 512s 512s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 512s 512s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 512s 512s api> summary(dclus1p) 512s 1 - level Cluster Sampling design 512s With (15) clusters. 512s dclus1p<-postStratify(dclus1, ~stype, pop.types) 512s Probabilities: 512s Min. 1st Qu. Median Mean 3rd Qu. Max. 512s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 512s Population size (PSUs): 757 512s Data variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> summary(rclus1p) 512s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 512s Unstratified cluster jacknife (JK1) with 15 replicates. 512s Variables: 512s [1] "cds" "stype" "name" "sname" "snum" "dname" 512s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 512s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 512s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 512s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 512s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 512s [37] "api.stu" "fpc" "pw" 512s 512s api> svymean(~api00, dclus1p) 512s mean SE 512s api00 642.31 23.921 512s 512s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 512s total SE 512s enroll 3680893 406293 512s 512s api> svymean(~api00, rclus1p) 512s mean SE 512s api00 642.31 26.934 512s 512s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 512s total SE 512s enroll 3680893 473431 512s > 512s BEGIN TEST badcal.R 512s 512s R version 4.4.3 (2025-02-28) -- "Trophy Case" 512s Copyright (C) 2025 The R Foundation for Statistical Computing 512s Platform: aarch64-unknown-linux-gnu 512s 512s R is free software and comes with ABSOLUTELY NO WARRANTY. 512s You are welcome to redistribute it under certain conditions. 512s Type 'license()' or 'licence()' for distribution details. 512s 512s R is a collaborative project with many contributors. 512s Type 'contributors()' for more information and 512s 'citation()' on how to cite R or R packages in publications. 512s 512s Type 'demo()' for some demos, 'help()' for on-line help, or 512s 'help.start()' for an HTML browser interface to help. 512s Type 'q()' to quit R. 512s 512s > ## 512s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 512s > ## 512s > library(survey) 512s Loading required package: grid 512s Loading required package: Matrix 513s Loading required package: survival 513s 513s Attaching package: 'survey' 513s 513s The following object is masked from 'package:graphics': 513s 513s dotchart 513s 513s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 513s > des <- svydesign(ids=~1, weights=~w, data=data) 513s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 513s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 513s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 513s > 513s BEGIN TEST brewer_cpp.R 514s 514s R version 4.4.3 (2025-02-28) -- "Trophy Case" 514s Copyright (C) 2025 The R Foundation for Statistical Computing 514s Platform: aarch64-unknown-linux-gnu 514s 514s R is free software and comes with ABSOLUTELY NO WARRANTY. 514s You are welcome to redistribute it under certain conditions. 514s Type 'license()' or 'licence()' for distribution details. 514s 514s R is a collaborative project with many contributors. 514s Type 'contributors()' for more information and 514s 'citation()' on how to cite R or R packages in publications. 514s 514s Type 'demo()' for some demos, 'help()' for on-line help, or 514s 'help.start()' for an HTML browser interface to help. 514s Type 'q()' to quit R. 514s 514s > ## pps="brewer" can't use rcpp 514s > ## this checks that it doesn't 514s > library(survey) 514s Loading required package: grid 514s Loading required package: Matrix 515s Loading required package: survival 515s > data(election) 515s 515s Attaching package: 'survey' 515s 515s The following object is masked from 'package:graphics': 515s 515s dotchart 515s 515s > 515s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 515s > options(survey.use_rcpp=TRUE) 515s > a<-svytotal(~Bush+Kerry+Nader, dpps_br) 515s > options(survey.use_rcpp=FALSE) 515s > b<-svytotal(~Bush+Kerry+Nader, dpps_br) 515s > 515s > stopifnot(identical(a,b)) 515s > 515s BEGIN TEST bycovmat.R 515s 515s R version 4.4.3 (2025-02-28) -- "Trophy Case" 515s Copyright (C) 2025 The R Foundation for Statistical Computing 515s Platform: aarch64-unknown-linux-gnu 515s 515s R is free software and comes with ABSOLUTELY NO WARRANTY. 515s You are welcome to redistribute it under certain conditions. 515s Type 'license()' or 'licence()' for distribution details. 515s 515s R is a collaborative project with many contributors. 515s Type 'contributors()' for more information and 515s 'citation()' on how to cite R or R packages in publications. 515s 515s Type 'demo()' for some demos, 'help()' for on-line help, or 515s 'help.start()' for an HTML browser interface to help. 515s Type 'q()' to quit R. 515s 515s > 515s > library(survey) 515s Loading required package: grid 515s Loading required package: Matrix 516s Loading required package: survival 516s > data(api) 516s 516s Attaching package: 'survey' 516s 516s The following object is masked from 'package:graphics': 516s 516s dotchart 516s 516s > options(survey.replicates.mse=TRUE) 516s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 516s > rclus1<-as.svrepdesign(dclus1) 516s > 516s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 516s + covmat=TRUE,drop.empty.groups=FALSE) 516s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 516s + covmat=TRUE,drop.empty.groups=TRUE) 516s > 516s > stopifnot(all.equal( 516s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 516s + )) 516s > stopifnot(all.equal( 516s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 516s + )) 516s > 516s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 516s > all <- svytotal(~ell+mobility+meals, dclus1) 516s > 516s > stopifnot(all(abs(vcov(svycontrast(all, 516s + list(quote(ell/mobility), 516s + quote(mobility/mobility), 516s + quote(ell/meals),quote(mobility/meals)))) 516s + -vcov(rat))<1e-10)) 516s > 516s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 516s > 516s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 516s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 516s > 516s > con<-svycontrast(all, 516s + list(quote(ell/mobility), 516s + quote(mobility/mobility), 516s + quote(ell/meals),quote(mobility/meals))) 516s > 516s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 516s > 516s > options(survey.replicates.mse=FALSE) 516s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 516s > rclus1<-as.svrepdesign(dclus1) 516s > 516s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 516s + covmat=TRUE,drop.empty.groups=FALSE) 516s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 516s + covmat=TRUE,drop.empty.groups=TRUE) 516s > 516s > stopifnot(all.equal( 516s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 516s + )) 516s > stopifnot(all.equal( 516s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 516s + )) 516s > 516s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 516s > all <- svytotal(~ell+mobility+meals, dclus1) 516s > 516s > stopifnot(all(abs(vcov(svycontrast(all, 516s + list(quote(ell/mobility), 516s + quote(mobility/mobility), 516s + quote(ell/meals),quote(mobility/meals)))) 516s + -vcov(rat))<1e-10)) 516s > 516s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 516s > 516s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 516s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 516s > 516s > con<-svycontrast(all, 516s + list(quote(ell/mobility), 516s + quote(mobility/mobility), 516s + quote(ell/meals),quote(mobility/meals))) 516s > 516s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 516s > 516s > 516s > 516s BEGIN TEST caleg.R 516s 516s R version 4.4.3 (2025-02-28) -- "Trophy Case" 516s Copyright (C) 2025 The R Foundation for Statistical Computing 516s Platform: aarch64-unknown-linux-gnu 516s 516s R is free software and comes with ABSOLUTELY NO WARRANTY. 516s You are welcome to redistribute it under certain conditions. 516s Type 'license()' or 'licence()' for distribution details. 516s 516s R is a collaborative project with many contributors. 516s Type 'contributors()' for more information and 516s 'citation()' on how to cite R or R packages in publications. 516s 516s Type 'demo()' for some demos, 'help()' for on-line help, or 516s 'help.start()' for an HTML browser interface to help. 516s Type 'q()' to quit R. 516s 517s > ## 517s > ## Calibration examples 517s > ## 517s > 517s > 517s > ## Example of calibration to first-stage clusters 517s > library(survey) 517s Loading required package: grid 517s Loading required package: Matrix 518s Loading required package: survival 518s 518s Attaching package: 'survey' 518s 518s The following object is masked from 'package:graphics': 518s 518s dotchart 518s 518s > data(api) 518s > 518s > clusters<-table(apiclus2$dnum) 518s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 518s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 518s > 518s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 518s > 518s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 518s > 518s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 518s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 518s > 518s > names(pop)<-names(clusters) 518s > 518s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 518s > 518s > svymean(~api99, dclus2) 518s mean SE 518s api99 642.14 31.434 518s > svymean(~api99, dclus2g) 518s mean SE 518s api99 654.49 29.82 518s > 518s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 518s dnum api99 se 518s 83 83 694.3333 0.0000 518s 132 132 505.0000 0.0000 518s 152 152 574.0000 0.0000 518s 173 173 894.7500 0.0000 518s 198 198 533.7500 0.0000 518s 200 200 589.8000 6.8335 518s 228 228 477.0000 0.0000 518s 295 295 646.4000 0.0000 518s 302 302 903.5000 0.0000 518s 403 403 852.4000 0.0000 518s 452 452 533.0000 0.0000 518s 480 480 614.2000 0.0000 518s 523 523 580.5000 0.0000 518s 534 534 564.6000 0.0000 518s 549 549 896.2000 0.0000 518s 552 552 730.0000 0.0000 518s 570 570 518.4000 7.5478 518s 575 575 800.8000 4.2513 518s 596 596 785.6000 2.4155 518s 620 620 591.6000 10.5869 518s 638 638 560.2000 4.0954 518s 674 674 760.0000 0.0000 518s 679 679 610.2500 0.0000 518s 687 687 718.6667 0.0000 518s 701 701 651.5000 0.0000 518s 711 711 690.5000 0.0000 518s 731 731 702.0000 2.1744 518s 768 768 562.5000 0.0000 518s 781 781 854.4000 0.7456 518s > 518s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 519s dnum api99 se 519s 83 83 694.3333 0 519s 132 132 505.0000 0 519s 152 152 574.0000 0 519s 173 173 894.7500 0 519s 198 198 533.7500 0 519s 200 200 567.5455 0 519s 228 228 477.0000 0 519s 295 295 646.4000 0 519s 302 302 903.5000 0 519s 403 403 852.4000 0 519s 452 452 533.0000 0 519s 480 480 614.2000 0 519s 523 523 580.5000 0 519s 534 534 564.6000 0 519s 549 549 896.2000 0 519s 552 552 730.0000 0 519s 570 570 548.9444 0 519s 575 575 824.5357 0 519s 596 596 787.5714 0 519s 620 620 609.3750 0 519s 638 638 585.6429 0 519s 674 674 760.0000 0 519s 679 679 610.2500 0 519s 687 687 718.6667 0 519s 701 701 651.5000 0 519s 711 711 690.5000 0 519s 731 731 700.6667 0 519s 768 768 562.5000 0 519s 781 781 851.0000 0 519s > 519s > ## Averaging to first stage 519s > 519s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 519s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 519s > 519s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 519s > 519s > svytotal(~enroll,dclus1g) 519s total SE 519s enroll 3811472 0 519s > svytotal(~api.stu,dclus1g) 519s total SE 519s api.stu 3242857 38967 519s > 519s > #variation within clusters should be zero 519s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 519s [1] TRUE 519s > 519s > ##bounded weights 519s > dclus1g<-calibrate(dclus1, ~enroll, pop) 519s > range(weights(dclus1g)/weights(dclus1)) 519s [1] 0.7906782 1.7891164 519s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 519s > range(weights(dclus1gb)/weights(dclus1)) 519s [1] 0.7198751 1.5000000 519s > 519s > ## Ratio estimators 519s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 519s > svytotal(~api.stu,dstrat) 519s total SE 519s api.stu 3086009 99477 519s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 519s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 519s > predict(common, total=total.enroll) 519s $total 519s enroll 519s api.stu 3190038 519s 519s $se 519s enroll 519s api.stu 29565.98 519s 519s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 519s > svytotal(~api.stu, dstratg) 519s total SE 519s api.stu 3190038 29566 519s > 519s > ## postStratify vs calibrate in stratified sample (Ben French) 519s > set.seed(17) 519s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 519s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 519s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 519s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 519s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 519s > postStratify(des,~w,popw)->dps 519s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 519s > 519s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 519s [1] TRUE 519s > 519s > ## missing data in calibrated design 519s > dps$variables$z[1]<-NA 519s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 519s 519s Call: 519s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 519s 519s Survey design: 519s postStratify(des, ~w, popw) 519s 519s Coefficients: 519s Estimate Std. Error t value Pr(>|t|) 519s (Intercept) -0.1203 0.3380 -0.356 0.722 519s z 6.2118 0.6451 9.630 <2e-16 *** 519s x 2.2602 0.2514 8.992 <2e-16 *** 519s --- 519s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 519s 519s (Dispersion parameter for quasibinomial family taken to be 1.919987) 519s 519s Number of Fisher Scoring iterations: 9 519s 519s > 519s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 519s > # should match the ratio estmate above 519s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 519s > svytotal(~api.stu, dstratgh) 519s total SE 519s api.stu 3190038 29566 519s > 519s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 519s > bnds <- list( 519s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 519s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 519s > lapply(bnds, head) 519s $lower 519s [1] 1 1 -Inf -Inf -Inf -Inf 519s 519s $upper 519s [1] 1 1 Inf Inf Inf Inf 519s 519s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 519s > svytotal(~api.stu, dstratg1) 519s total SE 519s api.stu 3190133 29561 519s > head(weights(dstrat)) 519s 1 2 3 4 5 6 519s 44.21 44.21 44.21 44.21 44.21 44.21 519s > head(weights(dstratg1)) 519s 1 2 3 4 5 6 519s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 519s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 519s [1] TRUE 519s > 519s > ## individual boundary constraints as constant values (Daniel Oehm) 519s > bnds <- list( 519s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 519s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 519s > lapply(bnds, head) 519s $lower 519s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 519s 519s $upper 519s [1] 44.21 44.21 Inf Inf Inf Inf 519s 519s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 519s > svytotal(~api.stu, dstratg2) 519s total SE 519s api.stu 3190133 29561 519s > head(weights(dstrat)) 519s 1 2 3 4 5 6 519s 44.21 44.21 44.21 44.21 44.21 44.21 519s > head(weights(dstratg2)) 519s 1 2 3 4 5 6 519s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 519s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 519s [1] TRUE 519s > 519s > # sparse matrix support (Daniel Oehm) 519s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 519s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 519s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 519s > svymean(~api00, dclus1g) 519s mean SE 519s api00 642.31 23.921 519s > svytotal(~enroll, dclus1g) 519s total SE 519s enroll 3680893 406293 519s > 519s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 519s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 519s > svymean(~api00, dclus1g) 519s mean SE 519s api00 642.31 23.921 519s > svytotal(~enroll, dclus1g) 519s total SE 519s enroll 3680893 406293 519s > 519s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 519s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 519s > svymean(~api00, dclus1g) 519s mean SE 519s api00 642.31 23.921 519s > svytotal(~enroll, dclus1g) 519s total SE 519s enroll 3680893 406293 519s > 519s BEGIN TEST check.R 519s 519s R version 4.4.3 (2025-02-28) -- "Trophy Case" 519s Copyright (C) 2025 The R Foundation for Statistical Computing 519s Platform: aarch64-unknown-linux-gnu 519s 519s R is free software and comes with ABSOLUTELY NO WARRANTY. 519s You are welcome to redistribute it under certain conditions. 519s Type 'license()' or 'licence()' for distribution details. 519s 519s R is a collaborative project with many contributors. 519s Type 'contributors()' for more information and 519s 'citation()' on how to cite R or R packages in publications. 519s 519s Type 'demo()' for some demos, 'help()' for on-line help, or 519s 'help.start()' for an HTML browser interface to help. 519s Type 'q()' to quit R. 519s 519s > library(survey) 519s Loading required package: grid 519s Loading required package: Matrix 520s Loading required package: survival 520s 520s Attaching package: 'survey' 520s 520s > The following object is masked from 'package:graphics': 520s 520s dotchart 520s 520s data(fpc) 520s > ## test various possibilities for svydesign 520s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 520s Warning message: 520s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 520s No weights or probabilities supplied, assuming equal probability 520s Warning message: 520s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 520s No weights or probabilities supplied, assuming equal probability 520s Warning message: 520s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 520s No weights or probabilities supplied, assuming equal probability 520s variables = ~x, data = fpc, nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7413 520s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 520s data = fpc, nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7413 520s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 520s data = fpc, nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 44.2 6.237 520s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 520s nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.525 0.7796 520s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 520s data = fpc, nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7413 520s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 520s nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.525 0.7796 520s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 520s > a 520s 1 - level Cluster Sampling design (with replacement) 520s With (5) clusters. 520s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.525 0.838 520s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 520s > a 520s 1 - level Cluster Sampling design (with replacement) 520s With (5) clusters. 520s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 520s nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7938 520s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 520s > a 520s 2 - level Cluster Sampling design (with replacement) 520s With (2, 8) clusters. 520s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 520s data = fpc) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.5465 520s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 520s > a 520s 2 - level Cluster Sampling design (with replacement) 520s With (2, 8) clusters. 520s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 520s > svymean(~x,a) 520s mean SE 520s x 5.525 0.5188 520s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 520s variables = fpc[, "x", drop = FALSE], nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7413Warning message: 520s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 520s No weights or probabilities supplied, assuming equal probability 520s 520s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 520s > a 520s Stratified Independent Sampling design (with replacement) 520s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 520s variables = fpc[, 4:6], nest = TRUE) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7413 520s > 520s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 520s > a 520s 1 - level Cluster Sampling design 520s With (5) clusters. 520s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 520s 4:6], fpc = rep(27, 8)) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.7165 520s > 520s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 520s > a 520s Stratified Independent Sampling design 520s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 520s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 520s > svymean(~x,a) 520s mean SE 520s x 5.4481 0.616 520s > 520s BEGIN TEST confintrep.R 520s 520s R version 4.4.3 (2025-02-28) -- "Trophy Case" 520s Copyright (C) 2025 The R Foundation for Statistical Computing 520s Platform: aarch64-unknown-linux-gnu 520s 520s R is free software and comes with ABSOLUTELY NO WARRANTY. 520s You are welcome to redistribute it under certain conditions. 520s Type 'license()' or 'licence()' for distribution details. 520s 520s R is a collaborative project with many contributors. 520s Type 'contributors()' for more information and 520s 'citation()' on how to cite R or R packages in publications. 520s 520s Type 'demo()' for some demos, 'help()' for on-line help, or 520s 'help.start()' for an HTML browser interface to help. 520s Type 'q()' to quit R. 520s 521s > library(survey) 521s Loading required package: grid 521s Loading required package: Matrix 522s Loading required package: survival 522s 522s Attaching package: 'survey' 522s 522s > The following object is masked from 'package:graphics': 522s 522s dotchart 522s 522s data(api) 522s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 522s Warning message: 522s In as.svrepdesign.default(dclus2) : 522s Finite population corrections after first stage have been dropped 522s > rclus2<-as.svrepdesign(dclus2) 522s > 522s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial) 522s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint") 522s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial) 522s > if(anyNA(confint(mrep))) stop("NA in confint") 522s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint") 522s > 522s BEGIN TEST contrast-replicates.R 522s 522s R version 4.4.3 (2025-02-28) -- "Trophy Case" 522s Copyright (C) 2025 The R Foundation for Statistical Computing 522s Platform: aarch64-unknown-linux-gnu 522s 522s R is free software and comes with ABSOLUTELY NO WARRANTY. 522s You are welcome to redistribute it under certain conditions. 522s Type 'license()' or 'licence()' for distribution details. 522s 522s R is a collaborative project with many contributors. 522s Type 'contributors()' for more information and 522s 'citation()' on how to cite R or R packages in publications. 522s 522s Type 'demo()' for some demos, 'help()' for on-line help, or 522s 'help.start()' for an HTML browser interface to help. 522s Type 'q()' to quit R. 522s 522s > ## test use of replicates in svyby, svycontrast 522s > library(survey) 522s Loading required package: grid 522s Loading required package: Matrix 523s Loading required package: survival 523s 523s Attaching package: 'survey' 523s 523s > 523s > data(api) 523s The following object is masked from 'package:graphics': 523s 523s dotchart 523s 523s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 523s > rclus1<-as.svrepdesign(dclus1) 523s > 523s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 523s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 523s > vcov(c_without) 523s contrast 523s contrast 0.06862947 523s > 523s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 523s > 523s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 523s > 523s > v_with<- vcov(rclus1, c_with$replicates) 524s > 524s > r<- attr(meanlogs_with, "replicates") 524s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 524s > 524s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 524s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 524s > 524s BEGIN TEST coxph-termtest.R 524s 524s R version 4.4.3 (2025-02-28) -- "Trophy Case" 524s Copyright (C) 2025 The R Foundation for Statistical Computing 524s Platform: aarch64-unknown-linux-gnu 524s 524s R is free software and comes with ABSOLUTELY NO WARRANTY. 524s You are welcome to redistribute it under certain conditions. 524s Type 'license()' or 'licence()' for distribution details. 524s 524s R is a collaborative project with many contributors. 524s Type 'contributors()' for more information and 524s 'citation()' on how to cite R or R packages in publications. 524s 524s Type 'demo()' for some demos, 'help()' for on-line help, or 524s 'help.start()' for an HTML browser interface to help. 524s Type 'q()' to quit R. 524s 524s > library(survey) 524s Loading required package: grid 524s Loading required package: Matrix 525s Loading required package: survival 525s > library(survival) 525s > set.seed(2021-6-25) 525s > test1 <- list(time=c(4,3,1,1,2,2,3), 525s + status=c(1,1,1,0,1,1,0), 525s + x1=as.factor(rbinom(7, 2, 0.5)), 525s + x=c(0,2,1,1,1,0,0)) 525s > # Fit a stratified model 525s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 525s 525s Attaching package: 'survey' 525s 525s The following object is masked from 'package:graphics': 525s 525s dotchart 525s 525s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 525s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 525s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 525s > 525s > data(pbc, package="survival") 525s > 525s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 525s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 525s > pbc$randprob<-fitted(biasmodel) 525s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 525s > 525s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 525s > library(splines) 525s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 525s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 525s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 525s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 525s > 525s BEGIN TEST deff.R 525s 525s R version 4.4.3 (2025-02-28) -- "Trophy Case" 525s Copyright (C) 2025 The R Foundation for Statistical Computing 525s Platform: aarch64-unknown-linux-gnu 525s 525s R is free software and comes with ABSOLUTELY NO WARRANTY. 525s You are welcome to redistribute it under certain conditions. 525s Type 'license()' or 'licence()' for distribution details. 525s 525s R is a collaborative project with many contributors. 525s Type 'contributors()' for more information and 525s 'citation()' on how to cite R or R packages in publications. 