0s autopkgtest [22:36:42]: starting date and time: 2025-03-15 22:36:42+0000 0s autopkgtest [22:36:42]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:36:42]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.63wvue2x/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-16.secgroup --name adt-plucky-amd64-r-cran-survey-20250315-223641-juju-7f2275-prod-proposed-migration-environment-2-9cfdce76-ee4e-49d2-b03d-fd8c64f2317b --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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/ 50s autopkgtest [22:37:32]: testbed dpkg architecture: amd64 50s autopkgtest [22:37:32]: testbed apt version: 2.9.31ubuntu1 51s autopkgtest [22:37:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [22:37:33]: testbed release detected to be: None 52s autopkgtest [22:37:34]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 53s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 53s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 53s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 53s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 53s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 53s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 53s Fetched 1265 kB in 1s (1036 kB/s) 55s Reading package lists... 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s Calculating upgrade... 56s The following package was automatically installed and is no longer required: 56s libnl-genl-3-200 56s Use 'sudo apt autoremove' to remove it. 57s The following NEW packages will be installed: 57s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 57s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 57s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 57s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 57s The following packages will be upgraded: 57s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 57s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 57s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 57s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 57s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 57s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 57s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 57s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 57s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 57s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 57s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 57s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 57s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 57s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 57s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 57s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 57s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 57s parted pci.ids pciutils pinentry-curses python-apt-common python3 57s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 57s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 57s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 57s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 57s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 57s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 57s xz-utils 57s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 829 MB of archives. 57s After this operation, 325 MB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 58s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 59s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 59s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 60s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 60s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 60s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 60s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 60s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 60s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 60s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 60s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 60s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 60s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 60s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 60s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 60s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 60s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 61s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 61s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 61s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 61s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 61s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 61s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 61s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 61s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 61s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 61s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 61s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 61s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 61s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 61s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 61s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 61s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 61s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 61s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 61s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 61s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 61s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 61s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 61s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 61s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 61s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 61s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 61s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 61s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 61s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 61s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 61s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 61s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 61s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 61s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 61s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 61s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 61s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 61s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 61s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 61s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 61s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 61s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 61s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 62s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 62s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 62s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 62s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 62s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 62s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 62s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 62s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 62s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 62s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 62s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 62s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 62s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 62s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 62s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 62s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 62s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 62s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 62s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 62s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 62s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 62s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 62s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 62s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 62s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 62s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 62s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 62s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 62s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 62s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 62s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 62s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 62s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 62s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 62s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 62s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 62s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 63s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 63s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 63s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 63s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 63s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 63s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 63s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 81s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 81s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 81s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 81s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 81s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 81s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 81s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 81s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 83s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 84s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 88s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 88s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 88s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 88s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 88s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 88s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 89s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 89s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 89s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 89s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 89s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 89s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 89s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 89s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 89s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 89s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 89s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 89s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 89s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 89s Preconfiguring packages ... 90s Fetched 829 MB in 32s (25.6 MB/s) 90s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109140 files and directories currently installed.) 90s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 90s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 90s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 90s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 90s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 90s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 91s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 91s Checking for services that may need to be restarted... 91s Checking init scripts... 91s Checking for services that may need to be restarted... 91s Checking init scripts... 91s Stopping some services possibly affected by the upgrade (will be restarted later): 91s cron: stopping...done. 91s 91s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 91s Setting up libc6:amd64 (2.41-1ubuntu1) ... 91s Checking for services that may need to be restarted... 91s Checking init scripts... 91s Restarting services possibly affected by the upgrade: 91s cron: restarting...done. 91s 91s Services restarted successfully. 91s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 94s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ... 94s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 94s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ... 94s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 94s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ... 94s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 94s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ... 94s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 95s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ... 95s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 95s Setting up libudev1:amd64 (257.3-1ubuntu3) ... 95s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 95s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 95s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 95s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 95s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 95s Preparing to unpack .../libselinux1_3.7-3ubuntu3_amd64.deb ... 95s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ... 95s Setting up libselinux1:amd64 (3.7-3ubuntu3) ... 95s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 97s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 97s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 97s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 97s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 97s Setting up python3-minimal (3.13.2-2) ... 97s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 97s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 97s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 97s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 97s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 98s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 98s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 98s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 98s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 98s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 98s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 98s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 98s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 98s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 98s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 98s Selecting previously unselected package libdebuginfod-common. 98s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 98s Unpacking libdebuginfod-common (0.192-4) ... 98s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 98s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 98s Setting up libsemanage-common (3.7-2.1build1) ... 98s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109155 files and directories currently installed.) 99s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 99s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 99s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 99s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 99s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 99s Unpacking libglib2.0-0t64:amd64 (2.84.0-1) 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.../23-parted_3.6-5_amd64.deb ... 101s Unpacking parted (3.6-5) over (3.6-4build1) ... 101s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 101s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 101s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 101s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 101s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 101s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 101s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 101s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 101s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 101s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 102s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 102s Unpacking strace 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(2.44-3ubuntu1) over (2.44-2ubuntu1) ... 102s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 102s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 102s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 102s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 102s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 102s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 102s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 102s Unpacking hwdata (0.393-3) over (0.392-1) ... 102s Selecting previously unselected package pnp.ids. 102s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 102s Unpacking pnp.ids (0.393-3) ... 102s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 102s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 102s Selecting previously unselected package bpftool. 102s Preparing to unpack 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.../56-initramfs-tools_0.146ubuntu1_all.deb ... 107s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 107s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 107s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 107s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 107s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 107s Selecting previously unselected package libdebuginfod1t64:amd64. 107s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 107s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 107s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 107s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 107s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 107s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 107s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 107s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 107s Selecting previously unselected package linux-modules-6.14.0-10-generic. 108s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 108s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 108s Selecting previously unselected package linux-image-6.14.0-10-generic. 108s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 108s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 108s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 108s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 108s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 109s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 109s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-image-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 109s Preparing to unpack .../68-linux-virtual_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 109s Preparing to unpack .../69-linux-image-virtual_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-image-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 109s Preparing to unpack .../70-linux-headers-virtual_6.14.0-10.10_amd64.deb ... 109s Unpacking linux-headers-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 109s Selecting previously unselected package linux-headers-6.14.0-10. 109s Preparing to unpack .../71-linux-headers-6.14.0-10_6.14.0-10.10_all.deb ... 109s Unpacking linux-headers-6.14.0-10 (6.14.0-10.10) ... 113s Selecting previously unselected package linux-headers-6.14.0-10-generic. 113s Preparing to unpack .../72-linux-headers-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 113s Unpacking linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 114s Preparing to unpack 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(1.0.6-6) over (1.0.6-5) ... 115s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 115s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 115s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 115s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 115s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 115s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 115s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 115s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 115s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 115s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 115s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 115s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 115s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 115s Setting up media-types (13.0.0) ... 115s Installing new version of config file /etc/mime.types ... 115s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 115s Setting up ubuntu-kernel-accessories (1.549) ... 115s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 115s Setting up pci.ids (0.0~2025.03.09-1) ... 115s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 115s Setting up apt-utils (2.9.33) ... 115s Setting up libdebuginfod-common (0.192-4) ... 116s Setting up exfatprogs (1.2.8-1) ... 116s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 116s Setting up bpftool (7.6.0+6.14.0-10.10) ... 116s Setting up libestr0:amd64 (0.1.11-2) ... 116s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 116s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 116s Setting up dosfstools (4.2-1.2) ... 116s Setting up rsyslog (8.2412.0-2ubuntu2) ... 116s info: The user `syslog' is already a member of `adm'. 117s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 117s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 117s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 117s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 117s Setting up systemd (257.3-1ubuntu3) ... 117s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 117s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 117s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 118s Setting up libparted2t64:amd64 (3.6-5) ... 118s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 118s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 118s Setting up linux-headers-generic (6.14.0-10.10) ... 118s Setting up libjemalloc2:amd64 (5.3.0-3) ... 118s Setting up locales (2.41-1ubuntu1) ... 118s Installing new version of config file /etc/locale.alias ... 119s Generating locales (this might take a while)... 120s en_US.UTF-8... done 120s Generation complete. 120s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 120s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 120s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 120s Installing new version of config file /etc/apparmor.d/fusermount3 ... 120s Installing new version of config file /etc/apparmor.d/lsusb ... 120s Installing new version of config file /etc/apparmor.d/openvpn ... 121s Reloading AppArmor profiles 123s Setting up libftdi1-2:amd64 (1.5-8build1) ... 123s Setting up libglib2.0-data (2.84.0-1) ... 123s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 123s Setting up libncurses6:amd64 (6.5+20250216-2) ... 123s Setting up strace (6.13+ds-1ubuntu1) ... 123s Setting up xz-utils (5.6.4-1) ... 123s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 124s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 124s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 124s Setting up udev (257.3-1ubuntu3) ... 124s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 127s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 127s Setting up libpci3:amd64 (1:3.13.0-2) ... 127s Setting up whiptail (0.52.24-4ubuntu2) ... 127s Setting up python-apt-common (2.9.9build1) ... 127s Setting up pnp.ids (0.393-3) ... 127s Setting up libnl-3-200:amd64 (3.7.0-1) ... 127s Setting up python3.13-minimal (3.13.2-2) ... 127s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 127s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 127s Setting up libc-dev-bin (2.41-1ubuntu1) ... 127s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 127s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 128s Setting up rsync (3.4.1+ds1-3) ... 128s rsync.service is a disabled or a static unit not running, not starting it. 128s Setting up python3.13-gdbm (3.13.2-2) ... 128s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 128s Setting up systemd-resolved (257.3-1ubuntu3) ... 129s Setting up initramfs-tools-bin (0.146ubuntu1) ... 129s Setting up ncurses-term (6.5+20250216-2) ... 129s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 129s Setting up libpython3.13:amd64 (3.13.2-2) ... 129s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 129s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 129s Setting up systemd-sysv (257.3-1ubuntu3) ... 129s Setting up linux-headers-virtual (6.14.0-10.10) ... 129s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 129s Setting up python3.13 (3.13.2-2) ... 130s Setting up htop (3.4.0-2) ... 130s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 132s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 132s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 132s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 132s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 132s Setting up parted (3.6-5) ... 132s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 132s Setting up python3 (3.13.2-2) ... 132s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 132s Setting up python3-markupsafe (2.1.5-1build4) ... 133s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 135s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 135s Setting up hwdata (0.393-3) ... 135s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 135s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 135s No schema files found: doing nothing. 135s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 135s Setting up linux-perf (6.14.0-10.10) ... 135s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 135s Setting up pciutils (1:3.13.0-2) ... 135s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 135s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 135s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 135s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 136s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 136s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 136s Setting up curl (8.12.1-3ubuntu1) ... 136s Setting up linux-image-virtual (6.14.0-10.10) ... 136s Setting up initramfs-tools-core (0.146ubuntu1) ... 136s Setting up linux-tools-common (6.14.0-10.10) ... 136s Setting up python3-systemd (235-1build6) ... 136s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 136s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 136s Setting up linux-image-generic (6.14.0-10.10) ... 136s Setting up python3-dbus (1.3.2-5build5) ... 136s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 136s Setting up initramfs-tools (0.146ubuntu1) ... 136s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 136s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 136s update-initramfs: deferring update (trigger activated) 136s Setting up linux-generic (6.14.0-10.10) ... 136s Setting up ubuntu-minimal (1.549) ... 136s Setting up python3-apt (2.9.9build1) ... 136s Setting up python3-bcrypt (4.2.0-2.1build1) ... 136s Setting up python3-yaml (6.0.2-1build2) ... 136s Setting up libfwupd3:amd64 (2.0.6-4) ... 136s Setting up python3-lazr.uri (1.0.6-6) ... 136s Setting up binutils (2.44-3ubuntu1) ... 136s Setting up ubuntu-standard (1.549) ... 136s Setting up cloud-init-base (25.1-0ubuntu3) ... 138s Setting up linux-virtual (6.14.0-10.10) ... 138s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 138s Setting up python3-gi (3.50.0-4build1) ... 138s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 138s Setting up fwupd (2.0.6-4) ... 139s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 139s fwupd.service is a disabled or a static unit not running, not starting it. 139s Setting up cloud-init (25.1-0ubuntu3) ... 139s Processing triggers for man-db (2.13.0-1) ... 141s Processing triggers for dbus (1.16.2-1ubuntu1) ... 141s Processing triggers for shared-mime-info (2.4-5) ... 141s Warning: program compiled against libxml 212 using older 209 141s Processing triggers for libc-bin (2.41-1ubuntu1) ... 