525s 525s Type 'demo()' for some demos, 'help()' for on-line help, or 525s 'help.start()' for an HTML browser interface to help. 525s Type 'q()' to quit R. 525s 525s > ## from Takahiro Tsuchiya 525s > library(survey) 525s Loading required package: grid 525s Loading required package: Matrix 526s Loading required package: survival 526s 526s Attaching package: 'survey' 526s 526s > The following object is masked from 'package:graphics': 526s 526s dotchart 526s 526s kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 526s + 1 1 15 100 20 526s + 2 2 143 100 200 526s + 3 3 21 100 11 526s + 4 4 51 100 25 526s + 5 5 337 100 550 526s + 6 6 50 100 30 526s + 7 7 274 100 250 526s + 8 8 145 100 100 526s + 9 9 15 100 10 526s + 10 10 86 100 55 526s + ",open="r"),header=TRUE) 526s > close(tmp) 526s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 526s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 526s mean SE DEff 526s uriage 113.700 35.626 1.0101 526s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 526s uriage 526s uriage 1.010101 526s > 526s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 526s total SE DEff 526s uriage 113700 35626 1.0101 526s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 526s uriage 526s uriage 1.010101 526s > 526s > 526s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 526s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 526s mean SE DEff 526s uriage 243.914 48.752 1.9741 526s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 526s uriage 526s uriage 1.974067 526s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 526s total SE DEff 526s uriage 305136 184965 18.157 526s > (N.hat <- sum(weights(des.pps))) 526s [1] 1251 526s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 526s uriage 526s uriage 18.15669 526s > 526s BEGIN TEST defftest.R 526s 526s R version 4.4.3 (2025-02-28) -- "Trophy Case" 526s Copyright (C) 2025 The R Foundation for Statistical Computing 526s Platform: aarch64-unknown-linux-gnu 526s 526s R is free software and comes with ABSOLUTELY NO WARRANTY. 526s You are welcome to redistribute it under certain conditions. 526s Type 'license()' or 'licence()' for distribution details. 526s 526s R is a collaborative project with many contributors. 526s Type 'contributors()' for more information and 526s 'citation()' on how to cite R or R packages in publications. 526s 526s Type 'demo()' for some demos, 'help()' for on-line help, or 526s 'help.start()' for an HTML browser interface to help. 526s Type 'q()' to quit R. 526s 527s > library(survey) 527s Loading required package: grid 527s Loading required package: Matrix 527s Loading required package: survival 528s 528s Attaching package: 'survey' 528s 528s The following object is masked from 'package:graphics': 528s 528s dotchart 528s 528s > 528s > data(api) 528s > 528s > ## one-stage cluster sample 528s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 528s > 528s > # svyglm model 528s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 528s > 528s > #deffs returned from svyglm model - implausibly high 528s > deff(mod) 528s (Intercept) enroll api.stu 528s 1.919945 2.500983 2.686102 528s > #> (Intercept) enroll api.stu 528s > #> 351.3500 457.6799 491.5567 528s > 528s > # run mod with same data and glm() 528s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 528s > 528s > # manually calculate deffs 528s > 528s > clust_se <- summary(mod)$coefficients[,2] 528s > srs_se <- summary(srs_mod)$coefficients[,2] 528s > 528s > deffs <- clust_se^2 / srs_se^2 528s > stopifnot(all.equal(deffs, deff(mod))) 528s > 528s > 528s BEGIN TEST degf-svrepdesign.R 528s 528s R version 4.4.3 (2025-02-28) -- "Trophy Case" 528s Copyright (C) 2025 The R Foundation for Statistical Computing 528s Platform: aarch64-unknown-linux-gnu 528s 528s R is free software and comes with ABSOLUTELY NO WARRANTY. 528s You are welcome to redistribute it under certain conditions. 528s Type 'license()' or 'licence()' for distribution details. 528s 528s R is a collaborative project with many contributors. 528s Type 'contributors()' for more information and 528s 'citation()' on how to cite R or R packages in publications. 528s 528s Type 'demo()' for some demos, 'help()' for on-line help, or 528s 'help.start()' for an HTML browser interface to help. 528s Type 'q()' to quit R. 528s 528s > library(survey) 528s Loading required package: grid 528s Loading required package: Matrix 529s Loading required package: survival 529s 529s Attaching package: 'survey' 529s 529s The following object is masked from 'package:graphics': 529s 529s dotchart 529s 529s > data(scd) 529s > 529s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1), 529s + c(0,1,0,1,1,0)) 529s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights) 529s Warning message: 529s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) : 529s No sampling weights provided: equal probability assumed 529s > 529s > stopifnot(degf(scdrep)==3) 529s > 529s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4) 529s > stopifnot(degf(scdrep)==4) 529s > 529s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2) 529s Warning message: 529s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 529s No sampling weights provided: equal probability assumed 529s > stopifnot(degf(scdrep)==2) 529s > 529s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 529s + warning=function(w) w) 529s > 529s > stopifnot(inherits(msg,"warning")) 529s > 529s > 529s > 529s > 529s BEGIN TEST domain.R 529s Warning message: 529s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 529s No sampling weights provided: equal probability assumed 529s 529s R version 4.4.3 (2025-02-28) -- "Trophy Case" 529s Copyright (C) 2025 The R Foundation for Statistical Computing 529s Platform: aarch64-unknown-linux-gnu 529s 529s R is free software and comes with ABSOLUTELY NO WARRANTY. 529s You are welcome to redistribute it under certain conditions. 529s Type 'license()' or 'licence()' for distribution details. 529s 529s R is a collaborative project with many contributors. 529s Type 'contributors()' for more information and 529s 'citation()' on how to cite R or R packages in publications. 529s 529s Type 'demo()' for some demos, 'help()' for on-line help, or 529s 'help.start()' for an HTML browser interface to help. 529s Type 'q()' to quit R. 529s 529s > ## 529s > ## Domain means can be written as ratio estimators or as regression coefficients 529s > ## 529s > ## This code checks that subsetting the design object gives the same results as 529s > ## these approaches. 529s > ## 529s > 529s > 529s > library(survey) 529s Loading required package: grid 529s Loading required package: Matrix 530s Loading required package: survival 531s 531s Attaching package: 'survey' 531s 531s > data(fpc) 531s The following object is masked from 'package:graphics': 531s 531s dotchart 531s 531s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 531s > dsub<-subset(dfpc,x>4) 531s > (m1<-svymean(~x,design=dsub)) 531s mean SE 531s x 6.195 0.7555 531s > 531s > ## These should give the same domain estimates and standard errors 531s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 531s I(x > 4) x se 531s FALSE FALSE 3.314286 0.3117042 531s TRUE TRUE 6.195000 0.7555129 531s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 531s > summary(m3) 531s 531s Call: 531s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 531s 531s Survey design: 531s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 531s nest = TRUE) 531s 531s Coefficients: 531s Estimate Std. Error t value Pr(>|t|) 531s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 531s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 531s --- 531s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 531s 531s (Dispersion parameter for gaussian family taken to be 2.557379) 531s 531s Number of Fisher Scoring iterations: 2 531s 531s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 531s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 531s dfpc) 531s Ratios= 531s as.numeric(x > 4) 531s I(x * (x > 4)) 6.195 531s SEs= 531s as.numeric(x > 4) 531s I(x * (x > 4)) 0.7555129 531s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 531s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 531s > 531s > ## with strata 531s > data(api) 531s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 531s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 531s > m2<-svyglm(enroll~comp.imp-1, dstrat) 531s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 531s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 531s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 531s > 531s > ## with calibration 531s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 531s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 531s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 531s 1 - level Cluster Sampling design 531s With (15) clusters. 531s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 531s > 531s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 531s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 531s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 531s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 531s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 531s > 531s > ## with raking 531s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 531s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 531s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 531s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 531s > m2<-svyglm(api00~comp.imp-1, dclus1r) 531s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 531s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 531s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 531s > 531s > 531s > 531s > ## 531s > ## based on bug report from Takahiro Tsuchiya for version 3.4 531s > ## 531s > rei<-read.table(tmp<-textConnection( 531s + " id N n.a h n.ah n.h sub y 531s + 1 1 300 20 1 12 5 TRUE 1 531s + 2 2 300 20 1 12 5 TRUE 2 531s + 3 3 300 20 1 12 5 TRUE 3 531s + 4 4 300 20 1 12 5 TRUE 4 531s + 5 5 300 20 1 12 5 TRUE 5 531s + 6 6 300 20 1 12 5 FALSE NA 531s + 7 7 300 20 1 12 5 FALSE NA 531s + 8 8 300 20 1 12 5 FALSE NA 531s + 9 9 300 20 1 12 5 FALSE NA 531s + 10 10 300 20 1 12 5 FALSE NA 531s + 11 11 300 20 1 12 5 FALSE NA 531s + 12 12 300 20 1 12 5 FALSE NA 531s + 13 13 300 20 2 8 3 TRUE 6 531s + 14 14 300 20 2 8 3 TRUE 7 531s + 15 15 300 20 2 8 3 TRUE 8 531s + 16 16 300 20 2 8 3 FALSE NA 531s + 17 17 300 20 2 8 3 FALSE NA 531s + 18 18 300 20 2 8 3 FALSE NA 531s + 19 19 300 20 2 8 3 FALSE NA 531s + 20 20 300 20 2 8 3 FALSE NA 531s + "), header=TRUE) 531s > close(tmp) 531s > 531s > 531s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 531s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 531s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 531s > 531s > rei$y<-rei$y*(rei$y>3) 531s > ## based on Sarndal et al (9.4.14) 531s > rei$w.ah <- rei$n.ah / rei$n.a 531s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 531s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 531s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 531s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 531s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 531s > 531s > a.rei$f.h<-with(a.rei, n.h/n.ah) 531s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 531s > 531s > a.rei$f<-with(a.rei, n.a/N) 531s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 531s > 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))) 531s > 531s > V 531s [1] 70761.47 531s > Vphase1 531s [1] 44325.47 531s > Vphase2 531s [1] 26436 531s > vcov(tot2) 531s [,1] 531s [1,] 70761.47 531s attr(,"phases") 531s attr(,"phases")$phase1 531s [,1] 531s [1,] 44325.47 531s 531s attr(,"phases")$phase2 531s [,1] 531s [1,] 26436 531s 531s > 531s > ## comparing to regression 531s > reg<-svyglm(y~I(y<4), design=des.rei2) 531s > mn<-svymean(~y, subset(des.rei2,y>3)) 531s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 531s [1] TRUE 531s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 531s [1] TRUE 531s > vcov(mn) 531s [,1] 531s [1,] 0.3292258 531s attr(,"phases") 531s attr(,"phases")$phase1 531s [,1] 531s [1,] 0.1599264 531s 531s attr(,"phases")$phase2 531s [,1] 531s [1,] 0.1692994 531s 531s > vcov(reg) 531s (Intercept) I(y < 4)TRUE 531s (Intercept) 0.3292258 -0.3292258 531s I(y < 4)TRUE -0.3292258 0.5901907 531s attr(,"phases") 531s attr(,"phases")$phase1 531s (Intercept) I(y < 4)TRUE 531s (Intercept) 0.1599264 -0.1599264 531s I(y < 4)TRUE -0.1599264 0.2588542 531s 531s attr(,"phases")$phase2 531s (Intercept) I(y < 4)TRUE 531s (Intercept) 0.1692994 -0.1692994 531s I(y < 4)TRUE -0.1692994 0.3313365 531s 531s > 531s > 531s BEGIN TEST fpc.R 531s 531s R version 4.4.3 (2025-02-28) -- "Trophy Case" 531s Copyright (C) 2025 The R Foundation for Statistical Computing 531s Platform: aarch64-unknown-linux-gnu 531s 531s R is free software and comes with ABSOLUTELY NO WARRANTY. 531s You are welcome to redistribute it under certain conditions. 531s Type 'license()' or 'licence()' for distribution details. 531s 531s R is a collaborative project with many contributors. 531s Type 'contributors()' for more information and 531s 'citation()' on how to cite R or R packages in publications. 531s 531s Type 'demo()' for some demos, 'help()' for on-line help, or 531s 'help.start()' for an HTML browser interface to help. 531s Type 'q()' to quit R. 531s 531s > library(survey) 531s Loading required package: grid 531s Loading required package: Matrix 532s Loading required package: survival 532s 532s Attaching package: 'survey' 532s 532s The following object is masked from 'package:graphics': 532s 532s dotchart 532s 532s > ## check many permutations of fpc specification 532s > example(fpc) 532s 532s fpc> data(fpc) 532s 532s fpc> fpc 532s stratid psuid weight nh Nh x 532s 1 1 1 3 5 15 2.8 532s 2 1 2 3 5 15 4.1 532s 3 1 3 3 5 15 6.8 532s 4 1 4 3 5 15 6.8 532s 5 1 5 3 5 15 9.2 532s 6 2 1 4 3 12 3.7 532s 7 2 2 4 3 12 6.6 532s 8 2 3 4 3 12 4.2 532s 532s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 532s fpc+ data=fpc, nest=TRUE) 532s 532s fpc> withoutfpc 532s Stratified Independent Sampling design (with replacement) 532s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 532s data=fpc, nest=TRUE) 532s 532s fpc> svymean(~x, withoutfpc) 532s mean SE 532s x 5.4481 0.7413 532s 532s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 532s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 532s 532s fpc> withfpc 532s Stratified Independent Sampling design 532s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 532s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 532s 532s fpc> svymean(~x, withfpc) 532s mean SE 532s x 5.4481 0.616 532s 532s fpc> ## Other equivalent forms 532s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 532s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 532s 532s fpc> svymean(~x, withfpc) 532s mean SE 532s x 5.4481 0.616 532s 532s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 532s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 532s 532s fpc> svymean(~x, withfpc) 532s mean SE 532s x 5.4481 0.616 532s 532s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 532s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 532s 532s fpc> svymean(~x, withfpc) 532s mean SE 532s x 5.4481 0.616 532s 532s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 532s fpc+ variables=~x,data=fpc,nest=TRUE) 532s 532s fpc> svymean(~x, withfpc) 532s mean SE 532s x 5.4481 0.616 532s 532s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 532s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 532s 532s fpc> svymean(~x, withfpc) 532s mean SE 532s x 5.4481 0.616 532s > 532s > 532s BEGIN TEST glm-scoping.R 532s 532s R version 4.4.3 (2025-02-28) -- "Trophy Case" 532s Copyright (C) 2025 The R Foundation for Statistical Computing 532s Platform: aarch64-unknown-linux-gnu 532s 532s R is free software and comes with ABSOLUTELY NO WARRANTY. 532s You are welcome to redistribute it under certain conditions. 532s Type 'license()' or 'licence()' for distribution details. 532s 532s R is a collaborative project with many contributors. 532s Type 'contributors()' for more information and 532s 'citation()' on how to cite R or R packages in publications. 532s 532s Type 'demo()' for some demos, 'help()' for on-line help, or 532s 'help.start()' for an HTML browser interface to help. 532s Type 'q()' to quit R. 532s 532s > ## bug report from Thomas Leeper, fixed in version 3.32-3 532s > 532s > library("survey") 532s Loading required package: grid 532s Loading required package: Matrix 533s Loading required package: survival 534s 534s Attaching package: 'survey' 534s 534s The following object is masked from 'package:graphics': 534s 534s dotchart 534s 534s > data(api) 534s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 534s > 534s > # pass `family` directly (WORKS!) 534s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 534s Stratified Independent Sampling design 534s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 534s fpc = ~fpc) 534s 534s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 534s family = gaussian()) 534s 534s Coefficients: 534s (Intercept) ell meals mobility 534s 820.8873 -0.4806 -3.1415 0.2257 534s 534s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 534s Null Deviance: 3023000 534s Residual Deviance: 1029000 AIC: 2308 534s > 534s > # passing `family` via ... (WORKS!) 534s > myfun1 <- function(formula, design, ...) { 534s + svyglm(formula, design = design, ...) 534s + } 534s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 534s Stratified Independent Sampling design 534s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 534s fpc = ~fpc) 534s 534s Call: svyglm(formula = formula, design = design, family = ..1) 534s 534s Coefficients: 534s (Intercept) ell meals mobility 534s 820.8873 -0.4806 -3.1415 0.2257 534s 534s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 534s Null Deviance: 3023000 534s Residual Deviance: 1029000 AIC: 2308 534s > 534s > # passing `family` via default argument (DOES NOT WORK!) 534s > myfun2 <- function(formula, design, family = gaussian()) { 534s + svyglm(formula, design = design, family = family) 534s + } 534s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 534s Stratified Independent Sampling design 534s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 534s fpc = ~fpc) 534s 534s Call: svyglm(formula = formula, design = design, family = family) 534s 534s Coefficients: 534s (Intercept) ell meals mobility 534s 820.8873 -0.4806 -3.1415 0.2257 534s 534s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 534s Null Deviance: 3023000 534s Residual Deviance: 1029000 AIC: 2308 534s > 534s BEGIN TEST kalton.R 534s 534s R version 4.4.3 (2025-02-28) -- "Trophy Case" 534s Copyright (C) 2025 The R Foundation for Statistical Computing 534s Platform: aarch64-unknown-linux-gnu 534s 534s R is free software and comes with ABSOLUTELY NO WARRANTY. 534s You are welcome to redistribute it under certain conditions. 534s Type 'license()' or 'licence()' for distribution details. 534s 534s R is a collaborative project with many contributors. 534s Type 'contributors()' for more information and 534s 'citation()' on how to cite R or R packages in publications. 534s 534s Type 'demo()' for some demos, 'help()' for on-line help, or 534s 'help.start()' for an HTML browser interface to help. 534s Type 'q()' to quit R. 534s 534s > library(survey) 534s Loading required package: grid 534s Loading required package: Matrix 535s Loading required package: survival 535s 535s Attaching package: 'survey' 535s 535s The following object is masked from 'package:graphics': 535s 535s dotchart 535s 535s > 535s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 535s > 535s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 535s > 535s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 535s > 535s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 535s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 535s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 535s > 535s > dkalton<-svydesign(id=~1,data=kaltonsample) 535s > 535s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 535s > 535s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 535s > 535s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 535s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 535s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 535s > 535s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 535s Warning message: 535s In svydesign.default(id = ~1, data = kaltonsample) : 535s No weights or probabilities supplied, assuming equal probability 535s > 535s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 535s > 535s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 535s > 535s > 535s > #table A 535s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 4.00 1.00 1.38 535s 2 1.20 1.07 1.10 535s 3 1.70 1.20 4.00 535s 4 1.83 1.65 1.79 535s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 4.00 1.00 1.37 535s 2 1.20 1.07 1.10 535s 3 1.70 1.20 4.00 535s 4 1.83 1.65 1.79 535s > 535s > #table B 535s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 1.81 1.45 2.02 535s 2 1.08 0.87 1.21 535s 3 2.20 1.76 2.45 535s 4 1.83 1.47 2.04 535s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 1.81 1.45 2.02 535s 2 1.08 0.87 1.21 535s 3 2.20 1.76 2.45 535s 4 1.83 1.47 2.04 535s > 535s > #table C 535s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 1.82 1.50 1.97 535s 2 1.09 0.78 1.24 535s 3 2.19 1.88 2.34 535s 4 1.83 1.52 1.98 535s > 535s > #table D 535s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 1.21 1.17 1.14 535s 2 1.43 1.40 1.36 535s 3 1.66 1.62 1.59 535s 4 1.88 1.85 1.81 535s > 535s > #table G 535s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 1.87 1.46 1.98 535s 2 1.08 0.74 1.27 535s 3 2.17 2.09 2.18 535s 4 1.89 1.49 1.99 535s > 535s > #table G 535s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 535s b 535s a 1 2 3 535s 1 1.81 1.48 1.99 535s 2 1.08 0.75 1.26 535s 3 2.20 2.00 2.20 535s 4 1.83 1.50 2.00 535s > 535s BEGIN TEST logranktest.R 535s 535s R version 4.4.3 (2025-02-28) -- "Trophy Case" 535s Copyright (C) 2025 The R Foundation for Statistical Computing 535s Platform: aarch64-unknown-linux-gnu 535s 535s R is free software and comes with ABSOLUTELY NO WARRANTY. 535s You are welcome to redistribute it under certain conditions. 535s Type 'license()' or 'licence()' for distribution details. 535s 535s R is a collaborative project with many contributors. 535s Type 'contributors()' for more information and 535s 'citation()' on how to cite R or R packages in publications. 535s 535s Type 'demo()' for some demos, 'help()' for on-line help, or 535s 'help.start()' for an HTML browser interface to help. 535s Type 'q()' to quit R. 535s 535s > ## StackOverflow 63333282 535s > 535s > library(survey) 535s Loading required package: grid 535s Loading required package: Matrix 536s Loading required package: survival 536s 536s Attaching package: 'survey' 536s 536s > The following object is masked from 'package:graphics': 536s 536s dotchart 536s 536s D = data.frame(unique_id = 1:135, 536s + 536s + weights = rep(1,135), 536s + 536s + 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 , 536s + 536s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 536s + 536s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 536s + 536s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 536s + 536s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 536s + 536s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 536s + 536s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 536s + 536s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 536s + 536s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 536s + 536s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 536s + 536s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 536s + 536s + 2.35699896, 2.94956000, 8.85381736), 536s + 536s + 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, 536s + 536s + 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, 536s + 536s + 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), 536s + 536s + group = c(rep("group1", 40), rep("group2", 95))) 536s > 536s > 536s > 536s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 536s > 536s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 536s > 536s > a<-svylogrank(formula = svykm_formula, design = svy_design) 536s > 536s > ii<-with(D, order(event_time, event_flag)) 536s > 536s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 536s > 536s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 536s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 536s > 536s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 537s > 537s > 537s > stopifnot(all.equal(a[[2]],b[[2]])) 537s > 537s > stopifnot(all.equal(a[[2]],d[[2]])) 537s > 537s > stopifnot(all.equal(a[[2]],f[-1])) 537s > 537s > 537s BEGIN TEST lonely.psu.R 537s 537s R version 4.4.3 (2025-02-28) -- "Trophy Case" 537s Copyright (C) 2025 The R Foundation for Statistical Computing 537s Platform: aarch64-unknown-linux-gnu 537s 537s R is free software and comes with ABSOLUTELY NO WARRANTY. 537s You are welcome to redistribute it under certain conditions. 537s Type 'license()' or 'licence()' for distribution details. 537s 537s R is a collaborative project with many contributors. 537s Type 'contributors()' for more information and 537s 'citation()' on how to cite R or R packages in publications. 537s 537s Type 'demo()' for some demos, 'help()' for on-line help, or 537s 'help.start()' for an HTML browser interface to help. 537s Type 'q()' to quit R. 537s 537s > 537s > ## lonely PSUs by design 537s > library(survey) 537s Loading required package: grid 537s Loading required package: Matrix 538s Loading required package: survival 538s 538s Attaching package: 'survey' 538s 538s The following object is masked from 'package:graphics': 538s 538s dotchart 538s 538s > data(api) 538s > ## not certainty PSUs by fpc 538s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 538s > summary(ds) 538s Stratified Independent Sampling design (with replacement) 538s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 538s Probabilities: 538s Min. 1st Qu. Median Mean 3rd Qu. Max. 538s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 538s Stratum Sizes: 538s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 538s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 538s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 538s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 538s Data variables: 538s [1] "cds" "stype" "name" "sname" "snum" "dname" 538s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 538s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 538s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 538s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 538s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 538s [37] "api.stu" "fpc" "pw" 538s > 538s > options(survey.lonely.psu="fail") 538s > try(svymean(~api00,ds)) 538s > try(svymean(~api00, as.svrepdesign(ds))) 538s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 538s Stratum (413) has only one PSU at stage 1 538s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 538s Stratum413has only one PSU 538s > options(survey.lonely.psu="remove") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.8058 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.8058 538s > options(survey.lonely.psu="certainty") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.8058 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.8058 538s > options(survey.lonely.psu="adjust") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.8281 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.8267 538s > options(survey.lonely.psu="average") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 6.0096 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.8217 538s > 538s > ## fpc specified 538s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 538s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 538s > summary(ds) 538s Stratified Independent Sampling design 538s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 538s fpc = fpc) 538s Probabilities: 538s Min. 1st Qu. Median Mean 3rd Qu. Max. 538s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 538s Stratum Sizes: 538s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 538s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 538s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 538s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 538s Population stratum sizes (PSUs): 538s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 538s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 538s Data variables: 538s [1] "cds" "stype" "name" "sname" "snum" "dname" 538s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 538s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 538s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 538s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 538s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 538s [37] "api.stu" "fpc" "pw" 538s > 538s > options(survey.lonely.psu="fail") 538s > try(svymean(~api00,ds)) 538s mean SE 538s api00 644.17 5.7344 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.7344 538s > options(survey.lonely.psu="remove") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.7344 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.7344 538s > options(survey.lonely.psu="certainty") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.7344 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.7344 538s > options(survey.lonely.psu="adjust") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.7344 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.7344 538s > options(survey.lonely.psu="average") 538s > svymean(~api00,ds) 538s mean SE 538s api00 644.17 5.7344 538s > svymean(~api00, as.svrepdesign(ds)) 538s mean SE 538s api00 644.17 5.7501 538s > 538s > rs<-as.svrepdesign(ds) 538s > svytotal(~api00,rs) 538s total SE 538s api00 3989986 35616 538s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 538s [1] TRUE 538s > 538s > ## lonely PSUs after subsetting 538s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 538s > ds1<-ds[-31,] 538s > summary(ds1) 538s Stratified Independent Sampling design (with replacement) 538s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 538s dnum != 413)) 538s Probabilities: 538s Min. 1st Qu. Median Mean 3rd Qu. Max. 538s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 538s Stratum Sizes: 538s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 538s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 538s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 538s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 538s Data variables: 538s [1] "cds" "stype" "name" "sname" "snum" "dname" 538s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 538s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 538s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 538s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 538s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 538s [37] "api.stu" "fpc" "pw" 538s > 538s > options(survey.lonely.psu="fail") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="remove") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="certainty") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="adjust") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="average") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 5.8909 538s > 538s > ## with adjustment 538s > options(survey.adjust.domain.lonely=TRUE) 538s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 538s > ds1<-ds[-31,] 538s > summary(ds1) 538s Stratified Independent Sampling design (with replacement) 538s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 538s dnum != 413)) 538s Probabilities: 538s Min. 1st Qu. Median Mean 3rd Qu. Max. 538s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 538s Stratum Sizes: 538s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 538s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 538s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 538s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 538s Data variables: 538s [1] "cds" "stype" "name" "sname" "snum" "dname" 538s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 538s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 538s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 538s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 538s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 538s [37] "api.stu" "fpc" "pw" 538s > 538s > options(survey.lonely.psu="fail") 538s > try(svymean(~api00,ds1)) 538s Warning message: 538s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 538s Stratum (406) has only one PSU at stage 1 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="remove") 538s > svymean(~api00,ds1) 538s Warning message: 538s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 538s Stratum (406) has only one PSU at stage 1 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="certainty") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 5.8909 538s > options(survey.lonely.psu="adjust") 538s > svymean(~api00,ds1) 538s Warning message: 538s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 538s Stratum (406) has only one PSU at stage 1 538s mean SE 538s api00 645.14 5.9119 538s > options(survey.lonely.psu="average") 538s > svymean(~api00,ds1) 538s mean SE 538s api00 645.14 6.0914 538s > 538s > ## checks for `svytotal()` 538s > 538s > df_w_singleton <- data.frame( 538s + Stratum = c(1, 1, 2, 2, 3), 538s + PSU = c(1, 2, 3, 4, 5), 538s + Design_Weight = c(10.5, 10.5, 20, 20, 15), 538s + Sex = c("M", "F", "F", "M", "M"), 538s + Age = c(30.5, 40.5, 35, 52, 44), 538s + Height = c(6.2, 5.0, 5.3, 5.7, 5.5) 538s + ) 538s > 538s > design_w_singleton <- survey::svydesign( 538s + data = df_w_singleton, 538s + ids = ~ PSU, strata = ~ Stratum, 538s + weights = ~ Design_Weight 538s + ) 538s > 538s > options("survey.lonely.psu" = "remove") 538s > 538s > stopifnot(all.equal( 538s + target = 126625, 538s + current = as.numeric( 538s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 538s + ) 538s + )) 538s > 538s > options("survey.lonely.psu" = "certainty") 538s > 538s > stopifnot(all.equal( 538s + target = 126625, 538s + current = as.numeric( 538s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 538s + ) 538s + )) 538s > 538s > options("survey.lonely.psu" = "adjust") 538s > 538s > stopifnot(all.equal( 538s + target = 127579.8, 538s + current = as.numeric( 538s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 538s + ), 538s + scale = 127579.8, tolerance = 0.000001 538s + )) 538s Warning message: 538s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 538s Stratum (406) has only one PSU at stage 1 538s Warning message: 538s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 538s Stratum (406) has only one PSU at stage 1 538s > 538s BEGIN TEST mtcars-var.R 538s 538s R version 4.4.3 (2025-02-28) -- "Trophy Case" 538s Copyright (C) 2025 The R Foundation for Statistical Computing 538s Platform: aarch64-unknown-linux-gnu 538s 538s R is free software and comes with ABSOLUTELY NO WARRANTY. 538s You are welcome to redistribute it under certain conditions. 538s Type 'license()' or 'licence()' for distribution details. 538s 538s R is a collaborative project with many contributors. 538s Type 'contributors()' for more information and 538s 'citation()' on how to cite R or R packages in publications. 538s 538s Type 'demo()' for some demos, 'help()' for on-line help, or 538s 'help.start()' for an HTML browser interface to help. 538s Type 'q()' to quit R. 538s 538s > library(survey) 538s Loading required package: grid 538s Loading required package: Matrix 539s Loading required package: survival 540s > 540s > # don't throw an error on domains of size 1, just return NA 540s > input <- mtcars 540s > input$carb <- factor(input$carb) 540s > design <- svydesign(ids = ~0, weights = NULL, data = input) 540s 540s Attaching package: 'survey' 540s 540s The following object is masked from 'package:graphics': 540s 540s dotchart 540s 540s > svyby( 540s + ~mpg, 540s + ~carb, 540s + design, 540s + svyvar 540s + ) 540s carb mpg se 540s 1 1 36.01619 11.2823286 540s 2 2 29.94444 9.0030898 540s 3 3 1.11000 0.4604066 540s 4 4 15.29656 4.3174617 540s 6 6 NA NA 540s 8 8 NA NA 540s > 540s > 540s > ## same n with na.rm=TRUE as subset(, !is.na) 540s > input$mpg[1]<-NA 540s > design <- svydesign(ids = ~0, weights = NULL, data = input) 540s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 540s + svyvar(~mpg, subset(design, !is.na(mpg))))) 540s > 540s BEGIN TEST multistage-rcpp.R 540s 540s R version 4.4.3 (2025-02-28) -- "Trophy Case" 540s Copyright (C) 2025 The R Foundation for Statistical Computing 540s Platform: aarch64-unknown-linux-gnu 540s 540s R is free software and comes with ABSOLUTELY NO WARRANTY. 540s You are welcome to redistribute it under certain conditions. 540s Type 'license()' or 'licence()' for distribution details. 540s 540s R is a collaborative project with many contributors. 540s Type 'contributors()' for more information and 540s 'citation()' on how to cite R or R packages in publications. 540s 540s Type 'demo()' for some demos, 'help()' for on-line help, or 540s 'help.start()' for an HTML browser interface to help. 540s Type 'q()' to quit R. 540s 540s > ## temporarily disable while it's being fixed 540s > ## q("no") 540s > 540s > ## 540s > ## Check that multistage() and multistage_rcpp() give same results 540s > ## for different options. 540s > ## 540s > library(survey) 540s Loading required package: grid 540s Loading required package: Matrix 541s Loading required package: survival 541s 541s Attaching package: 'survey' 541s 541s The following object is masked from 'package:graphics': 541s 541s dotchart 541s 541s > 541s > # Check for a simple random sample ---- 541s > 541s > data('api', package = 'survey') 541s > api_srs_design <- svydesign( 541s + data = apisrs, 541s + ids = ~ 1, 541s + weights = ~ 1 541s + ) 541s > 541s > x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob) 541s > 541s > base_r_result <- survey:::multistage(x = x, 541s + clusters = api_srs_design$cluster, 541s + stratas = api_srs_design$strata, 541s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=TRUE, stage = 1, cal = NULL) 541s > 541s > rcpp_result <- survey:::multistage_rcpp(x = x, 541s + clusters = api_srs_design$cluster, 541s + stratas = api_srs_design$strata, 541s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=TRUE, stage = 1, cal = NULL) 541s > 541s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 541s + stop("Differences between `multistage()` and `multistage_rcpp()` for SRS") 541s + } 541s > 541s > # Check for a stratified simple random sample ---- 541s > 541s > apistrat_design <- svydesign( 541s + data = apistrat, 541s + id =~ 1, 541s + strata =~ stype, 541s + weights =~ pw, 541s + fpc =~ fpc 541s + ) 541s > 541s > x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob) 541s > 541s > base_r_result <- survey:::multistage(x = x, 541s + clusters = apistrat_design$cluster, 541s + stratas = apistrat_design$strata, 541s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=TRUE, stage = 1, cal = NULL) 541s > 541s > rcpp_result <- survey:::multistage_rcpp(x = x, 541s + clusters = apistrat_design$cluster, 541s + stratas = apistrat_design$strata, 541s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=TRUE, stage = 1, cal = NULL) 541s > 541s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 541s + stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample") 541s + } 541s > 541s > ##_ Check whether expected true zeroes are actually computed as zeroes ---- 541s > 541s > x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob)) 541s > 541s > base_r_result <- survey:::multistage(x = x, 541s + clusters = apistrat_design$cluster, 541s + stratas = apistrat_design$strata, 541s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=TRUE, stage = 1, cal = NULL) 541s > 541s > rcpp_result <- survey:::multistage_rcpp(x = x, 541s + clusters = apistrat_design$cluster, 541s + stratas = apistrat_design$strata, 541s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=TRUE, stage = 1, cal = NULL) 541s > 541s > if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) { 541s + stop("Computations which should equal zero do not.") 541s + } 541s > 541s > # Create a stratified, multistage design ---- 541s > 541s > data(mu284) 541s > 541s > ## Create three strata, the third of which has only one PSU 541s > mu284_stratified <- rbind( 541s + transform(mu284, stratum = 1, 541s + y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)), 541s + transform(mu284, stratum = 2, 541s + y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)), 541s + transform(mu284[1,], stratum = 3, 541s + y2 = y1 + 2) 541s + ) 541s > 541s > ## Create domain variables which yield a lonely PSU or a lonely SSU 541s > mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19) 541s > mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1) 541s > 541s > ## Create a survey design object with no lonely PSUs 541s > dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3), 541s + strata = ~ stratum, nest = TRUE, 541s + id = ~ id1 + id2, fpc = ~ n1 + n2) 541s > ## Create a survey design with one lonely PSU 541s > dmu284_strat_w_lonely <- svydesign(data = mu284_stratified, 541s + strata = ~ stratum, nest = TRUE, 541s + id = ~ id1 + id2, fpc = ~ n1 + n2) 541s > ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU 541s > dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU) 541s > dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU) 541s > 541s > 541s > # Check same results for different values of 'lonely PSU' options ---- 541s > 541s > lonely_psu_options <- c(certainty = 'certainty', 541s + remove = 'remove', 541s + average = 'average', 541s + adjust = 'adjust') 541s > one_stage_options <- c(TRUE, FALSE) 541s > 541s > design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 541s + 'one.stage' = one_stage_options, 541s + stringsAsFactors = FALSE) 541s > design_lonely_psu_comparisons[['results_match']] <- NA 541s > 541s > ##_ Check for lonely PSUs caused by design ---- 541s > for (i in seq_len(nrow(design_lonely_psu_comparisons))) { 541s + survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i] 541s + one.stage <- design_lonely_psu_comparisons[['one.stage']][i] 541s + options('survey.lonely.psu' = survey.lonely.psu) 541s + 541s + x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob) 541s + 541s + base_r_result <- survey:::multistage(x = x, 541s + clusters = dmu284_strat_w_lonely$cluster, 541s + stratas = dmu284_strat_w_lonely$strata, 541s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=one.stage, stage = 1, cal = NULL) 541s + 541s + rcpp_result <- survey:::multistage_rcpp(x = x, 541s + clusters = dmu284_strat_w_lonely$cluster, 541s + stratas = dmu284_strat_w_lonely$strata, 541s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=one.stage, stage = 1, cal = NULL) 541s + 541s + design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 541s + } 541s > 541s > print(design_lonely_psu_comparisons) 541s survey.lonely.psu one.stage results_match 541s 1 certainty TRUE TRUE 541s 2 remove TRUE TRUE 541s 3 average TRUE TRUE 541s 4 adjust TRUE TRUE 541s 5 certainty FALSE TRUE 541s 6 remove FALSE TRUE 541s 7 average FALSE TRUE 541s 8 adjust FALSE TRUE 541s > if (!all(design_lonely_psu_comparisons$results_match)) { 541s + stop("Results for design lonely PSUs differ between base R and Rcpp implementations.") 541s + } 541s > 541s > ##_ Check for domain lonely PSUs caused by subsetting ---- 541s > 541s > domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 541s + 'survey.adjust.domain.lonely' = c(FALSE, TRUE), 541s + 'one.stage' = one_stage_options, 541s + stringsAsFactors = FALSE) 541s > domain_lonely_psu_comparisons[['results_match']] <- NA 541s > 541s > for (i in seq_len(nrow(domain_lonely_psu_comparisons))) { 541s + 541s + options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i]) 541s + options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i]) 541s + one.stage <- domain_lonely_psu_comparisons[['one.stage']][i] 541s + 541s + 541s + x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob) 541s + suppressWarnings({ 541s + base_r_result <- survey:::multistage(x = x, 541s + clusters = dmu284_strat_domain_lonely_psu$cluster, 541s + stratas = dmu284_strat_domain_lonely_psu$strata, 541s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 541s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=one.stage, stage = 1, cal = NULL) 541s + }) 541s + 541s + rcpp_result <- survey:::multistage_rcpp(x = x, 541s + clusters = dmu284_strat_domain_lonely_psu$cluster, 541s + stratas = dmu284_strat_domain_lonely_psu$strata, 541s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 541s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=one.stage, stage = 1, cal = NULL) 541s + 541s + domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 541s + } 541s > 541s > print(domain_lonely_psu_comparisons) 541s survey.lonely.psu survey.adjust.domain.lonely one.stage results_match 541s 1 certainty FALSE TRUE TRUE 541s 2 remove FALSE TRUE TRUE 541s 3 average FALSE TRUE TRUE 541s 4 adjust FALSE TRUE TRUE 541s 5 certainty TRUE TRUE TRUE 541s 6 remove TRUE TRUE TRUE 541s 7 average TRUE TRUE TRUE 541s 8 adjust TRUE TRUE TRUE 541s 9 certainty FALSE FALSE TRUE 541s 10 remove FALSE FALSE TRUE 541s 11 average FALSE FALSE TRUE 541s 12 adjust FALSE FALSE TRUE 541s 13 certainty TRUE FALSE TRUE 541s 14 remove TRUE FALSE TRUE 541s 15 average TRUE FALSE TRUE 541s 16 adjust TRUE FALSE TRUE 541s > if (!all(domain_lonely_psu_comparisons$results_match)) { 541s + stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.") 541s + } 541s > 541s > # Checks for edge cases ---- 541s > 541s > ## Zero records ---- 541s > 541s > zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent") 541s > 541s > zero_row_result <- survey:::multistage_rcpp( 541s + x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]), 541s + clusters = zero_row_design$cluster, 541s + stratas = zero_row_design$strata, 541s + nPSUs = zero_row_design$fpc$sampsize, 541s + fpcs = zero_row_design$fpc$popsize, 541s + lonely.psu=getOption("survey.lonely.psu"), 541s + one.stage=one.stage, stage = 1, cal = NULL 541s + ) 541s > 541s > if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) { 541s + stop("`multistage_rcpp()` should return zeros for zero-row inputs.") 541s + } 541s > 541s > 541s Warning messages: 541s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 541s At least one stratum contains only one PSU at stage 1 541s BEGIN TEST multistage.R 541s 541s R version 4.4.3 (2025-02-28) -- "Trophy Case" 541s Copyright (C) 2025 The R Foundation for Statistical Computing 541s Platform: aarch64-unknown-linux-gnu 541s 541s R is free software and comes with ABSOLUTELY NO WARRANTY. 541s You are welcome to redistribute it under certain conditions. 541s Type 'license()' or 'licence()' for distribution details. 541s 541s R is a collaborative project with many contributors. 541s Type 'contributors()' for more information and 541s 'citation()' on how to cite R or R packages in publications. 541s 541s Type 'demo()' for some demos, 'help()' for on-line help, or 541s 'help.start()' for an HTML browser interface to help. 541s Type 'q()' to quit R. 541s 541s > ## 541s > ## Check that multistage samples still work 541s > ## 541s > library(survey) 541s Loading required package: grid 542s Loading required package: Matrix 542s Loading required package: survival 543s > example(mu284) 543s 543s Attaching package: 'survey' 543s 543s The following object is masked from 'package:graphics': 543s 543s dotchart 543s 543s 543s mu284> data(mu284) 543s 543s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 543s 2 - level Cluster Sampling design 543s With (5, 15) clusters. 543s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 543s 543s mu284> (ytotal<-svytotal(~y1, dmu284)) 543s total SE 543s y1 15080 2274.3 543s 543s mu284> vcov(ytotal) 543s y1 543s y1 5172234 543s > 543s > 543s BEGIN TEST na_action.R 543s 543s R version 4.4.3 (2025-02-28) -- "Trophy Case" 543s Copyright (C) 2025 The R Foundation for Statistical Computing 543s Platform: aarch64-unknown-linux-gnu 543s 543s R is free software and comes with ABSOLUTELY NO WARRANTY. 543s You are welcome to redistribute it under certain conditions. 543s Type 'license()' or 'licence()' for distribution details. 543s 543s R is a collaborative project with many contributors. 543s Type 'contributors()' for more information and 543s 'citation()' on how to cite R or R packages in publications. 543s 543s Type 'demo()' for some demos, 'help()' for on-line help, or 543s 'help.start()' for an HTML browser interface to help. 543s Type 'q()' to quit R. 543s 543s > ## from Terry Therneau 543s > library(survey) 543s Loading required package: grid 543s Loading required package: Matrix 544s Loading required package: survival 544s 544s Attaching package: 'survey' 544s 544s > load("naa.rda") 544s > 544s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 544s The following object is masked from 'package:graphics': 544s 544s dotchart 544s 544s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 544s > all.equal(coef(fit1e),coef(fit1o)) 544s [1] TRUE 544s > all.equal(vcov(fit1e),vcov(fit1o)) 544s [1] TRUE 544s > 544s BEGIN TEST newquantile.R 544s 544s R version 4.4.3 (2025-02-28) -- "Trophy Case" 544s Copyright (C) 2025 The R Foundation for Statistical Computing 544s Platform: aarch64-unknown-linux-gnu 544s 544s R is free software and comes with ABSOLUTELY NO WARRANTY. 544s You are welcome to redistribute it under certain conditions. 544s Type 'license()' or 'licence()' for distribution details. 544s 544s R is a collaborative project with many contributors. 544s Type 'contributors()' for more information and 544s 'citation()' on how to cite R or R packages in publications. 544s 544s Type 'demo()' for some demos, 'help()' for on-line help, or 544s 'help.start()' for an HTML browser interface to help. 544s Type 'q()' to quit R. 544s 544s > ## quantiles with equal weights 544s > 544s > library(survey) 544s Loading required package: grid 544s Loading required package: Matrix 545s Loading required package: survival 545s 545s Attaching package: 'survey' 545s 545s > data(api) 545s The following object is masked from 'package:graphics': 545s 545s dotchart 545s 546s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 546s > 546s > 546s > for(i in 1:9){ 546s + print(i) 546s + all.equal( 546s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 546s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 546s + ) 546s + 546s + } 546s [1] 1 546s [1] 2 546s [1] 3 546s [1] 4 546s [1] 5 546s [1] 6 546s [1] 7 546s [1] 8 546s [1] 9 546s > 546s BEGIN TEST nwts-cch.R 546s 546s R version 4.4.3 (2025-02-28) -- "Trophy Case" 546s Copyright (C) 2025 The R Foundation for Statistical Computing 546s Platform: aarch64-unknown-linux-gnu 546s 546s R is free software and comes with ABSOLUTELY NO WARRANTY. 546s You are welcome to redistribute it under certain conditions. 546s Type 'license()' or 'licence()' for distribution details. 546s 546s R is a collaborative project with many contributors. 546s Type 'contributors()' for more information and 546s 'citation()' on how to cite R or R packages in publications. 546s 546s Type 'demo()' for some demos, 'help()' for on-line help, or 546s 'help.start()' for an HTML browser interface to help. 546s Type 'q()' to quit R. 546s 546s > library(survey) 546s Loading required package: grid 546s Loading required package: Matrix 547s Loading required package: survival 547s > library(survival) 547s > data(nwtco) 547s 547s Attaching package: 'survey' 547s 547s The following object is masked from 'package:graphics': 547s 547s dotchart 547s 547s > 547s > ntwco<-subset(nwtco, !is.na(edrel)) 547s > 547s > load("nwtco-subcohort.rda") 547s > nwtco$subcohort<-subcohort 547s > 547s > d_BorganII <- twophase(id=list(~seqno,~seqno), 547s + strata=list(NULL,~interaction(instit,rel)), 547s + data=nwtco, subset=~I(rel |subcohort)) 547s > 547s > ##Coefficient results same as Splus with code from 547s > ## http://faculty.washington.edu/norm/software.html 547s > ## SE slightly larger due to using sandwich variance. 547s > 547s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 547s Call: 547s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 547s I(age/12), design = d_BorganII) 547s 547s coef exp(coef) se(coef) robust se z p 547s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 547s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 547s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 547s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 547s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 547s 547s Likelihood ratio test= on 5 df, p= 547s n= 1062, number of events= 571 547s > 547s > ## 547s > ## This gives higher standard errors. calibrate() does not recompute the 547s > ## finite population correction if a calibration variable happens to predict 547s > ## sampling perfectly. It probably should. 547s > ## 547s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 547s + strata=list(NULL,~rel), 547s + data=nwtco, subset=~I(rel |subcohort)), 547s + phase=2, formula=~interaction(instit,rel), 547s + epsilon=1e-10) 548s > 548s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 548s Call: 548s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 548s I(age/12), design = d_BorganIIps) 548s 548s coef exp(coef) se(coef) robust se z p 548s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 548s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 548s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 548s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 548s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 548s 548s Likelihood ratio test= on 5 df, p= 548s n= 1062, number of events= 571 548s > 548s BEGIN TEST nwts.R 548s 548s R version 4.4.3 (2025-02-28) -- "Trophy Case" 548s Copyright (C) 2025 The R Foundation for Statistical Computing 548s Platform: aarch64-unknown-linux-gnu 548s 548s R is free software and comes with ABSOLUTELY NO WARRANTY. 548s You are welcome to redistribute it under certain conditions. 548s Type 'license()' or 'licence()' for distribution details. 548s 548s R is a collaborative project with many contributors. 548s Type 'contributors()' for more information and 548s 'citation()' on how to cite R or R packages in publications. 