142s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 142s /etc/kernel/postinst.d/initramfs-tools: 142s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 142s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 153s /etc/kernel/postinst.d/zz-update-grub: 153s Sourcing file `/etc/default/grub' 153s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 153s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 153s Generating grub configuration file ... 153s Found linux image: /boot/vmlinuz-6.14.0-10-generic 153s Found initrd image: /boot/initrd.img-6.14.0-10-generic 153s Found linux image: /boot/vmlinuz-6.12.0-16-generic 153s Found initrd image: /boot/initrd.img-6.12.0-16-generic 154s Found linux image: /boot/vmlinuz-6.11.0-8-generic 154s Found initrd image: /boot/initrd.img-6.11.0-8-generic 154s Warning: os-prober will not be executed to detect other bootable partitions. 154s Systems on them will not be added to the GRUB boot configuration. 154s Check GRUB_DISABLE_OS_PROBER documentation entry. 154s Adding boot menu entry for UEFI Firmware Settings ... 154s done 154s Processing triggers for initramfs-tools (0.146ubuntu1) ... 154s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 154s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Solving dependencies... 166s The following packages will be REMOVED: 166s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 166s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 166s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 166s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 166s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 166s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 166s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 166s linux-tools-6.12.0-16-generic* 167s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 167s After this operation, 545 MB disk space will be freed. 167s (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 ... 148643 files and directories currently installed.) 167s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 167s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 167s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 167s Removing libpython3.12t64:amd64 (3.12.9-1) ... 167s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 167s Removing libnsl2:amd64 (1.3.0-3build3) ... 167s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 167s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 168s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 170s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 171s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 173s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 173s /etc/kernel/postrm.d/initramfs-tools: 173s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 173s /etc/kernel/postrm.d/zz-update-grub: 173s Sourcing file `/etc/default/grub' 173s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 173s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 173s Generating grub configuration file ... 173s Found linux image: /boot/vmlinuz-6.14.0-10-generic 173s Found initrd image: /boot/initrd.img-6.14.0-10-generic 174s Found linux image: /boot/vmlinuz-6.12.0-16-generic 174s Found initrd image: /boot/initrd.img-6.12.0-16-generic 174s Warning: os-prober will not be executed to detect other bootable partitions. 174s Systems on them will not be added to the GRUB boot configuration. 174s Check GRUB_DISABLE_OS_PROBER documentation entry. 174s Adding boot menu entry for UEFI Firmware Settings ... 174s done 174s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 174s W: Removing the running kernel 174s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 174s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 174s /etc/kernel/postrm.d/initramfs-tools: 174s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 174s /etc/kernel/postrm.d/zz-update-grub: 174s Sourcing file `/etc/default/grub' 174s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 174s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 174s Generating grub configuration file ... 174s Found linux image: /boot/vmlinuz-6.14.0-10-generic 174s Found initrd image: /boot/initrd.img-6.14.0-10-generic 175s Warning: os-prober will not be executed to detect other bootable partitions. 175s Systems on them will not be added to the GRUB boot configuration. 175s Check GRUB_DISABLE_OS_PROBER documentation entry. 175s Adding boot menu entry for UEFI Firmware Settings ... 175s done 175s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 175s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 177s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 177s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 177s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 177s Processing triggers for libc-bin (2.41-1ubuntu1) ... 177s (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 ... 76972 files and directories currently installed.) 177s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 177s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 177s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 177s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 177s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 177s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 177s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 177s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 177s autopkgtest [22:39:39]: upgrading testbed (apt dist-upgrade and autopurge) 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 179s Entering ResolveByKeep 179s 179s Calculating upgrade... 180s The following packages will be upgraded: 180s libc-bin libc-dev-bin libc6 libc6-dev locales 180s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Need to get 10.5 MB of archives. 180s After this operation, 1024 B of additional disk space will be used. 180s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 181s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 181s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 181s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 181s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 182s Preconfiguring packages ... 182s Fetched 10.5 MB in 2s (6426 kB/s) 182s (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 ... 76968 files and directories currently installed.) 182s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 182s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 182s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 182s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 182s Setting up libc6:amd64 (2.41-1ubuntu2) ... 183s (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 ... 76968 files and directories currently installed.) 183s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 183s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 183s Setting up libc-bin (2.41-1ubuntu2) ... 183s (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 ... 76968 files and directories currently installed.) 183s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 183s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 183s Setting up locales (2.41-1ubuntu2) ... 184s Generating locales (this might take a while)... 186s en_US.UTF-8... done 186s Generation complete. 186s Setting up libc-dev-bin (2.41-1ubuntu2) ... 186s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 186s Processing triggers for man-db (2.13.0-1) ... 186s Processing triggers for systemd (257.3-1ubuntu3) ... 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s Starting pkgProblemResolver with broken count: 0 188s Starting 2 pkgProblemResolver with broken count: 0 188s Done 189s Solving dependencies... 189s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s autopkgtest [22:39:51]: rebooting testbed after setup commands that affected boot 213s autopkgtest [22:40:15]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 216s autopkgtest [22:40:18]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 218s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (dsc) [2340 B] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (tar) [2341 kB] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-survey 4.4-2-2 (diff) [4580 B] 218s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC 218s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 218s gpgv: issuer "plessy@debian.org" 218s gpgv: Can't check signature: No public key 218s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found 219s autopkgtest [22:40:21]: testing package r-cran-survey version 4.4-2-2 219s autopkgtest [22:40:21]: build not needed 223s autopkgtest [22:40:25]: test run-unit-test: preparing testbed 223s Reading package lists... 224s Building dependency tree... 224s Reading state information... 224s Starting pkgProblemResolver with broken count: 0 224s Starting 2 pkgProblemResolver with broken count: 0 224s Done 225s The following NEW packages will be installed: 225s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 225s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 225s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 225s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 225s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 225s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 225s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 225s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 225s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler node-normalize.css 225s r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 225s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 225s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 225s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 225s r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 225s r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby 225s r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi 225s r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign 225s r-cran-formula r-cran-future r-cran-future.apply r-cran-generics 225s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable 225s r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms 225s r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr 225s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 225s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 225s r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats 225s r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools 225s r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr 225s r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly 225s r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 225s r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress 225s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg r-cran-r.cache 225s r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6 225s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 225s r-cran-rcppeigen r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes 225s r-cran-reformulas r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang 225s r-cran-rpart r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape 225s r-cran-sparsem r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr 225s r-cran-survey r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 225s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 225s r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun 225s r-cran-yaml r-cran-zip r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip 225s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded. 225s Need to get 172 MB of archives. 225s After this operation, 346 MB of additional disk space will be used. 225s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 226s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 226s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 226s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 226s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 226s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 226s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 226s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 226s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 226s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 226s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 226s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 226s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 226s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 226s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 227s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 227s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 227s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 227s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 227s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 227s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 227s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 227s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 227s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 227s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 227s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 227s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 227s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 227s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 227s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 227s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 227s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 227s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 227s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 227s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 227s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 227s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 227s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 228s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 228s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 228s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 228s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 228s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 228s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 228s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 228s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 228s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 228s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 228s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 230s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 230s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B] 230s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 230s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB] 230s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cardata all 3.0.5-1 [1819 kB] 230s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-formula all 1.2-5-1 [158 kB] 230s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 230s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 230s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 230s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 230s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 231s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 231s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-boot all 1.3-31-1 [635 kB] 231s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 231s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 231s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 231s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB] 231s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nloptr amd64 2.1.1-1 [251 kB] 231s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 231s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 231s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reformulas all 0.4.0-1 [91.5 kB] 231s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 231s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 231s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lme4 amd64 1.1-36-1 [4135 kB] 231s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 231s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 232s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 232s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 232s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 232s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 232s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 232s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 232s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 232s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 232s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 232s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 232s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 232s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 232s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 232s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 232s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 232s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 232s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringi amd64 1.8.4-1build1 [927 kB] 232s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 232s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB] 232s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 232s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 232s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 232s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 232s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 232s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 233s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 233s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 233s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 233s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 233s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 233s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 233s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 234s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 234s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-deriv all 4.1.6-1 [151 kB] 234s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 234s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB] 234s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-doby all 4.6.25-1 [4772 kB] 234s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 234s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.51+dfsg-1 [574 kB] 234s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 234s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 234s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 234s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 234s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pbkrtest all 0.5.3-1 [178 kB] 234s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sparsem amd64 1.84-2-1 [813 kB] 234s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixmodels all 0.5-3-1 [361 kB] 234s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB] 235s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB] 235s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpparmadillo amd64 14.2.3-1-1 [864 kB] 235s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-class amd64 7.3-23-1 [92.7 kB] 235s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] 235s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-e1071 amd64 1.7-16-1 [565 kB] 235s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB] 235s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-iterators all 1.0.14-1 [336 kB] 235s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-foreach all 1.5.2-1 [124 kB] 235s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 235s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelmetrics amd64 1.2.2.2-1build1 [128 kB] 235s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] 235s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-proc amd64 1.18.5-1 [966 kB] 235s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tzdb amd64 0.4.0-2 [521 kB] 235s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clock amd64 0.7.2-1 [1903 kB] 235s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gower amd64 1.0.2-1 [210 kB] 235s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hardhat all 1.4.0+dfsg-1 [565 kB] 235s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rpart amd64 4.1.24-1 [670 kB] 235s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-shape all 1.4.6.1-1 [749 kB] 235s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-diagram all 1.6.5-2 [656 kB] 235s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-kernsmooth amd64 2.23-26-1 [94.5 kB] 235s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB] 235s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-globals all 0.16.3-1 [120 kB] 235s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 235s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-parallelly amd64 1.42.0-1 [540 kB] 235s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 235s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 235s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progressr all 0.15.1-1 [353 kB] 235s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-squarem all 2021.1-1 [179 kB] 235s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lava all 1.8.1+dfsg-1 [2191 kB] 235s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prodlim amd64 2024.06.25-1 [415 kB] 235s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ipred amd64 0.9-15-1 [386 kB] 235s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timechange amd64 0.3.0-1 [178 kB] 235s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1009 kB] 236s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timedate amd64 4041.110-1 [1208 kB] 236s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 236s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB] 236s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-caret amd64 7.0-1+dfsg-1 [3460 kB] 236s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-conquer amd64 1.3.3-1 [499 kB] 236s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-quantreg amd64 6.00-1 [1454 kB] 236s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-foreign amd64 0.8.88-1 [250 kB] 236s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 236s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB] 236s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB] 236s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB] 236s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB] 236s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB] 236s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit64 amd64 4.6.0-1-1ubuntu2 [501 kB] 236s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] 236s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB] 236s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB] 236s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB] 236s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-haven amd64 2.5.4-1 [346 kB] 236s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-curl amd64 6.2.1+dfsg-1ubuntu1 [197 kB] 236s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB] 236s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB] 236s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readxl amd64 1.4.4-1 [360 kB] 236s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-writexl amd64 1.5.1-1 [158 kB] 236s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 236s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.oo all 1.27.0-1 [979 kB] 236s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.utils all 2.13.0-1 [1423 kB] 236s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-zip amd64 2.3.2-1 [156 kB] 236s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-openxlsx amd64 4.2.8-1 [2056 kB] 236s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rio all 1.2.3-1 [546 kB] 236s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-car all 3.1-3-1 [1525 kB] 237s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-zoo amd64 1.8-13-1 [999 kB] 237s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lmtest amd64 0.9.40-1 [396 kB] 237s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sandwich all 3.1-1-1 [1483 kB] 237s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-aer all 1.2-14-1 [2597 kB] 237s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB] 237s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB] 237s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB] 237s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB] 237s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hexbin amd64 1.28.5-1 [1581 kB] 237s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB] 237s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB] 237s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 237s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.cache all 0.16.0-1 [113 kB] 237s Get:201 http://ftpmaster.internal/ubuntu plucky/main amd64 tcl8.6 amd64 8.6.16+dfsg-1 [14.9 kB] 237s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 tcl amd64 8.6.14build1 [4124 B] 237s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.rsp all 0.46.0+ds-1 [1412 kB] 238s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB] 238s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survey amd64 4.4-2-2 [3453 kB] 239s Preconfiguring packages ... 239s Fetched 172 MB in 13s (13.3 MB/s) 239s Selecting previously unselected package fonts-dejavu-mono. 239s (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 ... 76968 files and directories currently installed.) 239s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8_all.deb ... 239s Unpacking fonts-dejavu-mono (2.37-8) ... 239s Selecting previously unselected package fonts-dejavu-core. 239s Preparing to unpack .../001-fonts-dejavu-core_2.37-8_all.deb ... 239s Unpacking fonts-dejavu-core (2.37-8) ... 239s Selecting previously unselected package fontconfig-config. 239s Preparing to unpack .../002-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 239s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 239s Selecting previously unselected package libfontconfig1:amd64. 239s Preparing to unpack .../003-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 239s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 239s Selecting previously unselected package fontconfig. 239s Preparing to unpack .../004-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 239s Unpacking fontconfig (2.15.0-2ubuntu1) ... 239s Selecting previously unselected package fonts-glyphicons-halflings. 239s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 239s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 239s Selecting previously unselected package fonts-mathjax. 239s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 239s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 240s Selecting previously unselected package libblas3:amd64. 240s Preparing to unpack .../007-libblas3_3.12.1-2_amd64.deb ... 240s Unpacking libblas3:amd64 (3.12.1-2) ... 240s Selecting previously unselected package libpixman-1-0:amd64. 240s Preparing to unpack .../008-libpixman-1-0_0.44.0-3_amd64.deb ... 240s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 240s Selecting previously unselected package libxcb-render0:amd64. 240s Preparing to unpack .../009-libxcb-render0_1.17.0-2_amd64.deb ... 240s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 240s Selecting previously unselected package libxcb-shm0:amd64. 240s Preparing to unpack .../010-libxcb-shm0_1.17.0-2_amd64.deb ... 240s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 240s Selecting previously unselected package libxrender1:amd64. 240s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 240s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 240s Selecting previously unselected package libcairo2:amd64. 240s Preparing to unpack .../012-libcairo2_1.18.2-2_amd64.deb ... 240s Unpacking libcairo2:amd64 (1.18.2-2) ... 240s Selecting previously unselected package libdatrie1:amd64. 