548s 548s Type 'demo()' for some demos, 'help()' for on-line help, or 548s 'help.start()' for an HTML browser interface to help. 548s Type 'q()' to quit R. 548s 548s > 548s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 548s > ## data from Norman Breslow's web page. 548s > library(survey) 548s Loading required package: grid 548s Loading required package: Matrix 549s Loading required package: survival 549s 549s Attaching package: 'survey' 549s 549s The following object is masked from 'package:graphics': 549s 549s dotchart 549s 549s > load("nwts.rda") 549s > nwtsnb<-nwts 549s > nwtsnb$case<-nwts$case-nwtsb$case 549s > nwtsnb$control<-nwts$control-nwtsb$control 549s > 549s > a<-rbind(nwtsb,nwtsnb) 549s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 549s > 549s > b<-rbind(a,a) 549s > b$rel<-rep(c(1,0),each=32) 549s > b$n<-ifelse(b$rel,b$case,b$control) 549s > 549s > index<-rep(1:64,b$n) 549s > 549s > nwt.exp<-b[index,c(1:3,6,7)] 549s > nwt.exp$id<-1:4088 549s > 549s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 549s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 550s > 550s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 550s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 550s > 550s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 550s > 550s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 550s 550s Call: 550s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 550s family = quasibinomial) 550s 550s Survey design: 550s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 550s subset = subset, data = data, pps = pps) 550s 550s Coefficients: 550s Estimate Std. Error t value Pr(>|t|) 550s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 550s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 550s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 550s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 550s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 550s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 550s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 550s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s (Dispersion parameter for quasibinomial family taken to be 1.000876) 550s 550s Number of Fisher Scoring iterations: 4 550s 550s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 550s 550s Call: 550s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 550s family = quasibinomial) 550s 550s Survey design: 550s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 550s subset = subset, data = data, pps = pps) 550s 550s Coefficients: 550s Estimate Std. Error t value Pr(>|t|) 550s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 550s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 550s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 550s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 550s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 550s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 550s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 550s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s (Dispersion parameter for quasibinomial family taken to be 1.000876) 550s 550s Number of Fisher Scoring iterations: 4 550s 550s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 550s 550s Call: 550s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 550s family = quasibinomial) 550s 550s Survey design: 550s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 550s rel)) 550s 550s Coefficients: 550s Estimate Std. Error t value Pr(>|t|) 550s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 550s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 550s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 550s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 550s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 550s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 550s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 550s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s (Dispersion parameter for quasibinomial family taken to be 1.000876) 550s 550s Number of Fisher Scoring iterations: 4 550s 550s > 550s > ## check subsets of calibrated designs. 550s > summary(svyglm(rel~factor(stage), 550s + family=quasibinomial,design=subset(dccs8,histol==1))) 550s 550s Call: 550s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 550s histol == 1), family = quasibinomial) 550s 550s Survey design: 550s subset(dccs8, histol == 1) 550s 550s Coefficients: 550s Estimate Std. Error t value Pr(>|t|) 550s (Intercept) -2.7160 0.1083 -25.085Warning messages: 550s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 550s 2: In summary.glm(g) : 550s observations with zero weight not used for calculating dispersion 550s 3: In summary.glm(glm.object) : 550s observations with zero weight not used for calculating dispersion 550s 4: In `[.twophase2`(design, nas == 0, ) : 550s 1 strata have only one PSU in this subset. 550s 5: In `[.twophase2`(design, nas == 0, ) : 550s 1 strata have only one PSU in this subset. 550s < 2e-16 *** 550s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 550s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 550s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s (Dispersion parameter for quasibinomial family taken to be 1.001333) 550s 550s Number of Fisher Scoring iterations: 4 550s 550s > summary(svyglm(rel~factor(stage), 550s + family=quasibinomial,design=subset(gccs8,histol==1))) 550s 550s Call: 550s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 550s histol == 1), family = quasibinomial) 550s 550s Survey design: 550s subset(gccs8, histol == 1) 550s 550s Coefficients: 550s Estimate Std. Error t value Pr(>|t|) 550s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 550s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 550s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 550s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 550s --- 550s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 550s 550s (Dispersion parameter for quasibinomial family taken to be 1.001333) 550s 550s Number of Fisher Scoring iterations: 4 550s 550s > 550s > 550s Warning messages: 550s 1: In summary.glm(g) : 550s observations with zero weight not used for calculating dispersion 550s 2: In summary.glm(glm.object) : 550s observations with zero weight not used for calculating dispersion 550s BEGIN TEST poisson.R 550s 550s R version 4.4.3 (2025-02-28) -- "Trophy Case" 550s Copyright (C) 2025 The R Foundation for Statistical Computing 550s Platform: aarch64-unknown-linux-gnu 550s 550s R is free software and comes with ABSOLUTELY NO WARRANTY. 550s You are welcome to redistribute it under certain conditions. 550s Type 'license()' or 'licence()' for distribution details. 550s 550s R is a collaborative project with many contributors. 550s Type 'contributors()' for more information and 550s 'citation()' on how to cite R or R packages in publications. 550s 550s Type 'demo()' for some demos, 'help()' for on-line help, or 550s 'help.start()' for an HTML browser interface to help. 550s Type 'q()' to quit R. 550s 550s > ## check poisson sampling 550s > library(survey) 550s Loading required package: grid 550s Loading required package: Matrix 551s Loading required package: survival 551s 551s Attaching package: 'survey' 551s 551s > data(api) 551s The following object is masked from 'package:graphics': 551s 551s dotchart 551s 551s > set.seed(2021-7-15) 551s > apipop$prob<-apipop$api00/1000 551s > insample<-rbinom(nrow(apipop),1,apipop$prob) 551s > apipois<-apipop[insample,] 551s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 551s > 551s > stopifnot(isTRUE(all.equal( 551s + as.vector(SE(svytotal(~api00,design=des))), 551s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 551s + ))) 551s > 551s > 551s BEGIN TEST pps.R 552s 552s R version 4.4.3 (2025-02-28) -- "Trophy Case" 552s Copyright (C) 2025 The R Foundation for Statistical Computing 552s Platform: aarch64-unknown-linux-gnu 552s 552s R is free software and comes with ABSOLUTELY NO WARRANTY. 552s You are welcome to redistribute it under certain conditions. 552s Type 'license()' or 'licence()' for distribution details. 552s 552s R is a collaborative project with many contributors. 552s Type 'contributors()' for more information and 552s 'citation()' on how to cite R or R packages in publications. 552s 552s Type 'demo()' for some demos, 'help()' for on-line help, or 552s 'help.start()' for an HTML browser interface to help. 552s Type 'q()' to quit R. 552s 552s > library(survey) 552s Loading required package: grid 552s Loading required package: Matrix 553s Loading required package: survival 553s 553s Attaching package: 'survey' 553s 553s The following object is masked from 'package:graphics': 553s 553s dotchart 553s 553s > data(election) 553s > 553s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 553s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 553s > svytotal(~Bush+Kerry+Nader, dpps) 553s total SE 553s Bush 64518472 2447629 553s Kerry 51202102 2450787 553s Nader 478530 102420 553s > svytotal(~Bush+Kerry+Nader, dppswr) 553s total SE 553s Bush 64518472 2671455 553s Kerry 51202102 2679433 553s Nader 478530 105303 553s > 553s > ##subsets 553s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 553s total SE 553s Bush 34944285 5399833 553s Kerry 25581714 4028434 553s Nader 478530 102420 553s > 553s > ##multistage: should agree with STRS analysis 553s > data(api) 553s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 553s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 553s > 553s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 553s [1] TRUE 553s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 553s [1] TRUE 553s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 553s [1] TRUE 553s > 553s > ## the new without-replacement methods 553s > data(election) 553s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 553s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 553s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 553s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 553s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 553s > ## Yates-Grundy type 553s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 553s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 553s > 553s > ## The with-replacement approximation 553s > svytotal(~Bush+Kerry+Nader, dpps_ht) 553s total SE 553s Bush 64518472 2604404 553s Kerry 51202102 2523712 553s Nader 478530 102326 553s > svytotal(~Bush+Kerry+Nader, dpps_yg) 553s total SE 553s Bush 64518472 2406526 553s Kerry 51202102 2408091 553s Nader 478530 101664 553s > svytotal(~Bush+Kerry+Nader, dpps_hr) 553s total SE 553s Bush 64518472 2624662 553s Kerry 51202102 2525222 553s Nader 478530 102793 553s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 553s total SE 553s Bush 64518472 2436738 553s Kerry 51202102 2439845 553s Nader 478530 102016 553s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 553s total SE 553s Bush 64518472 2472753 553s Kerry 51202102 2426842 553s Nader 478530 102595 553s > svytotal(~Bush+Kerry+Nader, dpps_br) 553s total SE 553s Bush 64518472 2447629 553s Kerry 51202102 2450787 553s Nader 478530 102420 553s > svytotal(~Bush+Kerry+Nader, dpps_ov) 553s total SE 553s Bush 64518472 2939608 553s Kerry 51202102 1964632 553s Nader 478530 104373 553s > 553s > ## subsets 553s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 553s total SE 553s Bush 34944285 5406348 553s Kerry 25581714 4047741 553s Nader 478530 102326 553s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 553s total SE 553s Bush 34944285 5377659 553s Kerry 25581714 4010908 553s Nader 478530 102016 553s > 553s > ## counts 553s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 553s I(Nader > 0) counts se 553s FALSE FALSE 19 0 553s TRUE TRUE 21 0 553s > 553s BEGIN TEST qrule-swiss.R 553s 553s R version 4.4.3 (2025-02-28) -- "Trophy Case" 553s Copyright (C) 2025 The R Foundation for Statistical Computing 553s Platform: aarch64-unknown-linux-gnu 553s 553s R is free software and comes with ABSOLUTELY NO WARRANTY. 553s You are welcome to redistribute it under certain conditions. 553s Type 'license()' or 'licence()' for distribution details. 553s 553s R is a collaborative project with many contributors. 553s Type 'contributors()' for more information and 553s 'citation()' on how to cite R or R packages in publications. 553s 553s Type 'demo()' for some demos, 'help()' for on-line help, or 553s 'help.start()' for an HTML browser interface to help. 553s Type 'q()' to quit R. 553s 553s > library(survey) 553s Loading required package: grid 553s Loading required package: Matrix 554s Loading required package: survival 554s > 554s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1) 554s 554s Attaching package: 'survey' 554s 554s The following object is masked from 'package:graphics': 554s 554s dotchart 554s 554s > 554s > design_no_strat <- svydesign(id = ~id, 554s + probs = ~probs, 554s + data = data_no_strat, 554s + fpc = ~fpc) 554s > 554s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99) 554s > 554s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE, 554s + interval.type = "mean", qrule = "hf1") 554s > 554s > stopifnot(all(diff(res$x[,"quantile"])>=0)) 554s > 554s > 554s > 554s BEGIN TEST quantile.R 555s 555s R version 4.4.3 (2025-02-28) -- "Trophy Case" 555s Copyright (C) 2025 The R Foundation for Statistical Computing 555s Platform: aarch64-unknown-linux-gnu 555s 555s R is free software and comes with ABSOLUTELY NO WARRANTY. 555s You are welcome to redistribute it under certain conditions. 555s Type 'license()' or 'licence()' for distribution details. 555s 555s R is a collaborative project with many contributors. 555s Type 'contributors()' for more information and 555s 'citation()' on how to cite R or R packages in publications. 555s 555s Type 'demo()' for some demos, 'help()' for on-line help, or 555s 'help.start()' for an HTML browser interface to help. 555s Type 'q()' to quit R. 555s 555s > library(survey) 555s Loading required package: grid 555s Loading required package: Matrix 556s Loading required package: survival 556s 556s Attaching package: 'survey' 556s 556s The following object is masked from 'package:graphics': 556s 556s dotchart 556s 556s > set.seed(42) 556s > 556s > df<-data.frame(x=exp(rnorm(1000))) 556s > df$y<-round(df$x,1) 556s > ddf<-svydesign(id=~1,data=df) 556s Warning message: 556s In svydesign.default(id = ~1, data = df) : 556s No weights or probabilities supplied, assuming equal probability 556s > rdf<-as.svrepdesign(ddf) 556s > 556s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 556s 0.01 0.1 0.5 0.9 0.99 556s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 556s > 556s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 557s x 557s q0.01 0.01554946 557s q0.1 0.01425828 557s q0.5 0.03428012 557s q0.9 0.16457488 557s q0.99 1.88672412 557s > 557s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 557s 0.01 0.1 0.5 0.9 0.99 557s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 557s > 557s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 557s x 557s q0.01 0.01556240 557s q0.1 0.01420086 557s q0.5 0.03430175 557s q0.9 0.16461019 557s q0.99 1.88818131 557s > 557s > 557s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 557s $quantiles 557s 0.01 0.1 0.5 0.9 0.99 557s y 0.02352941 0.2230769 0.9340909 3.55 9.4 557s 557s $CIs 557s , , y 557s 557s 0.01 0.1 0.5 0.9 0.99 557s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 557s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 557s 557s 557s > 557s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 557s Statistic: 557s y 557s q0.01 0.1 557s q0.1 0.3 557s q0.5 1.0 557s q0.9 3.6 557s q0.99 9.4 557s SE: 557s y 557s q0.01 0.02547977 557s q0.1 0.02547977 557s q0.5 0.02547977 557s q0.9 0.15287859 557s q0.99 1.88302540 557s > 557s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 557s $quantiles 557s 0.01 0.1 0.5 0.9 0.99 557s y 0.02352941 0.2230769 0.9340909 3.55 9.4 557s 557s $CIs 557s , , y 557s 557s 0.01 0.1 0.5 0.9 0.99 557s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 557s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 557s 557s 557s > 557s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 557s Statistic: 557s y 557s q0.01 0.1 557s q0.1 0.3 557s q0.5 1.0 557s q0.9 3.6 557s q0.99 9.4 557s SE: 557s y 557s q0.01 0.02551067 557s q0.1 0.02551067 557s q0.5 0.02551067 557s q0.9 0.15306404 557s q0.99 1.88450896 557s > 557s > 557s > 557s > df<-data.frame(x=exp(rnorm(20))) 557s > df$y<-round(df$x,1) 557s > ddf<-svydesign(id=~1,data=df) 557s Warning message: 557s In svydesign.default(id = ~1, data = df) : 557s No weights or probabilities supplied, assuming equal probability 557s > rdf<-as.svrepdesign(ddf) 557s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 557s 0.01 0.1 0.5 0.9 0.99 557s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 557s > 557s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 557s x 557s q0.01 0.00000000 557s q0.1 0.04598541 557s q0.5 0.25943731 557s q0.9 2.12343073 557s q0.99 1.91998924 557s > 557s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 557s 0.01 0.1 0.5 0.9 0.99 557s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 557s > 557s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 557s x 557s q0.01 0.00000000 557s q0.1 0.04732818 557s q0.5 0.24957966 557s q0.9 2.25211815 557s q0.99 2.04043154 557s > 557s > 557s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 557s $quantiles 557s 0.01 0.1 0.5 0.9 0.99 557s y 0.1 0.15 0.75 2.4 8.68 557s 557s $CIs 557s , , y 557s 557s 0.01 0.1 0.5 0.9 0.99 557s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 557s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 557s 557s 557s > 557s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 557s Statistic: 557s y 557s q0.01 0.10 557s q0.1 0.20 557s q0.5 0.80 557s q0.9 2.40 557s q0.99 8.68 557s SE: 557s y 557s q0.01 0.00000000 557s q0.1 0.02611112 557s q0.5 0.26542051 557s q0.9 2.10908603 557s q0.99 1.91777710 557s > 557s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 557s $quantiles 557s 0.01 0.1 0.5 0.9 0.99 557s y 0.1 0.15 0.75 2.4 8.68 557s 557s $CIs 557s , , y 557s 557s 0.01 0.1 0.5 0.9 0.99 557s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 557s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 557s 557s 557s > 557s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 557s Statistic: 557s y 557s q0.01 0.10 557s q0.1 0.20 557s q0.5 0.80 557s q0.9 2.40 557s q0.99 8.68 557s SE: 557s y 557s q0.01 0.00000000 557s q0.1 0.02551067 557s q0.5 0.25244616 557s q0.9 2.23558589 557s q0.99 2.03881114 557s > 557s BEGIN TEST quantiles-chile.R 557s 557s R version 4.4.3 (2025-02-28) -- "Trophy Case" 557s Copyright (C) 2025 The R Foundation for Statistical Computing 557s Platform: aarch64-unknown-linux-gnu 557s 557s R is free software and comes with ABSOLUTELY NO WARRANTY. 557s You are welcome to redistribute it under certain conditions. 557s Type 'license()' or 'licence()' for distribution details. 557s 557s R is a collaborative project with many contributors. 557s Type 'contributors()' for more information and 557s 'citation()' on how to cite R or R packages in publications. 557s 557s Type 'demo()' for some demos, 'help()' for on-line help, or 557s 'help.start()' for an HTML browser interface to help. 557s Type 'q()' to quit R. 557s 557s > library(survey) 557s Loading required package: grid 557s Loading required package: Matrix 558s Loading required package: survival 558s 558s Attaching package: 'survey' 558s 558s The following object is masked from 'package:graphics': 558s 558s dotchart 558s 558s > datos <- readRDS("datos_ejemplo.rds") 558s > 558s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 558s > set.seed(234262762) 558s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 558s > options(survey.lonely.psu="remove") 558s > 558s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 558s > 558s > suppressWarnings({ 558s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 558s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 558s + }) 558s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 558s [1] TRUE 558s > 558s > suppressWarnings({ 558s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 558s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 558s + }) 558s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 558s [1] TRUE 558s > 558s BEGIN TEST rakecheck.R 559s 559s R version 4.4.3 (2025-02-28) -- "Trophy Case" 559s Copyright (C) 2025 The R Foundation for Statistical Computing 559s Platform: aarch64-unknown-linux-gnu 559s 559s R is free software and comes with ABSOLUTELY NO WARRANTY. 559s You are welcome to redistribute it under certain conditions. 559s Type 'license()' or 'licence()' for distribution details. 559s 559s R is a collaborative project with many contributors. 559s Type 'contributors()' for more information and 559s 'citation()' on how to cite R or R packages in publications. 559s 559s Type 'demo()' for some demos, 'help()' for on-line help, or 559s 'help.start()' for an HTML browser interface to help. 559s Type 'q()' to quit R. 559s 559s > library(survey) 559s Loading required package: grid 559s Loading required package: Matrix 560s Loading required package: survival 560s 560s Attaching package: 'survey' 560s 560s The following object is masked from 'package:graphics': 560s 560s dotchart 560s 560s > 560s > data(api) 560s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 560s > rclus1 <- as.svrepdesign(dclus1) 560s > 560s > ## population marginal totals for each stratum 560s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 560s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 560s > 560s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 560s > 560s > svymean(~api00, rclus1r) 560s mean SE 560s api00 641.23 26.873 560s > svytotal(~enroll, rclus1r) 560s total SE 560s enroll 3647300 463511 560s > 560s > ff<-~stype+sch.wide 560s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 560s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 560s > 560s > svymean(~api00,rclus1g) 560s mean SE 560s api00 641.23 26.874 560s > svytotal(~enroll,rclus1g) 560s total SE 560s enroll 3647280 463582 560s > 560s > summary(weights(rclus1g)/weights(rclus1r)) 560s V1 V2 V3 V4 V5 V6 560s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 560s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 560s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 560s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 560s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 560s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 560s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 560s V7 V8 V9 V10 V11 560s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 560s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 560s Median :1 Median :1 Median :1 Median :1 Median :1 560s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 560s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 560s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 560s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 560s V12 V13 V14 V15 560s Min. :0.9997 Min. :1 Min. :1 Min. :1 560s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 560s Median :1.0001 Median :1 Median :1 Median :1 560s Mean :1.0000 Mean :1 Mean :1 Mean :1 560s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 560s Max. :1.0002 Max. :1 Max. :1 Max. :1 560s NA's :37 NA's :13 NA's :1 NA's :12 560s > 560s > 560s > ## Do it for a design without replicate weights 560s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 560s > 560s > svymean(~api00, dclus1r) 560s mean SE 560s api00 641.23 23.704 560s > svytotal(~enroll, dclus1r) 560s total SE 560s enroll 3647300 400603 560s > 560s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 560s > 560s > svymean(~api00,dclus1g) 560s mean SE 560s api00 641.23 23.704 560s > svytotal(~enroll,dclus1g) 560s total SE 560s enroll 3647280 400603 560s > 560s > summary(weights(dclus1g)/weights(dclus1r)) 560s Min. 1st Qu. Median Mean 3rd Qu. Max. 560s 1 1 1 1 1 1 560s > 560s > 560s > 560s > ## Example of raking with partial joint distributions 560s > pop.table <- xtabs(~stype+sch.wide,apipop) 560s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 560s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 560s + list(pop.table, pop.imp)) 560s > svymean(~api00, dclus1r2) 560s mean SE 560s api00 642.62 22.732 560s > 560s > ff1 <-~stype*sch.wide+comp.imp 560s > 560s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 560s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 560s > 560s > svymean(~api00, dclus1g2) 560s mean SE 560s api00 642.61 22.731 560s > 560s > summary(weights(dclus1r2)/weights(dclus1g2)) 560s Min. 1st Qu. Median Mean 3rd Qu. Max. 560s 0.999 1.000 1.000 1.000 1.000 1.002 560s > 560s BEGIN TEST raowuboot.R 560s 560s R version 4.4.3 (2025-02-28) -- "Trophy Case" 560s Copyright (C) 2025 The R Foundation for Statistical Computing 560s Platform: aarch64-unknown-linux-gnu 560s 560s R is free software and comes with ABSOLUTELY NO WARRANTY. 560s You are welcome to redistribute it under certain conditions. 560s Type 'license()' or 'licence()' for distribution details. 560s 560s R is a collaborative project with many contributors. 560s Type 'contributors()' for more information and 560s 'citation()' on how to cite R or R packages in publications. 560s 560s Type 'demo()' for some demos, 'help()' for on-line help, or 560s 'help.start()' for an HTML browser interface to help. 560s Type 'q()' to quit R. 560s 560s > ## regression test for bug reported by Richard Valliant 560s > library(survey) 560s Loading required package: grid 560s Loading required package: Matrix 561s Loading required package: survival 562s 562s Attaching package: 'survey' 562s 562s > s<-subbootweights(c(1,1),1:2, 50) 562s The following object is masked from 'package:graphics': 562s 562s dotchart 562s 562s > stopifnot(all(s$repweights$weights %in% c(0,2))) 562s > 562s BEGIN TEST regTermTest-missing.R 562s 562s R version 4.4.3 (2025-02-28) -- "Trophy Case" 562s Copyright (C) 2025 The R Foundation for Statistical Computing 562s Platform: aarch64-unknown-linux-gnu 562s 562s R is free software and comes with ABSOLUTELY NO WARRANTY. 562s You are welcome to redistribute it under certain conditions. 562s Type 'license()' or 'licence()' for distribution details. 562s 562s R is a collaborative project with many contributors. 562s Type 'contributors()' for more information and 562s 'citation()' on how to cite R or R packages in publications. 562s 562s Type 'demo()' for some demos, 'help()' for on-line help, or 562s 'help.start()' for an HTML browser interface to help. 562s Type 'q()' to quit R. 562s 562s > library(survey) 562s Loading required package: grid 562s Loading required package: Matrix 563s Loading required package: survival 563s > data(nhanes) 563s 563s Attaching package: 'survey' 563s 563s The following object is masked from 'package:graphics': 563s 563s dotchart 563s 563s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 563s > 563s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 563s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 563s > 563s > ta<-regTermTest(a, ~HI_CHOL) 563s > tb<-regTermTest(b, ~HI_CHOL) 563s > 563s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 563s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 563s > 563s BEGIN TEST regpredict.R 563s 563s R version 4.4.3 (2025-02-28) -- "Trophy Case" 563s Copyright (C) 2025 The R Foundation for Statistical Computing 563s Platform: aarch64-unknown-linux-gnu 563s 563s R is free software and comes with ABSOLUTELY NO WARRANTY. 563s You are welcome to redistribute it under certain conditions. 563s Type 'license()' or 'licence()' for distribution details. 563s 563s R is a collaborative project with many contributors. 563s Type 'contributors()' for more information and 563s 'citation()' on how to cite R or R packages in publications. 563s 563s Type 'demo()' for some demos, 'help()' for on-line help, or 563s 'help.start()' for an HTML browser interface to help. 563s Type 'q()' to quit R. 563s 563s > library(survey) 563s Loading required package: grid 563s Loading required package: Matrix 564s Loading required package: survival 564s > data(api) 564s 564s Attaching package: 'survey' 564s 564s The following object is masked from 'package:graphics': 564s 564s dotchart 564s 564s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 565s > 565s > 565s > ## regression estimator of total, three ways 565s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 565s > npop <- sum(!is.na(apipop$enroll)) 565s > 565s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 565s > a <- predict(api.reg, newdata=pop, total=npop) 565s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 565s > 565s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 565s [1] TRUE 565s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 565s [1] TRUE 565s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 565s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 565s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 565s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 565s + } 565s > 565s > ## classical ratio estimator, four ways. 565s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 565s + family=quasi(link="identity", var="mu")) 565s > 565s > a <- predict(api.reg2, newdata=pop, total=npop) 565s > b <- svytotal(~api.stu, 565s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 565s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 565s > 565s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 565s [1] TRUE 565s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 565s [1] TRUE 565s > all.equal(as.vector(coef(a)),as.vector(e$total)) 565s [1] TRUE 565s > all.equal(as.vector(SE(a)), as.vector(e$se)) 565s [1] TRUE 565s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 565s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 565s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 565s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 565s + } 565s > 565s BEGIN TEST rss_scores.R 565s 565s R version 4.4.3 (2025-02-28) -- "Trophy Case" 565s Copyright (C) 2025 The R Foundation for Statistical Computing 565s Platform: aarch64-unknown-linux-gnu 565s 565s R is free software and comes with ABSOLUTELY NO WARRANTY. 565s You are welcome to redistribute it under certain conditions. 565s Type 'license()' or 'licence()' for distribution details. 565s 565s R is a collaborative project with many contributors. 565s Type 'contributors()' for more information and 565s 'citation()' on how to cite R or R packages in publications. 565s 565s Type 'demo()' for some demos, 'help()' for on-line help, or 565s 'help.start()' for an HTML browser interface to help. 565s Type 'q()' to quit R. 565s 565s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 565s > library(survey) 565s Loading required package: grid 565s Loading required package: Matrix 566s Loading required package: survival 566s 566s Attaching package: 'survey' 566s 566s The following object is masked from 'package:graphics': 566s 566s dotchart 566s 566s > data(myco) 566s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 566s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 566s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 566s > 566s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 566s > 566s > s<-svyscoretest(m_full, ~Scar) 566s > stopifnot(abs(s[1]-10.73)<0.05) 566s > 566s > t<-svyscoretest(m_full,~Scar,method="individual") 566s > stopifnot(abs(coef(t)- -32.61)<0.1) 566s > stopifnot(abs(vcov(t)-99.1)<0.1) 566s > 566s > 566s BEGIN TEST scoping.R 566s 566s R version 4.4.3 (2025-02-28) -- "Trophy Case" 566s Copyright (C) 2025 The R Foundation for Statistical Computing 566s Platform: aarch64-unknown-linux-gnu 566s 566s R is free software and comes with ABSOLUTELY NO WARRANTY. 566s You are welcome to redistribute it under certain conditions. 566s Type 'license()' or 'licence()' for distribution details. 566s 566s R is a collaborative project with many contributors. 566s Type 'contributors()' for more information and 566s 'citation()' on how to cite R or R packages in publications. 566s 566s Type 'demo()' for some demos, 'help()' for on-line help, or 566s 'help.start()' for an HTML browser interface to help. 566s Type 'q()' to quit R. 566s 566s > 566s > ## regression test for testing regression 566s > 566s > library(survey) 566s Loading required package: grid 566s Loading required package: Matrix 567s Loading required package: survival 567s 567s Attaching package: 'survey' 567s 567s The following object is masked from 'package:graphics': 567s 567s dotchart 567s 567s > data(api) 567s > 567s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 567s > 567s > 567s > f<-function(){ 567s + form<-acs.46~stype 567s + svyglm(formula=form, design = dstrat) 567s + } 567s > 567s > g<-function(form){ 567s + svyglm(formula=form, design = dstrat) 567s + } 567s > f() 567s Stratified Independent Sampling design 567s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 567s fpc = ~fpc) 567s 567s Call: svyglm(formula = form, design = dstrat) 567s 567s Coefficients: 567s (Intercept) stypeH stypeM 567s 28.7449 0.7551 0.4022 567s 567s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 567s (66 observations deleted due to missingness) 567s Null Deviance: 1838 567s Residual Deviance: 1835 AIC: 719.8 567s > g(acs.46~stype) 567s Stratified Independent Sampling design 567s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 567s fpc = ~fpc) 567s 567s Call: svyglm(formula = form, design = dstrat) 567s 567s Coefficients: 567s (Intercept) stypeH stypeM 567s 28.7449 0.7551 0.4022 567s 567s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 567s (66 observations deleted due to missingness) 567s Null Deviance: 1838 567s Residual Deviance: 1835 AIC: 719.8 567s > 567s > f<-function(){ 567s + form<-Surv(acs.46)~stype 567s + svycoxph(formula=form, design = dstrat) 567s + } 567s > 567s > g<-function(form){ 567s + svycoxph(formula=form, design = dstrat) 567s + } 567s > 567s > f() 567s Call: 567s svycoxph(formula = form, design = dstrat) 567s 567s coef exp(coef) se(coef) robust se z p 567s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 567s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 567s 567s Likelihood ratio test= on 2 df, p= 567s n= 134, number of events= 134 567s (66 observations deleted due to missingness) 567s > g(Surv(acs.46)~stype) 567s Call: 567s svycoxph(formula = form, design = dstrat) 567s 567s coef exp(coef) se(coef) robust se z p 567s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 567s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 567s 567s Likelihood ratio test= on 2 df, p= 567s n= 134, number of events= 134 567s (66 observations deleted due to missingness) 567s > 567s > ## check coxph for a single predictor 567s > svycoxph(Surv(acs.46)~api00,design=dstrat) 567s Call: 567s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 567s 567s coef exp(coef) se(coef) robust se z p 567s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 567s 567s Likelihood ratio test= on 1 df, p= 567s n= 134, number of events= 134 567s (66 observations deleted due to missingness) 567s > 567s BEGIN TEST survcurve.R 567s 567s R version 4.4.3 (2025-02-28) -- "Trophy Case" 567s Copyright (C) 2025 The R Foundation for Statistical Computing 567s Platform: aarch64-unknown-linux-gnu 567s 567s R is free software and comes with ABSOLUTELY NO WARRANTY. 567s You are welcome to redistribute it under certain conditions. 567s Type 'license()' or 'licence()' for distribution details. 567s 567s R is a collaborative project with many contributors. 567s Type 'contributors()' for more information and 567s 'citation()' on how to cite R or R packages in publications. 567s 567s Type 'demo()' for some demos, 'help()' for on-line help, or 567s 'help.start()' for an HTML browser interface to help. 567s Type 'q()' to quit R. 567s 568s > library(survey) 568s Loading required package: grid 568s Loading required package: Matrix 568s Loading required package: survival 569s 569s Attaching package: 'survey' 569s 569s The following object is masked from 'package:graphics': 569s 569s dotchart 569s 569s > library(survival) 569s > 569s > pbc2<-rbind(pbc,pbc) 569s > pbc2$id<-rep(1:418,2) 569s > 569s > dpbc1<-svydesign(id=~1, data=pbc) 569s Warning message: 569s In svydesign.default(id = ~1, data = pbc) : 569s No weights or probabilities supplied, assuming equal probability 569s > dpbc2<-svydesign(id=~id, data=pbc2) 569s Warning message: 569s > 569s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 569s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 569s In svydesign.default(id = ~id, data = pbc2) : 569s No weights or probabilities supplied, assuming equal probability 569s > 569s > (c1<-confint(s1,(1:5)*365)) 569s 0.025 0.975 569s 365 0.6446215 0.8594153 569s 730 0.5410938 0.7766848 569s 1095 0.2683127 0.5103356 569s 1460 0.1444731 0.3722001 569s 1825 0.1009672 0.3204713 569s > (c2<-confint(s2,(1:5)*365)) 569s 0.025 0.975 569s 365 0.6446215 0.8594153 569s 730 0.5410938 0.7766848 569s 1095 0.2683127 0.5103356 569s 1460 0.1444731 0.3722001 569s 1825 0.1009672 0.3204713 569s > all.equal(c1, c2) 569s [1] TRUE 569s > 569s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 569s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 569s > 569s > d<-data.frame(bili=c(5,10)) 569s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 569s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 571s > 571s > (pc1<-confint(p1[[1]],(1:5)*365)) 571s 0.025 0.975 571s 365 0.8410027 0.9266263 571s 730 0.7371114 0.8548312 571s 1095 0.5517779 0.7018583 571s 1460 0.4335073 0.5992819 571s 1825 0.3260899 0.5046241 571s > (pc2<-confint(p2[[1]],(1:5)*365)) 571s 0.025 0.975 571s 365 0.8409490 0.9267054 571s 730 0.7370152 0.8549432 571s 1095 0.5515848 0.7019513 571s 1460 0.4332252 0.5992968 571s 1825 0.3257172 0.5045795 571s > all.equal(pc1, pc2) 571s [1] "Mean relative difference: 0.0002070722" 571s > 571s > (q1<-quantile(p1[[2]])) 571s 0.75 0.5 0.25 571s 489 930 1492 571s > (q2<-quantile(p2[[2]])) 571s 0.75 0.5 0.25 571s 489 930 1492 571s > all.equal(q1,q2) 571s [1] TRUE 571s > 571s BEGIN TEST svyby-strings.R 571s 571s R version 4.4.3 (2025-02-28) -- "Trophy Case" 571s Copyright (C) 2025 The R Foundation for Statistical Computing 571s Platform: aarch64-unknown-linux-gnu 571s 571s R is free software and comes with ABSOLUTELY NO WARRANTY. 571s You are welcome to redistribute it under certain conditions. 571s Type 'license()' or 'licence()' for distribution details. 571s 571s R is a collaborative project with many contributors. 571s Type 'contributors()' for more information and 571s 'citation()' on how to cite R or R packages in publications. 571s 571s Type 'demo()' for some demos, 'help()' for on-line help, or 571s 'help.start()' for an HTML browser interface to help. 571s Type 'q()' to quit R. 571s 571s > 571s > ## check that stringsAsFactors fixes the string levels problem 571s > data(api, package = "survey") 571s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 573s > est0 <- 573s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 573s > 573s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 573s > 573s BEGIN TEST svyby_bug.R 573s 573s R version 4.4.3 (2025-02-28) -- "Trophy Case" 573s Copyright (C) 2025 The R Foundation for Statistical Computing 573s Platform: aarch64-unknown-linux-gnu 573s 573s R is free software and comes with ABSOLUTELY NO WARRANTY. 573s You are welcome to redistribute it under certain conditions. 573s Type 'license()' or 'licence()' for distribution details. 573s 573s R is a collaborative project with many contributors. 573s Type 'contributors()' for more information and 573s 'citation()' on how to cite R or R packages in publications. 573s 573s Type 'demo()' for some demos, 'help()' for on-line help, or 573s 'help.start()' for an HTML browser interface to help. 573s Type 'q()' to quit R. 573s 573s > library(survey) 573s Loading required package: grid 573s Loading required package: Matrix 574s Loading required package: survival 574s > options(warn=2) 574s > 574s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 574s > data(api) 574s 574s Attaching package: 'survey' 574s 574s The following object is masked from 'package:graphics': 574s 574s dotchart 574s 574s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 574s > svyby(~api99, ~stype, dclus1, svymean ) 574s stype api99 se 574s E E 607.7917 22.81660 574s H H 595.7143 41.76400 574s M M 608.6000 32.56064 574s > 574s > set.seed(123) 574s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 574s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 574s > 574s > # subsetting w/ na.rm = FALSE... 574s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 574s mean SE 574s api99 NA NA 574s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 574s mean SE 574s api99 595.71 41.764 574s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 574s mean SE 574s api99 NA NA 574s > 574s > # ... looks like this: 574s > svyby(~api99, ~stype, dclus1.na , svymean ) 574s stype api99 se 574s E E NA NA 574s H H 595.7143 41.764 574s M M NA NA 574s > 574s > # subsetting w/ na.rm = TRUE... 574s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 574s mean SE 574s api99 606.53 22.901 574s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 574s mean SE 574s api99 595.71 41.764 574s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 574s mean SE 574s api99 613.39 33.224 574s > 574s > # ... looks like this 574s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 574s stype api99 se 574s E E 606.5319 22.90084 574s H H 595.7143 41.76400 574s M M 613.3913 33.22358 574s > 574s > # Without missing values, this works: 574s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 574s stype api99 se 574s E E 607.7917 22.81660 574s H H 595.7143 41.76400 574s M M 608.6000 32.56064 574s > 574s > # ... but this breaks! 574s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 574s stype api99 se 574s E E 606.5319 22.90084 574s H H 595.7143 41.76400 574s M M 613.3913 33.22358 574s > 574s > # ... and i don't think this is the expected behavior 574s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 574s stype api99 se 574s E E NA NA 574s H H 595.7143 41.764 574s M M NA NA 574s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 574s stype api99 se 574s E E 606.5319 22.90084 574s H H 595.7143 41.76400 574s M M 613.3913 33.22358 574s > 574s > 574s > ## Now some more as tests 574s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 574s stype api99 se 574s E E 2894629.0 792809.8 574s H H 282283.9 101492.9 574s M M 477513.4 107555.5 574s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 574s stype api99/api00 se.api99/api00 574s E E 0.9367750 0.006365702 574s H H 0.9630485 0.010520785 574s M M 0.9682246 0.009390982 574s > 574s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 574s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 574s stype (Intercept) se.(Intercept) 574s E E 606.5319 22.90084 574s H H 595.7143 41.76400 574s M M 613.3913 33.22358 574s > 574s BEGIN TEST svyby_se.R 574s 574s R version 4.4.3 (2025-02-28) -- "Trophy Case" 574s Copyright (C) 2025 The R Foundation for Statistical Computing 574s Platform: aarch64-unknown-linux-gnu 574s 574s R is free software and comes with ABSOLUTELY NO WARRANTY. 574s You are welcome to redistribute it under certain conditions. 574s Type 'license()' or 'licence()' for distribution details. 574s 574s R is a collaborative project with many contributors. 574s Type 'contributors()' for more information and 574s 'citation()' on how to cite R or R packages in publications. 574s 574s Type 'demo()' for some demos, 'help()' for on-line help, or 574s 'help.start()' for an HTML browser interface to help. 574s Type 'q()' to quit R. 574s 574s > library(survey) 574s Loading required package: grid 574s Loading required package: Matrix 575s Loading required package: survival 576s 576s Attaching package: 'survey' 576s 576s > data(api) 576s The following object is masked from 'package:graphics': 576s 576s dotchart 576s 576s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 576s > 576s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 576s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 576s > 576s > 576s > stopifnot(all.equal(SE(a),SE(b))) 576s > 576s BEGIN TEST svycontrast.R 576s 576s R version 4.4.3 (2025-02-28) -- "Trophy Case" 576s Copyright (C) 2025 The R Foundation for Statistical Computing 576s Platform: aarch64-unknown-linux-gnu 576s 576s R is free software and comes with ABSOLUTELY NO WARRANTY. 576s You are welcome to redistribute it under certain conditions. 576s Type 'license()' or 'licence()' for distribution details. 576s 576s R is a collaborative project with many contributors. 576s Type 'contributors()' for more information and 576s 'citation()' on how to cite R or R packages in publications. 576s 576s Type 'demo()' for some demos, 'help()' for on-line help, or 576s 'help.start()' for an HTML browser interface to help. 576s Type 'q()' to quit R. 576s 576s > library(survey) 576s Loading required package: grid 576s Loading required package: Matrix 577s Loading required package: survival 577s 577s Attaching package: 'survey' 577s 577s The following object is masked from 'package:graphics': 577s 577s dotchart 577s 577s > data(api) 577s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 577s > rclus2<-as.svrepdesign(dclus2) 577s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 577s > svycontrast(model, c(ell=1,meals=0)) 577s contrast SE 577s contrast -2.0592 1.6177 577s > a<-svycontrast(model, c(0,1,0,0)) 577s > 577s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 577s > svycontrast(model2, c(ell=1,meals=0)) 577s contrast SE 577s contrast -2.0592 1.6177 577s > a2<-svycontrast(model2, c(0,1,0,0)) 577s > stopifnot(!is.null(a2$replicates)) 577s > 577s BEGIN TEST svyivreg-var.R 577s 577s R version 4.4.3 (2025-02-28) -- "Trophy Case" 577s Copyright (C) 2025 The R Foundation for Statistical Computing 577s Platform: aarch64-unknown-linux-gnu 577s 577s R is free software and comes with ABSOLUTELY NO WARRANTY. 577s You are welcome to redistribute it under certain conditions. 577s Type 'license()' or 'licence()' for distribution details. 577s 577s R is a collaborative project with many contributors. 577s Type 'contributors()' for more information and 577s 'citation()' on how to cite R or R packages in publications. 577s 577s Type 'demo()' for some demos, 'help()' for on-line help, or 577s 'help.start()' for an HTML browser interface to help. 577s Type 'q()' to quit R. 577s 577s > 577s > library(survey) 577s Loading required package: grid 577s Loading required package: Matrix 578s Loading required package: survival 578s 578s Attaching package: 'survey' 578s 578s The following object is masked from 'package:graphics': 578s 578s dotchart 578s 578s > data(api) 579s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 579s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 579s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 579s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 579s > 579s BEGIN TEST svyivreg.R 579s 579s R version 4.4.3 (2025-02-28) -- "Trophy Case" 579s Copyright (C) 2025 The R Foundation for Statistical Computing 579s Platform: aarch64-unknown-linux-gnu 579s 579s R is free software and comes with ABSOLUTELY NO WARRANTY. 579s You are welcome to redistribute it under certain conditions. 579s Type 'license()' or 'licence()' for distribution details. 579s 579s R is a collaborative project with many contributors. 579s Type 'contributors()' for more information and 579s 'citation()' on how to cite R or R packages in publications. 579s 579s Type 'demo()' for some demos, 'help()' for on-line help, or 579s 'help.start()' for an HTML browser interface to help. 579s Type 'q()' to quit R. 579s 579s > library(survey) 579s Loading required package: grid 579s Loading required package: Matrix 580s Loading required package: survival 580s > library(AER) 580s 580s Attaching package: 'survey' 580s 580s The following object is masked from 'package:graphics': 580s 580s dotchart 580s 580s Loading required package: car 580s Loading required package: carData 580s Loading required package: lmtest 580s Loading required package: zoo 580s 580s Attaching package: 'zoo' 580s 580s The following objects are masked from 'package:base': 580s 580s as.Date, as.Date.numeric 580s 580s Loading required package: sandwich 580s > 580s > load("cigsw.rda") 580s > 580s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 580s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 580s > 580s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 580s [1] TRUE 580s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 580s [1] TRUE 580s > 580s BEGIN TEST svyolr-rake-subset.R 580s 580s R version 4.4.3 (2025-02-28) -- "Trophy Case" 580s Copyright (C) 2025 The R Foundation for Statistical Computing 580s Platform: aarch64-unknown-linux-gnu 580s 580s R is free software and comes with ABSOLUTELY NO WARRANTY. 580s You are welcome to redistribute it under certain conditions. 580s Type 'license()' or 'licence()' for distribution details. 580s 580s R is a collaborative project with many contributors. 580s Type 'contributors()' for more information and 580s 'citation()' on how to cite R or R packages in publications. 580s 580s Type 'demo()' for some demos, 'help()' for on-line help, or 580s 'help.start()' for an HTML browser interface to help. 580s Type 'q()' to quit R. 580s 580s > library(survey) 580s Loading required package: grid 580s Loading required package: Matrix 581s Loading required package: survival 582s 582s Attaching package: 'survey' 582s 582s The following object is masked from 'package:graphics': 582s 582s dotchart 582s 582s > data(api) 582s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 582s > 582s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 582s > 582s > ## population marginal totals for each stratum 582s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 582s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 582s > 582s > 582s > ## rake with the population totals 582s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 582s > 582s > # works 582s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 582s > 582s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 582s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 582s > 582s > # fails in 4.1 (should work because NA values are subsetted out) 582s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 582s > 582s BEGIN TEST svyolr.R 582s 582s R version 4.4.3 (2025-02-28) -- "Trophy Case" 582s Copyright (C) 2025 The R Foundation for Statistical Computing 582s Platform: aarch64-unknown-linux-gnu 582s 582s R is free software and comes with ABSOLUTELY NO WARRANTY. 582s You are welcome to redistribute it under certain conditions. 582s Type 'license()' or 'licence()' for distribution details. 582s 582s R is a collaborative project with many contributors. 582s Type 'contributors()' for more information and 582s 'citation()' on how to cite R or R packages in publications. 582s 582s Type 'demo()' for some demos, 'help()' for on-line help, or 582s 'help.start()' for an HTML browser interface to help. 582s Type 'q()' to quit R. 582s 582s > library(survey) 582s Loading required package: grid 582s Loading required package: Matrix 583s Loading required package: survival 583s 583s Attaching package: 'survey' 583s 583s The following object is masked from 'package:graphics': 583s 583s dotchart 583s 583s > 583s > ################################################################################ 583s > # Example from svyolr: runs OK 583s > data(api) 583s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 583s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 583s > 583s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 583s > m 583s Call: 583s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 583s 583s Coefficients: 583s avg.ed mobility stypeH stypeM 583s -2.6999217 0.0325042 -1.7574715 -0.6191463 583s 583s Intercepts: 583s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 583s -8.857919 -6.586464 -4.924938 583s > 583s > ## Use regTermTest for testing multiple parameters 583s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 583s > ################################################################################ 583s > 583s > ################################################################################ 583s > # If we wrap everything into a function: error b/c it looks for design variable 583s > # dclus1 in .GlobalEnv 583s > 583s > foo <- function(x){ 583s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 583s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 583s + 583s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 583s + ## Use regTermTest for testing multiple parameters 583s + regTermTest(m, ~avg.ed+stype, method="LRT") 583s + } 583s > 583s > # OK 583s > foo(apiclus1) 583s Working (Rao-Scott+F) LRT for avg.ed stype 583s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 583s Working 2logLR = 0.6580304 p= 0.73257 583s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 583s > 583s > # Clean-up everything but apiclus1 and foo 583s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 583s > 583s > # Error 583s > test2<-foo(apiclus1) 583s > ################################################################################ 583s > all.equal(test,test2) 583s [1] TRUE 583s > 583s > 583s BEGIN TEST toy_example_for_postStratify.R 583s 583s R version 4.4.3 (2025-02-28) -- "Trophy Case" 583s Copyright (C) 2025 The R Foundation for Statistical Computing 583s Platform: aarch64-unknown-linux-gnu 583s 583s R is free software and comes with ABSOLUTELY NO WARRANTY. 583s You are welcome to redistribute it under certain conditions. 583s Type 'license()' or 'licence()' for distribution details. 583s 583s R is a collaborative project with many contributors. 583s Type 'contributors()' for more information and 583s 'citation()' on how to cite R or R packages in publications. 583s 583s Type 'demo()' for some demos, 'help()' for on-line help, or 583s 'help.start()' for an HTML browser interface to help. 583s Type 'q()' to quit R. 583s 583s > library(survey) 583s Loading required package: grid 583s Loading required package: Matrix 584s Loading required package: survival 585s 585s Attaching package: 'survey' 585s 585s The following object is masked from 'package:graphics': 585s 585s dotchart 585s 585s > 585s > # Dummy data for testing nonresponse adjustments 585s > toy <- data.frame(id = 1:10, 585s + dummy = 1, 585s + class = c(rep("A", 5), rep("B", 5)), 585s + responded = c(rep(TRUE, 8), FALSE, FALSE), 585s + weight = rep(100, 10)) 585s > 585s > # With jackknife replicate weights 585s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 585s > diag(toy_repweights) <- rep(0, 10) 585s > 585s > # Scramble up which person is in which jackknife group 585s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 585s > 585s > toy_design <- svrepdesign(variables = toy[, 1:4], 585s + weights = toy$weight, 585s + repweights = toy_repweights, 585s + type = "JK1", 585s + scale = 0.9) 585s > 585s > # Get the sum of the weights for the full sample 585s > poptotals <- as.data.frame(svyby(formula = ~dummy, 585s + by = ~class, 585s + design = toy_design, 585s + FUN = survey::svytotal)) 585s > 585s > poptotals$Freq <- poptotals$dummy 585s > poptotals$dummy <- NULL 585s > poptotals$se <- NULL 585s > 585s > # Adjust the weights of the responding sample to match to the full sample 585s > adjusted <- postStratify(design = subset(toy_design, responded), 585s + strata = ~class, 585s + population = poptotals) 585s > 585s > # This works for the weights... 585s > svyby(formula = ~dummy, 585s + by = ~class, 585s + design = adjusted, 585s + FUN = survey::svytotal) 585s class dummy se 585s A A 500 0 585s B B 500 0 585s > 585s > # ...and some, but not all, the replicate weights 585s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 585s > 585s > 585s > 585s BEGIN TEST twophase.R 585s 585s R version 4.4.3 (2025-02-28) -- "Trophy Case" 585s Copyright (C) 2025 The R Foundation for Statistical Computing 585s Platform: aarch64-unknown-linux-gnu 585s 585s R is free software and comes with ABSOLUTELY NO WARRANTY. 585s You are welcome to redistribute it under certain conditions. 585s Type 'license()' or 'licence()' for distribution details. 585s 585s R is a collaborative project with many contributors. 585s Type 'contributors()' for more information and 585s 'citation()' on how to cite R or R packages in publications. 585s 585s Type 'demo()' for some demos, 'help()' for on-line help, or 585s 'help.start()' for an HTML browser interface to help. 585s Type 'q()' to quit R. 585s 585s > library(survey) 585s Loading required package: grid 585s Loading required package: Matrix 586s Loading required package: survival 586s 586s Attaching package: 'survey' 586s 586s The following object is masked from 'package:graphics': 586s 586s dotchart 586s 586s > 586s > ## two-phase simple random sampling. 