240s Preparing to unpack .../013-libdatrie1_0.2.13-3build1_amd64.deb ... 240s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 240s Selecting previously unselected package libdeflate0:amd64. 240s Preparing to unpack .../014-libdeflate0_1.23-1_amd64.deb ... 240s Unpacking libdeflate0:amd64 (1.23-1) ... 240s Selecting previously unselected package libgfortran5:amd64. 240s Preparing to unpack .../015-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 240s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 240s Selecting previously unselected package libgomp1:amd64. 240s Preparing to unpack .../016-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 240s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 240s Selecting previously unselected package libgraphite2-3:amd64. 240s Preparing to unpack .../017-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 240s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 240s Selecting previously unselected package libharfbuzz0b:amd64. 240s Preparing to unpack .../018-libharfbuzz0b_10.2.0-1_amd64.deb ... 240s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 240s Selecting previously unselected package x11-common. 240s Preparing to unpack .../019-x11-common_1%3a7.7+23ubuntu3_all.deb ... 240s Unpacking x11-common (1:7.7+23ubuntu3) ... 240s Selecting previously unselected package libice6:amd64. 240s Preparing to unpack .../020-libice6_2%3a1.1.1-1_amd64.deb ... 240s Unpacking libice6:amd64 (2:1.1.1-1) ... 240s Selecting previously unselected package libjpeg-turbo8:amd64. 240s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 240s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 240s Selecting previously unselected package libjpeg8:amd64. 240s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_amd64.deb ... 240s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 240s Selecting previously unselected package libjs-bootstrap. 240s Preparing to unpack .../023-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 240s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 240s Selecting previously unselected package libjs-highlight.js. 240s Preparing to unpack .../024-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 240s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 240s Selecting previously unselected package libjs-jquery. 240s Preparing to unpack .../025-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 240s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 240s Selecting previously unselected package libjs-jquery-datatables. 240s Preparing to unpack .../026-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 240s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 240s Selecting previously unselected package liblapack3:amd64. 240s Preparing to unpack .../027-liblapack3_3.12.1-2_amd64.deb ... 240s Unpacking liblapack3:amd64 (3.12.1-2) ... 240s Selecting previously unselected package liblerc4:amd64. 240s Preparing to unpack .../028-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 240s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 240s Selecting previously unselected package libthai-data. 240s Preparing to unpack .../029-libthai-data_0.1.29-2build1_all.deb ... 240s Unpacking libthai-data (0.1.29-2build1) ... 240s Selecting previously unselected package libthai0:amd64. 240s Preparing to unpack .../030-libthai0_0.1.29-2build1_amd64.deb ... 240s Unpacking libthai0:amd64 (0.1.29-2build1) ... 241s Selecting previously unselected package libpango-1.0-0:amd64. 241s Preparing to unpack .../031-libpango-1.0-0_1.56.2-1_amd64.deb ... 241s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 241s Selecting previously unselected package libpangoft2-1.0-0:amd64. 241s Preparing to unpack .../032-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 241s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 241s Selecting previously unselected package libpangocairo-1.0-0:amd64. 241s Preparing to unpack .../033-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 241s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 241s Selecting previously unselected package libpaper2:amd64. 241s Preparing to unpack .../034-libpaper2_2.2.5-0.3_amd64.deb ... 241s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 241s Selecting previously unselected package libpaper-utils. 241s Preparing to unpack .../035-libpaper-utils_2.2.5-0.3_amd64.deb ... 241s Unpacking libpaper-utils (2.2.5-0.3) ... 241s Selecting previously unselected package libsharpyuv0:amd64. 241s Preparing to unpack .../036-libsharpyuv0_1.5.0-0.1_amd64.deb ... 241s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 241s Selecting previously unselected package libsm6:amd64. 241s Preparing to unpack .../037-libsm6_2%3a1.2.4-1_amd64.deb ... 241s Unpacking libsm6:amd64 (2:1.2.4-1) ... 241s Selecting previously unselected package libtcl8.6:amd64. 241s Preparing to unpack .../038-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 241s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 241s Selecting previously unselected package libjbig0:amd64. 241s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 241s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 241s Selecting previously unselected package libwebp7:amd64. 241s Preparing to unpack .../040-libwebp7_1.5.0-0.1_amd64.deb ... 241s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 241s Selecting previously unselected package libtiff6:amd64. 241s Preparing to unpack .../041-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 241s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 241s Selecting previously unselected package libxft2:amd64. 241s Preparing to unpack .../042-libxft2_2.3.6-1build1_amd64.deb ... 241s Unpacking libxft2:amd64 (2.3.6-1build1) ... 241s Selecting previously unselected package libxss1:amd64. 241s Preparing to unpack .../043-libxss1_1%3a1.2.3-1build3_amd64.deb ... 241s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 241s Selecting previously unselected package libtk8.6:amd64. 241s Preparing to unpack .../044-libtk8.6_8.6.16-1_amd64.deb ... 241s Unpacking libtk8.6:amd64 (8.6.16-1) ... 241s Selecting previously unselected package libxt6t64:amd64. 241s Preparing to unpack .../045-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 241s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 241s Selecting previously unselected package zip. 241s Preparing to unpack .../046-zip_3.0-14ubuntu2_amd64.deb ... 241s Unpacking zip (3.0-14ubuntu2) ... 241s Selecting previously unselected package unzip. 241s Preparing to unpack .../047-unzip_6.0-28ubuntu6_amd64.deb ... 241s Unpacking unzip (6.0-28ubuntu6) ... 241s Selecting previously unselected package xdg-utils. 241s Preparing to unpack .../048-xdg-utils_1.2.1-2ubuntu1_all.deb ... 241s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 241s Selecting previously unselected package r-base-core. 241s Preparing to unpack .../049-r-base-core_4.4.3-1_amd64.deb ... 241s Unpacking r-base-core (4.4.3-1) ... 242s Selecting previously unselected package r-cran-littler. 242s Preparing to unpack .../050-r-cran-littler_0.3.20-2_amd64.deb ... 242s Unpacking r-cran-littler (0.3.20-2) ... 242s Selecting previously unselected package littler. 242s Preparing to unpack .../051-littler_0.3.20-2_all.deb ... 242s Unpacking littler (0.3.20-2) ... 242s Selecting previously unselected package node-normalize.css. 242s Preparing to unpack .../052-node-normalize.css_8.0.1-5_all.deb ... 242s Unpacking node-normalize.css (8.0.1-5) ... 242s Selecting previously unselected package r-cran-abind. 242s Preparing to unpack .../053-r-cran-abind_1.4-8-1_all.deb ... 242s Unpacking r-cran-abind (1.4-8-1) ... 242s Selecting previously unselected package r-cran-cardata. 242s Preparing to unpack .../054-r-cran-cardata_3.0.5-1_all.deb ... 242s Unpacking r-cran-cardata (3.0.5-1) ... 242s Selecting previously unselected package r-cran-formula. 242s Preparing to unpack .../055-r-cran-formula_1.2-5-1_all.deb ... 242s Unpacking r-cran-formula (1.2-5-1) ... 242s Selecting previously unselected package r-cran-mass. 242s Preparing to unpack .../056-r-cran-mass_7.3-64-1_amd64.deb ... 242s Unpacking r-cran-mass (7.3-64-1) ... 242s Selecting previously unselected package r-cran-lattice. 242s Preparing to unpack .../057-r-cran-lattice_0.22-6-1_amd64.deb ... 242s Unpacking r-cran-lattice (0.22-6-1) ... 242s Selecting previously unselected package r-cran-nlme. 242s Preparing to unpack .../058-r-cran-nlme_3.1.167-1_amd64.deb ... 242s Unpacking r-cran-nlme (3.1.167-1) ... 242s Selecting previously unselected package r-cran-matrix. 242s Preparing to unpack .../059-r-cran-matrix_1.7-3-1_amd64.deb ... 242s Unpacking r-cran-matrix (1.7-3-1) ... 242s Selecting previously unselected package r-cran-mgcv. 242s Preparing to unpack .../060-r-cran-mgcv_1.9-1-1_amd64.deb ... 242s Unpacking r-cran-mgcv (1.9-1-1) ... 242s Selecting previously unselected package r-cran-nnet. 242s Preparing to unpack .../061-r-cran-nnet_7.3-20-1_amd64.deb ... 242s Unpacking r-cran-nnet (7.3-20-1) ... 242s Selecting previously unselected package r-cran-boot. 242s Preparing to unpack .../062-r-cran-boot_1.3-31-1_all.deb ... 242s Unpacking r-cran-boot (1.3-31-1) ... 242s Selecting previously unselected package r-cran-pkgkitten. 242s Preparing to unpack .../063-r-cran-pkgkitten_0.2.4-1_all.deb ... 242s Unpacking r-cran-pkgkitten (0.2.4-1) ... 242s Selecting previously unselected package r-cran-rcpp. 242s Preparing to unpack .../064-r-cran-rcpp_1.0.14-1_amd64.deb ... 242s Unpacking r-cran-rcpp (1.0.14-1) ... 242s Selecting previously unselected package r-cran-minqa. 242s Preparing to unpack .../065-r-cran-minqa_1.2.8-1_amd64.deb ... 242s Unpacking r-cran-minqa (1.2.8-1) ... 242s Selecting previously unselected package libnlopt0:amd64. 242s Preparing to unpack .../066-libnlopt0_2.7.1-6ubuntu3_amd64.deb ... 242s Unpacking libnlopt0:amd64 (2.7.1-6ubuntu3) ... 242s Selecting previously unselected package r-cran-nloptr. 242s Preparing to unpack .../067-r-cran-nloptr_2.1.1-1_amd64.deb ... 242s Unpacking r-cran-nloptr (2.1.1-1) ... 242s Selecting previously unselected package r-cran-rbibutils. 242s Preparing to unpack .../068-r-cran-rbibutils_2.3-1_amd64.deb ... 242s Unpacking r-cran-rbibutils (2.3-1) ... 242s Selecting previously unselected package r-cran-rdpack. 242s Preparing to unpack .../069-r-cran-rdpack_2.6.2-1syncable1_all.deb ... 242s Unpacking r-cran-rdpack (2.6.2-1syncable1) ... 243s Selecting previously unselected package r-cran-reformulas. 243s Preparing to unpack .../070-r-cran-reformulas_0.4.0-1_all.deb ... 243s Unpacking r-cran-reformulas (0.4.0-1) ... 243s Selecting previously unselected package r-cran-rcppeigen. 243s Preparing to unpack .../071-r-cran-rcppeigen_0.3.4.0.2-1_amd64.deb ... 243s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 243s Selecting previously unselected package r-cran-statmod. 243s Preparing to unpack .../072-r-cran-statmod_1.5.0-1_amd64.deb ... 243s Unpacking r-cran-statmod (1.5.0-1) ... 243s Selecting previously unselected package r-cran-lme4. 243s Preparing to unpack .../073-r-cran-lme4_1.1-36-1_amd64.deb ... 243s Unpacking r-cran-lme4 (1.1-36-1) ... 243s Selecting previously unselected package r-cran-backports. 243s Preparing to unpack .../074-r-cran-backports_1.5.0-2_amd64.deb ... 243s Unpacking r-cran-backports (1.5.0-2) ... 243s Selecting previously unselected package r-cran-cli. 243s Preparing to unpack .../075-r-cran-cli_3.6.4-1_amd64.deb ... 243s Unpacking r-cran-cli (3.6.4-1) ... 243s Selecting previously unselected package r-cran-generics. 243s Preparing to unpack .../076-r-cran-generics_0.1.3-1_all.deb ... 243s Unpacking r-cran-generics (0.1.3-1) ... 243s Selecting previously unselected package r-cran-glue. 243s Preparing to unpack .../077-r-cran-glue_1.8.0-1_amd64.deb ... 243s Unpacking r-cran-glue (1.8.0-1) ... 243s Selecting previously unselected package r-cran-rlang. 243s Preparing to unpack .../078-r-cran-rlang_1.1.5-1_amd64.deb ... 243s Unpacking r-cran-rlang (1.1.5-1) ... 243s Selecting previously unselected package r-cran-lifecycle. 243s Preparing to unpack .../079-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 243s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 243s Selecting previously unselected package r-cran-magrittr. 243s Preparing to unpack .../080-r-cran-magrittr_2.0.3-1_amd64.deb ... 243s Unpacking r-cran-magrittr (2.0.3-1) ... 243s Selecting previously unselected package r-cran-utf8. 243s Preparing to unpack .../081-r-cran-utf8_1.2.4-1_amd64.deb ... 243s Unpacking r-cran-utf8 (1.2.4-1) ... 243s Selecting previously unselected package r-cran-vctrs. 243s Preparing to unpack .../082-r-cran-vctrs_0.6.5-1_amd64.deb ... 243s Unpacking r-cran-vctrs (0.6.5-1) ... 243s Selecting previously unselected package r-cran-pillar. 243s Preparing to unpack .../083-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 243s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 243s Selecting previously unselected package r-cran-r6. 243s Preparing to unpack .../084-r-cran-r6_2.6.1-1_all.deb ... 243s Unpacking r-cran-r6 (2.6.1-1) ... 243s Selecting previously unselected package r-cran-fansi. 243s Preparing to unpack .../085-r-cran-fansi_1.0.5-1_amd64.deb ... 243s Unpacking r-cran-fansi (1.0.5-1) ... 243s Selecting previously unselected package r-cran-pkgconfig. 243s Preparing to unpack .../086-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 243s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 243s Selecting previously unselected package r-cran-tibble. 243s Preparing to unpack .../087-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 243s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 244s Selecting previously unselected package r-cran-withr. 244s Preparing to unpack .../088-r-cran-withr_3.0.2+dfsg-1_all.deb ... 244s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 244s Selecting previously unselected package r-cran-tidyselect. 244s Preparing to unpack .../089-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 244s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 244s Selecting previously unselected package r-cran-dplyr. 244s Preparing to unpack .../090-r-cran-dplyr_1.1.4-4_amd64.deb ... 244s Unpacking r-cran-dplyr (1.1.4-4) ... 244s Selecting previously unselected package r-cran-purrr. 244s Preparing to unpack .../091-r-cran-purrr_1.0.4-1_amd64.deb ... 244s Unpacking r-cran-purrr (1.0.4-1) ... 244s Selecting previously unselected package r-cran-stringi. 244s Preparing to unpack .../092-r-cran-stringi_1.8.4-1build1_amd64.deb ... 244s Unpacking r-cran-stringi (1.8.4-1build1) ... 244s Selecting previously unselected package r-cran-stringr. 244s Preparing to unpack .../093-r-cran-stringr_1.5.1-1_all.deb ... 244s Unpacking r-cran-stringr (1.5.1-1) ... 244s Selecting previously unselected package r-cran-cpp11. 244s Preparing to unpack .../094-r-cran-cpp11_0.5.2-1_all.deb ... 244s Unpacking r-cran-cpp11 (0.5.2-1) ... 244s Selecting previously unselected package r-cran-tidyr. 244s Preparing to unpack .../095-r-cran-tidyr_1.3.1-1_amd64.deb ... 244s Unpacking r-cran-tidyr (1.3.1-1) ... 244s Selecting previously unselected package r-cran-broom. 244s Preparing to unpack .../096-r-cran-broom_1.0.7+dfsg-1_all.deb ... 244s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 244s Selecting previously unselected package r-cran-numderiv. 244s Preparing to unpack .../097-r-cran-numderiv_2016.8-1.1-3_all.deb ... 244s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 244s Selecting previously unselected package r-cran-gtable. 244s Preparing to unpack .../098-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 244s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 244s Selecting previously unselected package r-cran-isoband. 244s Preparing to unpack .../099-r-cran-isoband_0.2.7-1_amd64.deb ... 244s Unpacking r-cran-isoband (0.2.7-1) ... 244s Selecting previously unselected package r-cran-farver. 244s Preparing to unpack .../100-r-cran-farver_2.1.2-1_amd64.deb ... 244s Unpacking r-cran-farver (2.1.2-1) ... 244s Selecting previously unselected package r-cran-labeling. 244s Preparing to unpack .../101-r-cran-labeling_0.4.3-1_all.deb ... 244s Unpacking r-cran-labeling (0.4.3-1) ... 244s Selecting previously unselected package r-cran-colorspace. 244s Preparing to unpack .../102-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 244s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 244s Selecting previously unselected package r-cran-munsell. 244s Preparing to unpack .../103-r-cran-munsell_0.5.1-1_all.deb ... 244s Unpacking r-cran-munsell (0.5.1-1) ... 244s Selecting previously unselected package r-cran-rcolorbrewer. 244s Preparing to unpack .../104-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 244s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 244s Selecting previously unselected package r-cran-viridislite. 244s Preparing to unpack .../105-r-cran-viridislite_0.4.2-2_all.deb ... 244s Unpacking r-cran-viridislite (0.4.2-2) ... 244s Selecting previously unselected package r-cran-scales. 244s Preparing to unpack .../106-r-cran-scales_1.3.0-1_all.deb ... 244s Unpacking r-cran-scales (1.3.0-1) ... 244s Selecting previously unselected package r-cran-ggplot2. 244s Preparing to unpack .../107-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 244s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 245s Selecting previously unselected package r-cran-cowplot. 245s Preparing to unpack .../108-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 245s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 245s Selecting previously unselected package r-cran-deriv. 245s Preparing to unpack .../109-r-cran-deriv_4.1.6-1_all.deb ... 245s Unpacking r-cran-deriv (4.1.6-1) ... 245s Selecting previously unselected package r-cran-modelr. 245s Preparing to unpack .../110-r-cran-modelr_0.1.11-1_all.deb ... 245s Unpacking r-cran-modelr (0.1.11-1) ... 245s Selecting previously unselected package r-cran-microbenchmark. 245s Preparing to unpack .../111-r-cran-microbenchmark_1.5.0-1_amd64.deb ... 245s Unpacking r-cran-microbenchmark (1.5.0-1) ... 245s Selecting previously unselected package r-cran-doby. 245s Preparing to unpack .../112-r-cran-doby_4.6.25-1_all.deb ... 245s Unpacking r-cran-doby (4.6.25-1) ... 245s Selecting previously unselected package r-cran-evaluate. 245s Preparing to unpack .../113-r-cran-evaluate_1.0.3-1_all.deb ... 245s Unpacking r-cran-evaluate (1.0.3-1) ... 245s Selecting previously unselected package r-cran-xfun. 245s Preparing to unpack .../114-r-cran-xfun_0.51+dfsg-1_amd64.deb ... 245s Unpacking r-cran-xfun (0.51+dfsg-1) ... 245s Selecting previously unselected package r-cran-highr. 245s Preparing to unpack .../115-r-cran-highr_0.11+dfsg-1_all.deb ... 245s Unpacking r-cran-highr (0.11+dfsg-1) ... 245s Selecting previously unselected package r-cran-yaml. 245s Preparing to unpack .../116-r-cran-yaml_2.3.10-1_amd64.deb ... 245s Unpacking r-cran-yaml (2.3.10-1) ... 245s Selecting previously unselected package libjs-mathjax. 245s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 245s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 246s Selecting previously unselected package r-cran-knitr. 246s Preparing to unpack .../118-r-cran-knitr_1.49+dfsg-1_all.deb ... 246s Unpacking r-cran-knitr (1.49+dfsg-1) ... 246s Selecting previously unselected package r-cran-pbkrtest. 246s Preparing to unpack .../119-r-cran-pbkrtest_0.5.3-1_all.deb ... 246s Unpacking r-cran-pbkrtest (0.5.3-1) ... 246s Selecting previously unselected package r-cran-sparsem. 246s Preparing to unpack .../120-r-cran-sparsem_1.84-2-1_amd64.deb ... 246s Unpacking r-cran-sparsem (1.84-2-1) ... 246s Selecting previously unselected package r-cran-matrixmodels. 246s Preparing to unpack .../121-r-cran-matrixmodels_0.5-3-1_all.deb ... 246s Unpacking r-cran-matrixmodels (0.5-3-1) ... 246s Selecting previously unselected package r-cran-survival. 246s Preparing to unpack .../122-r-cran-survival_3.8-3-1_amd64.deb ... 246s Unpacking r-cran-survival (3.8-3-1) ... 246s Selecting previously unselected package r-cran-matrixstats. 246s Preparing to unpack .../123-r-cran-matrixstats_1.5.0-1_amd64.deb ... 246s Unpacking r-cran-matrixstats (1.5.0-1) ... 246s Selecting previously unselected package r-cran-rcpparmadillo. 246s Preparing to unpack .../124-r-cran-rcpparmadillo_14.2.3-1-1_amd64.deb ... 246s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 246s Selecting previously unselected package r-cran-class. 246s Preparing to unpack .../125-r-cran-class_7.3-23-1_amd64.deb ... 246s Unpacking r-cran-class (7.3-23-1) ... 246s Selecting previously unselected package r-cran-proxy. 246s Preparing to unpack .../126-r-cran-proxy_0.4-27-1_amd64.deb ... 246s Unpacking r-cran-proxy (0.4-27-1) ... 247s Selecting previously unselected package r-cran-e1071. 247s Preparing to unpack .../127-r-cran-e1071_1.7-16-1_amd64.deb ... 247s Unpacking r-cran-e1071 (1.7-16-1) ... 247s Selecting previously unselected package r-cran-codetools. 247s Preparing to unpack .../128-r-cran-codetools_0.2-20-1_all.deb ... 247s Unpacking r-cran-codetools (0.2-20-1) ... 247s Selecting previously unselected package r-cran-iterators. 247s Preparing to unpack .../129-r-cran-iterators_1.0.14-1_all.deb ... 247s Unpacking r-cran-iterators (1.0.14-1) ... 247s Selecting previously unselected package r-cran-foreach. 247s Preparing to unpack .../130-r-cran-foreach_1.5.2-1_all.deb ... 247s Unpacking r-cran-foreach (1.5.2-1) ... 247s Selecting previously unselected package r-cran-data.table. 247s Preparing to unpack .../131-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ... 247s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 247s Selecting previously unselected package r-cran-modelmetrics. 247s Preparing to unpack .../132-r-cran-modelmetrics_1.2.2.2-1build1_amd64.deb ... 247s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 247s Selecting previously unselected package r-cran-plyr. 247s Preparing to unpack .../133-r-cran-plyr_1.8.9-1_amd64.deb ... 247s Unpacking r-cran-plyr (1.8.9-1) ... 247s Selecting previously unselected package r-cran-proc. 247s Preparing to unpack .../134-r-cran-proc_1.18.5-1_amd64.deb ... 247s Unpacking r-cran-proc (1.18.5-1) ... 247s Selecting previously unselected package r-cran-tzdb. 247s Preparing to unpack .../135-r-cran-tzdb_0.4.0-2_amd64.deb ... 247s Unpacking r-cran-tzdb (0.4.0-2) ... 247s Selecting previously unselected package r-cran-clock. 247s Preparing to unpack .../136-r-cran-clock_0.7.2-1_amd64.deb ... 247s Unpacking r-cran-clock (0.7.2-1) ... 247s Selecting previously unselected package r-cran-gower. 247s Preparing to unpack .../137-r-cran-gower_1.0.2-1_amd64.deb ... 247s Unpacking r-cran-gower (1.0.2-1) ... 247s Selecting previously unselected package r-cran-hardhat. 247s Preparing to unpack .../138-r-cran-hardhat_1.4.0+dfsg-1_all.deb ... 247s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ... 247s Selecting previously unselected package r-cran-rpart. 247s Preparing to unpack .../139-r-cran-rpart_4.1.24-1_amd64.deb ... 247s Unpacking r-cran-rpart (4.1.24-1) ... 247s Selecting previously unselected package r-cran-shape. 247s Preparing to unpack .../140-r-cran-shape_1.4.6.1-1_all.deb ... 247s Unpacking r-cran-shape (1.4.6.1-1) ... 247s Selecting previously unselected package r-cran-diagram. 247s Preparing to unpack .../141-r-cran-diagram_1.6.5-2_all.deb ... 247s Unpacking r-cran-diagram (1.6.5-2) ... 247s Selecting previously unselected package r-cran-kernsmooth. 247s Preparing to unpack .../142-r-cran-kernsmooth_2.23-26-1_amd64.deb ... 247s Unpacking r-cran-kernsmooth (2.23-26-1) ... 247s Selecting previously unselected package r-cran-digest. 247s Preparing to unpack .../143-r-cran-digest_0.6.37-1_amd64.deb ... 247s Unpacking r-cran-digest (0.6.37-1) ... 247s Selecting previously unselected package r-cran-globals. 247s Preparing to unpack .../144-r-cran-globals_0.16.3-1_all.deb ... 247s Unpacking r-cran-globals (0.16.3-1) ... 247s Selecting previously unselected package r-cran-listenv. 247s Preparing to unpack .../145-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 247s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 247s Selecting previously unselected package r-cran-parallelly. 247s Preparing to unpack .../146-r-cran-parallelly_1.42.0-1_amd64.deb ... 247s Unpacking r-cran-parallelly (1.42.0-1) ... 247s Selecting previously unselected package r-cran-future. 247s Preparing to unpack .../147-r-cran-future_1.34.0+dfsg-1_all.deb ... 247s Unpacking r-cran-future (1.34.0+dfsg-1) ... 248s Selecting previously unselected package r-cran-future.apply. 248s Preparing to unpack .../148-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 248s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 248s Selecting previously unselected package r-cran-progressr. 248s Preparing to unpack .../149-r-cran-progressr_0.15.1-1_all.deb ... 248s Unpacking r-cran-progressr (0.15.1-1) ... 248s Selecting previously unselected package r-cran-squarem. 248s Preparing to unpack .../150-r-cran-squarem_2021.1-1_all.deb ... 248s Unpacking r-cran-squarem (2021.1-1) ... 248s Selecting previously unselected package r-cran-lava. 248s Preparing to unpack .../151-r-cran-lava_1.8.1+dfsg-1_all.deb ... 248s Unpacking r-cran-lava (1.8.1+dfsg-1) ... 248s Selecting previously unselected package r-cran-prodlim. 248s Preparing to unpack .../152-r-cran-prodlim_2024.06.25-1_amd64.deb ... 248s Unpacking r-cran-prodlim (2024.06.25-1) ... 248s Selecting previously unselected package r-cran-ipred. 248s Preparing to unpack .../153-r-cran-ipred_0.9-15-1_amd64.deb ... 248s Unpacking r-cran-ipred (0.9-15-1) ... 248s Selecting previously unselected package r-cran-timechange. 248s Preparing to unpack .../154-r-cran-timechange_0.3.0-1_amd64.deb ... 248s Unpacking r-cran-timechange (0.3.0-1) ... 248s Selecting previously unselected package r-cran-lubridate. 248s Preparing to unpack .../155-r-cran-lubridate_1.9.4+dfsg-1_amd64.deb ... 248s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 248s Selecting previously unselected package r-cran-timedate. 248s Preparing to unpack .../156-r-cran-timedate_4041.110-1_amd64.deb ... 248s Unpacking r-cran-timedate (4041.110-1) ... 248s Selecting previously unselected package r-cran-recipes. 248s Preparing to unpack .../157-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 248s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 248s Selecting previously unselected package r-cran-reshape2. 248s Preparing to unpack .../158-r-cran-reshape2_1.4.4-2build1_amd64.deb ... 248s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 248s Selecting previously unselected package r-cran-caret. 248s Preparing to unpack .../159-r-cran-caret_7.0-1+dfsg-1_amd64.deb ... 248s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 248s Selecting previously unselected package r-cran-conquer. 248s Preparing to unpack .../160-r-cran-conquer_1.3.3-1_amd64.deb ... 248s Unpacking r-cran-conquer (1.3.3-1) ... 248s Selecting previously unselected package r-cran-quantreg. 248s Preparing to unpack .../161-r-cran-quantreg_6.00-1_amd64.deb ... 248s Unpacking r-cran-quantreg (6.00-1) ... 248s Selecting previously unselected package r-cran-foreign. 248s Preparing to unpack .../162-r-cran-foreign_0.8.88-1_amd64.deb ... 248s Unpacking r-cran-foreign (0.8.88-1) ... 248s Selecting previously unselected package r-cran-ellipsis. 248s Preparing to unpack .../163-r-cran-ellipsis_0.3.2-2_amd64.deb ... 248s Unpacking r-cran-ellipsis (0.3.2-2) ... 248s Selecting previously unselected package r-cran-forcats. 248s Preparing to unpack .../164-r-cran-forcats_1.0.0-1_all.deb ... 248s Unpacking r-cran-forcats (1.0.0-1) ... 248s Selecting previously unselected package r-cran-hms. 248s Preparing to unpack .../165-r-cran-hms_1.1.3-1_all.deb ... 248s Unpacking r-cran-hms (1.1.3-1) ... 248s Selecting previously unselected package r-cran-clipr. 248s Preparing to unpack .../166-r-cran-clipr_0.8.0-1_all.deb ... 248s Unpacking r-cran-clipr (0.8.0-1) ... 248s Selecting previously unselected package r-cran-crayon. 249s Preparing to unpack .../167-r-cran-crayon_1.5.3-1_all.deb ... 