586s > data(pbc, package="survival") 586s > pbc$id<-1:nrow(pbc) 586s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 586s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 586s Two-phase sparse-matrix design: 586s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 586s subset = subset, data = data, pps = pps) 586s Phase 1: 586s Independent Sampling design (with replacement) 586s svydesign(ids = ~id) 586s Phase 2: 586s Independent Sampling design 586s svydesign(ids = ~id, fpc = `*phase1*`) 586s > m<-svymean(~bili, d2pbc) 586s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 586s [1] TRUE 586s > all.equal(as.vector(SE(m)), 586s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 586s + tolerance=0.002) 586s [1] TRUE 586s > 586s > ## two-stage sampling as two-phase 586s > data(mu284) 586s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 586s > mu284.1<-mu284[ii,] 586s > mu284.1$id<-1:nrow(mu284.1) 586s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 586s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 586s > ## first phase cluster sample, second phase stratified within cluster 586s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 586s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 586s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 586s NULL), data = mu284.1, subset = ~sub, method = "approx") 586s Phase 1: 586s 1 - level Cluster Sampling design 586s With (5) clusters. 586s svydesign(ids = ~id1, fpc = ~n1) 586s Phase 2: 586s Stratified Independent Sampling design 586s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 586s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 586s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 586s Two-phase sparse-matrix design: 586s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 586s subset = subset, data = data, pps = pps) 586s Phase 1: 586s 1 - level Cluster Sampling design 586s With (5) clusters. 586s svydesign(ids = ~id1, fpc = ~n1) 586s Phase 2: 586s Stratified Independent Sampling design 586s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 586s > summary(d2mu284) 586s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 586s NULL), data = mu284.1, subset = ~sub, method = "approx") 586s Phase 1: 586s 1 - level Cluster Sampling design 586s With (5) clusters. 586s svydesign(ids = ~id1, fpc = ~n1) 586s Probabilities: 586s Min. 1st Qu. Median Mean 3rd Qu. Max. 586s 0.1 0.1 0.1 0.1 0.1 0.1 586s Population size (PSUs): 50 586s Phase 2: 586s Stratified Independent Sampling design 586s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 586s Probabilities: 586s Min. 1st Qu. Median Mean 3rd Qu. Max. 586s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 586s Stratum Sizes: 586s 19 31 45 47 50 586s obs 3 3 3 3 3 586s design.PSU 3 3 3 3 3 586s actual.PSU 3 3 3 3 3 586s Population stratum sizes (PSUs): 586s 19 31 45 47 50 586s 5 7 8 5 9 586s Data variables: 586s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 586s > t1<-svytotal(~y1, dmu284) 586s > t2<-svytotal(~y1, d2mu284) 586s > t22<-svytotal(~y1,d22mu284) 586s > m1<-svymean(~y1, dmu284) 586s > m2<-svymean(~y1, d2mu284) 586s > m22<-svymean(~y1, d22mu284) 586s > all.equal(coef(t1),coef(t2)) 586s [1] TRUE 586s > all.equal(coef(t1),coef(t22)) 586s [1] TRUE 586s > all.equal(coef(m1),coef(m2)) 586s [1] TRUE 586s > all.equal(coef(m1),coef(m22)) 586s [1] TRUE 586s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 586s [1] TRUE 586s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 586s [1] TRUE 586s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 586s [1] TRUE 586s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 586s [1] TRUE 586s > 586s > ## case-cohort design 586s > ##this example requires R 2.3.1 or later for cch and data. 586s > library("survival") 586s > data(nwtco, package="survival") 586s > ## unstratified, equivalent to Lin & Ying (1993) 586s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 586s + subset=~I(in.subcohort | rel), data=nwtco)) 587s Two-phase sparse-matrix design: 587s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 587s subset = subset, data = data, pps = pps) 587s Phase 1: 587s Independent Sampling design (with replacement) 587s svydesign(ids = ~seqno) 587s Phase 2: 587s Stratified Independent Sampling design 587s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 587s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 587s + design=dcchs) 587s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 587s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 587s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 587s + design=dcchs) 587s > all.equal(coef(cch1),coef(cch1.2)) 587s [1] TRUE 587s > all.equal(SE(cch1),SE(cch1.2)) 587s [1] TRUE 587s > ## Using survival::cch 587s > subcoh <- nwtco$in.subcohort 587s > selccoh <- with(nwtco, rel==1|subcoh==1) 587s > ccoh.data <- nwtco[selccoh,] 587s > ccoh.data$subcohort <- subcoh[selccoh] 587s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 587s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 587s + cohort.size=4028, method="LinYing", robust=TRUE) 587s > 587s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 587s [1] TRUE 587s > ## cch has smaller variances by a factor of 1.0005 because 587s > ## there is a (n/(n-1)) in the survey phase1 varianace 587s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 587s [1] TRUE 587s > 587s > 587s > ## bug report from Takahiro Tsuchiya for version 3.4 587s > ## We used to not match Sarndal exactly, because our old phase-one 587s > ## estimator had a small bias for finite populations 587s > rei<-read.table(tmp<-textConnection( 587s + " id N n.a h n.ah n.h sub y 587s + 1 1 300 20 1 12 5 TRUE 1 587s + 2 2 300 20 1 12 5 TRUE 2 587s + 3 3 300 20 1 12 5 TRUE 3 587s + 4 4 300 20 1 12 5 TRUE 4 587s + 5 5 300 20 1 12 5 TRUE 5 587s + 6 6 300 20 1 12 5 FALSE NA 587s + 7 7 300 20 1 12 5 FALSE NA 587s + 8 8 300 20 1 12 5 FALSE NA 587s + 9 9 300 20 1 12 5 FALSE NA 587s + 10 10 300 20 1 12 5 FALSE NA 587s + 11 11 300 20 1 12 5 FALSE NA 587s + 12 12 300 20 1 12 5 FALSE NA 587s + 13 13 300 20 2 8 3 TRUE 6 587s + 14 14 300 20 2 8 3 TRUE 7 587s + 15 15 300 20 2 8 3 TRUE 8 587s + 16 16 300 20 2 8 3 FALSE NA 587s + 17 17 300 20 2 8 3 FALSE NA 587s + 18 18 300 20 2 8 3 FALSE NA 587s + 19 19 300 20 2 8 3 FALSE NA 587s + 20 20 300 20 2 8 3 FALSE NA 587s + "), header=TRUE) 587s > close(tmp) 587s > 587s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 587s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 587s > tot<- svytotal(~y, des.rei) 587s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 587s + fpc=list(~N,NULL), subset=~sub, data=rei) 587s > tot2<- svytotal(~y, des.rei2) 587s > 587s > ## based on Sarndal et al (9.4.14) 587s > rei$w.ah <- rei$n.ah / rei$n.a 587s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 587s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 587s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 587s > 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)) 587s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 587s > 587s > a.rei$f.h<-with(a.rei, n.h/n.ah) 587s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 587s > 587s > a.rei$f<-with(a.rei, n.a/N) 587s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 587s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 587s > 587s > V 587s [1] 36522.63 587s > Vphase1 587s [1] 24072.63 587s > Vphase2 587s [1] 12450 587s > vcov(tot) 587s y 587s y 35911.05 587s attr(,"phases") 587s attr(,"phases")$phase1 587s [,1] 587s [1,] 23461.05 587s 587s attr(,"phases")$phase2 587s y 587s y 12450 587s 587s > vcov(tot2) 587s [,1] 587s [1,] 36522.63 587s attr(,"phases") 587s attr(,"phases")$phase1 587s [,1] 587s [1,] 24072.63 587s 587s attr(,"phases")$phase2 587s [,1] 587s [1,] 12450 587s 587s > ## phase 2 identical 587s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 587s [1] TRUE 587s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 587s [1] TRUE 587s > ## phase 1 differs by 2.6% for old twophase estimator 587s > Vphase1/attr(vcov(tot),"phases")$phase1 587s [,1] 587s [1,] 1.026068 587s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 587s [1] TRUE 587s > 587s > 587s autopkgtest [16:08:57]: test run-unit-test: -----------------------] 588s autopkgtest [16:08:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 588s run-unit-test PASS 588s autopkgtest [16:08:58]: test pkg-r-autopkgtest: preparing testbed 727s autopkgtest [16:11:17]: testbed dpkg architecture: arm64 727s autopkgtest [16:11:17]: testbed apt version: 2.9.33 728s autopkgtest [16:11:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 728s autopkgtest [16:11:18]: testbed release detected to be: plucky 729s autopkgtest [16:11:19]: updating testbed package index (apt update) 730s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 730s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 730s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 730s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 730s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 731s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 731s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 731s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 731s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 731s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 731s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 732s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 732s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 732s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 733s Fetched 1078 kB in 3s (375 kB/s) 734s Reading package lists... 735s + lsb_release --codename --short 735s + RELEASE=plucky 735s + cat 735s + [ plucky != trusty ] 735s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 735s Reading package lists... 735s Building dependency tree... 735s Reading state information... 736s Calculating upgrade... 736s Calculating upgrade... 737s The following packages will be upgraded: 737s pinentry-curses python3-jinja2 strace 737s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 737s Need to get 647 kB of archives. 737s After this operation, 11.3 kB of additional disk space will be used. 737s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 738s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 738s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 739s Fetched 647 kB in 1s (572 kB/s) 739s (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 ... 117701 files and directories currently installed.) 739s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 739s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 739s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 739s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 739s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 739s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 739s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 739s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 740s Setting up strace (6.13+ds-1ubuntu1) ... 740s Processing triggers for man-db (2.13.0-1) ... 740s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 740s + /usr/lib/apt/apt-helper analyze-pattern ?true 740s + uname -r 740s + sed s/\./\\./g 740s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 740s + + tail -n+2 740s apt list ?obsolete 740s + cut -d/ -f1 740s + grep -v ^linux-.*6\.14\.0-10-generic.* 741s + obsolete_pkgs=linux-headers-6.11.0-8-generic 741s linux-headers-6.11.0-8 741s linux-image-6.11.0-8-generic 741s linux-modules-6.11.0-8-generic 741s linux-tools-6.11.0-8-generic 741s linux-tools-6.11.0-8 741s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 741s Reading package lists... 741s Building dependency tree... 741s Reading state information... 742s Solving dependencies... 742s The following packages will be REMOVED: 742s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 742s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 742s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 742s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 743s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 743s After this operation, 267 MB disk space will be freed. 743s (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 ... 117701 files and directories currently installed.) 743s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 743s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 743s Removing libpython3.12t64:arm64 (3.12.9-1) ... 743s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 743s Removing libnsl2:arm64 (1.3.0-3build3) ... 743s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 743s Removing libunwind8:arm64 (1.6.2-3.1) ... 743s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 743s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 745s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 745s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 745s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 745s /etc/kernel/postrm.d/initramfs-tools: 745s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 746s /etc/kernel/postrm.d/zz-flash-kernel: 746s flash-kernel: Kernel 6.11.0-8-generic has been removed. 746s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 746s /etc/kernel/postrm.d/zz-update-grub: 746s Sourcing file `/etc/default/grub' 746s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 746s Generating grub configuration file ... 746s Found linux image: /boot/vmlinuz-6.14.0-10-generic 746s Found initrd image: /boot/initrd.img-6.14.0-10-generic 747s Warning: os-prober will not be executed to detect other bootable partitions. 747s Systems on them will not be added to the GRUB boot configuration. 747s Check GRUB_DISABLE_OS_PROBER documentation entry. 747s Adding boot menu entry for UEFI Firmware Settings ... 747s done 747s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 747s Processing triggers for libc-bin (2.41-1ubuntu1) ... 747s (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 ... 81650 files and directories currently installed.) 747s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 747s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 747s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 747s + grep -q trusty /etc/lsb-release 747s + [ ! -d /usr/share/doc/unattended-upgrades ] 747s + [ ! -d /usr/share/doc/lxd ] 747s + [ ! -d /usr/share/doc/lxd-client ] 747s + [ ! -d /usr/share/doc/snapd ] 747s + type iptables 747s + cat 747s + chmod 755 /etc/rc.local 747s + . /etc/rc.local 747s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 747s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 747s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 747s + uname -m 747s + [ aarch64 = ppc64le ] 747s + [ -d /run/systemd/system ] 747s + systemd-detect-virt --quiet --vm 747s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 747s + cat 747s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 747s + echo COMPRESS=lz4 747s autopkgtest [16:11:37]: upgrading testbed (apt dist-upgrade and autopurge) 748s Reading package lists... 748s Building dependency tree... 748s Reading state information... 749s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 749s Starting 2 pkgProblemResolver with broken count: 0 749s Done 750s Entering ResolveByKeep 751s 751s Calculating upgrade... 751s The following packages will be upgraded: 751s libc-bin libc-dev-bin libc6 libc6-dev locales 752s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 752s Need to get 9530 kB of archives. 752s After this operation, 0 B of additional disk space will be used. 752s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 754s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 754s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 757s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 758s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 764s Preconfiguring packages ... 764s Fetched 9530 kB in 12s (807 kB/s) 764s (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 ... 81647 files and directories currently installed.) 764s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 764s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 764s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 764s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 764s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 765s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 765s Setting up libc6:arm64 (2.41-1ubuntu2) ... 765s (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 ... 81647 files and directories currently installed.) 765s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 765s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 765s Setting up libc-bin (2.41-1ubuntu2) ... 765s (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 ... 81647 files and directories currently installed.) 765s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 765s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 766s Setting up locales (2.41-1ubuntu2) ... 767s Generating locales (this might take a while)... 769s en_US.UTF-8... done 769s Generation complete. 769s Setting up libc-dev-bin (2.41-1ubuntu2) ... 769s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 769s Processing triggers for man-db (2.13.0-1) ... 770s Processing triggers for systemd (257.3-1ubuntu3) ... 771s Reading package lists... 771s Building dependency tree... 771s Reading state information... 771s Starting pkgProblemResolver with broken count: 0 772s Starting 2 pkgProblemResolver with broken count: 0 772s Done 772s Solving dependencies... 773s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 773s autopkgtest [16:12:03]: rebooting testbed after setup commands that affected boot 800s Reading package lists... 800s Building dependency tree... 800s Reading state information... 800s Starting pkgProblemResolver with broken count: 0 800s Starting 2 pkgProblemResolver with broken count: 0 800s Done 801s The following NEW packages will be installed: 801s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 801s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 801s fonts-glyphicons-halflings fonts-mathjax g++ g++-14 g++-14-aarch64-linux-gnu 801s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 801s gcc-aarch64-linux-gnu gfortran gfortran-14 gfortran-14-aarch64-linux-gnu 801s gfortran-aarch64-linux-gnu icu-devtools libasan8 libblas-dev libblas3 801s libbz2-dev libcairo2 libcc1-0 libdatrie1 libdeflate-dev libdeflate0 801s libfontconfig1 libgcc-14-dev libgfortran-14-dev libgfortran5 libgomp1 801s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 801s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 801s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 801s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 801s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 801s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 801s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 801s libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 libthai-data 801s libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7 801s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler 801s node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core 801s r-base-dev r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 801s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 801s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 801s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 801s r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 801s r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby 801s r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi 801s r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign 801s r-cran-formula r-cran-future r-cran-future.apply r-cran-generics 801s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable 801s r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms 801s r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr 801s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 801s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 801s r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats 801s r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools 801s r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr 801s r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly 801s r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 801s r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress 801s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg 801s r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rbibutils 801s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 801s r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 801s r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang r-cran-rpart 801s r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape r-cran-sparsem 801s r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey 801s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 801s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 801s r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun 801s r-cran-yaml r-cran-zip r-cran-zoo unzip x11-common xdg-utils zip zlib1g-dev 802s 0 upgraded, 255 newly installed, 0 to remove and 0 not upgraded. 802s Need to get 259 MB of archives. 802s After this operation, 671 MB of additional disk space will be used. 802s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 803s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 803s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 815s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 815s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 815s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 815s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 815s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 815s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 815s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 818s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 820s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 823s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 824s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 826s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 829s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 852s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 853s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 853s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 853s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 855s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 868s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 868s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 868s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 868s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 868s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 868s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 869s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 870s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 870s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 870s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 870s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 871s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 873s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 874s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 874s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 887s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 887s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 887s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 887s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 887s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 887s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 887s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 887s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 887s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 887s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 888s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 888s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 888s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 888s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 888s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 888s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 888s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 889s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 889s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 889s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 902s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 902s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 902s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 902s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 902s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 902s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 902s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 903s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 903s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 903s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 906s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 910s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 911s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 911s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 911s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 911s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 911s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 912s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 912s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 912s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 912s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 912s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 912s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 912s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 913s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 913s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 914s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 914s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 914s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 915s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 915s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 916s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 916s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 916s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 916s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 916s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 916s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 917s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 917s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 917s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 917s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 917s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 947s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB] 947s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B] 947s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 947s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 948s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 948s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 948s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 948s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 