249s Unpacking r-cran-crayon (1.5.3-1) ... 249s Selecting previously unselected package r-cran-bit. 249s Preparing to unpack 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previously unselected package r-cran-haven. 249s Preparing to unpack .../174-r-cran-haven_2.5.4-1_amd64.deb ... 249s Unpacking r-cran-haven (2.5.4-1) ... 249s Selecting previously unselected package r-cran-curl. 249s Preparing to unpack .../175-r-cran-curl_6.2.1+dfsg-1ubuntu1_amd64.deb ... 249s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ... 249s Selecting previously unselected package r-cran-rematch. 249s Preparing to unpack .../176-r-cran-rematch_2.0.0-1_all.deb ... 249s Unpacking r-cran-rematch (2.0.0-1) ... 249s Selecting previously unselected package r-cran-cellranger. 249s Preparing to unpack .../177-r-cran-cellranger_1.1.0-3_all.deb ... 249s Unpacking r-cran-cellranger (1.1.0-3) ... 249s Selecting previously unselected package r-cran-readxl. 249s Preparing to unpack .../178-r-cran-readxl_1.4.4-1_amd64.deb ... 249s Unpacking r-cran-readxl (1.4.4-1) ... 249s Selecting previously unselected package r-cran-writexl. 249s Preparing to unpack .../179-r-cran-writexl_1.5.1-1_amd64.deb 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... 254s Setting up r-cran-isoband (0.2.7-1) ... 254s Setting up r-cran-diagram (1.6.5-2) ... 254s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 254s Setting up r-cran-zoo (1.8-13-1) ... 254s Setting up r-cran-matrix (1.7-3-1) ... 254s Setting up r-cran-kernsmooth (2.23-26-1) ... 254s Setting up r-cran-knitr (1.49+dfsg-1) ... 254s Setting up r-cran-mgcv (1.9-1-1) ... 254s Setting up r-cran-cachem (1.1.0-1) ... 254s Setting up r-cran-lmtest (0.9.40-1) ... 254s Setting up r-cran-rcpparmadillo (14.2.3-1-1) ... 254s Setting up r-cran-tzdb (0.4.0-2) ... 254s Setting up r-cran-globals (0.16.3-1) ... 254s Setting up r-cran-vctrs (0.6.5-1) ... 254s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 254s Setting up r-cran-mitools (2.4-2build1) ... 254s Setting up r-cran-pillar (1.10.1+dfsg-1) ... 254s Setting up r-cran-ellipsis (0.3.2-2) ... 254s Setting up r-cran-minqa (1.2.8-1) ... 254s Setting up r-cran-stringr (1.5.1-1) ... 254s Setting up r-cran-class (7.3-23-1) ... 254s Setting up 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r-cran-lava (1.8.1+dfsg-1) ... 254s Setting up r-cran-purrr (1.0.4-1) ... 254s Setting up r-cran-e1071 (1.7-16-1) ... 254s Setting up r-cran-blob (1.2.4-1) ... 254s Setting up r-cran-hardhat (1.4.0+dfsg-1) ... 254s Setting up r-cran-dplyr (1.1.4-4) ... 254s Setting up r-cran-reformulas (0.4.0-1) ... 254s Setting up r-cran-rsqlite (2.3.9-1) ... 254s Setting up r-cran-progress (1.2.3-1) ... 254s Setting up r-cran-lubridate (1.9.4+dfsg-1) ... 254s Setting up r-cran-r.utils (2.13.0-1) ... 254s Setting up r-cran-vroom (1.6.5-1) ... 254s Setting up r-cran-prodlim (2024.06.25-1) ... 254s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 254s Setting up r-cran-cellranger (1.1.0-3) ... 254s Setting up r-cran-rpart (4.1.24-1) ... 254s Setting up r-cran-ipred (0.9-15-1) ... 254s Setting up r-cran-lme4 (1.1-36-1) ... 254s Setting up r-cran-readr (2.1.5-1) ... 254s Setting up r-cran-tidyr (1.3.1-1) ... 254s Setting up r-cran-recipes (1.1.0+dfsg-1) ... 254s Setting up r-cran-r.cache (0.16.0-1) ... 254s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 254s Setting up r-cran-readxl (1.4.4-1) ... 254s Setting up r-cran-haven (2.5.4-1) ... 254s Setting up r-cran-caret (7.0-1+dfsg-1) ... 254s Setting up r-cran-broom (1.0.7+dfsg-1) ... 254s Setting up r-cran-conquer (1.3.3-1) ... 254s Setting up r-cran-r.rsp (0.46.0+ds-1) ... 254s Setting up r-cran-rio (1.2.3-1) ... 254s Setting up r-cran-quantreg (6.00-1) ... 254s Setting up r-cran-modelr (0.1.11-1) ... 254s Setting up r-cran-doby (4.6.25-1) ... 254s Setting up r-cran-pbkrtest (0.5.3-1) ... 254s Setting up r-cran-car (3.1-3-1) ... 254s Setting up r-cran-aer (1.2-14-1) ... 254s Processing triggers for libc-bin (2.41-1ubuntu2) ... 254s Processing triggers for man-db (2.13.0-1) ... 256s Processing triggers for install-info (7.1.1-1) ... 257s autopkgtest [22:40:59]: test run-unit-test: [----------------------- 257s BEGIN TEST 3stage2phase.R 257s 257s R version 4.4.3 (2025-02-28) -- "Trophy Case" 257s Copyright (C) 2025 The R Foundation for Statistical Computing 257s Platform: x86_64-pc-linux-gnu 257s 257s R is free software and comes with ABSOLUTELY NO WARRANTY. 257s You are welcome to redistribute it under certain conditions. 257s Type 'license()' or 'licence()' for distribution details. 257s 257s R is a collaborative project with many contributors. 257s Type 'contributors()' for more information and 257s 'citation()' on how to cite R or R packages in publications. 257s 257s Type 'demo()' for some demos, 'help()' for on-line help, or 257s 'help.start()' for an HTML browser interface to help. 257s Type 'q()' to quit R. 257s 257s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 257s > ## motivated by dietary biomarker substudy in HCHS 257s > 257s > library(survey) 257s Loading required package: grid 257s Loading required package: Matrix 258s Loading required package: survival 258s > 258s > load("simdata1.RData") 258s 258s Attaching package: 'survey' 258s 258s The following object is masked from 'package:graphics': 258s 258s dotchart 258s 258s > 258s > twophase.full = twophase(id=list(~block+house+ind,~1), 258s + strata=list(~strat,NULL), 258s + probs=list(~P.block+P.house+P.ind,NULL), 258s + subset=~phase2, 258s + data=simdata1,method='full') 259s > 259s > twophase.approx = twophase(id=list(~block+house+ind,~1), 259s + strata=list(~strat,NULL), 259s + probs=list(~P.block+P.house+P.ind,NULL), 259s + subset=~phase2, 259s + data=simdata1,method='approx') 259s > 259s > twophase.rep = twophase(id=list(~block,~1), 259s + strata=list(~strat,NULL), 259s + probs=list(~I(P.block*P.house*P.ind),NULL), 259s + subset=~phase2, 259s + data=simdata1,method='full') 259s > 259s > 259s > twophase.repapprox = twophase(id=list(~block,~1), 259s + strata=list(~strat,NULL), 259s + probs=list(~I(P.block*P.house*P.ind),NULL), 259s + subset=~phase2, 259s + data=simdata1,method='approx') 259s > 259s > 259s > svymean(~age, twophase.full) 259s mean SE 259s age 41.116 0.8114 259s > svymean(~age, twophase.approx) 259s mean SE 259s age 41.116 0.6693 259s > svymean(~age, twophase.rep) 259s mean SE 259s age 41.116 0.784 259s > svymean(~age, twophase.repapprox) 259s mean SE 259s age 41.116 0.6592 259s > 259s BEGIN TEST DBIcheck.R 259s 259s R version 4.4.3 (2025-02-28) -- "Trophy Case" 259s Copyright (C) 2025 The R Foundation for Statistical Computing 259s Platform: x86_64-pc-linux-gnu 259s 259s R is free software and comes with ABSOLUTELY NO WARRANTY. 259s You are welcome to redistribute it under certain conditions. 259s Type 'license()' or 'licence()' for distribution details. 259s 259s R is a collaborative project with many contributors. 259s Type 'contributors()' for more information and 259s 'citation()' on how to cite R or R packages in publications. 259s 259s Type 'demo()' for some demos, 'help()' for on-line help, or 259s 'help.start()' for an HTML browser interface to help. 259s Type 'q()' to quit R. 259s 259s > 259s > library(survey) 259s Loading required package: grid 259s Loading required package: Matrix 260s Loading required package: survival 260s > library(RSQLite) 260s 260s Attaching package: 'survey' 260s 260s The following object is masked from 'package:graphics': 260s 260s dotchart 260s 260s > 260s > data(api) 260s > apiclus1$api_stu<-apiclus1$api.stu 260s > apiclus1$comp_imp<-apiclus1$comp.imp 260s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 260s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 260s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 260s > 260s > m<-svymean(~api00+stype,dclus1) 260s > m.db<-svymean(~api00+stype, dbclus1) 260s > all.equal(coef(m),coef(m.db)) 260s [1] TRUE 260s > all.equal(vcov(m), vcov(m.db)) 260s [1] TRUE 260s > 260s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 260s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 261s > all.equal(coef(r), coef(r.db)) 261s [1] TRUE 261s > all.equal(SE(r), SE(r.db)) 261s [1] TRUE 261s > 261s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 261s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 261s > all.equal(coef(b), coef(b.db)) 261s [1] TRUE 261s > all.equal(SE(b), SE(b.db)) 261s [1] TRUE 261s > all.equal(deff(b), deff(b.db)) 261s [1] TRUE 261s > 261s > l<-svyglm(api00~api99+mobility, design=dclus1) 261s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 261s > all.equal(coef(l),coef(l.db)) 261s [1] TRUE 261s > all.equal(vcov(l), vcov(l.db)) 261s [1] TRUE 261s > 261s > dclus1<-update(dclus1, apidiff=api00-api99) 261s > dclus1<-update(dclus1, apipct= apidiff/api99) 261s > dbclus1<-update(dbclus1, apidiff=api00-api99) 261s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 261s > 261s > u<-svymean(~api00+apidiff+apipct, dclus1) 261s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 261s > all.equal(u, u.db) 261s [1] TRUE 261s > 261s > all.equal(nrow(dclus1),nrow(dbclus1)) 261s [1] TRUE 261s > all.equal(nrow(subset(dclus1,stype=="E")), 261s + nrow(subset(dbclus1,stype=="E"))) 261s [1] "Mean relative difference: 0.2708333" 261s > 261s > ## replicate weights 261s > rclus1<-as.svrepdesign(dclus1) 261s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 261s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 261s > m<-svymean(~api00+api99,rclus1) 261s > m.db<-svymean(~api00+api99,db_rclus1) 261s > all.equal(m,m.db) 261s [1] TRUE 261s > 261s > summary(db_rclus1) 261s DB-backed replicate weight design 261s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 261s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 261s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 261s Unstratified cluster jacknife (JK1) with 15 replicates. 261s Variables: 261s [1] "row_names" "cds" "stype" "name" "sname" 261s [6] "snum" "dname" "dnum" "cname" "cnum" 261s [11] "flag" "pcttest" "api00" "api99" "target" 261s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 261s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 261s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 261s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 261s [36] "emer" "enroll" "api_stu" "fpc" "pw" 261s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 261s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 261s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 261s [56] "wt15" 261s > 261s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 261s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 261s > all.equal(s,s.db) 261s [1] TRUE 261s > 261s BEGIN TEST anova-svycoxph.R 261s 261s R version 4.4.3 (2025-02-28) -- "Trophy Case" 261s Copyright (C) 2025 The R Foundation for Statistical Computing 261s Platform: x86_64-pc-linux-gnu 261s 261s R is free software and comes with ABSOLUTELY NO WARRANTY. 261s You are welcome to redistribute it under certain conditions. 261s Type 'license()' or 'licence()' for distribution details. 261s 261s R is a collaborative project with many contributors. 261s Type 'contributors()' for more information and 261s 'citation()' on how to cite R or R packages in publications. 261s 261s Type 'demo()' for some demos, 'help()' for on-line help, or 261s 'help.start()' for an HTML browser interface to help. 261s Type 'q()' to quit R. 261s 261s > 261s > library(survey) 261s Loading required package: grid 261s Loading required package: Matrix 262s Loading required package: survival 262s 262s Attaching package: 'survey' 262s 262s The following object is masked from 'package:graphics': 262s 262s dotchart 262s 262s > example(svycoxph, ask=FALSE) 262s 262s svycxp> ## Somewhat unrealistic example of nonresponse bias. 262s svycxp> data(pbc, package="survival") 262s 262s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 262s 262s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 262s 262s svycxp> pbc$randprob<-fitted(biasmodel) 262s 262s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 262s 262s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 262s 262s svycxp> rpbc<-as.svrepdesign(dpbc) 262s 262s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 262s Call: 262s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 262s albumin, design = dpbc) 262s 262s coef exp(coef) se(coef) robust se z p 262s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 262s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 262s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 262s 262s Likelihood ratio test= on 3 df, p= 262s n= 312, number of events= 144 262s 262s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 262s Call: 262s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 262s protime + albumin, design = rpbc) 262s 262s coef exp(coef) se(coef) z p 262s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 262s protime 0.24487 1.27745 0.09373 2.612 0.00899 262s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 262s 262s Likelihood ratio test=NA on 3 df, p=NA 262s n= 312, number of events= 144 262s 262s svycxp> s<-predict(model,se=TRUE, type="curve", 262s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 262s 262s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 262s 262s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 262s 262s svycxp> quantile(s[[1]], ci=TRUE) 262s 0.75 0.5 0.25 262s 1435 2503 3574 262s attr(,"ci") 262s 0.025 0.975 262s 0.75 1217 1786 262s 0.5 2256 3170 262s 0.25 3222 Inf 262s 262s svycxp> confint(s[[2]], parm=365*(1:5)) 262s 0.025 0.975 262s 365 0.8375139 0.9453781 262s 730 0.7382750 0.8999016 262s 1095 0.4784105 0.7478460 262s 1460 0.3192009 0.6206764 262s 1825 0.2149475 0.5292978 262s > m<-update(model, .~.+I(protime^2)) 262s > a<-anova(m,model) 262s > b<-anova(m, model,force=TRUE) 262s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 262s > 262s BEGIN TEST api.R 263s 263s R version 4.4.3 (2025-02-28) -- "Trophy Case" 263s Copyright (C) 2025 The R Foundation for Statistical Computing 263s Platform: x86_64-pc-linux-gnu 263s 263s R is free software and comes with ABSOLUTELY NO WARRANTY. 263s You are welcome to redistribute it under certain conditions. 263s Type 'license()' or 'licence()' for distribution details. 263s 263s R is a collaborative project with many contributors. 263s Type 'contributors()' for more information and 263s 'citation()' on how to cite R or R packages in publications. 263s 263s Type 'demo()' for some demos, 'help()' for on-line help, or 263s 'help.start()' for an HTML browser interface to help. 263s Type 'q()' to quit R. 263s 263s > library(survey) 263s Loading required package: grid 263s Loading required package: Matrix 264s Loading required package: survival 264s 264s Attaching package: 'survey' 264s 264s The following object is masked from 'package:graphics': 264s 264s dotchart 264s 264s > options(survey.replicates.mse=TRUE) 264s > example(api) 264s 264s api> library(survey) 264s 264s api> data(api) 264s 264s api> mean(apipop$api00) 264s [1] 664.7126 264s 264s api> sum(apipop$enroll, na.rm=TRUE) 264s [1] 3811472 264s 264s api> #stratified sample 264s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 264s 264s api> summary(dstrat) 264s Stratified Independent Sampling design 264s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 264s Stratum Sizes: 264s E H M 264s obs 100 50 50 264s design.PSU 100 50 50 264s actual.PSU 100 50 50 264s Population stratum sizes (PSUs): 264s E H M 264s 4421 755 1018 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "pw" "fpc" 264s 264s api> svymean(~api00, dstrat) 264s mean SE 264s api00 662.29 9.4089 264s 264s api> svytotal(~enroll, dstrat, na.rm=TRUE) 264s total SE 264s enroll 3687178 114642 264s 264s api> # one-stage cluster sample 264s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 264s 264s api> summary(dclus1) 264s 1 - level Cluster Sampling design 264s With (15) clusters. 264s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 264s Population size (PSUs): 757 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> svymean(~api00, dclus1) 264s mean SE 264s api00 644.17 23.542 264s 264s api> svytotal(~enroll, dclus1, na.rm=TRUE) 264s total SE 264s enroll 3404940 932235 264s 264s api> # two-stage cluster sample 264s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 264s 264s api> summary(dclus2) 264s 2 - level Cluster Sampling design 264s With (40, 126) clusters. 264s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 264s Population size (PSUs): 757 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "pw" "fpc1" "fpc2" 264s 264s api> svymean(~api00, dclus2) 264s mean SE 264s api00 670.81 30.099 264s 264s api> svytotal(~enroll, dclus2, na.rm=TRUE) 264s total SE 264s enroll 2639273 799638 264s 264s api> # two-stage `with replacement' 264s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 264s 264s api> summary(dclus2wr) 264s 2 - level Cluster Sampling design (with replacement) 264s With (40, 126) clusters. 264s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "pw" "fpc1" "fpc2" 264s 264s api> svymean(~api00, dclus2wr) 264s mean SE 264s api00 670.81 30.712 264s 264s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 264s total SE 264s enroll 2639273 820261 264s 264s api> # convert to replicate weights 264s api> rclus1<-as.svrepdesign(dclus1) 264s 264s api> summary(rclus1) 264s Call: as.svrepdesign.default(dclus1) 264s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 264s Variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> svymean(~api00, rclus1) 264s mean SE 264s api00 644.17 26.335 264s 264s api> svytotal(~enroll, rclus1, na.rm=TRUE) 264s total SE 264s enroll 3404940 932235 264s 264s api> # post-stratify on school type 264s api> pop.types<-xtabs(~stype, data=apipop) 264s 264s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 264s 264s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 264s 264s api> summary(dclus1p) 264s 1 - level Cluster Sampling design 264s With (15) clusters. 264s dclus1p<-postStratify(dclus1, ~stype, pop.types) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 264s Population size (PSUs): 757 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> summary(rclus1p) 264s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 264s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 264s Variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> svymean(~api00, dclus1p) 264s mean SE 264s api00 642.31 23.921 264s 264s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 264s total SE 264s enroll 3680893 406293 264s 264s api> svymean(~api00, rclus1p) 264s mean SE 264s api00 642.31 26.936 264s 264s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 264s total SE 264s enroll 3680893 473434 264s > 264s > options(survey.replicates.mse=FALSE) 264s > example(api) 264s 264s api> library(survey) 264s 264s api> data(api) 264s 264s api> mean(apipop$api00) 264s [1] 664.7126 264s 264s api> sum(apipop$enroll, na.rm=TRUE) 264s [1] 3811472 264s 264s api> #stratified sample 264s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 264s 264s api> summary(dstrat) 264s Stratified Independent Sampling design 264s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 264s Stratum Sizes: 264s E H M 264s obs 100 50 50 264s design.PSU 100 50 50 264s actual.PSU 100 50 50 264s Population stratum sizes (PSUs): 264s E H M 264s 4421 755 1018 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "pw" "fpc" 264s 264s api> svymean(~api00, dstrat) 264s mean SE 264s api00 662.29 9.4089 264s 264s api> svytotal(~enroll, dstrat, na.rm=TRUE) 264s total SE 264s enroll 3687178 114642 264s 264s api> # one-stage cluster sample 264s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 264s 264s api> summary(dclus1) 264s 1 - level Cluster Sampling design 264s With (15) clusters. 264s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 264s Population size (PSUs): 757 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> svymean(~api00, dclus1) 264s mean SE 264s api00 644.17 23.542 264s 264s api> svytotal(~enroll, dclus1, na.rm=TRUE) 264s total SE 264s enroll 3404940 932235 264s 264s api> # two-stage cluster sample 264s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 264s 264s api> summary(dclus2) 264s 2 - level Cluster Sampling design 264s With (40, 126) clusters. 264s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 264s Population size (PSUs): 757 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "pw" "fpc1" "fpc2" 264s 264s api> svymean(~api00, dclus2) 264s mean SE 264s api00 670.81 30.099 264s 264s api> svytotal(~enroll, dclus2, na.rm=TRUE) 264s total SE 264s enroll 2639273 799638 264s 264s api> # two-stage `with replacement' 264s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 264s 264s api> summary(dclus2wr) 264s 2 - level Cluster Sampling design (with replacement) 264s With (40, 126) clusters. 264s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "pw" "fpc1" "fpc2" 264s 264s api> svymean(~api00, dclus2wr) 264s mean SE 264s api00 670.81 30.712 264s 264s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 264s total SE 264s enroll 2639273 820261 264s 264s api> # convert to replicate weights 264s api> rclus1<-as.svrepdesign(dclus1) 264s 264s api> summary(rclus1) 264s Call: as.svrepdesign.default(dclus1) 264s Unstratified cluster jacknife (JK1) with 15 replicates. 264s Variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> svymean(~api00, rclus1) 264s mean SE 264s api00 644.17 26.329 264s 264s api> svytotal(~enroll, rclus1, na.rm=TRUE) 264s total SE 264s enroll 3404940 932235 264s 264s api> # post-stratify on school type 264s api> pop.types<-xtabs(~stype, data=apipop) 264s 264s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 264s 264s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 264s 264s api> summary(dclus1p) 264s 1 - level Cluster Sampling design 264s With (15) clusters. 264s dclus1p<-postStratify(dclus1, ~stype, pop.types) 264s Probabilities: 264s Min. 1st Qu. Median Mean 3rd Qu. Max. 264s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 264s Population size (PSUs): 757 264s Data variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> summary(rclus1p) 264s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 264s Unstratified cluster jacknife (JK1) with 15 replicates. 264s Variables: 264s [1] "cds" "stype" "name" "sname" "snum" "dname" 264s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 264s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 264s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 264s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 264s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 264s [37] "api.stu" "fpc" "pw" 264s 264s api> svymean(~api00, dclus1p) 264s mean SE 264s api00 642.31 23.921 264s 264s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 264s total SE 264s enroll 3680893 406293 264s 264s api> svymean(~api00, rclus1p) 264s mean SE 264s api00 642.31 26.934 264s 264s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 264s total SE 264s enroll 3680893 473431 264s > 264s BEGIN TEST badcal.R 264s 264s R version 4.4.3 (2025-02-28) -- "Trophy Case" 264s Copyright (C) 2025 The R Foundation for Statistical Computing 264s Platform: x86_64-pc-linux-gnu 264s 264s R is free software and comes with ABSOLUTELY NO WARRANTY. 264s You are welcome to redistribute it under certain conditions. 264s Type 'license()' or 'licence()' for distribution details. 264s 264s R is a collaborative project with many contributors. 264s Type 'contributors()' for more information and 264s 'citation()' on how to cite R or R packages in publications. 264s 264s Type 'demo()' for some demos, 'help()' for on-line help, or 264s 'help.start()' for an HTML browser interface to help. 264s Type 'q()' to quit R. 264s 264s > ## 264s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 264s > ## 264s > library(survey) 264s Loading required package: grid 264s Loading required package: Matrix 266s Loading required package: survival 266s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 266s > des <- svydesign(ids=~1, weights=~w, data=data) 266s 266s Attaching package: 'survey' 266s 266s The following object is masked from 'package:graphics': 266s 266s dotchart 266s 266s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 266s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 266s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 266s > 266s BEGIN TEST brewer_cpp.R 266s 266s R version 4.4.3 (2025-02-28) -- "Trophy Case" 266s Copyright (C) 2025 The R Foundation for Statistical Computing 266s Platform: x86_64-pc-linux-gnu 266s 266s R is free software and comes with ABSOLUTELY NO WARRANTY. 266s You are welcome to redistribute it under certain conditions. 266s Type 'license()' or 'licence()' for distribution details. 266s 266s R is a collaborative project with many contributors. 266s Type 'contributors()' for more information and 266s 'citation()' on how to cite R or R packages in publications. 266s 266s Type 'demo()' for some demos, 'help()' for on-line help, or 266s 'help.start()' for an HTML browser interface to help. 266s Type 'q()' to quit R. 266s 266s > ## pps="brewer" can't use rcpp 266s > ## this checks that it doesn't 266s > library(survey) 266s Loading required package: grid 266s Loading required package: Matrix 267s Loading required package: survival 268s 268s Attaching package: 'survey' 268s 268s > data(election) 268s The following object is masked from 'package:graphics': 268s 268s dotchart 268s 268s > 268s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 268s > options(survey.use_rcpp=TRUE) 268s > a<-svytotal(~Bush+Kerry+Nader, dpps_br) 268s > options(survey.use_rcpp=FALSE) 268s > b<-svytotal(~Bush+Kerry+Nader, dpps_br) 268s > 268s > stopifnot(identical(a,b)) 268s > 268s BEGIN TEST bycovmat.R 268s 268s R version 4.4.3 (2025-02-28) -- "Trophy Case" 268s Copyright (C) 2025 The R Foundation for Statistical Computing 268s Platform: x86_64-pc-linux-gnu 268s 268s R is free software and comes with ABSOLUTELY NO WARRANTY. 268s You are welcome to redistribute it under certain conditions. 268s Type 'license()' or 'licence()' for distribution details. 268s 268s R is a collaborative project with many contributors. 268s Type 'contributors()' for more information and 268s 'citation()' on how to cite R or R packages in publications. 268s 268s Type 'demo()' for some demos, 'help()' for on-line help, or 268s 'help.start()' for an HTML browser interface to help. 268s Type 'q()' to quit R. 268s 268s > 268s > library(survey) 268s Loading required package: grid 268s Loading required package: Matrix 269s Loading required package: survival 269s > data(api) 269s 269s Attaching package: 'survey' 269s 269s The following object is masked from 'package:graphics': 269s 269s dotchart 269s 269s > options(survey.replicates.mse=TRUE) 269s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 269s > rclus1<-as.svrepdesign(dclus1) 269s > 269s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 269s + covmat=TRUE,drop.empty.groups=FALSE) 270s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 270s + covmat=TRUE,drop.empty.groups=TRUE) 270s > 270s > stopifnot(all.equal( 270s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 270s + )) 270s > stopifnot(all.equal( 270s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 270s + )) 270s > 270s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 270s > all <- svytotal(~ell+mobility+meals, dclus1) 270s > 270s > stopifnot(all(abs(vcov(svycontrast(all, 270s + list(quote(ell/mobility), 270s + quote(mobility/mobility), 270s + quote(ell/meals),quote(mobility/meals)))) 270s + -vcov(rat))<1e-10)) 270s > 270s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 270s > 270s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 270s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 270s > 270s > con<-svycontrast(all, 270s + list(quote(ell/mobility), 270s + quote(mobility/mobility), 270s + quote(ell/meals),quote(mobility/meals))) 270s > 270s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 270s > 270s > options(survey.replicates.mse=FALSE) 270s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 270s > rclus1<-as.svrepdesign(dclus1) 270s > 270s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 270s + covmat=TRUE,drop.empty.groups=FALSE) 270s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 270s + covmat=TRUE,drop.empty.groups=TRUE) 270s > 270s > stopifnot(all.equal( 270s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 270s + )) 270s > stopifnot(all.equal( 270s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 270s + )) 270s > 270s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 270s > all <- svytotal(~ell+mobility+meals, dclus1) 270s > 270s > stopifnot(all(abs(vcov(svycontrast(all, 270s + list(quote(ell/mobility), 270s + quote(mobility/mobility), 270s + quote(ell/meals),quote(mobility/meals)))) 270s + -vcov(rat))<1e-10)) 270s > 270s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 270s > 270s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 270s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 270s > 270s > con<-svycontrast(all, 270s + list(quote(ell/mobility), 270s + quote(mobility/mobility), 270s + quote(ell/meals),quote(mobility/meals))) 270s > 270s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 270s > 270s > 270s > 270s BEGIN TEST caleg.R 270s 270s R version 4.4.3 (2025-02-28) -- "Trophy Case" 270s Copyright (C) 2025 The R Foundation for Statistical Computing 270s Platform: x86_64-pc-linux-gnu 270s 270s R is free software and comes with ABSOLUTELY NO WARRANTY. 270s You are welcome to redistribute it under certain conditions. 270s Type 'license()' or 'licence()' for distribution details. 270s 270s R is a collaborative project with many contributors. 270s Type 'contributors()' for more information and 270s 'citation()' on how to cite R or R packages in publications. 270s 270s Type 'demo()' for some demos, 'help()' for on-line help, or 270s 'help.start()' for an HTML browser interface to help. 270s Type 'q()' to quit R. 270s 270s > ## 270s > ## Calibration examples 270s > ## 270s > 270s > 270s > ## Example of calibration to first-stage clusters 270s > library(survey) 270s Loading required package: grid 270s Loading required package: Matrix 271s Loading required package: survival 271s > data(api) 271s 271s Attaching package: 'survey' 271s 271s The following object is masked from 'package:graphics': 271s 271s dotchart 271s 271s > 271s > clusters<-table(apiclus2$dnum) 271s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 271s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 271s > 271s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 271s > 271s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 271s > 271s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 271s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 271s > 271s > names(pop)<-names(clusters) 271s > 271s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 271s > 271s > svymean(~api99, dclus2) 271s mean SE 271s api99 642.14 31.434 271s > svymean(~api99, dclus2g) 271s mean SE 271s api99 654.49 29.82 271s > 271s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 271s dnum api99 se 271s 83 83 694.3333 0.0000 271s 132 132 505.0000 0.0000 271s 152 152 574.0000 0.0000 271s 173 173 894.7500 0.0000 271s 198 198 533.7500 0.0000 271s 200 200 589.8000 6.8335 271s 228 228 477.0000 0.0000 271s 295 295 646.4000 0.0000 271s 302 302 903.5000 0.0000 271s 403 403 852.4000 0.0000 271s 452 452 533.0000 0.0000 271s 480 480 614.2000 0.0000 271s 523 523 580.5000 0.0000 271s 534 534 564.6000 0.0000 271s 549 549 896.2000 0.0000 271s 552 552 730.0000 0.0000 271s 570 570 518.4000 7.5478 271s 575 575 800.8000 4.2513 271s 596 596 785.6000 2.4155 271s 620 620 591.6000 10.5869 271s 638 638 560.2000 4.0954 271s 674 674 760.0000 0.0000 271s 679 679 610.2500 0.0000 271s 687 687 718.6667 0.0000 271s 701 701 651.5000 0.0000 271s 711 711 690.5000 0.0000 271s 731 731 702.0000 2.1744 271s 768 768 562.5000 0.0000 271s 781 781 854.4000 0.7456 271s > 271s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 272s dnum api99 se 272s 83 83 694.3333 0 272s 132 132 505.0000 0 272s 152 152 574.0000 0 272s 173 173 894.7500 0 272s 198 198 533.7500 0 272s 200 200 567.5455 0 272s 228 228 477.0000 0 272s 295 295 646.4000 0 272s 302 302 903.5000 0 272s 403 403 852.4000 0 272s 452 452 533.0000 0 272s 480 480 614.2000 0 272s 523 523 580.5000 0 272s 534 534 564.6000 0 272s 549 549 896.2000 0 272s 552 552 730.0000 0 272s 570 570 548.9444 0 272s 575 575 824.5357 0 272s 596 596 787.5714 0 272s 620 620 609.3750 0 272s 638 638 585.6429 0 272s 674 674 760.0000 0 272s 679 679 610.2500 0 272s 687 687 718.6667 0 272s 701 701 651.5000 0 272s 711 711 690.5000 0 272s 731 731 700.6667 0 272s 768 768 562.5000 0 272s 781 781 851.0000 0 272s > 272s > ## Averaging to first stage 272s > 272s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 272s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 272s > 272s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 272s > 272s > svytotal(~enroll,dclus1g) 272s total SE 272s enroll 3811472 0 272s > svytotal(~api.stu,dclus1g) 272s total SE 272s api.stu 3242857 38967 272s > 272s > #variation within clusters should be zero 272s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 272s [1] TRUE 272s > 272s > ##bounded weights 272s > dclus1g<-calibrate(dclus1, ~enroll, pop) 272s > range(weights(dclus1g)/weights(dclus1)) 272s [1] 0.7906782 1.7891164 272s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 272s > range(weights(dclus1gb)/weights(dclus1)) 272s [1] 0.7198751 1.5000000 272s > 272s > ## Ratio estimators 272s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 272s > svytotal(~api.stu,dstrat) 272s total SE 272s api.stu 3086009 99477 272s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 272s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 272s > predict(common, total=total.enroll) 272s $total 272s enroll 272s api.stu 3190038 272s 272s $se 272s enroll 272s api.stu 29565.98 272s 272s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 272s > svytotal(~api.stu, dstratg) 272s total SE 272s api.stu 3190038 29566 272s > 272s > ## postStratify vs calibrate in stratified sample (Ben French) 272s > set.seed(17) 272s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 272s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 272s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 272s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 272s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 272s > postStratify(des,~w,popw)->dps 272s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 272s > 272s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 272s [1] TRUE 272s > 272s > ## missing data in calibrated design 272s > dps$variables$z[1]<-NA 272s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 272s 272s Call: 272s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 272s 272s Survey design: 272s postStratify(des, ~w, popw) 272s 272s Coefficients: 272s Estimate Std. Error t value Pr(>|t|) 272s (Intercept) -0.1203 0.3380 -0.356 0.722 272s z 6.2118 0.6451 9.630 <2e-16 *** 272s x 2.2602 0.2514 8.992 <2e-16 *** 272s --- 272s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 272s 272s (Dispersion parameter for quasibinomial family taken to be 1.919987) 272s 272s Number of Fisher Scoring iterations: 9 272s 272s > 272s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 272s > # should match the ratio estmate above 272s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 272s > svytotal(~api.stu, dstratgh) 272s total SE 272s api.stu 3190038 29566 272s > 272s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 272s > bnds <- list( 272s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 272s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 272s > lapply(bnds, head) 272s $lower 272s [1] 1 1 -Inf -Inf -Inf -Inf 272s 272s $upper 272s [1] 1 1 Inf Inf Inf Inf 272s 272s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 272s > svytotal(~api.stu, dstratg1) 272s total SE 272s api.stu 3190133 29561 272s > head(weights(dstrat)) 272s 1 2 3 4 5 6 272s 44.21 44.21 44.21 44.21 44.21 44.21 272s > head(weights(dstratg1)) 272s 1 2 3 4 5 6 272s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 272s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 272s [1] TRUE 272s > 272s > ## individual boundary constraints as constant values (Daniel Oehm) 272s > bnds <- list( 272s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 272s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 272s > lapply(bnds, head) 272s $lower 272s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 272s 272s $upper 272s [1] 44.21 44.21 Inf Inf Inf Inf 272s 272s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 272s > svytotal(~api.stu, dstratg2) 272s total SE 272s api.stu 3190133 29561 272s > head(weights(dstrat)) 272s 1 2 3 4 5 6 272s 44.21 44.21 44.21 44.21 44.21 44.21 272s > head(weights(dstratg2)) 272s 1 2 3 4 5 6 272s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 272s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 272s [1] TRUE 272s > 272s > # sparse matrix support (Daniel Oehm) 272s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 272s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 272s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 272s > svymean(~api00, dclus1g) 272s mean SE 272s api00 642.31 23.921 272s > svytotal(~enroll, dclus1g) 272s total SE 272s enroll 3680893 406293 272s > 272s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 272s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 272s > svymean(~api00, dclus1g) 272s mean SE 272s api00 642.31 23.921 272s > svytotal(~enroll, dclus1g) 272s total SE 272s enroll 3680893 406293 272s > 272s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 272s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 272s > svymean(~api00, dclus1g) 272s mean SE 272s api00 642.31 23.921 272s > svytotal(~enroll, dclus1g) 272s total SE 272s enroll 3680893 406293 272s > 272s BEGIN TEST check.R 272s 272s R version 4.4.3 (2025-02-28) -- "Trophy Case" 272s Copyright (C) 2025 The R Foundation for Statistical Computing 272s Platform: x86_64-pc-linux-gnu 272s 272s R is free software and comes with ABSOLUTELY NO WARRANTY. 272s You are welcome to redistribute it under certain conditions. 272s Type 'license()' or 'licence()' for distribution details. 272s 272s R is a collaborative project with many contributors. 272s Type 'contributors()' for more information and 272s 'citation()' on how to cite R or R packages in publications. 272s 272s Type 'demo()' for some demos, 'help()' for on-line help, or 272s 'help.start()' for an HTML browser interface to help. 272s Type 'q()' to quit R. 272s 272s > library(survey) 272s Loading required package: grid 272s Loading required package: Matrix 273s Loading required package: survival 274s 274s Attaching package: 'survey' 274s 274s > data(fpc) 274s The following object is masked from 'package:graphics': 274s 274s dotchart 274s 274s > ## test various possibilities for svydesign 274s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 274s variables = ~x, data = fpc, nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7413 274s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 274s data = fpc, nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7413 274s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 274s data = fpc, nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 44.2 6.237 274s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 274s nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.525 0.7796 274s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 274s data = fpc, nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7413 274s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 274s nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.525 0.7796 274s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 274s > a 274s 1 - level Cluster Sampling design (with replacement) 274s With (5) clusters. 274s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.525 0.838 274s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 274s > a 274s 1 - level Cluster Sampling design (with replacement) 274s With (5) clusters. 274s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 274s nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7938 274s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 274s > a 274s 2 - level Cluster Sampling design (with replacement) 274s With (2, 8) clusters. 274s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 274s data = fpc) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.5465 274s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 274s > a 274s 2 - level Cluster Sampling design (with replacement) 274s With (2, 8) clusters. 274s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 274s > svymean(~x,a) 274s mean SE 274s x 5.525 0.5188 274s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 274s > Warning message: 274s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 274s No weights or probabilities supplied, assuming equal probability 274s Warning message: 274s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 274s No weights or probabilities supplied, assuming equal probability 274s Warning message: 274s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 274s No weights or probabilities supplied, assuming equal probability 274s Warning message: 274s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 274s No weights or probabilities supplied, assuming equal probability 274s a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 274s variables = fpc[, "x", drop = FALSE], nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7413 274s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 274s > a 274s Stratified Independent Sampling design (with replacement) 274s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 274s variables = fpc[, 4:6], nest = TRUE) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7413 274s > 274s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 274s > a 274s 1 - level Cluster Sampling design 274s With (5) clusters. 274s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 274s 4:6], fpc = rep(27, 8)) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.7165 274s > 274s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 274s > a 274s Stratified Independent Sampling design 274s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 274s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 274s > svymean(~x,a) 274s mean SE 274s x 5.4481 0.616 274s > 274s BEGIN TEST confintrep.R 274s 274s R version 4.4.3 (2025-02-28) -- "Trophy Case" 274s Copyright (C) 2025 The R Foundation for Statistical Computing 274s Platform: x86_64-pc-linux-gnu 274s 274s R is free software and comes with ABSOLUTELY NO WARRANTY. 274s You are welcome to redistribute it under certain conditions. 274s Type 'license()' or 'licence()' for distribution details. 274s 274s R is a collaborative project with many contributors. 274s Type 'contributors()' for more information and 274s 'citation()' on how to cite R or R packages in publications. 274s 274s Type 'demo()' for some demos, 'help()' for on-line help, or 274s 'help.start()' for an HTML browser interface to help. 274s Type 'q()' to quit R. 274s 274s > library(survey) 274s Loading required package: grid 274s Loading required package: Matrix 275s Loading required package: survival 275s > data(api) 275s 275s Attaching package: 'survey' 275s 275s The following object is masked from 'package:graphics': 275s 275s dotchart 275s 275s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 275s > rclus2<-as.svrepdesign(dclus2) 275s > 275s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial) 275s Warning message: 275s In as.svrepdesign.default(dclus2) : 275s Finite population corrections after first stage have been dropped 275s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint") 275s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial) 275s > if(anyNA(confint(mrep))) stop("NA in confint") 275s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint") 275s > 275s BEGIN TEST contrast-replicates.R 275s 275s R version 4.4.3 (2025-02-28) -- "Trophy Case" 275s Copyright (C) 2025 The R Foundation for Statistical Computing 275s Platform: x86_64-pc-linux-gnu 275s 275s R is free software and comes with ABSOLUTELY NO WARRANTY. 275s You are welcome to redistribute it under certain conditions. 275s Type 'license()' or 'licence()' for distribution details. 275s 275s R is a collaborative project with many contributors. 275s Type 'contributors()' for more information and 275s 'citation()' on how to cite R or R packages in publications. 275s 275s Type 'demo()' for some demos, 'help()' for on-line help, or 275s 'help.start()' for an HTML browser interface to help. 275s Type 'q()' to quit R. 275s 275s > ## test use of replicates in svyby, svycontrast 275s > library(survey) 275s Loading required package: grid 275s Loading required package: Matrix 276s Loading required package: survival 276s > 276s > data(api) 276s 276s Attaching package: 'survey' 276s 276s The following object is masked from 'package:graphics': 276s 276s dotchart 276s 276s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 276s > rclus1<-as.svrepdesign(dclus1) 276s > 276s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 276s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 276s > vcov(c_without) 276s contrast 276s contrast 0.06862947 276s > 276s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 276s > 276s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 276s > 276s > v_with<- vcov(rclus1, c_with$replicates) 276s > 276s > r<- attr(meanlogs_with, "replicates") 276s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 276s > 276s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 276s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 276s > 276s BEGIN TEST coxph-termtest.R 277s 277s R version 4.4.3 (2025-02-28) -- "Trophy Case" 277s Copyright (C) 2025 The R Foundation for Statistical Computing 277s Platform: x86_64-pc-linux-gnu 277s 277s R is free software and comes with ABSOLUTELY NO WARRANTY. 277s You are welcome to redistribute it under certain conditions. 277s Type 'license()' or 'licence()' for distribution details. 277s 277s R is a collaborative project with many contributors. 277s Type 'contributors()' for more information and 277s 'citation()' on how to cite R or R packages in publications. 277s 277s Type 'demo()' for some demos, 'help()' for on-line help, or 277s 'help.start()' for an HTML browser interface to help. 277s Type 'q()' to quit R. 277s 277s > library(survey) 277s Loading required package: grid 277s Loading required package: Matrix 277s Loading required package: survival 278s > library(survival) 278s > set.seed(2021-6-25) 278s > test1 <- list(time=c(4,3,1,1,2,2,3), 278s + status=c(1,1,1,0,1,1,0), 278s + x1=as.factor(rbinom(7, 2, 0.5)), 278s + x=c(0,2,1,1,1,0,0)) 278s > # Fit a stratified model 278s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 278s 278s Attaching package: 'survey' 278s 278s The following object is masked from 'package:graphics': 278s 278s dotchart 278s 278s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 278s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 278s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 278s > 278s > data(pbc, package="survival") 278s > 278s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 278s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 278s > pbc$randprob<-fitted(biasmodel) 278s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 278s > 278s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 278s > library(splines) 278s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 278s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 278s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 278s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 278s > 278s BEGIN TEST deff.R 278s 278s R version 4.4.3 (2025-02-28) -- "Trophy Case" 278s Copyright (C) 2025 The R Foundation for Statistical Computing 278s Platform: x86_64-pc-linux-gnu 278s 278s R is free software and comes with ABSOLUTELY NO WARRANTY. 278s You are welcome to redistribute it under certain conditions. 278s Type 'license()' or 'licence()' for distribution details. 278s 278s R is a collaborative project with many contributors. 278s Type 'contributors()' for more information and 278s 'citation()' on how to cite R or R packages in publications. 278s 278s Type 'demo()' for some demos, 'help()' for on-line help, or 278s 'help.start()' for an HTML browser interface to help. 278s Type 'q()' to quit R. 278s 278s > ## from Takahiro Tsuchiya 278s > library(survey) 278s Loading required package: grid 278s Loading required package: Matrix 279s Loading required package: survival 279s 279s Attaching package: 'survey' 279s 279s > kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 279s + 1 1 15 100 20 279s + 2 2 143 100 200 279s The following object is masked from 'package:graphics': 279s 279s dotchart 279s 279s + 3 3 21 100 11 279s + 4 4 51 100 25 279s + 5 5 337 100 550 279s + 6 6 50 100 30 279s + 7 7 274 100 250 279s + 8 8 145 100 100 279s + 9 9 15 100 10 279s + 10 10 86 100 55 279s + ",open="r"),header=TRUE) 279s > close(tmp) 279s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 279s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 279s mean SE DEff 279s uriage 113.700 35.626 1.0101 279s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 279s uriage 279s uriage 1.010101 279s > 279s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 279s total SE DEff 279s uriage 113700 35626 1.0101 279s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 279s uriage 279s uriage 1.010101 279s > 279s > 279s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 279s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 279s mean SE DEff 279s uriage 243.914 48.752 1.9741 279s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 279s uriage 279s uriage 1.974067 279s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 279s total SE DEff 279s uriage 305136 184965 18.157 279s > (N.hat <- sum(weights(des.pps))) 279s [1] 1251 279s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 279s uriage 279s uriage 18.15669 279s > 279s BEGIN TEST defftest.R 279s 279s R version 4.4.3 (2025-02-28) -- "Trophy Case" 279s Copyright (C) 2025 The R Foundation for Statistical Computing 279s Platform: x86_64-pc-linux-gnu 279s 279s R is free software and comes with ABSOLUTELY NO WARRANTY. 279s You are welcome to redistribute it under certain conditions. 279s Type 'license()' or 'licence()' for distribution details. 279s 279s R is a collaborative project with many contributors. 279s Type 'contributors()' for more information and 279s 'citation()' on how to cite R or R packages in publications. 279s 279s Type 'demo()' for some demos, 'help()' for on-line help, or 279s 'help.start()' for an HTML browser interface to help. 279s Type 'q()' to quit R. 279s 279s > library(survey) 279s Loading required package: grid 279s Loading required package: Matrix 280s Loading required package: survival 280s 280s Attaching package: 'survey' 280s 280s > 280s > data(api) 280s The following object is masked from 'package:graphics': 280s 280s dotchart 280s 281s > 281s > ## one-stage cluster sample 281s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 281s > 281s > # svyglm model 281s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 281s > 281s > #deffs returned from svyglm model - implausibly high 281s > deff(mod) 281s (Intercept) enroll api.stu 281s 1.919945 2.500983 2.686102 281s > #> (Intercept) enroll api.stu 281s > #> 351.3500 457.6799 491.5567 281s > 281s > # run mod with same data and glm() 281s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 281s > 281s > # manually calculate deffs 281s > 281s > clust_se <- summary(mod)$coefficients[,2] 281s > srs_se <- summary(srs_mod)$coefficients[,2] 281s > 281s > deffs <- clust_se^2 / srs_se^2 281s > stopifnot(all.equal(deffs, deff(mod))) 281s > 281s > 281s BEGIN TEST degf-svrepdesign.R 281s 281s R version 4.4.3 (2025-02-28) -- "Trophy Case" 281s Copyright (C) 2025 The R Foundation for Statistical Computing 281s Platform: x86_64-pc-linux-gnu 281s 281s R is free software and comes with ABSOLUTELY NO WARRANTY. 281s You are welcome to redistribute it under certain conditions. 281s Type 'license()' or 'licence()' for distribution details. 281s 281s R is a collaborative project with many contributors. 281s Type 'contributors()' for more information and 281s 'citation()' on how to cite R or R packages in publications. 281s 281s Type 'demo()' for some demos, 'help()' for on-line help, or 281s 'help.start()' for an HTML browser interface to help. 281s Type 'q()' to quit R. 281s 281s > library(survey) 281s Loading required package: grid 281s Loading required package: Matrix 282s Loading required package: survival 282s 282s Attaching package: 'survey' 282s 282s > data(scd) 282s The following object is masked from 'package:graphics': 282s 282s dotchart 282s 282s > 282s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1), 282s + c(0,1,0,1,1,0)) 282s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights) 282s > Warning message: 282s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) : 282s No sampling weights provided: equal probability assumed 282s 282s > stopifnot(degf(scdrep)==3) 282s > 282s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4) 282s > stopifnot(degf(scdrep)==4) 282s > 282s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2) 282s > stopifnot(degf(scdrep)==2) 282s > 282s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 282s + warning=function(w) w) 282s > 282s > stopifnot(inherits(msg,"warning")) 282s > 282s > 282s > 282s > 282s BEGIN TEST domain.R 282s Warning message: 282s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 282s No sampling weights provided: equal probability assumed 282s Warning message: 282s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 282s No sampling weights provided: equal probability assumed 282s 282s R version 4.4.3 (2025-02-28) -- "Trophy Case" 282s Copyright (C) 2025 The R Foundation for Statistical Computing 282s Platform: x86_64-pc-linux-gnu 282s 282s R is free software and comes with ABSOLUTELY NO WARRANTY. 282s You are welcome to redistribute it under certain conditions. 282s Type 'license()' or 'licence()' for distribution details. 282s 282s R is a collaborative project with many contributors. 282s Type 'contributors()' for more information and 282s 'citation()' on how to cite R or R packages in publications. 282s 282s Type 'demo()' for some demos, 'help()' for on-line help, or 282s 'help.start()' for an HTML browser interface to help. 282s Type 'q()' to quit R. 282s 282s > ## 282s > ## Domain means can be written as ratio estimators or as regression coefficients 282s > ## 282s > ## This code checks that subsetting the design object gives the same results as 282s > ## these approaches. 