948s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 948s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 948s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cardata all 3.0.5-1 [1819 kB] 950s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-formula all 1.2-5-1 [158 kB] 950s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 951s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 953s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 956s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 960s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 964s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nnet arm64 7.3-20-1 [113 kB] 965s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-boot all 1.3-31-1 [635 kB] 965s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 965s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB] 968s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-minqa arm64 1.2.8-1 [112 kB] 968s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnlopt0 arm64 2.7.1-6ubuntu3 [179 kB] 968s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nloptr arm64 2.1.1-1 [251 kB] 969s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rbibutils arm64 2.3-1 [1016 kB] 970s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 971s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-reformulas all 0.4.0-1 [91.5 kB] 971s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcppeigen arm64 0.3.4.0.2-1 [1422 kB] 972s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB] 973s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lme4 arm64 1.1-36-1 [4108 kB] 978s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-backports arm64 1.5.0-2 [121 kB] 978s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 979s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 979s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 979s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB] 982s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 982s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 982s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 982s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 984s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 984s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB] 984s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 985s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 985s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB] 985s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 986s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyselect arm64 1.2.1+dfsg-1 [222 kB] 986s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dplyr arm64 1.1.4-4 [1534 kB] 988s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-purrr arm64 1.0.4-1 [552 kB] 988s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringi arm64 1.8.4-1build1 [902 kB] 989s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 990s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB] 990s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 991s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 994s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 994s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 994s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 996s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB] 997s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 997s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB] 999s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB] 999s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 999s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 1000s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 1001s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 1006s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 1006s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-deriv all 4.1.6-1 [151 kB] 1007s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-modelr all 0.1.11-1 [195 kB] 1007s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-microbenchmark arm64 1.5.0-1 [67.5 kB] 1007s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-doby all 4.6.25-1 [4772 kB] 1012s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB] 1012s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.51+dfsg-1 [573 kB] 1013s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 1013s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 1013s Get:172 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 1019s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 1020s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pbkrtest all 0.5.3-1 [178 kB] 1020s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sparsem arm64 1.84-2-1 [812 kB] 1021s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrixmodels all 0.5-3-1 [361 kB] 1021s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 1029s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB] 1030s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpparmadillo arm64 14.2.3-1-1 [843 kB] 1031s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-class arm64 7.3-23-1 [90.5 kB] 1031s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-proxy arm64 0.4-27-1 [181 kB] 1031s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-e1071 arm64 1.7-16-1 [563 kB] 1032s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-codetools all 0.2-20-1 [90.5 kB] 1032s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-iterators all 1.0.14-1 [336 kB] 1032s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-foreach all 1.5.2-1 [124 kB] 1032s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-data.table arm64 1.17.0+dfsg-1 [2129 kB] 1035s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-modelmetrics arm64 1.2.2.2-1build1 [121 kB] 1035s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-plyr arm64 1.8.9-1 [831 kB] 1036s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-proc arm64 1.18.5-1 [963 kB] 1037s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tzdb arm64 0.4.0-2 [512 kB] 1037s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-clock arm64 0.7.2-1 [1829 kB] 1039s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gower arm64 1.0.2-1 [208 kB] 1039s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hardhat all 1.4.0+dfsg-1 [565 kB] 1040s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 1041s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-shape all 1.4.6.1-1 [749 kB] 1041s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-diagram all 1.6.5-2 [656 kB] 1042s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-kernsmooth arm64 2.23-26-1 [93.3 kB] 1042s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB] 1043s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-globals all 0.16.3-1 [120 kB] 1043s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 1043s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-parallelly arm64 1.42.0-1 [540 kB] 1043s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 1044s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 1045s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-progressr all 0.15.1-1 [353 kB] 1045s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-squarem all 2021.1-1 [179 kB] 1045s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lava all 1.8.1+dfsg-1 [2191 kB] 1047s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-prodlim arm64 2024.06.25-1 [415 kB] 1048s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ipred arm64 0.9-15-1 [386 kB] 1048s Get:209 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-timechange arm64 0.3.0-1 [172 kB] 1048s Get:210 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lubridate arm64 1.9.4+dfsg-1 [1009 kB] 1049s Get:211 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-timedate arm64 4041.110-1 [1210 kB] 1050s Get:212 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 1052s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-reshape2 arm64 1.4.4-2build1 [110 kB] 1052s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-caret arm64 7.0-1+dfsg-1 [3461 kB] 1056s Get:215 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-conquer arm64 1.3.3-1 [440 kB] 1056s Get:216 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-quantreg arm64 6.00-1 [1436 kB] 1058s Get:217 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-foreign arm64 0.8.88-1 [243 kB] 1058s Get:218 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 1058s Get:219 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-forcats all 1.0.0-1 [369 kB] 1058s Get:220 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hms all 1.1.3-1 [96.5 kB] 1059s Get:221 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-clipr all 0.8.0-1 [53.5 kB] 1059s Get:222 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB] 1059s Get:223 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bit arm64 4.6.0+dfsg-1 [450 kB] 1059s Get:224 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bit64 arm64 4.6.0-1-1ubuntu2 [497 kB] 1060s Get:225 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-prettyunits all 1.2.0-1 [162 kB] 1060s Get:226 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-progress all 1.2.3-1 [91.9 kB] 1060s Get:227 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vroom arm64 1.6.5-1 [832 kB] 1061s Get:228 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-readr arm64 2.1.5-1 [756 kB] 1062s Get:229 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-haven arm64 2.5.4-1 [338 kB] 1062s Get:230 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB] 1062s Get:231 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rematch all 2.0.0-1 [18.3 kB] 1062s Get:232 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cellranger all 1.1.0-3 [102 kB] 1063s Get:233 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-readxl arm64 1.4.4-1 [341 kB] 1063s Get:234 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-writexl arm64 1.5.1-1 [159 kB] 1063s Get:235 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 1063s Get:236 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.oo all 1.27.0-1 [979 kB] 1064s Get:237 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r.utils all 2.13.0-1 [1423 kB] 1066s Get:238 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-zip arm64 2.3.2-1 [147 kB] 1066s Get:239 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openxlsx arm64 4.2.8-1 [2018 kB] 1068s Get:240 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rio all 1.2.3-1 [546 kB] 1068s Get:241 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-car all 3.1-3-1 [1525 kB] 1070s Get:242 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-zoo arm64 1.8-13-1 [996 kB] 1071s Get:243 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lmtest arm64 0.9.40-1 [396 kB] 1071s Get:244 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sandwich all 3.1-1-1 [1483 kB] 1073s Get:245 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-aer all 1.2-14-1 [2597 kB] 1076s Get:246 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-blob all 1.2.4-1 [49.8 kB] 1076s Get:247 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB] 1076s Get:248 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB] 1076s Get:249 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-dbi all 1.2.3-1 [853 kB] 1077s Get:250 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-hexbin arm64 1.28.5-1 [1580 kB] 1079s Get:251 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB] 1079s Get:252 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mitools all 2.4-2build1 [265 kB] 1079s Get:253 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 1079s Get:254 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rsqlite arm64 2.3.9-1 [1247 kB] 1080s Get:255 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survey arm64 4.4-2-2 [3448 kB] 1085s Preconfiguring packages ... 1085s Fetched 259 MB in 4min 43s (915 kB/s) 1085s Selecting previously unselected package libisl23:arm64. 1085s (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 ... 81647 files and directories currently installed.) 1085s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ... 1085s Unpacking libisl23:arm64 (0.27-1) ... 1085s Selecting previously unselected package libmpc3:arm64. 1085s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ... 1085s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 1085s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 1085s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1085s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1085s Selecting previously unselected package cpp-14. 1085s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 1085s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 1085s Selecting previously unselected package cpp-aarch64-linux-gnu. 1085s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1085s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1085s Selecting previously unselected package cpp. 1086s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 1086s Unpacking cpp (4:14.2.0-1ubuntu1) ... 1086s Selecting previously unselected package libcc1-0:arm64. 1086s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libgomp1:arm64. 1086s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libitm1:arm64. 1086s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libasan8:arm64. 1086s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package liblsan0:arm64. 1086s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libtsan2:arm64. 1086s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libubsan1:arm64. 1086s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libhwasan0:arm64. 1086s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_arm64.deb ... 1086s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ... 1086s Selecting previously unselected package libgcc-14-dev:arm64. 1086s Preparing to unpack .../014-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1086s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 1086s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 1086s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1086s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1087s Selecting previously unselected package gcc-14. 1087s Preparing to unpack .../016-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 1087s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 1087s Selecting previously unselected package gcc-aarch64-linux-gnu. 1087s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1087s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1087s Selecting previously unselected package gcc. 1087s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 1087s Unpacking gcc (4:14.2.0-1ubuntu1) ... 1087s Selecting previously unselected package libstdc++-14-dev:arm64. 1087s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1087s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 1087s Selecting previously unselected package g++-14-aarch64-linux-gnu. 1087s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1087s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1087s Selecting previously unselected package g++-14. 1087s Preparing to unpack .../021-g++-14_14.2.0-17ubuntu3_arm64.deb ... 1087s Unpacking g++-14 (14.2.0-17ubuntu3) ... 1087s Selecting previously unselected package g++-aarch64-linux-gnu. 1087s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1087s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1087s Selecting previously unselected package g++. 1087s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 1087s Unpacking g++ (4:14.2.0-1ubuntu1) ... 1087s Selecting previously unselected package build-essential. 1087s Preparing to unpack .../024-build-essential_12.10ubuntu1_arm64.deb ... 1087s Unpacking build-essential (12.10ubuntu1) ... 1087s Selecting previously unselected package dctrl-tools. 1087s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ... 1087s Unpacking dctrl-tools (2.24-3build3) ... 1087s Selecting previously unselected package fonts-dejavu-mono. 1087s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ... 1087s Unpacking fonts-dejavu-mono (2.37-8) ... 1087s Selecting previously unselected package fonts-dejavu-core. 1087s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ... 1088s Unpacking fonts-dejavu-core (2.37-8) ... 1088s Selecting previously unselected package fontconfig-config. 1088s Preparing to unpack .../028-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 1088s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 1088s Selecting previously unselected package libfontconfig1:arm64. 1088s Preparing to unpack .../029-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 1088s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 1088s Selecting previously unselected package fontconfig. 1088s Preparing to unpack .../030-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 1088s Unpacking fontconfig (2.15.0-2ubuntu1) ... 1088s Selecting previously unselected package fonts-glyphicons-halflings. 1088s Preparing to unpack .../031-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 1088s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 1088s Selecting previously unselected package fonts-mathjax. 1088s Preparing to unpack .../032-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 1088s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 1088s Selecting previously unselected package libgfortran5:arm64. 1088s Preparing to unpack .../033-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 1088s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 1088s Selecting previously unselected package libgfortran-14-dev:arm64. 1088s Preparing to unpack .../034-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1088s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 1088s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 1088s Preparing to unpack .../035-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1088s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1088s Selecting previously unselected package gfortran-14. 1089s Preparing to unpack .../036-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 1089s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 1089s Selecting previously unselected package gfortran-aarch64-linux-gnu. 1089s Preparing to unpack .../037-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1089s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1089s Selecting previously unselected package gfortran. 1089s Preparing to unpack .../038-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 1089s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 1089s Selecting previously unselected package icu-devtools. 1089s Preparing to unpack .../039-icu-devtools_76.1-1ubuntu2_arm64.deb ... 1089s Unpacking icu-devtools (76.1-1ubuntu2) ... 1089s Selecting previously unselected package libblas3:arm64. 1089s Preparing to unpack .../040-libblas3_3.12.1-2_arm64.deb ... 1089s Unpacking libblas3:arm64 (3.12.1-2) ... 1089s Selecting previously unselected package libblas-dev:arm64. 1089s Preparing to unpack .../041-libblas-dev_3.12.1-2_arm64.deb ... 1089s Unpacking libblas-dev:arm64 (3.12.1-2) ... 1089s Selecting previously unselected package libbz2-dev:arm64. 1089s Preparing to unpack .../042-libbz2-dev_1.0.8-6_arm64.deb ... 1089s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 1089s Selecting previously unselected package libpixman-1-0:arm64. 1089s Preparing to unpack .../043-libpixman-1-0_0.44.0-3_arm64.deb ... 1089s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 1089s Selecting previously unselected package libxcb-render0:arm64. 1089s Preparing to unpack .../044-libxcb-render0_1.17.0-2_arm64.deb ... 1089s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 1089s Selecting previously unselected package libxcb-shm0:arm64. 1089s Preparing to unpack .../045-libxcb-shm0_1.17.0-2_arm64.deb ... 1089s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 1089s Selecting previously unselected package libxrender1:arm64. 1089s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 1089s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 1089s Selecting previously unselected package libcairo2:arm64. 1089s Preparing to unpack .../047-libcairo2_1.18.2-2_arm64.deb ... 1089s Unpacking libcairo2:arm64 (1.18.2-2) ... 1089s Selecting previously unselected package libdatrie1:arm64. 1089s Preparing to unpack .../048-libdatrie1_0.2.13-3build1_arm64.deb ... 1089s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 1089s Selecting previously unselected package libdeflate0:arm64. 1089s Preparing to unpack .../049-libdeflate0_1.23-1_arm64.deb ... 1089s Unpacking libdeflate0:arm64 (1.23-1) ... 1089s Selecting previously unselected package libdeflate-dev:arm64. 1089s Preparing to unpack .../050-libdeflate-dev_1.23-1_arm64.deb ... 1089s Unpacking libdeflate-dev:arm64 (1.23-1) ... 1089s Selecting previously unselected package libgraphite2-3:arm64. 1089s Preparing to unpack .../051-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 1089s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 1089s Selecting previously unselected package libharfbuzz0b:arm64. 1089s Preparing to unpack .../052-libharfbuzz0b_10.2.0-1_arm64.deb ... 1089s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 1089s Selecting previously unselected package x11-common. 1089s Preparing to unpack .../053-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1089s Unpacking x11-common (1:7.7+23ubuntu3) ... 1089s Selecting previously unselected package libice6:arm64. 1089s Preparing to unpack .../054-libice6_2%3a1.1.1-1_arm64.deb ... 1089s Unpacking libice6:arm64 (2:1.1.1-1) ... 1089s Selecting previously unselected package libicu-dev:arm64. 1089s Preparing to unpack .../055-libicu-dev_76.1-1ubuntu2_arm64.deb ... 1089s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 1090s Selecting previously unselected package libjpeg-turbo8:arm64. 1090s Preparing to unpack .../056-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 1090s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 1090s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 1090s Preparing to unpack .../057-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 1090s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 1090s Selecting previously unselected package libjpeg8:arm64. 1090s Preparing to unpack .../058-libjpeg8_8c-2ubuntu11_arm64.deb ... 1090s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1090s Selecting previously unselected package libjpeg8-dev:arm64. 1090s Preparing to unpack .../059-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 1090s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 1090s Selecting previously unselected package libjpeg-dev:arm64. 1090s Preparing to unpack .../060-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 1090s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 1090s Selecting previously unselected package libjs-bootstrap. 1090s Preparing to unpack .../061-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 1090s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 1090s Selecting previously unselected package libjs-highlight.js. 1090s Preparing to unpack .../062-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 1090s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 1090s Selecting previously unselected package libjs-jquery. 1090s Preparing to unpack .../063-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 1090s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1090s Selecting previously unselected package libjs-jquery-datatables. 1090s Preparing to unpack .../064-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 1090s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 1090s Selecting previously unselected package liblapack3:arm64. 1090s Preparing to unpack .../065-liblapack3_3.12.1-2_arm64.deb ... 1090s Unpacking liblapack3:arm64 (3.12.1-2) ... 1090s Selecting previously unselected package liblapack-dev:arm64. 1090s Preparing to unpack .../066-liblapack-dev_3.12.1-2_arm64.deb ... 1090s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 1090s Selecting previously unselected package liblerc4:arm64. 1090s Preparing to unpack .../067-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 1090s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 1090s Selecting previously unselected package libncurses-dev:arm64. 1090s Preparing to unpack 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libpcre2-posix3:arm64 (10.45-1) ... 1091s Selecting previously unselected package libpcre2-dev:arm64. 1091s Preparing to unpack .../079-libpcre2-dev_10.45-1_arm64.deb ... 1091s Unpacking libpcre2-dev:arm64 (10.45-1) ... 1091s Selecting previously unselected package libpkgconf3:arm64. 1091s Preparing to unpack .../080-libpkgconf3_1.8.1-4_arm64.deb ... 1091s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 1091s Selecting previously unselected package zlib1g-dev:arm64. 1091s Preparing to unpack .../081-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 1091s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1091s Selecting previously unselected package libpng-dev:arm64. 1091s Preparing to unpack .../082-libpng-dev_1.6.47-1_arm64.deb ... 1091s Unpacking libpng-dev:arm64 (1.6.47-1) ... 1091s Selecting previously unselected package libreadline-dev:arm64. 1091s Preparing to unpack .../083-libreadline-dev_8.2-6_arm64.deb ... 1091s Unpacking libreadline-dev:arm64 (8.2-6) ... 1091s Selecting previously unselected package libsharpyuv0:arm64. 1091s Preparing to unpack .../084-libsharpyuv0_1.5.0-0.1_arm64.deb ... 1091s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 1091s Selecting previously unselected package libsm6:arm64. 1091s Preparing to unpack .../085-libsm6_2%3a1.2.4-1_arm64.deb ... 1091s Unpacking libsm6:arm64 (2:1.2.4-1) ... 1091s Selecting previously unselected package libtcl8.6:arm64. 1091s Preparing to unpack .../086-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 1091s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 1091s Selecting previously unselected package libjbig0:arm64. 1091s Preparing to unpack .../087-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 1091s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 1091s Selecting previously unselected package libwebp7:arm64. 1091s Preparing to unpack .../088-libwebp7_1.5.0-0.1_arm64.deb ... 1091s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 1091s Selecting previously unselected package libtiff6:arm64. 1091s Preparing to unpack .../089-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 1091s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 1091s Selecting previously unselected package libxft2:arm64. 1091s Preparing to unpack .../090-libxft2_2.3.6-1build1_arm64.deb ... 1091s Unpacking libxft2:arm64 (2.3.6-1build1) ... 1092s Selecting previously unselected package libxss1:arm64. 1092s Preparing to unpack .../091-libxss1_1%3a1.2.3-1build3_arm64.deb ... 1092s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 1092s Selecting previously unselected package libtk8.6:arm64. 1092s Preparing to unpack .../092-libtk8.6_8.6.16-1_arm64.deb ... 1092s Unpacking libtk8.6:arm64 (8.6.16-1) ... 1092s Selecting previously unselected package libxt6t64:arm64. 1092s Preparing to unpack .../093-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 1092s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 1092s Selecting previously unselected package zip. 1092s Preparing to unpack .../094-zip_3.0-14ubuntu2_arm64.deb ... 1092s Unpacking zip (3.0-14ubuntu2) ... 1092s Selecting previously unselected package unzip. 1092s Preparing to unpack .../095-unzip_6.0-28ubuntu6_arm64.deb ... 1092s Unpacking unzip (6.0-28ubuntu6) ... 