282s > ## 282s > 282s > 282s > library(survey) 282s Loading required package: grid 282s Loading required package: Matrix 283s Loading required package: survival 284s 284s Attaching package: 'survey' 284s 284s > The following object is masked from 'package:graphics': 284s 284s dotchart 284s 284s data(fpc) 284s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 284s > dsub<-subset(dfpc,x>4) 284s > (m1<-svymean(~x,design=dsub)) 284s mean SE 284s x 6.195 0.7555 284s > 284s > ## These should give the same domain estimates and standard errors 284s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 284s I(x > 4) x se 284s FALSE FALSE 3.314286 0.3117042 284s TRUE TRUE 6.195000 0.7555129 284s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 284s > summary(m3) 284s 284s Call: 284s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 284s 284s Survey design: 284s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 284s nest = TRUE) 284s 284s Coefficients: 284s Estimate Std. Error t value Pr(>|t|) 284s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 284s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 284s --- 284s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 284s 284s (Dispersion parameter for gaussian family taken to be 2.557379) 284s 284s Number of Fisher Scoring iterations: 2 284s 284s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 284s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 284s dfpc) 284s Ratios= 284s as.numeric(x > 4) 284s I(x * (x > 4)) 6.195 284s SEs= 284s as.numeric(x > 4) 284s I(x * (x > 4)) 0.7555129 284s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 284s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 284s > 284s > ## with strata 284s > data(api) 284s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 284s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 284s > m2<-svyglm(enroll~comp.imp-1, dstrat) 284s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 284s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 284s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 284s > 284s > ## with calibration 284s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 284s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 284s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 284s 1 - level Cluster Sampling design 284s With (15) clusters. 284s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 284s > 284s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 284s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 284s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 284s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 284s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 284s > 284s > ## with raking 284s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 284s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 284s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 284s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 284s > m2<-svyglm(api00~comp.imp-1, dclus1r) 284s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 284s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 284s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 284s > 284s > 284s > 284s > ## 284s > ## based on bug report from Takahiro Tsuchiya for version 3.4 284s > ## 284s > rei<-read.table(tmp<-textConnection( 284s + " id N n.a h n.ah n.h sub y 284s + 1 1 300 20 1 12 5 TRUE 1 284s + 2 2 300 20 1 12 5 TRUE 2 284s + 3 3 300 20 1 12 5 TRUE 3 284s + 4 4 300 20 1 12 5 TRUE 4 284s + 5 5 300 20 1 12 5 TRUE 5 284s + 6 6 300 20 1 12 5 FALSE NA 284s + 7 7 300 20 1 12 5 FALSE NA 284s + 8 8 300 20 1 12 5 FALSE NA 284s + 9 9 300 20 1 12 5 FALSE NA 284s + 10 10 300 20 1 12 5 FALSE NA 284s + 11 11 300 20 1 12 5 FALSE NA 284s + 12 12 300 20 1 12 5 FALSE NA 284s + 13 13 300 20 2 8 3 TRUE 6 284s + 14 14 300 20 2 8 3 TRUE 7 284s + 15 15 300 20 2 8 3 TRUE 8 284s + 16 16 300 20 2 8 3 FALSE NA 284s + 17 17 300 20 2 8 3 FALSE NA 284s + 18 18 300 20 2 8 3 FALSE NA 284s + 19 19 300 20 2 8 3 FALSE NA 284s + 20 20 300 20 2 8 3 FALSE NA 284s + "), header=TRUE) 284s > close(tmp) 284s > 284s > 284s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 284s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 284s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 284s > 284s > rei$y<-rei$y*(rei$y>3) 284s > ## based on Sarndal et al (9.4.14) 284s > rei$w.ah <- rei$n.ah / rei$n.a 284s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 284s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 284s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 284s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 284s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 284s > 284s > a.rei$f.h<-with(a.rei, n.h/n.ah) 284s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 284s > 284s > a.rei$f<-with(a.rei, n.a/N) 284s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 284s > 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))) 284s > 284s > V 284s [1] 70761.47 284s > Vphase1 284s [1] 44325.47 284s > Vphase2 284s [1] 26436 284s > vcov(tot2) 284s [,1] 284s [1,] 70761.47 284s attr(,"phases") 284s attr(,"phases")$phase1 284s [,1] 284s [1,] 44325.47 284s 284s attr(,"phases")$phase2 284s [,1] 284s [1,] 26436 284s 284s > 284s > ## comparing to regression 284s > reg<-svyglm(y~I(y<4), design=des.rei2) 284s > mn<-svymean(~y, subset(des.rei2,y>3)) 284s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 284s [1] TRUE 284s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 284s [1] TRUE 284s > vcov(mn) 284s [,1] 284s [1,] 0.3292258 284s attr(,"phases") 284s attr(,"phases")$phase1 284s [,1] 284s [1,] 0.1599264 284s 284s attr(,"phases")$phase2 284s [,1] 284s [1,] 0.1692994 284s 284s > vcov(reg) 284s (Intercept) I(y < 4)TRUE 284s (Intercept) 0.3292258 -0.3292258 284s I(y < 4)TRUE -0.3292258 0.5901907 284s attr(,"phases") 284s attr(,"phases")$phase1 284s (Intercept) I(y < 4)TRUE 284s (Intercept) 0.1599264 -0.1599264 284s I(y < 4)TRUE -0.1599264 0.2588542 284s 284s attr(,"phases")$phase2 284s (Intercept) I(y < 4)TRUE 284s (Intercept) 0.1692994 -0.1692994 284s I(y < 4)TRUE -0.1692994 0.3313365 284s 284s > 284s > 284s BEGIN TEST fpc.R 284s 284s R version 4.4.3 (2025-02-28) -- "Trophy Case" 284s Copyright (C) 2025 The R Foundation for Statistical Computing 284s Platform: x86_64-pc-linux-gnu 284s 284s R is free software and comes with ABSOLUTELY NO WARRANTY. 284s You are welcome to redistribute it under certain conditions. 284s Type 'license()' or 'licence()' for distribution details. 284s 284s R is a collaborative project with many contributors. 284s Type 'contributors()' for more information and 284s 'citation()' on how to cite R or R packages in publications. 284s 284s Type 'demo()' for some demos, 'help()' for on-line help, or 284s 'help.start()' for an HTML browser interface to help. 284s Type 'q()' to quit R. 284s 284s > library(survey) 284s Loading required package: grid 284s Loading required package: Matrix 285s Loading required package: survival 286s 286s Attaching package: 'survey' 286s 286s The following object is masked from 'package:graphics': 286s 286s dotchart 286s 286s > ## check many permutations of fpc specification 286s > example(fpc) 286s 286s fpc> data(fpc) 286s 286s fpc> fpc 286s stratid psuid weight nh Nh x 286s 1 1 1 3 5 15 2.8 286s 2 1 2 3 5 15 4.1 286s 3 1 3 3 5 15 6.8 286s 4 1 4 3 5 15 6.8 286s 5 1 5 3 5 15 9.2 286s 6 2 1 4 3 12 3.7 286s 7 2 2 4 3 12 6.6 286s 8 2 3 4 3 12 4.2 286s 286s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 286s fpc+ data=fpc, nest=TRUE) 286s 286s fpc> withoutfpc 286s Stratified Independent Sampling design (with replacement) 286s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 286s data=fpc, nest=TRUE) 286s 286s fpc> svymean(~x, withoutfpc) 286s mean SE 286s x 5.4481 0.7413 286s 286s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 286s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 286s 286s fpc> withfpc 286s Stratified Independent Sampling design 286s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 286s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 286s 286s fpc> svymean(~x, withfpc) 286s mean SE 286s x 5.4481 0.616 286s 286s fpc> ## Other equivalent forms 286s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 286s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 286s 286s fpc> svymean(~x, withfpc) 286s mean SE 286s x 5.4481 0.616 286s 286s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 286s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 286s 286s fpc> svymean(~x, withfpc) 286s mean SE 286s x 5.4481 0.616 286s 286s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 286s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 286s 286s fpc> svymean(~x, withfpc) 286s mean SE 286s x 5.4481 0.616 286s 286s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 286s fpc+ variables=~x,data=fpc,nest=TRUE) 286s 286s fpc> svymean(~x, withfpc) 286s mean SE 286s x 5.4481 0.616 286s 286s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 286s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 286s 286s fpc> svymean(~x, withfpc) 286s mean SE 286s x 5.4481 0.616 286s > 286s > 286s BEGIN TEST glm-scoping.R 286s 286s R version 4.4.3 (2025-02-28) -- "Trophy Case" 286s Copyright (C) 2025 The R Foundation for Statistical Computing 286s Platform: x86_64-pc-linux-gnu 286s 286s R is free software and comes with ABSOLUTELY NO WARRANTY. 286s You are welcome to redistribute it under certain conditions. 286s Type 'license()' or 'licence()' for distribution details. 286s 286s R is a collaborative project with many contributors. 286s Type 'contributors()' for more information and 286s 'citation()' on how to cite R or R packages in publications. 286s 286s Type 'demo()' for some demos, 'help()' for on-line help, or 286s 'help.start()' for an HTML browser interface to help. 286s Type 'q()' to quit R. 286s 286s > ## bug report from Thomas Leeper, fixed in version 3.32-3 286s > 286s > library("survey") 286s Loading required package: grid 286s Loading required package: Matrix 287s Loading required package: survival 287s 287s Attaching package: 'survey' 287s 287s The following object is masked from 'package:graphics': 287s 287s dotchart 287s 287s > data(api) 287s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 287s > 287s > # pass `family` directly (WORKS!) 287s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 287s Stratified Independent Sampling design 287s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 287s fpc = ~fpc) 287s 287s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 287s family = gaussian()) 287s 287s Coefficients: 287s (Intercept) ell meals mobility 287s 820.8873 -0.4806 -3.1415 0.2257 287s 287s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 287s Null Deviance: 3023000 287s Residual Deviance: 1029000 AIC: 2308 287s > 287s > # passing `family` via ... (WORKS!) 287s > myfun1 <- function(formula, design, ...) { 287s + svyglm(formula, design = design, ...) 287s + } 287s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 287s Stratified Independent Sampling design 287s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 287s fpc = ~fpc) 287s 287s Call: svyglm(formula = formula, design = design, family = ..1) 287s 287s Coefficients: 287s (Intercept) ell meals mobility 287s 820.8873 -0.4806 -3.1415 0.2257 287s 287s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 287s Null Deviance: 3023000 287s Residual Deviance: 1029000 AIC: 2308 287s > 287s > # passing `family` via default argument (DOES NOT WORK!) 287s > myfun2 <- function(formula, design, family = gaussian()) { 287s + svyglm(formula, design = design, family = family) 287s + } 287s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 287s Stratified Independent Sampling design 287s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 287s fpc = ~fpc) 287s 287s Call: svyglm(formula = formula, design = design, family = family) 287s 287s Coefficients: 287s (Intercept) ell meals mobility 287s 820.8873 -0.4806 -3.1415 0.2257 287s 287s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 287s Null Deviance: 3023000 287s Residual Deviance: 1029000 AIC: 2308 287s > 287s BEGIN TEST kalton.R 287s 287s R version 4.4.3 (2025-02-28) -- "Trophy Case" 287s Copyright (C) 2025 The R Foundation for Statistical Computing 287s Platform: x86_64-pc-linux-gnu 287s 287s R is free software and comes with ABSOLUTELY NO WARRANTY. 287s You are welcome to redistribute it under certain conditions. 287s Type 'license()' or 'licence()' for distribution details. 287s 287s R is a collaborative project with many contributors. 287s Type 'contributors()' for more information and 287s 'citation()' on how to cite R or R packages in publications. 287s 287s Type 'demo()' for some demos, 'help()' for on-line help, or 287s 'help.start()' for an HTML browser interface to help. 287s Type 'q()' to quit R. 287s 287s > library(survey) 287s Loading required package: grid 288s Loading required package: Matrix 288s Loading required package: survival 289s 289s Attaching package: 'survey' 289s 289s > 289s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 289s The following object is masked from 'package:graphics': 289s 289s dotchart 289s 289s > 289s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 289s > 289s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 289s > 289s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 289s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 289s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 289s > 289s > dkalton<-svydesign(id=~1,data=kaltonsample) 289s > 289s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 289s > 289s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 289s > 289s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 289s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 289s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 289s > 289s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 289s > 289s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 289s Warning message: 289s In svydesign.default(id = ~1, data = kaltonsample) : 289s No weights or probabilities supplied, assuming equal probability 289s > 289s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 289s > 289s > 289s > #table A 289s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 4.00 1.00 1.38 289s 2 1.20 1.07 1.10 289s 3 1.70 1.20 4.00 289s 4 1.83 1.65 1.79 289s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 4.00 1.00 1.37 289s 2 1.20 1.07 1.10 289s 3 1.70 1.20 4.00 289s 4 1.83 1.65 1.79 289s > 289s > #table B 289s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 1.81 1.45 2.02 289s 2 1.08 0.87 1.21 289s 3 2.20 1.76 2.45 289s 4 1.83 1.47 2.04 289s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 1.81 1.45 2.02 289s 2 1.08 0.87 1.21 289s 3 2.20 1.76 2.45 289s 4 1.83 1.47 2.04 289s > 289s > #table C 289s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 1.82 1.50 1.97 289s 2 1.09 0.78 1.24 289s 3 2.19 1.88 2.34 289s 4 1.83 1.52 1.98 289s > 289s > #table D 289s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 1.21 1.17 1.14 289s 2 1.43 1.40 1.36 289s 3 1.66 1.62 1.59 289s 4 1.88 1.85 1.81 289s > 289s > #table G 289s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 1.87 1.46 1.98 289s 2 1.08 0.74 1.27 289s 3 2.17 2.09 2.18 289s 4 1.89 1.49 1.99 289s > 289s > #table G 289s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 289s b 289s a 1 2 3 289s 1 1.81 1.48 1.99 289s 2 1.08 0.75 1.26 289s 3 2.20 2.00 2.20 289s 4 1.83 1.50 2.00 289s > 289s BEGIN TEST logranktest.R 289s 289s R version 4.4.3 (2025-02-28) -- "Trophy Case" 289s Copyright (C) 2025 The R Foundation for Statistical Computing 289s Platform: x86_64-pc-linux-gnu 289s 289s R is free software and comes with ABSOLUTELY NO WARRANTY. 289s You are welcome to redistribute it under certain conditions. 289s Type 'license()' or 'licence()' for distribution details. 289s 289s R is a collaborative project with many contributors. 289s Type 'contributors()' for more information and 289s 'citation()' on how to cite R or R packages in publications. 289s 289s Type 'demo()' for some demos, 'help()' for on-line help, or 289s 'help.start()' for an HTML browser interface to help. 289s Type 'q()' to quit R. 289s 289s > ## StackOverflow 63333282 289s > 289s > library(survey) 289s Loading required package: grid 289s Loading required package: Matrix 290s Loading required package: survival 290s > D = data.frame(unique_id = 1:135, 290s + 290s + weights = rep(1,135), 290s + 290s + 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 , 290s + 290s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 290s + 290s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 290s + 290s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 290s + 290s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 290s + 290s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 290s + 290s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 290s + 290s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 290s + 290s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 290s + 290s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 290s + 290s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 290s + 290s + 2.35699896, 2.94956000, 8.85381736), 290s + 290s + 290s Attaching package: 'survey' 290s 290s The following object is masked from 'package:graphics': 290s 290s dotchart 290s 290s 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, 290s + 290s + 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, 290s + 290s + 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), 290s + 290s + group = c(rep("group1", 40), rep("group2", 95))) 290s > 290s > 290s > 290s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 290s > 290s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 290s > 290s > a<-svylogrank(formula = svykm_formula, design = svy_design) 290s > 290s > ii<-with(D, order(event_time, event_flag)) 290s > 290s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 290s > 290s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 290s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 290s > 290s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 290s > 290s > 290s > stopifnot(all.equal(a[[2]],b[[2]])) 290s > 290s > stopifnot(all.equal(a[[2]],d[[2]])) 290s > 290s > stopifnot(all.equal(a[[2]],f[-1])) 290s > 290s > 290s BEGIN TEST lonely.psu.R 290s 290s R version 4.4.3 (2025-02-28) -- "Trophy Case" 290s Copyright (C) 2025 The R Foundation for Statistical Computing 290s Platform: x86_64-pc-linux-gnu 290s 290s R is free software and comes with ABSOLUTELY NO WARRANTY. 290s You are welcome to redistribute it under certain conditions. 290s Type 'license()' or 'licence()' for distribution details. 290s 290s R is a collaborative project with many contributors. 290s Type 'contributors()' for more information and 290s 'citation()' on how to cite R or R packages in publications. 290s 290s Type 'demo()' for some demos, 'help()' for on-line help, or 290s 'help.start()' for an HTML browser interface to help. 290s Type 'q()' to quit R. 290s 290s > 290s > ## lonely PSUs by design 290s > library(survey) 290s Loading required package: grid 290s Loading required package: Matrix 291s Loading required package: survival 291s > data(api) 291s 291s Attaching package: 'survey' 291s 291s The following object is masked from 'package:graphics': 291s 291s dotchart 291s 291s > ## not certainty PSUs by fpc 291s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 291s > summary(ds) 291s Stratified Independent Sampling design (with replacement) 291s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 291s Probabilities: 291s Min. 1st Qu. Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 291s Stratum (413) has only one PSU at stage 1 291s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 291s Stratum413has only one PSU 291s Median Mean 3rd Qu. Max. 291s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 291s Stratum Sizes: 291s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 291s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 291s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 291s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 291s Data variables: 291s [1] "cds" "stype" "name" "sname" "snum" "dname" 291s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 291s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 291s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 291s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 291s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 291s [37] "api.stu" "fpc" "pw" 291s > 291s > options(survey.lonely.psu="fail") 291s > try(svymean(~api00,ds)) 291s > try(svymean(~api00, as.svrepdesign(ds))) 291s > options(survey.lonely.psu="remove") 291s > svymean(~api00,ds) 291s mean SE 291s api00 644.17 5.8058 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.8058 292s > options(survey.lonely.psu="certainty") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 5.8058 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.8058 292s > options(survey.lonely.psu="adjust") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 5.8281 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.8267 292s > options(survey.lonely.psu="average") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 6.0096 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.8217 292s > 292s > ## fpc specified 292s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 292s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 292s > summary(ds) 292s Stratified Independent Sampling design 292s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 292s fpc = fpc) 292s Probabilities: 292s Min. 1st Qu. Median Mean 3rd Qu. Max. 292s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 292s Stratum Sizes: 292s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 292s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 292s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 292s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 292s Population stratum sizes (PSUs): 292s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 292s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 292s Data variables: 292s [1] "cds" "stype" "name" "sname" "snum" "dname" 292s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 292s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 292s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 292s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 292s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 292s [37] "api.stu" "fpc" "pw" 292s > 292s > options(survey.lonely.psu="fail") 292s > try(svymean(~api00,ds)) 292s mean SE 292s api00 644.17 5.7344 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.7344 292s > options(survey.lonely.psu="remove") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 5.7344 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.7344 292s > options(survey.lonely.psu="certainty") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 5.7344 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.7344 292s > options(survey.lonely.psu="adjust") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 5.7344 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.7344 292s > options(survey.lonely.psu="average") 292s > svymean(~api00,ds) 292s mean SE 292s api00 644.17 5.7344 292s > svymean(~api00, as.svrepdesign(ds)) 292s mean SE 292s api00 644.17 5.7501 292s > 292s > rs<-as.svrepdesign(ds) 292s > svytotal(~api00,rs) 292s total SE 292s api00 3989986 35616 292s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 292s [1] TRUE 292s > 292s > ## lonely PSUs after subsetting 292s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 292s > ds1<-ds[-31,] 292s > summary(ds1) 292s Stratified Independent Sampling design (with replacement) 292s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 292s dnum != 413)) 292s Probabilities: 292s Min. 1st Qu. Median Mean 3rd Qu. Max. 292s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 292s Stratum Sizes: 292s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 292s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 292s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 292s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 292s Data variables: 292s [1] "cds" "stype" "name" "sname" "snum" "dname" 292s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 292s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 292s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 292s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 292s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 292s [37] "api.stu" "fpc" "pw" 292s > 292s > options(survey.lonely.psu="fail") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="remove") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="certainty") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="adjust") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="average") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > 292s > ## with adjustment 292s > options(survey.adjust.domain.lonely=TRUE) 292s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 292s > ds1<-ds[-31,] 292s > summary(ds1) 292s Stratified Independent Sampling design (with replacement) 292s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 292s dnum != 413)) 292s Probabilities: 292s Min. 1st Qu. Median Mean 3rd Qu. Max. 292s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 292s Stratum Sizes: 292s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 292s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 292s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 292s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 292s Data variables: 292s [1] "cds" "stype" "name" "sname" "snum" "dname" 292s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 292s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 292s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 292s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 292s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 292s [37] "api.stu" "fpc" "pw" 292s > 292s > options(survey.lonely.psu="fail") 292s > try(svymean(~api00,ds1)) 292s Warning message: 292s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 292s Stratum (406) has only one PSU at stage 1 292s Warning message: 292s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 292s Stratum (406) has only one PSU at stage 1 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="remove") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="certainty") 292s > svymean(~api00,ds1) 292s mean SE 292s api00 645.14 5.8909 292s > options(survey.lonely.psu="adjust") 292s > svymean(~api00,ds1) 292s Warning message: 292s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 292s Stratum (406) has only one PSU at stage 1 292s mean SE 292s api00 645.14 5.9119 292s > options(survey.lonely.psu="average") 292s > svymean(~api00,ds1) 292s Warning message: 292s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 292s Stratum (406) has only one PSU at stage 1 292s mean SE 292s api00 645.14 6.0914 292s Warning message: 292s > 292s > ## checks for `svytotal()` 292s > 292s > df_w_singleton <- data.frame( 292s + Stratum = c(1, 1, 2, 2, 3), 292s + PSU = c(1, 2, 3, 4, 5), 292s + Design_Weight = c(10.5, 10.5, 20, 20, 15), 292s + Sex = c("M", "F", "F", "M", "M"), 292s + Age = c(30.5, 40.5, 35, 52, 44), 292s + Height = c(6.2, 5.0, 5.3, 5.7, 5.5) 292s + ) 292s > 292s > design_w_singleton <- survey::svydesign( 292s + data = df_w_singleton, 292s + ids = ~ PSU, strata = ~ Stratum, 292s + weights = ~ Design_Weight 292s + ) 292s > 292s > options("survey.lonely.psu" = "remove") 292s > 292s > stopifnot(all.equal( 292s + target = 126625, 292s + current = as.numeric( 292s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 292s + ) 292s + )) 292s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 292s Stratum (406) has only one PSU at stage 1 292s > 292s > options("survey.lonely.psu" = "certainty") 292s > 292s > stopifnot(all.equal( 292s + target = 126625, 292s + current = as.numeric( 292s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 292s + ) 292s + )) 292s > 292s > options("survey.lonely.psu" = "adjust") 292s > 292s > stopifnot(all.equal( 292s + target = 127579.8, 292s + current = as.numeric( 292s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 292s + ), 292s + scale = 127579.8, tolerance = 0.000001 292s + )) 292s > 292s BEGIN TEST mtcars-var.R 292s 292s R version 4.4.3 (2025-02-28) -- "Trophy Case" 292s Copyright (C) 2025 The R Foundation for Statistical Computing 292s Platform: x86_64-pc-linux-gnu 292s 292s R is free software and comes with ABSOLUTELY NO WARRANTY. 292s You are welcome to redistribute it under certain conditions. 292s Type 'license()' or 'licence()' for distribution details. 292s 292s R is a collaborative project with many contributors. 292s Type 'contributors()' for more information and 292s 'citation()' on how to cite R or R packages in publications. 292s 292s Type 'demo()' for some demos, 'help()' for on-line help, or 292s 'help.start()' for an HTML browser interface to help. 292s Type 'q()' to quit R. 292s 292s > library(survey) 292s Loading required package: grid 292s Loading required package: Matrix 293s Loading required package: survival 293s 293s Attaching package: 'survey' 293s 293s The following object is masked from 'package:graphics': 293s 293s dotchart 293s 293s > 293s > # don't throw an error on domains of size 1, just return NA 293s > input <- mtcars 293s > input$carb <- factor(input$carb) 293s > design <- svydesign(ids = ~0, weights = NULL, data = input) 293s > svyby( 293s + ~mpg, 293s + ~carb, 293s + design, 293s + svyvar 293s + ) 293s carb mpg se 293s 1 1 36.01619 11.2823286 293s 2 2 29.94444 9.0030898 293s 3 3 1.11000 0.4604066 293s 4 4 15.29656 4.3174617 293s 6 6 NA NA 293s 8 8 NA NA 293s > 293s > 293s > ## same n with na.rm=TRUE as subset(, !is.na) 293s > input$mpg[1]<-NA 293s > design <- svydesign(ids = ~0, weights = NULL, data = input) 293s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 293s + svyvar(~mpg, subset(design, !is.na(mpg))))) 293s > 293s BEGIN TEST multistage-rcpp.R 293s 293s R version 4.4.3 (2025-02-28) -- "Trophy Case" 293s Copyright (C) 2025 The R Foundation for Statistical Computing 293s Platform: x86_64-pc-linux-gnu 293s 293s R is free software and comes with ABSOLUTELY NO WARRANTY. 293s You are welcome to redistribute it under certain conditions. 293s Type 'license()' or 'licence()' for distribution details. 293s 293s R is a collaborative project with many contributors. 293s Type 'contributors()' for more information and 293s 'citation()' on how to cite R or R packages in publications. 293s 293s Type 'demo()' for some demos, 'help()' for on-line help, or 293s 'help.start()' for an HTML browser interface to help. 293s Type 'q()' to quit R. 293s 293s > ## temporarily disable while it's being fixed 293s > ## q("no") 293s > 293s > ## 293s > ## Check that multistage() and multistage_rcpp() give same results 293s > ## for different options. 293s > ## 293s > library(survey) 293s Loading required package: grid 293s Loading required package: Matrix 294s Loading required package: survival 294s 294s Attaching package: 'survey' 294s 294s > 294s > # Check for a simple random sample ---- 294s > The following object is masked from 'package:graphics': 294s 294s dotchart 294s 294s 294s > data('api', package = 'survey') 294s > api_srs_design <- svydesign( 294s + data = apisrs, 294s + ids = ~ 1, 294s + weights = ~ 1 294s + ) 294s > 294s > x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob) 294s > 294s > base_r_result <- survey:::multistage(x = x, 294s + clusters = api_srs_design$cluster, 294s + stratas = api_srs_design$strata, 294s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=TRUE, stage = 1, cal = NULL) 294s > 294s > rcpp_result <- survey:::multistage_rcpp(x = x, 294s + clusters = api_srs_design$cluster, 294s + stratas = api_srs_design$strata, 294s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=TRUE, stage = 1, cal = NULL) 294s > 294s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 294s + stop("Differences between `multistage()` and `multistage_rcpp()` for SRS") 294s + } 294s > 294s > # Check for a stratified simple random sample ---- 294s > 294s > apistrat_design <- svydesign( 294s + data = apistrat, 294s + id =~ 1, 294s + strata =~ stype, 294s + weights =~ pw, 294s + fpc =~ fpc 294s + ) 294s > 294s > x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob) 294s > 294s > base_r_result <- survey:::multistage(x = x, 294s + clusters = apistrat_design$cluster, 294s + stratas = apistrat_design$strata, 294s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=TRUE, stage = 1, cal = NULL) 294s > 294s > rcpp_result <- survey:::multistage_rcpp(x = x, 294s + clusters = apistrat_design$cluster, 294s + stratas = apistrat_design$strata, 294s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=TRUE, stage = 1, cal = NULL) 294s > 294s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 294s + stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample") 294s + } 294s > 294s > ##_ Check whether expected true zeroes are actually computed as zeroes ---- 294s > 294s > x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob)) 294s > 294s > base_r_result <- survey:::multistage(x = x, 294s + clusters = apistrat_design$cluster, 294s + stratas = apistrat_design$strata, 294s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=TRUE, stage = 1, cal = NULL) 294s > 294s > rcpp_result <- survey:::multistage_rcpp(x = x, 294s + clusters = apistrat_design$cluster, 294s + stratas = apistrat_design$strata, 294s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=TRUE, stage = 1, cal = NULL) 294s > 294s > if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) { 294s + stop("Computations which should equal zero do not.") 294s + } 294s > 294s > # Create a stratified, multistage design ---- 294s > 294s > data(mu284) 294s > 294s > ## Create three strata, the third of which has only one PSU 294s > mu284_stratified <- rbind( 294s + transform(mu284, stratum = 1, 294s + y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)), 294s + transform(mu284, stratum = 2, 294s + y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)), 294s + transform(mu284[1,], stratum = 3, 294s + y2 = y1 + 2) 294s + ) 294s > 294s > ## Create domain variables which yield a lonely PSU or a lonely SSU 294s > mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19) 294s > mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1) 294s > 294s > ## Create a survey design object with no lonely PSUs 294s > dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3), 294s + strata = ~ stratum, nest = TRUE, 294s + id = ~ id1 + id2, fpc = ~ n1 + n2) 294s > ## Create a survey design with one lonely PSU 294s > dmu284_strat_w_lonely <- svydesign(data = mu284_stratified, 294s + strata = ~ stratum, nest = TRUE, 294s + id = ~ id1 + id2, fpc = ~ n1 + n2) 294s > ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU 294s > dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU) 294s > dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU) 294s > 294s > 294s > # Check same results for different values of 'lonely PSU' options ---- 294s > 294s > lonely_psu_options <- c(certainty = 'certainty', 294s + remove = 'remove', 294s + average = 'average', 294s + adjust = 'adjust') 294s > one_stage_options <- c(TRUE, FALSE) 294s > 294s > design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 294s + 'one.stage' = one_stage_options, 294s + stringsAsFactors = FALSE) 294s > design_lonely_psu_comparisons[['results_match']] <- NA 294s > 294s > ##_ Check for lonely PSUs caused by design ---- 294s > for (i in seq_len(nrow(design_lonely_psu_comparisons))) { 294s + survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i] 294s + one.stage <- design_lonely_psu_comparisons[['one.stage']][i] 294s + options('survey.lonely.psu' = survey.lonely.psu) 294s + 294s + x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob) 294s + 294s + base_r_result <- survey:::multistage(x = x, 294s + clusters = dmu284_strat_w_lonely$cluster, 294s + stratas = dmu284_strat_w_lonely$strata, 294s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=one.stage, stage = 1, cal = NULL) 294s + 294s + rcpp_result <- survey:::multistage_rcpp(x = x, 294s + clusters = dmu284_strat_w_lonely$cluster, 294s + stratas = dmu284_strat_w_lonely$strata, 294s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 294s + lonely.psu=getOption("survey.lonely.psu"), 294s + one.stage=one.stage, stage = 1, cal = NULL) 294s + 294s + design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 294s + } 294s > 294s > print(design_lonely_psu_comparisons) 294s survey.lonely.psu one.stage results_match 295s 1 certainty TRUE TRUE 295s 2 remove TRUE TRUE 295s 3 average TRUE TRUE 295s 4 adjust TRUE TRUE 295s 5 certainty FALSE TRUE 295s 6 remove FALSE TRUE 295s 7 average FALSE TRUE 295s 8 adjust FALSE TRUE 295s > if (!all(design_lonely_psu_comparisons$results_match)) { 295s + stop("Results for design lonely PSUs differ between base R and Rcpp implementations.") 295s + } 295s > 295s > ##_ Check for domain lonely PSUs caused by subsetting ---- 295s > 295s > domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 295s + 'survey.adjust.domain.lonely' = c(FALSE, TRUE), 295s + 'one.stage' = one_stage_options, 295s + stringsAsFactors = FALSE) 295s > domain_lonely_psu_comparisons[['results_match']] <- NA 295s > 295s > for (i in seq_len(nrow(domain_lonely_psu_comparisons))) { 295s + 295s + options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i]) 295s + options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i]) 295s + one.stage <- domain_lonely_psu_comparisons[['one.stage']][i] 295s + 295s + 295s + x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob) 295s + suppressWarnings({ 295s + base_r_result <- survey:::multistage(x = x, 295s + clusters = dmu284_strat_domain_lonely_psu$cluster, 295s + stratas = dmu284_strat_domain_lonely_psu$strata, 295s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 295s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 295s + lonely.psu=getOption("survey.lonely.psu"), 295s + one.stage=one.stage, stage = 1, cal = NULL) 295s + }) 295s + 295s + rcpp_result <- survey:::multistage_rcpp(x = x, 295s + clusters = dmu284_strat_domain_lonely_psu$cluster, 295s + stratas = dmu284_strat_domain_lonely_psu$strata, 295s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 295s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 295s + lonely.psu=getOption("survey.lonely.psu"), 295s + one.stage=one.stage, stage = 1, cal = NULL) 295s + 295s + domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 295s + } 295s Warning messages: 295s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 295s At least one stratum contains only one PSU at stage 1 295s > 295s > print(domain_lonely_psu_comparisons) 295s survey.lonely.psu survey.adjust.domain.lonely one.stage results_match 295s 1 certainty FALSE TRUE TRUE 295s 2 remove FALSE TRUE TRUE 295s 3 average FALSE TRUE TRUE 295s 4 adjust FALSE TRUE TRUE 295s 5 certainty TRUE TRUE TRUE 295s 6 remove TRUE TRUE TRUE 295s 7 average TRUE TRUE TRUE 295s 8 adjust TRUE TRUE TRUE 295s 9 certainty FALSE FALSE TRUE 295s 10 remove FALSE FALSE TRUE 295s 11 average FALSE FALSE TRUE 295s 12 adjust FALSE FALSE TRUE 295s 13 certainty TRUE FALSE TRUE 295s 14 remove TRUE FALSE TRUE 295s 15 average TRUE FALSE TRUE 295s 16 adjust TRUE FALSE TRUE 295s > if (!all(domain_lonely_psu_comparisons$results_match)) { 295s + stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.") 295s + } 295s > 295s > # Checks for edge cases ---- 295s > 295s > ## Zero records ---- 295s > 295s > zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent") 295s > 295s > zero_row_result <- survey:::multistage_rcpp( 295s + x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]), 295s + clusters = zero_row_design$cluster, 295s + stratas = zero_row_design$strata, 295s + nPSUs = zero_row_design$fpc$sampsize, 295s + fpcs = zero_row_design$fpc$popsize, 295s + lonely.psu=getOption("survey.lonely.psu"), 295s + one.stage=one.stage, stage = 1, cal = NULL 295s + ) 295s > 295s > if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) { 295s + stop("`multistage_rcpp()` should return zeros for zero-row inputs.") 295s + } 295s > 295s > 295s BEGIN TEST multistage.R 295s 295s R version 4.4.3 (2025-02-28) -- "Trophy Case" 295s Copyright (C) 2025 The R Foundation for Statistical Computing 295s Platform: x86_64-pc-linux-gnu 295s 295s R is free software and comes with ABSOLUTELY NO WARRANTY. 295s You are welcome to redistribute it under certain conditions. 295s Type 'license()' or 'licence()' for distribution details. 295s 295s R is a collaborative project with many contributors. 295s Type 'contributors()' for more information and 295s 'citation()' on how to cite R or R packages in publications. 295s 295s Type 'demo()' for some demos, 'help()' for on-line help, or 295s 'help.start()' for an HTML browser interface to help. 295s Type 'q()' to quit R. 295s 295s > ## 295s > ## Check that multistage samples still work 295s > ## 295s > library(survey) 295s Loading required package: grid 295s Loading required package: Matrix 296s Loading required package: survival 296s 296s Attaching package: 'survey' 296s 296s The following object is masked from 'package:graphics': 296s 296s dotchart 296s 296s > example(mu284) 296s 296s mu284> data(mu284) 296s 296s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 296s 2 - level Cluster Sampling design 296s With (5, 15) clusters. 296s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 296s 296s mu284> (ytotal<-svytotal(~y1, dmu284)) 296s total SE 296s y1 15080 2274.3 296s 296s mu284> vcov(ytotal) 296s y1 296s y1 5172234 296s > 296s > 296s BEGIN TEST na_action.R 296s 296s R version 4.4.3 (2025-02-28) -- "Trophy Case" 296s Copyright (C) 2025 The R Foundation for Statistical Computing 296s Platform: x86_64-pc-linux-gnu 296s 296s R is free software and comes with ABSOLUTELY NO WARRANTY. 296s You are welcome to redistribute it under certain conditions. 296s Type 'license()' or 'licence()' for distribution details. 296s 296s R is a collaborative project with many contributors. 296s Type 'contributors()' for more information and 296s 'citation()' on how to cite R or R packages in publications. 296s 296s Type 'demo()' for some demos, 'help()' for on-line help, or 296s 'help.start()' for an HTML browser interface to help. 296s Type 'q()' to quit R. 296s 296s > ## from Terry Therneau 296s > library(survey) 296s Loading required package: grid 296s Loading required package: Matrix 297s Loading required package: survival 298s 298s Attaching package: 'survey' 298s 298s > load("naa.rda") 298s The following object is masked from 'package:graphics': 298s 298s dotchart 298s 298s > 298s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 298s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 298s > all.equal(coef(fit1e),coef(fit1o)) 298s [1] TRUE 298s > all.equal(vcov(fit1e),vcov(fit1o)) 298s [1] TRUE 298s > 298s BEGIN TEST newquantile.R 298s 298s R version 4.4.3 (2025-02-28) -- "Trophy Case" 298s Copyright (C) 2025 The R Foundation for Statistical Computing 298s Platform: x86_64-pc-linux-gnu 298s 298s R is free software and comes with ABSOLUTELY NO WARRANTY. 298s You are welcome to redistribute it under certain conditions. 298s Type 'license()' or 'licence()' for distribution details. 298s 298s R is a collaborative project with many contributors. 298s Type 'contributors()' for more information and 298s 'citation()' on how to cite R or R packages in publications. 298s 298s Type 'demo()' for some demos, 'help()' for on-line help, or 298s 'help.start()' for an HTML browser interface to help. 298s Type 'q()' to quit R. 298s 298s > ## quantiles with equal weights 298s > 298s > library(survey) 298s Loading required package: grid 298s Loading required package: Matrix 299s Loading required package: survival 299s 299s Attaching package: 'survey' 299s 299s The following object is masked from 'package:graphics': 299s 299s dotchart 299s 299s > data(api) 299s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 299s > 299s > 299s > for(i in 1:9){ 299s + print(i) 299s + all.equal( 299s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 299s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 299s + ) 299s + 299s + } 300s [1] 1 300s [1] 2 300s [1] 3 300s [1] 4 300s [1] 5 300s [1] 6 300s [1] 7 300s [1] 8 300s [1] 9 300s > 300s BEGIN TEST nwts-cch.R 300s 300s R version 4.4.3 (2025-02-28) -- "Trophy Case" 300s Copyright (C) 2025 The R Foundation for Statistical Computing 300s Platform: x86_64-pc-linux-gnu 300s 300s R is free software and comes with ABSOLUTELY NO WARRANTY. 300s You are welcome to redistribute it under certain conditions. 300s Type 'license()' or 'licence()' for distribution details. 300s 300s R is a collaborative project with many contributors. 300s Type 'contributors()' for more information and 300s 'citation()' on how to cite R or R packages in publications. 300s 300s Type 'demo()' for some demos, 'help()' for on-line help, or 300s 'help.start()' for an HTML browser interface to help. 300s Type 'q()' to quit R. 300s 300s > library(survey) 300s Loading required package: grid 300s Loading required package: Matrix 301s Loading required package: survival 301s > library(survival) 301s > data(nwtco) 301s 301s Attaching package: 'survey' 301s 301s The following object is masked from 'package:graphics': 301s 301s dotchart 301s 301s > 301s > ntwco<-subset(nwtco, !is.na(edrel)) 301s > 301s > load("nwtco-subcohort.rda") 301s > nwtco$subcohort<-subcohort 301s > 301s > d_BorganII <- twophase(id=list(~seqno,~seqno), 301s + strata=list(NULL,~interaction(instit,rel)), 301s + data=nwtco, subset=~I(rel |subcohort)) 302s > 302s > ##Coefficient results same as Splus with code from 302s > ## http://faculty.washington.edu/norm/software.html 302s > ## SE slightly larger due to using sandwich variance. 302s > 302s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 302s Call: 302s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 302s I(age/12), design = d_BorganII) 302s 302s coef exp(coef) se(coef) robust se z p 302s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 302s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 302s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 302s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 302s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 302s 302s Likelihood ratio test= on 5 df, p= 302s n= 1062, number of events= 571 302s > 302s > ## 302s > ## This gives higher standard errors. calibrate() does not recompute the 302s > ## finite population correction if a calibration variable happens to predict 302s > ## sampling perfectly. It probably should. 302s > ## 302s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 302s + strata=list(NULL,~rel), 302s + data=nwtco, subset=~I(rel |subcohort)), 302s + phase=2, formula=~interaction(instit,rel), 302s + epsilon=1e-10) 302s > 302s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 302s Call: 302s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 302s I(age/12), design = d_BorganIIps) 302s 302s coef exp(coef) se(coef) robust se z p 302s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 302s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 302s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 302s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 302s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 302s 302s Likelihood ratio test= on 5 df, p= 302s n= 1062, number of events= 571 302s > 302s BEGIN TEST nwts.R 302s 302s R version 4.4.3 (2025-02-28) -- "Trophy Case" 302s Copyright (C) 2025 The R Foundation for Statistical Computing 302s Platform: x86_64-pc-linux-gnu 302s 302s R is free software and comes with ABSOLUTELY NO WARRANTY. 302s You are welcome to redistribute it under certain conditions. 302s Type 'license()' or 'licence()' for distribution details. 302s 302s R is a collaborative project with many contributors. 302s Type 'contributors()' for more information and 302s 'citation()' on how to cite R or R packages in publications. 302s 302s Type 'demo()' for some demos, 'help()' for on-line help, or 302s 'help.start()' for an HTML browser interface to help. 302s Type 'q()' to quit R. 302s 302s > 302s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 302s > ## data from Norman Breslow's web page. 302s > library(survey) 302s Loading required package: grid 302s Loading required package: Matrix 303s Loading required package: survival 303s 303s Attaching package: 'survey' 303s 303s > load("nwts.rda") 303s > nwtsnb<-nwts 303s > nwtsnb$case<-nwts$case-nwtsb$case 303s The following object is masked from 'package:graphics': 303s 303s dotchart 303s 303s > nwtsnb$control<-nwts$control-nwtsb$control 303s > 303s > a<-rbind(nwtsb,nwtsnb) 303s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 303s > 303s > b<-rbind(a,a) 303s > b$rel<-rep(c(1,0),each=32) 303s > b$n<-ifelse(b$rel,b$case,b$control) 303s > 303s > index<-rep(1:64,b$n) 303s > 303s > nwt.exp<-b[index,c(1:3,6,7)] 303s > nwt.exp$id<-1:4088 303s > 303s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 303s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 304s > 304s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 304s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 304s > 304s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 304s > 304s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 304s 304s Call: 304s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 304s family = quasibinomial) 304s 304s Survey design: 304s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 304s subset = subset, data = data, pps = pps) 304s 304s Coefficients: 304s Estimate Std. Error t value Pr(>|t|) 304s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 304s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 304s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 304s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 304s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 304s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 304s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 304s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 304s --- 304s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 304s 304s (Dispersion parameter for quasibinomial family taken to be 1.000876) 304s 304s Number of Fisher Scoring iterations: 4 304s 304s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 304s 304s Call: 304s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 304s family = quasibinomial) 304s 304s Survey design: 304s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 304s subset = subset, data = data, pps = pps) 304s 304s Coefficients: 304s Estimate Std. Error t value Pr(>|t|) 304s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 304s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 304s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 304s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 304s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 304s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 304s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 304s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 304s --- 304s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 304s 304s (Dispersion parameter for quasibinomial family taken to be 1.000876) 304s 304s Number of Fisher Scoring iterations: 4 304s 304s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 304s 304s Call: 304s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 304s family = quasibinomial) 304s 304s Survey design: 304s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 304s rel)) 304s 304s Coefficients: 304s Estimate Std. Error t value Pr(>|t|) 304s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 304s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 304s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 304s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 304s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 304s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 304s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 304s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 304s --- 304s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 304s 304s (Dispersion parameter for quasibinomial family taken to be 1.000876) 304s 304s Number of Fisher Scoring iterations: 4 304s 304s > 304s > ## check subsets of calibrated designs. 304s > summary(svyglm(rel~factor(stage), 304s + family=quasibinomial,design=subset(dccs8,histol==1))) 304s 304s Call: 304s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 304s histol == 1), family = quasibinomial) 304s 304s Survey design: 304s subset(dccs8, histol == 1) 304s 304s Coefficients: 304s EstimateWarning messages: 304s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 304s 2: In summary.glm(g) : 304s observations with zero weight not used for calculating dispersion 304s 3: In summary.glm(glm.object) : 304s observations with zero weight not used for calculating dispersion 304s 4: In `[.twophase2`(design, nas == 0, ) : 304s 1 strata have only one PSU in this subset. 304s 5: In `[.twophase2`(design, nas == 0, ) : 304s 1 strata have only one PSU in this subset. 304s Std. Error t value Pr(>|t|) 304s (Intercept) -2.7160 0.1083 -25.085 < 2e-16 *** 304s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 304s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 304s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 304s --- 304s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 304s 304s (Dispersion parameter for quasibinomial family taken to be 1.001333) 304s 304s Number of Fisher Scoring iterations: 4 304s 304s > summary(svyglm(rel~factor(stage), 304s + family=quasibinomial,design=subset(gccs8,histol==1))) 304s 304s Call: 304s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 304s histol == 1), family = quasibinomial) 304s 304s Survey design: 304s subset(gccs8, histol == 1) 304s 304s Coefficients: 304s Estimate Std. Error t value Pr(>|t|) 304s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 304s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 304s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 304s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 304s --- 304s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 304s 304s (Dispersion parameter for quasibinomial family taken to be 1.001333) 304s 304s Number of Fisher Scoring iterations: 4 304s 304s > 304s > 304s Warning messages: 304s 1: In summary.glm(g) : 304s observations with zero weight not used for calculating dispersion 304s 2: In summary.glm(glm.object) : 304s observations with zero weight not used for calculating dispersion 304s BEGIN TEST poisson.R 304s 304s R version 4.4.3 (2025-02-28) -- "Trophy Case" 304s Copyright (C) 2025 The R Foundation for Statistical Computing 304s Platform: x86_64-pc-linux-gnu 304s 304s R is free software and comes with ABSOLUTELY NO WARRANTY. 304s You are welcome to redistribute it under certain conditions. 304s Type 'license()' or 'licence()' for distribution details. 304s 304s R is a collaborative project with many contributors. 304s Type 'contributors()' for more information and 304s 'citation()' on how to cite R or R packages in publications. 304s 304s Type 'demo()' for some demos, 'help()' for on-line help, or 304s 'help.start()' for an HTML browser interface to help. 304s Type 'q()' to quit R. 304s 304s > ## check poisson sampling 304s > library(survey) 304s Loading required package: grid 305s Loading required package: Matrix 306s Loading required package: survival 306s > data(api) 306s 306s Attaching package: 'survey' 306s 306s The following object is masked from 'package:graphics': 306s 306s dotchart 306s 306s > set.seed(2021-7-15) 306s > apipop$prob<-apipop$api00/1000 306s > insample<-rbinom(nrow(apipop),1,apipop$prob) 306s > apipois<-apipop[insample,] 306s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 306s > 306s > stopifnot(isTRUE(all.equal( 306s + as.vector(SE(svytotal(~api00,design=des))), 306s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 306s + ))) 306s > 306s > 306s BEGIN TEST pps.R 306s 306s R version 4.4.3 (2025-02-28) -- "Trophy Case" 306s Copyright (C) 2025 The R Foundation for Statistical Computing 306s Platform: x86_64-pc-linux-gnu 306s 306s R is free software and comes with ABSOLUTELY NO WARRANTY. 306s You are welcome to redistribute it under certain conditions. 306s Type 'license()' or 'licence()' for distribution details. 306s 306s R is a collaborative project with many contributors. 306s Type 'contributors()' for more information and 306s 'citation()' on how to cite R or R packages in publications. 