1092s Selecting previously unselected package xdg-utils. 1092s Preparing to unpack .../096-xdg-utils_1.2.1-2ubuntu1_all.deb ... 1092s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 1092s Selecting previously unselected package r-base-core. 1092s Preparing to unpack .../097-r-base-core_4.4.3-1_arm64.deb ... 1092s Unpacking r-base-core (4.4.3-1) ... 1092s Selecting previously unselected package r-cran-littler. 1092s Preparing to unpack .../098-r-cran-littler_0.3.20-2_arm64.deb ... 1092s Unpacking r-cran-littler (0.3.20-2) ... 1092s Selecting previously unselected package littler. 1092s Preparing to unpack .../099-littler_0.3.20-2_all.deb ... 1092s Unpacking littler (0.3.20-2) ... 1092s Selecting previously unselected package node-normalize.css. 1092s Preparing to unpack .../100-node-normalize.css_8.0.1-5_all.deb 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... 1093s Selecting previously unselected package r-cran-nlme. 1093s Preparing to unpack .../112-r-cran-nlme_3.1.167-1_arm64.deb ... 1093s Unpacking r-cran-nlme (3.1.167-1) ... 1093s Selecting previously unselected package r-cran-matrix. 1093s Preparing to unpack .../113-r-cran-matrix_1.7-3-1_arm64.deb ... 1093s Unpacking r-cran-matrix (1.7-3-1) ... 1093s Selecting previously unselected package r-cran-mgcv. 1093s Preparing to unpack .../114-r-cran-mgcv_1.9-1-1_arm64.deb ... 1093s Unpacking r-cran-mgcv (1.9-1-1) ... 1093s Selecting previously unselected package r-cran-nnet. 1093s Preparing to unpack .../115-r-cran-nnet_7.3-20-1_arm64.deb ... 1093s Unpacking r-cran-nnet (7.3-20-1) ... 1093s Selecting previously unselected package r-cran-boot. 1093s Preparing to unpack .../116-r-cran-boot_1.3-31-1_all.deb ... 1093s Unpacking r-cran-boot (1.3-31-1) ... 1093s Selecting previously unselected package r-cran-pkgkitten. 1093s Preparing to unpack .../117-r-cran-pkgkitten_0.2.4-1_all.deb ... 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Preparing to unpack .../123-r-cran-rdpack_2.6.2-1syncable1_all.deb ... 1094s Unpacking r-cran-rdpack (2.6.2-1syncable1) ... 1094s Selecting previously unselected package r-cran-reformulas. 1094s Preparing to unpack .../124-r-cran-reformulas_0.4.0-1_all.deb ... 1094s Unpacking r-cran-reformulas (0.4.0-1) ... 1094s Selecting previously unselected package r-cran-rcppeigen. 1094s Preparing to unpack .../125-r-cran-rcppeigen_0.3.4.0.2-1_arm64.deb ... 1094s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 1094s Selecting previously unselected package r-cran-statmod. 1094s Preparing to unpack .../126-r-cran-statmod_1.5.0-1_arm64.deb ... 1094s Unpacking r-cran-statmod (1.5.0-1) ... 1094s Selecting previously unselected package r-cran-lme4. 1094s Preparing to unpack .../127-r-cran-lme4_1.1-36-1_arm64.deb ... 1094s Unpacking r-cran-lme4 (1.1-36-1) ... 1094s Selecting previously unselected package r-cran-backports. 1094s Preparing to unpack .../128-r-cran-backports_1.5.0-2_arm64.deb ... 1094s Unpacking r-cran-backports (1.5.0-2) ... 1094s Selecting previously unselected package r-cran-cli. 1094s Preparing to unpack .../129-r-cran-cli_3.6.4-1_arm64.deb ... 1094s Unpacking r-cran-cli (3.6.4-1) ... 1094s Selecting previously unselected package r-cran-generics. 1094s Preparing to unpack .../130-r-cran-generics_0.1.3-1_all.deb ... 1094s Unpacking r-cran-generics (0.1.3-1) ... 1094s Selecting previously unselected package r-cran-glue. 1094s Preparing to unpack .../131-r-cran-glue_1.8.0-1_arm64.deb ... 1094s Unpacking r-cran-glue (1.8.0-1) ... 1094s Selecting previously unselected package r-cran-rlang. 1094s Preparing to unpack .../132-r-cran-rlang_1.1.5-1_arm64.deb ... 1094s Unpacking r-cran-rlang (1.1.5-1) ... 1094s Selecting previously unselected package r-cran-lifecycle. 1094s Preparing to unpack .../133-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 1094s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 1094s Selecting previously unselected package r-cran-magrittr. 1094s Preparing to unpack .../134-r-cran-magrittr_2.0.3-1_arm64.deb ... 1094s Unpacking r-cran-magrittr (2.0.3-1) ... 1094s Selecting previously unselected package r-cran-utf8. 1094s Preparing to unpack .../135-r-cran-utf8_1.2.4-1_arm64.deb ... 1094s Unpacking r-cran-utf8 (1.2.4-1) ... 1094s Selecting previously unselected package r-cran-vctrs. 1094s Preparing to unpack .../136-r-cran-vctrs_0.6.5-1_arm64.deb ... 1094s Unpacking r-cran-vctrs (0.6.5-1) ... 1094s Selecting previously unselected package r-cran-pillar. 1094s Preparing to unpack .../137-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 1094s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 1094s Selecting previously unselected package r-cran-r6. 1094s Preparing to unpack .../138-r-cran-r6_2.6.1-1_all.deb ... 1094s Unpacking r-cran-r6 (2.6.1-1) ... 1094s Selecting previously unselected package r-cran-fansi. 1094s Preparing to unpack .../139-r-cran-fansi_1.0.5-1_arm64.deb ... 1094s Unpacking r-cran-fansi (1.0.5-1) ... 1095s Selecting previously unselected package r-cran-pkgconfig. 1095s Preparing to unpack .../140-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 1095s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 1095s Selecting previously unselected package r-cran-tibble. 1095s Preparing to unpack .../141-r-cran-tibble_3.2.1+dfsg-3_arm64.deb ... 1095s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 1095s Selecting previously unselected package r-cran-withr. 1095s Preparing to unpack .../142-r-cran-withr_3.0.2+dfsg-1_all.deb ... 1095s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 1095s Selecting previously unselected package r-cran-tidyselect. 1095s Preparing to unpack .../143-r-cran-tidyselect_1.2.1+dfsg-1_arm64.deb ... 1095s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 1095s Selecting previously unselected package r-cran-dplyr. 1095s Preparing to unpack .../144-r-cran-dplyr_1.1.4-4_arm64.deb ... 1095s Unpacking r-cran-dplyr (1.1.4-4) ... 1095s Selecting previously unselected package r-cran-purrr. 1095s Preparing to unpack .../145-r-cran-purrr_1.0.4-1_arm64.deb ... 1095s Unpacking r-cran-purrr (1.0.4-1) ... 1095s Selecting previously unselected package r-cran-stringi. 1095s Preparing to unpack .../146-r-cran-stringi_1.8.4-1build1_arm64.deb ... 1095s Unpacking r-cran-stringi (1.8.4-1build1) ... 1095s Selecting previously unselected package r-cran-stringr. 1095s Preparing to unpack .../147-r-cran-stringr_1.5.1-1_all.deb ... 1095s Unpacking r-cran-stringr (1.5.1-1) ... 1095s Selecting previously unselected package r-cran-cpp11. 1095s Preparing to unpack .../148-r-cran-cpp11_0.5.2-1_all.deb ... 1095s Unpacking r-cran-cpp11 (0.5.2-1) ... 1095s Selecting previously unselected package r-cran-tidyr. 1095s Preparing to unpack .../149-r-cran-tidyr_1.3.1-1_arm64.deb ... 1095s Unpacking r-cran-tidyr (1.3.1-1) ... 1095s Selecting previously unselected package r-cran-broom. 1095s Preparing to unpack .../150-r-cran-broom_1.0.7+dfsg-1_all.deb ... 1095s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 1095s Selecting previously unselected package r-cran-numderiv. 1095s Preparing to unpack .../151-r-cran-numderiv_2016.8-1.1-3_all.deb ... 1095s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 1095s Selecting previously unselected package r-cran-gtable. 1095s Preparing to unpack .../152-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 1095s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 1095s Selecting previously unselected package r-cran-isoband. 1095s Preparing to unpack .../153-r-cran-isoband_0.2.7-1_arm64.deb ... 1095s Unpacking r-cran-isoband (0.2.7-1) ... 1095s Selecting previously unselected package r-cran-farver. 1095s Preparing to unpack .../154-r-cran-farver_2.1.2-1_arm64.deb ... 1095s Unpacking r-cran-farver (2.1.2-1) ... 1095s Selecting previously unselected package r-cran-labeling. 1095s Preparing to unpack .../155-r-cran-labeling_0.4.3-1_all.deb ... 1095s Unpacking r-cran-labeling (0.4.3-1) ... 1095s Selecting previously unselected package r-cran-colorspace. 1095s Preparing to unpack .../156-r-cran-colorspace_2.1-1+dfsg-1_arm64.deb ... 1095s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 1095s Selecting previously unselected package r-cran-munsell. 1095s Preparing to unpack .../157-r-cran-munsell_0.5.1-1_all.deb ... 1095s Unpacking r-cran-munsell (0.5.1-1) ... 1095s Selecting previously unselected package r-cran-rcolorbrewer. 1095s Preparing to unpack .../158-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 1095s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 1096s Selecting previously unselected package r-cran-viridislite. 1096s Preparing to unpack .../159-r-cran-viridislite_0.4.2-2_all.deb ... 1096s Unpacking r-cran-viridislite (0.4.2-2) ... 1096s Selecting previously unselected package r-cran-scales. 1096s Preparing to unpack .../160-r-cran-scales_1.3.0-1_all.deb ... 1096s Unpacking r-cran-scales (1.3.0-1) ... 1096s Selecting previously unselected package r-cran-ggplot2. 1096s Preparing to unpack .../161-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 1096s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 1096s Selecting previously unselected package r-cran-cowplot. 1096s Preparing to unpack .../162-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 1096s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 1096s Selecting previously unselected package r-cran-deriv. 1096s Preparing to unpack .../163-r-cran-deriv_4.1.6-1_all.deb ... 1096s Unpacking r-cran-deriv (4.1.6-1) ... 1096s Selecting previously unselected package r-cran-modelr. 1096s Preparing to unpack .../164-r-cran-modelr_0.1.11-1_all.deb ... 1096s Unpacking r-cran-modelr (0.1.11-1) ... 1096s Selecting previously unselected package r-cran-microbenchmark. 1096s Preparing to unpack .../165-r-cran-microbenchmark_1.5.0-1_arm64.deb ... 1096s Unpacking r-cran-microbenchmark (1.5.0-1) ... 1096s Selecting previously unselected package r-cran-doby. 1096s Preparing to unpack .../166-r-cran-doby_4.6.25-1_all.deb ... 1096s Unpacking r-cran-doby (4.6.25-1) ... 1096s Selecting previously unselected package r-cran-evaluate. 1096s Preparing to unpack .../167-r-cran-evaluate_1.0.3-1_all.deb ... 1096s Unpacking r-cran-evaluate (1.0.3-1) ... 1096s Selecting previously unselected package r-cran-xfun. 1096s Preparing to unpack .../168-r-cran-xfun_0.51+dfsg-1_arm64.deb ... 1096s Unpacking r-cran-xfun (0.51+dfsg-1) ... 1096s Selecting previously unselected package r-cran-highr. 1096s Preparing to unpack .../169-r-cran-highr_0.11+dfsg-1_all.deb ... 1096s Unpacking r-cran-highr (0.11+dfsg-1) ... 1096s Selecting previously unselected package r-cran-yaml. 1096s Preparing to unpack .../170-r-cran-yaml_2.3.10-1_arm64.deb ... 1096s Unpacking r-cran-yaml (2.3.10-1) ... 1096s Selecting previously unselected package libjs-mathjax. 1096s Preparing to unpack .../171-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 1096s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 1097s Selecting previously unselected package r-cran-knitr. 1097s Preparing to unpack .../172-r-cran-knitr_1.49+dfsg-1_all.deb ... 1097s Unpacking r-cran-knitr (1.49+dfsg-1) ... 1097s Selecting previously unselected package r-cran-pbkrtest. 1097s Preparing to unpack .../173-r-cran-pbkrtest_0.5.3-1_all.deb ... 1097s Unpacking r-cran-pbkrtest (0.5.3-1) ... 1097s Selecting previously unselected package r-cran-sparsem. 1097s Preparing to unpack .../174-r-cran-sparsem_1.84-2-1_arm64.deb ... 1097s Unpacking r-cran-sparsem (1.84-2-1) ... 1097s Selecting previously unselected package r-cran-matrixmodels. 1097s Preparing to unpack .../175-r-cran-matrixmodels_0.5-3-1_all.deb ... 1097s Unpacking r-cran-matrixmodels (0.5-3-1) ... 1097s Selecting previously unselected package r-cran-survival. 1097s Preparing to unpack .../176-r-cran-survival_3.8-3-1_arm64.deb ... 1097s Unpacking r-cran-survival (3.8-3-1) ... 1097s Selecting previously unselected package r-cran-matrixstats. 1097s Preparing to unpack .../177-r-cran-matrixstats_1.5.0-1_arm64.deb ... 1097s Unpacking r-cran-matrixstats (1.5.0-1) ... 1097s Selecting previously unselected package r-cran-rcpparmadillo. 1097s Preparing to unpack .../178-r-cran-rcpparmadillo_14.2.3-1-1_arm64.deb ... 1097s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 1097s Selecting previously unselected package r-cran-class. 1097s Preparing to unpack .../179-r-cran-class_7.3-23-1_arm64.deb ... 1097s Unpacking r-cran-class (7.3-23-1) ... 1097s Selecting previously unselected package r-cran-proxy. 1097s Preparing to unpack .../180-r-cran-proxy_0.4-27-1_arm64.deb ... 1097s Unpacking r-cran-proxy (0.4-27-1) ... 1097s Selecting previously unselected package r-cran-e1071. 1097s Preparing to unpack .../181-r-cran-e1071_1.7-16-1_arm64.deb ... 1097s Unpacking r-cran-e1071 (1.7-16-1) ... 1097s Selecting previously unselected package r-cran-codetools. 1097s Preparing to unpack .../182-r-cran-codetools_0.2-20-1_all.deb ... 1097s Unpacking r-cran-codetools (0.2-20-1) ... 1097s Selecting previously unselected package r-cran-iterators. 1098s Preparing to unpack .../183-r-cran-iterators_1.0.14-1_all.deb ... 1098s Unpacking r-cran-iterators (1.0.14-1) ... 1098s Selecting previously unselected package r-cran-foreach. 1098s Preparing to unpack .../184-r-cran-foreach_1.5.2-1_all.deb ... 1098s Unpacking r-cran-foreach (1.5.2-1) ... 1098s Selecting previously unselected package r-cran-data.table. 1098s Preparing to unpack .../185-r-cran-data.table_1.17.0+dfsg-1_arm64.deb ... 1098s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 1098s Selecting previously unselected package r-cran-modelmetrics. 1098s Preparing to unpack .../186-r-cran-modelmetrics_1.2.2.2-1build1_arm64.deb ... 1098s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 1098s Selecting previously unselected package r-cran-plyr. 1098s Preparing to unpack .../187-r-cran-plyr_1.8.9-1_arm64.deb ... 1098s Unpacking r-cran-plyr (1.8.9-1) ... 1098s Selecting previously unselected package r-cran-proc. 1098s Preparing to unpack .../188-r-cran-proc_1.18.5-1_arm64.deb ... 1098s Unpacking r-cran-proc (1.18.5-1) ... 1098s Selecting previously unselected package r-cran-tzdb. 1098s Preparing to unpack .../189-r-cran-tzdb_0.4.0-2_arm64.deb ... 1098s Unpacking r-cran-tzdb (0.4.0-2) ... 1098s Selecting previously unselected package r-cran-clock. 1098s Preparing to unpack .../190-r-cran-clock_0.7.2-1_arm64.deb ... 1098s Unpacking r-cran-clock (0.7.2-1) ... 1098s Selecting previously unselected package r-cran-gower. 1098s Preparing to unpack .../191-r-cran-gower_1.0.2-1_arm64.deb ... 1098s Unpacking r-cran-gower (1.0.2-1) ... 1098s Selecting previously unselected package r-cran-hardhat. 1098s Preparing to unpack .../192-r-cran-hardhat_1.4.0+dfsg-1_all.deb ... 1098s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ... 1098s Selecting previously unselected package r-cran-rpart. 1098s Preparing to unpack .../193-r-cran-rpart_4.1.24-1_arm64.deb ... 1098s Unpacking r-cran-rpart (4.1.24-1) ... 1098s Selecting previously unselected package r-cran-shape. 1098s Preparing to unpack .../194-r-cran-shape_1.4.6.1-1_all.deb ... 1098s Unpacking r-cran-shape (1.4.6.1-1) ... 1098s Selecting previously unselected package r-cran-diagram. 1098s Preparing to unpack .../195-r-cran-diagram_1.6.5-2_all.deb ... 1098s Unpacking r-cran-diagram (1.6.5-2) ... 1098s Selecting previously unselected package r-cran-kernsmooth. 1098s Preparing to unpack .../196-r-cran-kernsmooth_2.23-26-1_arm64.deb ... 1098s Unpacking r-cran-kernsmooth (2.23-26-1) ... 1098s Selecting previously unselected package r-cran-digest. 1098s Preparing to unpack .../197-r-cran-digest_0.6.37-1_arm64.deb ... 1098s Unpacking r-cran-digest (0.6.37-1) ... 1098s Selecting previously unselected package r-cran-globals. 1098s Preparing to unpack .../198-r-cran-globals_0.16.3-1_all.deb ... 1098s Unpacking r-cran-globals (0.16.3-1) ... 1098s Selecting previously unselected package r-cran-listenv. 1098s Preparing to unpack .../199-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 1098s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 1098s Selecting previously unselected package r-cran-parallelly. 1098s Preparing to unpack .../200-r-cran-parallelly_1.42.0-1_arm64.deb ... 1098s Unpacking r-cran-parallelly (1.42.0-1) ... 1098s Selecting previously unselected package r-cran-future. 1098s Preparing to unpack .../201-r-cran-future_1.34.0+dfsg-1_all.deb ... 1098s Unpacking r-cran-future (1.34.0+dfsg-1) ... 1099s Selecting previously unselected package r-cran-future.apply. 1099s Preparing to unpack .../202-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 1099s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 1099s Selecting previously unselected package r-cran-progressr. 1099s Preparing to unpack .../203-r-cran-progressr_0.15.1-1_all.deb ... 1099s Unpacking r-cran-progressr (0.15.1-1) ... 1099s Selecting previously unselected package r-cran-squarem. 1099s Preparing to unpack .../204-r-cran-squarem_2021.1-1_all.deb ... 1099s Unpacking r-cran-squarem (2021.1-1) ... 1099s Selecting previously unselected package r-cran-lava. 1099s Preparing to unpack .../205-r-cran-lava_1.8.1+dfsg-1_all.deb ... 1099s Unpacking r-cran-lava (1.8.1+dfsg-1) ... 1099s Selecting previously unselected package r-cran-prodlim. 1099s Preparing to unpack .../206-r-cran-prodlim_2024.06.25-1_arm64.deb ... 1099s Unpacking r-cran-prodlim (2024.06.25-1) ... 1099s Selecting previously unselected package r-cran-ipred. 1099s Preparing to unpack .../207-r-cran-ipred_0.9-15-1_arm64.deb ... 1099s Unpacking r-cran-ipred (0.9-15-1) ... 1099s Selecting previously unselected package r-cran-timechange. 1099s Preparing to unpack .../208-r-cran-timechange_0.3.0-1_arm64.deb ... 1099s Unpacking r-cran-timechange (0.3.0-1) ... 1099s Selecting previously unselected package r-cran-lubridate. 1099s Preparing to unpack .../209-r-cran-lubridate_1.9.4+dfsg-1_arm64.deb ... 1099s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 1099s Selecting previously unselected package r-cran-timedate. 1099s Preparing to unpack .../210-r-cran-timedate_4041.110-1_arm64.deb ... 1099s Unpacking r-cran-timedate (4041.110-1) ... 1099s Selecting previously unselected package r-cran-recipes. 1099s Preparing to unpack .../211-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 1099s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 1099s Selecting previously unselected package r-cran-reshape2. 1099s Preparing to unpack .../212-r-cran-reshape2_1.4.4-2build1_arm64.deb ... 1099s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 1099s Selecting previously unselected package r-cran-caret. 1099s Preparing to unpack .../213-r-cran-caret_7.0-1+dfsg-1_arm64.deb ... 1099s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 1099s Selecting previously unselected package r-cran-conquer. 1099s Preparing to unpack .../214-r-cran-conquer_1.3.3-1_arm64.deb ... 1099s Unpacking r-cran-conquer (1.3.3-1) ... 1099s Selecting previously unselected package r-cran-quantreg. 1099s Preparing to unpack .../215-r-cran-quantreg_6.00-1_arm64.deb ... 1099s Unpacking r-cran-quantreg (6.00-1) ... 1099s Selecting previously unselected package r-cran-foreign. 1099s Preparing to unpack .../216-r-cran-foreign_0.8.88-1_arm64.deb ... 1099s Unpacking r-cran-foreign (0.8.88-1) ... 1099s Selecting previously unselected package r-cran-ellipsis. 1099s Preparing to unpack .../217-r-cran-ellipsis_0.3.2-2_arm64.deb ... 1099s Unpacking r-cran-ellipsis (0.3.2-2) ... 1099s Selecting previously unselected package r-cran-forcats. 1099s Preparing to unpack .../218-r-cran-forcats_1.0.0-1_all.deb ... 1099s Unpacking r-cran-forcats (1.0.0-1) ... 1099s Selecting previously unselected package r-cran-hms. 1099s Preparing to unpack .../219-r-cran-hms_1.1.3-1_all.deb ... 1099s Unpacking r-cran-hms (1.1.3-1) ... 1099s Selecting previously unselected package r-cran-clipr. 1100s Preparing to unpack .../220-r-cran-clipr_0.8.0-1_all.deb ... 1100s Unpacking r-cran-clipr (0.8.0-1) ... 1100s Selecting previously unselected package r-cran-crayon. 1100s Preparing to unpack .../221-r-cran-crayon_1.5.3-1_all.deb ... 1100s Unpacking r-cran-crayon (1.5.3-1) ... 1100s Selecting previously unselected package r-cran-bit. 1100s Preparing to unpack .../222-r-cran-bit_4.6.0+dfsg-1_arm64.deb ... 1100s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 1100s Selecting previously unselected package r-cran-bit64. 1100s Preparing to unpack .../223-r-cran-bit64_4.6.0-1-1ubuntu2_arm64.deb ... 1100s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ... 1100s Selecting previously unselected package r-cran-prettyunits. 1100s Preparing to unpack .../224-r-cran-prettyunits_1.2.0-1_all.deb ... 1100s Unpacking r-cran-prettyunits (1.2.0-1) ... 1100s Selecting previously unselected package r-cran-progress. 1100s Preparing to unpack .../225-r-cran-progress_1.2.3-1_all.deb ... 1100s Unpacking r-cran-progress (1.2.3-1) ... 1100s Selecting previously unselected package r-cran-vroom. 1100s Preparing to unpack .../226-r-cran-vroom_1.6.5-1_arm64.deb ... 1100s Unpacking r-cran-vroom (1.6.5-1) ... 1100s Selecting previously unselected package r-cran-readr. 1100s Preparing to unpack .../227-r-cran-readr_2.1.5-1_arm64.deb ... 1100s Unpacking r-cran-readr (2.1.5-1) ... 1100s Selecting previously unselected package r-cran-haven. 1100s Preparing to unpack .../228-r-cran-haven_2.5.4-1_arm64.deb ... 1100s Unpacking r-cran-haven (2.5.4-1) ... 1100s Selecting previously unselected package r-cran-curl. 1100s Preparing to unpack .../229-r-cran-curl_6.2.1+dfsg-1ubuntu1_arm64.deb ... 1100s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 1100s Selecting previously unselected package r-cran-rematch. 1100s Preparing to unpack .../230-r-cran-rematch_2.0.0-1_all.deb ... 1100s Unpacking r-cran-rematch (2.0.0-1) ... 1100s Selecting previously unselected package r-cran-cellranger. 1100s Preparing to unpack .../231-r-cran-cellranger_1.1.0-3_all.deb ... 1100s Unpacking r-cran-cellranger (1.1.0-3) ... 1100s Selecting previously unselected package r-cran-readxl. 1100s Preparing to unpack .../232-r-cran-readxl_1.4.4-1_arm64.deb ... 1100s Unpacking r-cran-readxl (1.4.4-1) ... 1100s Selecting previously unselected package r-cran-writexl. 1100s Preparing to unpack .../233-r-cran-writexl_1.5.1-1_arm64.deb ... 1100s Unpacking r-cran-writexl (1.5.1-1) ... 1100s Selecting previously unselected package r-cran-r.methodss3. 1100s Preparing to unpack .../234-r-cran-r.methodss3_1.8.2-1_all.deb ... 1100s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 1100s Selecting previously unselected package r-cran-r.oo. 1100s Preparing to unpack .../235-r-cran-r.oo_1.27.0-1_all.deb ... 1100s Unpacking r-cran-r.oo (1.27.0-1) ... 1100s Selecting previously unselected package r-cran-r.utils. 1100s Preparing to unpack .../236-r-cran-r.utils_2.13.0-1_all.deb ... 1100s Unpacking r-cran-r.utils (2.13.0-1) ... 1100s Selecting previously unselected package r-cran-zip. 1100s Preparing to unpack .../237-r-cran-zip_2.3.2-1_arm64.deb ... 1100s Unpacking r-cran-zip (2.3.2-1) ... 1100s Selecting previously unselected package r-cran-openxlsx. 1100s Preparing to unpack .../238-r-cran-openxlsx_4.2.8-1_arm64.deb ... 1100s Unpacking r-cran-openxlsx (4.2.8-1) ... 1100s Selecting previously unselected package r-cran-rio. 1101s Preparing to unpack .../239-r-cran-rio_1.2.3-1_all.deb ... 1101s Unpacking r-cran-rio (1.2.3-1) ... 1101s Selecting previously unselected package r-cran-car. 1101s Preparing to unpack .../240-r-cran-car_3.1-3-1_all.deb ... 1101s Unpacking r-cran-car (3.1-3-1) ... 1101s Selecting previously unselected package r-cran-zoo. 1101s Preparing to unpack .../241-r-cran-zoo_1.8-13-1_arm64.deb ... 1101s Unpacking r-cran-zoo (1.8-13-1) ... 1101s Selecting previously unselected package r-cran-lmtest. 1101s Preparing to unpack .../242-r-cran-lmtest_0.9.40-1_arm64.deb ... 1101s Unpacking r-cran-lmtest (0.9.40-1) ... 1101s Selecting previously unselected package r-cran-sandwich. 1101s Preparing to unpack .../243-r-cran-sandwich_3.1-1-1_all.deb ... 1101s Unpacking r-cran-sandwich (3.1-1-1) ... 1101s Selecting previously unselected package r-cran-aer. 1101s Preparing to unpack .../244-r-cran-aer_1.2-14-1_all.deb ... 1101s Unpacking r-cran-aer (1.2-14-1) ... 1101s Selecting previously unselected package r-cran-blob. 1101s Preparing to unpack .../245-r-cran-blob_1.2.4-1_all.deb ... 1101s Unpacking r-cran-blob (1.2.4-1) ... 1101s Selecting previously unselected package r-cran-fastmap. 1101s Preparing to unpack .../246-r-cran-fastmap_1.2.0-1_arm64.deb ... 1101s Unpacking r-cran-fastmap (1.2.0-1) ... 1101s Selecting previously unselected package r-cran-cachem. 1101s Preparing to unpack .../247-r-cran-cachem_1.1.0-1_arm64.deb ... 1101s Unpacking r-cran-cachem (1.1.0-1) ... 1101s Selecting previously unselected package r-cran-dbi. 1101s Preparing to unpack .../248-r-cran-dbi_1.2.3-1_all.deb ... 1101s Unpacking r-cran-dbi (1.2.3-1) ... 1101s Selecting previously unselected package r-cran-hexbin. 1101s Preparing to unpack .../249-r-cran-hexbin_1.28.5-1_arm64.deb ... 1101s Unpacking r-cran-hexbin (1.28.5-1) ... 1101s Selecting previously unselected package r-cran-memoise. 1101s Preparing to unpack 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(0.5.3-1) ... 1105s Setting up r-cran-car (3.1-3-1) ... 1105s Setting up r-cran-aer (1.2-14-1) ... 1105s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1105s Processing triggers for man-db (2.13.0-1) ... 1106s Processing triggers for install-info (7.1.1-1) ... 1109s autopkgtest [16:17:39]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1109s autopkgtest [16:17:39]: test pkg-r-autopkgtest: [----------------------- 1110s Test: Try to load the R library survey 1110s 1110s R version 4.4.3 (2025-02-28) -- "Trophy Case" 1110s Copyright (C) 2025 The R Foundation for Statistical Computing 1110s Platform: aarch64-unknown-linux-gnu 1110s 1110s R is free software and comes with ABSOLUTELY NO WARRANTY. 1110s You are welcome to redistribute it under certain conditions. 1110s Type 'license()' or 'licence()' for distribution details. 1110s 1110s R is a collaborative project with many contributors. 1110s Type 'contributors()' for more information and 1110s 'citation()' on how to cite R or R packages in publications. 1110s 1110s Type 'demo()' for some demos, 'help()' for on-line help, or 1110s 'help.start()' for an HTML browser interface to help. 1110s Type 'q()' to quit R. 1110s 1110s Loading required package: grid 1110s > library('survey') 1110s Loading required package: Matrix 1111s Loading required package: survival 1111s 1111s Attaching package: ‘survey’ 1111s 1111s The following object is masked from ‘package:graphics’: 1111s 1111s dotchart 1111s 1111s > 1111s > 1111s Other tests are currently unsupported! 1111s They will be progressively added. 1111s autopkgtest [16:17:41]: test pkg-r-autopkgtest: -----------------------] 1113s autopkgtest [16:17:43]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1113s pkg-r-autopkgtest PASS 1113s autopkgtest [16:17:43]: @@@@@@@@@@@@@@@@@@@@ summary 1113s run-unit-test PASS 1113s pkg-r-autopkgtest PASS 1131s nova [W] Using flock in prodstack6-arm64 1131s Creating nova instance adt-plucky-arm64-r-cran-survey-20250315-155910-juju-7f2275-prod-proposed-migration-environment-15-abd818f3-07ad-4a60-93af-2ce6c4ce393e from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1131s nova [W] Timed out waiting for ce565855-495b-4843-b90d-d535922fc268 to get deleted. 1131s nova [W] Using flock in prodstack6-arm64 1131s Creating nova instance adt-plucky-arm64-r-cran-survey-20250315-155910-juju-7f2275-prod-proposed-migration-environment-15-abd818f3-07ad-4a60-93af-2ce6c4ce393e from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1131s nova [W] Timed out waiting for d94aaa05-334d-497c-a136-31cc1ee807c4 to get deleted.