306s 306s Type 'demo()' for some demos, 'help()' for on-line help, or 306s 'help.start()' for an HTML browser interface to help. 306s Type 'q()' to quit R. 306s 306s > library(survey) 306s Loading required package: grid 306s Loading required package: Matrix 307s Loading required package: survival 307s 307s Attaching package: 'survey' 307s 307s The following object is masked from 'package:graphics': 307s 307s dotchart 307s 307s > data(election) 307s > 307s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 307s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 307s > svytotal(~Bush+Kerry+Nader, dpps) 307s total SE 307s Bush 64518472 2447629 307s Kerry 51202102 2450787 307s Nader 478530 102420 307s > svytotal(~Bush+Kerry+Nader, dppswr) 307s total SE 307s Bush 64518472 2671455 307s Kerry 51202102 2679433 307s Nader 478530 105303 307s > 307s > ##subsets 307s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 307s total SE 307s Bush 34944285 5399833 307s Kerry 25581714 4028434 307s Nader 478530 102420 307s > 307s > ##multistage: should agree with STRS analysis 307s > data(api) 307s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 307s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 307s > 307s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 307s [1] TRUE 307s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 307s [1] TRUE 307s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 307s [1] TRUE 307s > 307s > ## the new without-replacement methods 307s > data(election) 307s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 307s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 307s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 307s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 307s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 307s > ## Yates-Grundy type 307s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 307s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 307s > 307s > ## The with-replacement approximation 307s > svytotal(~Bush+Kerry+Nader, dpps_ht) 307s total SE 307s Bush 64518472 2604404 307s Kerry 51202102 2523712 307s Nader 478530 102326 307s > svytotal(~Bush+Kerry+Nader, dpps_yg) 307s total SE 307s Bush 64518472 2406526 307s Kerry 51202102 2408091 307s Nader 478530 101664 307s > svytotal(~Bush+Kerry+Nader, dpps_hr) 307s total SE 307s Bush 64518472 2624662 307s Kerry 51202102 2525222 307s Nader 478530 102793 307s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 307s total SE 307s Bush 64518472 2436738 307s Kerry 51202102 2439845 307s Nader 478530 102016 307s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 307s total SE 307s Bush 64518472 2472753 307s Kerry 51202102 2426842 307s Nader 478530 102595 307s > svytotal(~Bush+Kerry+Nader, dpps_br) 307s total SE 307s Bush 64518472 2447629 307s Kerry 51202102 2450787 307s Nader 478530 102420 307s > svytotal(~Bush+Kerry+Nader, dpps_ov) 307s total SE 307s Bush 64518472 2939608 307s Kerry 51202102 1964632 307s Nader 478530 104373 307s > 307s > ## subsets 307s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 307s total SE 307s Bush 34944285 5406348 307s Kerry 25581714 4047741 307s Nader 478530 102326 307s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 307s total SE 307s Bush 34944285 5377659 307s Kerry 25581714 4010908 307s Nader 478530 102016 307s > 307s > ## counts 307s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 307s I(Nader > 0) counts se 307s FALSE FALSE 19 0 307s TRUE TRUE 21 0 307s > 307s BEGIN TEST qrule-swiss.R 308s 308s R version 4.4.3 (2025-02-28) -- "Trophy Case" 308s Copyright (C) 2025 The R Foundation for Statistical Computing 308s Platform: x86_64-pc-linux-gnu 308s 308s R is free software and comes with ABSOLUTELY NO WARRANTY. 308s You are welcome to redistribute it under certain conditions. 308s Type 'license()' or 'licence()' for distribution details. 308s 308s R is a collaborative project with many contributors. 308s Type 'contributors()' for more information and 308s 'citation()' on how to cite R or R packages in publications. 308s 308s Type 'demo()' for some demos, 'help()' for on-line help, or 308s 'help.start()' for an HTML browser interface to help. 308s Type 'q()' to quit R. 308s 308s > library(survey) 308s Loading required package: grid 308s Loading required package: Matrix 309s Loading required package: survival 309s > 309s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1) 309s 309s Attaching package: 'survey' 309s 309s The following object is masked from 'package:graphics': 309s 309s dotchart 309s 309s > 309s > design_no_strat <- svydesign(id = ~id, 309s + probs = ~probs, 309s + data = data_no_strat, 309s + fpc = ~fpc) 309s > 309s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99) 309s > 309s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE, 309s + interval.type = "mean", qrule = "hf1") 309s > 309s > stopifnot(all(diff(res$x[,"quantile"])>=0)) 309s > 309s > 309s > 309s BEGIN TEST quantile.R 309s 309s R version 4.4.3 (2025-02-28) -- "Trophy Case" 309s Copyright (C) 2025 The R Foundation for Statistical Computing 309s Platform: x86_64-pc-linux-gnu 309s 309s R is free software and comes with ABSOLUTELY NO WARRANTY. 309s You are welcome to redistribute it under certain conditions. 309s Type 'license()' or 'licence()' for distribution details. 309s 309s R is a collaborative project with many contributors. 309s Type 'contributors()' for more information and 309s 'citation()' on how to cite R or R packages in publications. 309s 309s Type 'demo()' for some demos, 'help()' for on-line help, or 309s 'help.start()' for an HTML browser interface to help. 309s Type 'q()' to quit R. 309s 309s > library(survey) 309s Loading required package: grid 309s Loading required package: Matrix 310s Loading required package: survival 311s > set.seed(42) 311s > 311s > df<-data.frame(x=exp(rnorm(1000))) 311s 311s Attaching package: 'survey' 311s 311s The following object is masked from 'package:graphics': 311s 311s dotchart 311s 311s > df$y<-round(df$x,1) 311s > ddf<-svydesign(id=~1,data=df) 311s Warning message: 311s In svydesign.default(id = ~1, data = df) : 311s No weights or probabilities supplied, assuming equal probability 311s > rdf<-as.svrepdesign(ddf) 311s > 311s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 311s 0.01 0.1 0.5 0.9 0.99 311s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 311s > 311s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 311s x 311s q0.01 0.01554946 311s q0.1 0.01425828 311s q0.5 0.03428012 311s q0.9 0.16457488 311s q0.99 1.88672412 311s > 311s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 311s 0.01 0.1 0.5 0.9 0.99 311s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 311s > 311s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 312s x 312s q0.01 0.01556240 312s q0.1 0.01420086 312s q0.5 0.03430175 312s q0.9 0.16461019 312s q0.99 1.88818131 312s > 312s > 312s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 312s $quantiles 312s 0.01 0.1 0.5 0.9 0.99 312s y 0.02352941 0.2230769 0.9340909 3.55 9.4 312s 312s $CIs 312s , , y 312s 312s 0.01 0.1 0.5 0.9 0.99 312s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 312s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 312s 312s 312s > 312s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 312s Statistic: 312s y 312s q0.01 0.1 312s q0.1 0.3 312s q0.5 1.0 312s q0.9 3.6 312s q0.99 9.4 312s SE: 312s y 312s q0.01 0.02547977 312s q0.1 0.02547977 312s q0.5 0.02547977 312s q0.9 0.15287859 312s q0.99 1.88302540 312s > 312s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 312s $quantiles 312s 0.01 0.1 0.5 0.9 0.99 312s y 0.02352941 0.2230769 0.9340909 3.55 9.4 312s 312s $CIs 312s , , y 312s 312s 0.01 0.1 0.5 0.9 0.99 312s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 312s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 312s 312s 312s > 312s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 312s Statistic: 312s y 312s q0.01 0.1 312s q0.1 0.3 312s q0.5 1.0 312s q0.9 3.6 312s q0.99 9.4 312s SE: 312s y 312s q0.01 0.02551067 312s q0.1 0.02551067 312s q0.5 0.02551067 312s q0.9 0.15306404 312s q0.99 1.88450896 312s > 312s > 312s > 312s > df<-data.frame(x=exp(rnorm(20))) 312s > df$y<-round(df$x,1) 312s > ddf<-svydesign(id=~1,data=df) 312s > rdf<-as.svrepdesign(ddf) 312s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 312s Warning message: 312s In svydesign.default(id = ~1, data = df) : 312s No weights or probabilities supplied, assuming equal probability 312s 0.01 0.1 0.5 0.9 0.99 312s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 312s > 312s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 312s x 312s q0.01 0.00000000 312s q0.1 0.04598541 312s q0.5 0.25943731 312s q0.9 2.12343073 312s q0.99 1.91998924 312s > 312s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 312s 0.01 0.1 0.5 0.9 0.99 312s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 312s > 312s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 312s x 312s q0.01 0.00000000 312s q0.1 0.04732818 312s q0.5 0.24957966 312s q0.9 2.25211815 312s q0.99 2.04043154 312s > 312s > 312s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 312s $quantiles 312s 0.01 0.1 0.5 0.9 0.99 312s y 0.1 0.15 0.75 2.4 8.68 312s 312s $CIs 312s , , y 312s 312s 0.01 0.1 0.5 0.9 0.99 312s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 312s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 312s 312s 312s > 312s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 312s Statistic: 312s y 312s q0.01 0.10 312s q0.1 0.20 312s q0.5 0.80 312s q0.9 2.40 312s q0.99 8.68 312s SE: 312s y 312s q0.01 0.00000000 312s q0.1 0.02611112 312s q0.5 0.26542051 312s q0.9 2.10908603 312s q0.99 1.91777710 312s > 312s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 312s $quantiles 312s 0.01 0.1 0.5 0.9 0.99 312s y 0.1 0.15 0.75 2.4 8.68 312s 312s $CIs 312s , , y 312s 312s 0.01 0.1 0.5 0.9 0.99 312s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 312s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 312s 312s 312s > 312s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 312s Statistic: 312s y 312s q0.01 0.10 312s q0.1 0.20 312s q0.5 0.80 312s q0.9 2.40 312s q0.99 8.68 312s SE: 312s y 312s q0.01 0.00000000 312s q0.1 0.02551067 312s q0.5 0.25244616 312s q0.9 2.23558589 312s q0.99 2.03881114 312s > 312s BEGIN TEST quantiles-chile.R 312s 312s R version 4.4.3 (2025-02-28) -- "Trophy Case" 312s Copyright (C) 2025 The R Foundation for Statistical Computing 312s Platform: x86_64-pc-linux-gnu 312s 312s R is free software and comes with ABSOLUTELY NO WARRANTY. 312s You are welcome to redistribute it under certain conditions. 312s Type 'license()' or 'licence()' for distribution details. 312s 312s R is a collaborative project with many contributors. 312s Type 'contributors()' for more information and 312s 'citation()' on how to cite R or R packages in publications. 312s 312s Type 'demo()' for some demos, 'help()' for on-line help, or 312s 'help.start()' for an HTML browser interface to help. 312s Type 'q()' to quit R. 312s 312s > library(survey) 312s Loading required package: grid 312s Loading required package: Matrix 313s Loading required package: survival 314s 314s Attaching package: 'survey' 314s 314s The following object is masked from 'package:graphics': 314s 314s dotchart 314s 314s > datos <- readRDS("datos_ejemplo.rds") 314s > 314s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 314s > set.seed(234262762) 314s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 314s > options(survey.lonely.psu="remove") 314s > 314s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 314s > 314s > suppressWarnings({ 314s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 314s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 314s + }) 314s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 314s [1] TRUE 314s > 314s > suppressWarnings({ 314s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 314s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 314s + }) 314s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 314s [1] TRUE 314s > 314s BEGIN TEST rakecheck.R 314s 314s R version 4.4.3 (2025-02-28) -- "Trophy Case" 314s Copyright (C) 2025 The R Foundation for Statistical Computing 314s Platform: x86_64-pc-linux-gnu 314s 314s R is free software and comes with ABSOLUTELY NO WARRANTY. 314s You are welcome to redistribute it under certain conditions. 314s Type 'license()' or 'licence()' for distribution details. 314s 314s R is a collaborative project with many contributors. 314s Type 'contributors()' for more information and 314s 'citation()' on how to cite R or R packages in publications. 314s 314s Type 'demo()' for some demos, 'help()' for on-line help, or 314s 'help.start()' for an HTML browser interface to help. 314s Type 'q()' to quit R. 314s 314s > library(survey) 314s Loading required package: grid 314s Loading required package: Matrix 315s Loading required package: survival 315s 315s Attaching package: 'survey' 315s 315s > 315s > data(api) 315s The following object is masked from 'package:graphics': 315s 315s dotchart 315s 315s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 315s > rclus1 <- as.svrepdesign(dclus1) 315s > 315s > ## population marginal totals for each stratum 315s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 315s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 315s > 315s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 315s > 315s > svymean(~api00, rclus1r) 315s mean SE 315s api00 641.23 26.873 315s > svytotal(~enroll, rclus1r) 315s total SE 315s enroll 3647300 463511 315s > 315s > ff<-~stype+sch.wide 315s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 315s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 315s > 315s > svymean(~api00,rclus1g) 315s mean SE 315s api00 641.23 26.874 315s > svytotal(~enroll,rclus1g) 315s total SE 315s enroll 3647280 463582 315s > 315s > summary(weights(rclus1g)/weights(rclus1r)) 315s V1 V2 V3 V4 V5 V6 315s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 315s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 315s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 315s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 315s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 315s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 315s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 315s V7 V8 V9 V10 V11 315s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 315s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 315s Median :1 Median :1 Median :1 Median :1 Median :1 315s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 315s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 315s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 315s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 315s V12 V13 V14 V15 315s Min. :0.9997 Min. :1 Min. :1 Min. :1 315s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 315s Median :1.0001 Median :1 Median :1 Median :1 315s Mean :1.0000 Mean :1 Mean :1 Mean :1 315s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 315s Max. :1.0002 Max. :1 Max. :1 Max. :1 315s NA's :37 NA's :13 NA's :1 NA's :12 315s > 315s > 315s > ## Do it for a design without replicate weights 315s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 315s > 315s > svymean(~api00, dclus1r) 315s mean SE 315s api00 641.23 23.704 315s > svytotal(~enroll, dclus1r) 315s total SE 315s enroll 3647300 400603 315s > 315s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 315s > 315s > svymean(~api00,dclus1g) 315s mean SE 315s api00 641.23 23.704 315s > svytotal(~enroll,dclus1g) 315s total SE 315s enroll 3647280 400603 315s > 315s > summary(weights(dclus1g)/weights(dclus1r)) 315s Min. 1st Qu. Median Mean 3rd Qu. Max. 315s 1 1 1 1 1 1 315s > 315s > 315s > 315s > ## Example of raking with partial joint distributions 315s > pop.table <- xtabs(~stype+sch.wide,apipop) 315s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 315s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 315s + list(pop.table, pop.imp)) 315s > svymean(~api00, dclus1r2) 315s mean SE 315s api00 642.62 22.732 315s > 315s > ff1 <-~stype*sch.wide+comp.imp 315s > 315s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 315s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 315s > 315s > svymean(~api00, dclus1g2) 315s mean SE 315s api00 642.61 22.731 315s > 315s > summary(weights(dclus1r2)/weights(dclus1g2)) 315s Min. 1st Qu. Median Mean 3rd Qu. Max. 315s 0.999 1.000 1.000 1.000 1.000 1.002 315s > 315s BEGIN TEST raowuboot.R 315s 315s R version 4.4.3 (2025-02-28) -- "Trophy Case" 315s Copyright (C) 2025 The R Foundation for Statistical Computing 315s Platform: x86_64-pc-linux-gnu 315s 315s R is free software and comes with ABSOLUTELY NO WARRANTY. 315s You are welcome to redistribute it under certain conditions. 315s Type 'license()' or 'licence()' for distribution details. 315s 315s R is a collaborative project with many contributors. 315s Type 'contributors()' for more information and 315s 'citation()' on how to cite R or R packages in publications. 315s 315s Type 'demo()' for some demos, 'help()' for on-line help, or 315s 'help.start()' for an HTML browser interface to help. 315s Type 'q()' to quit R. 315s 316s > ## regression test for bug reported by Richard Valliant 316s > library(survey) 316s Loading required package: grid 316s Loading required package: Matrix 317s Loading required package: survival 317s 317s Attaching package: 'survey' 317s 317s The following object is masked from 'package:graphics': 317s 317s dotchart 317s 317s > s<-subbootweights(c(1,1),1:2, 50) 317s > stopifnot(all(s$repweights$weights %in% c(0,2))) 317s > 317s BEGIN TEST regTermTest-missing.R 317s 317s R version 4.4.3 (2025-02-28) -- "Trophy Case" 317s Copyright (C) 2025 The R Foundation for Statistical Computing 317s Platform: x86_64-pc-linux-gnu 317s 317s R is free software and comes with ABSOLUTELY NO WARRANTY. 317s You are welcome to redistribute it under certain conditions. 317s Type 'license()' or 'licence()' for distribution details. 317s 317s R is a collaborative project with many contributors. 317s Type 'contributors()' for more information and 317s 'citation()' on how to cite R or R packages in publications. 317s 317s Type 'demo()' for some demos, 'help()' for on-line help, or 317s 'help.start()' for an HTML browser interface to help. 317s Type 'q()' to quit R. 317s 317s > library(survey) 317s Loading required package: grid 317s Loading required package: Matrix 318s Loading required package: survival 318s 318s Attaching package: 'survey' 318s 318s The following object is masked from 'package:graphics': 318s 318s dotchart 318s 318s > data(nhanes) 318s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 318s > 318s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 319s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 319s > 319s > ta<-regTermTest(a, ~HI_CHOL) 319s > tb<-regTermTest(b, ~HI_CHOL) 319s > 319s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 319s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 319s > 319s BEGIN TEST regpredict.R 319s 319s R version 4.4.3 (2025-02-28) -- "Trophy Case" 319s Copyright (C) 2025 The R Foundation for Statistical Computing 319s Platform: x86_64-pc-linux-gnu 319s 319s R is free software and comes with ABSOLUTELY NO WARRANTY. 319s You are welcome to redistribute it under certain conditions. 319s Type 'license()' or 'licence()' for distribution details. 319s 319s R is a collaborative project with many contributors. 319s Type 'contributors()' for more information and 319s 'citation()' on how to cite R or R packages in publications. 319s 319s Type 'demo()' for some demos, 'help()' for on-line help, or 319s 'help.start()' for an HTML browser interface to help. 319s Type 'q()' to quit R. 319s 319s > library(survey) 319s Loading required package: grid 319s Loading required package: Matrix 320s Loading required package: survival 320s 320s Attaching package: 'survey' 320s 320s > data(api) 320s The following object is masked from 'package:graphics': 320s 320s dotchart 320s 320s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 320s > 320s > 320s > ## regression estimator of total, three ways 320s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 320s > npop <- sum(!is.na(apipop$enroll)) 320s > 320s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 320s > a <- predict(api.reg, newdata=pop, total=npop) 320s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 320s > 320s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 320s [1] TRUE 320s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 320s [1] TRUE 320s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 320s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 320s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 320s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 320s + } 320s > 320s > ## classical ratio estimator, four ways. 320s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 320s + family=quasi(link="identity", var="mu")) 320s > 320s > a <- predict(api.reg2, newdata=pop, total=npop) 320s > b <- svytotal(~api.stu, 320s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 320s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 320s > 320s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 320s [1] TRUE 320s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 320s [1] TRUE 320s > all.equal(as.vector(coef(a)),as.vector(e$total)) 320s [1] TRUE 320s > all.equal(as.vector(SE(a)), as.vector(e$se)) 320s [1] TRUE 320s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 320s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 320s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 320s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 320s + } 320s > 320s BEGIN TEST rss_scores.R 320s 320s R version 4.4.3 (2025-02-28) -- "Trophy Case" 320s Copyright (C) 2025 The R Foundation for Statistical Computing 320s Platform: x86_64-pc-linux-gnu 320s 320s R is free software and comes with ABSOLUTELY NO WARRANTY. 320s You are welcome to redistribute it under certain conditions. 320s Type 'license()' or 'licence()' for distribution details. 320s 320s R is a collaborative project with many contributors. 320s Type 'contributors()' for more information and 320s 'citation()' on how to cite R or R packages in publications. 320s 320s Type 'demo()' for some demos, 'help()' for on-line help, or 320s 'help.start()' for an HTML browser interface to help. 320s Type 'q()' to quit R. 320s 320s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 320s > library(survey) 320s Loading required package: grid 320s Loading required package: Matrix 321s Loading required package: survival 321s 321s Attaching package: 'survey' 321s 321s The following object is masked from 'package:graphics': 321s 321s dotchart 321s 321s > data(myco) 321s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 321s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 322s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 322s > 322s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 322s > 322s > s<-svyscoretest(m_full, ~Scar) 322s > stopifnot(abs(s[1]-10.73)<0.05) 322s > 322s > t<-svyscoretest(m_full,~Scar,method="individual") 322s > stopifnot(abs(coef(t)- -32.61)<0.1) 322s > stopifnot(abs(vcov(t)-99.1)<0.1) 322s > 322s > 322s BEGIN TEST scoping.R 322s 322s R version 4.4.3 (2025-02-28) -- "Trophy Case" 322s Copyright (C) 2025 The R Foundation for Statistical Computing 322s Platform: x86_64-pc-linux-gnu 322s 322s R is free software and comes with ABSOLUTELY NO WARRANTY. 322s You are welcome to redistribute it under certain conditions. 322s Type 'license()' or 'licence()' for distribution details. 322s 322s R is a collaborative project with many contributors. 322s Type 'contributors()' for more information and 322s 'citation()' on how to cite R or R packages in publications. 322s 322s Type 'demo()' for some demos, 'help()' for on-line help, or 322s 'help.start()' for an HTML browser interface to help. 322s Type 'q()' to quit R. 322s 322s > 322s > ## regression test for testing regression 322s > 322s > library(survey) 322s Loading required package: grid 322s Loading required package: Matrix 323s Loading required package: survival 323s 323s Attaching package: 'survey' 323s 323s > The following object is masked from 'package:graphics': 323s 323s dotchart 323s 323s data(api) 323s > 323s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 323s > 323s > 323s > f<-function(){ 323s + form<-acs.46~stype 323s + svyglm(formula=form, design = dstrat) 323s + } 323s > 323s > g<-function(form){ 323s + svyglm(formula=form, design = dstrat) 323s + } 323s > f() 323s Stratified Independent Sampling design 323s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 323s fpc = ~fpc) 323s 323s Call: svyglm(formula = form, design = dstrat) 323s 323s Coefficients: 323s (Intercept) stypeH stypeM 323s 28.7449 0.7551 0.4022 323s 323s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 323s (66 observations deleted due to missingness) 323s Null Deviance: 1838 323s Residual Deviance: 1835 AIC: 719.8 323s > g(acs.46~stype) 323s Stratified Independent Sampling design 323s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 323s fpc = ~fpc) 323s 323s Call: svyglm(formula = form, design = dstrat) 323s 323s Coefficients: 323s (Intercept) stypeH stypeM 323s 28.7449 0.7551 0.4022 323s 323s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 323s (66 observations deleted due to missingness) 323s Null Deviance: 1838 323s Residual Deviance: 1835 AIC: 719.8 323s > 323s > f<-function(){ 323s + form<-Surv(acs.46)~stype 323s + svycoxph(formula=form, design = dstrat) 323s + } 323s > 323s > g<-function(form){ 323s + svycoxph(formula=form, design = dstrat) 323s + } 323s > 323s > f() 323s Call: 323s svycoxph(formula = form, design = dstrat) 323s 323s coef exp(coef) se(coef) robust se z p 323s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 323s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 323s 323s Likelihood ratio test= on 2 df, p= 323s n= 134, number of events= 134 323s (66 observations deleted due to missingness) 323s > g(Surv(acs.46)~stype) 323s Call: 323s svycoxph(formula = form, design = dstrat) 323s 323s coef exp(coef) se(coef) robust se z p 323s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 323s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 323s 323s Likelihood ratio test= on 2 df, p= 323s n= 134, number of events= 134 323s (66 observations deleted due to missingness) 323s > 323s > ## check coxph for a single predictor 323s > svycoxph(Surv(acs.46)~api00,design=dstrat) 323s Call: 323s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 323s 323s coef exp(coef) se(coef) robust se z p 323s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 323s 323s Likelihood ratio test= on 1 df, p= 323s n= 134, number of events= 134 323s (66 observations deleted due to missingness) 323s > 323s BEGIN TEST survcurve.R 324s 324s R version 4.4.3 (2025-02-28) -- "Trophy Case" 324s Copyright (C) 2025 The R Foundation for Statistical Computing 324s Platform: x86_64-pc-linux-gnu 324s 324s R is free software and comes with ABSOLUTELY NO WARRANTY. 324s You are welcome to redistribute it under certain conditions. 324s Type 'license()' or 'licence()' for distribution details. 324s 324s R is a collaborative project with many contributors. 324s Type 'contributors()' for more information and 324s 'citation()' on how to cite R or R packages in publications. 324s 324s Type 'demo()' for some demos, 'help()' for on-line help, or 324s 'help.start()' for an HTML browser interface to help. 324s Type 'q()' to quit R. 324s 324s > library(survey) 324s Loading required package: grid 324s Loading required package: Matrix 325s Loading required package: survival 325s 325s Attaching package: 'survey' 325s 325s > The following object is masked from 'package:graphics': 325s 325s dotchart 325s 325s library(survival) 325s > 325s > pbc2<-rbind(pbc,pbc) 325s > pbc2$id<-rep(1:418,2) 325s > 325s > dpbc1<-svydesign(id=~1, data=pbc) 325s Warning message: 325s In svydesign.default(id = ~1, data = pbc) : 325s No weights or probabilities supplied, assuming equal probability 325s > dpbc2<-svydesign(id=~id, data=pbc2) 325s > 325s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 325s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 325s Warning message: 325s In svydesign.default(id = ~id, data = pbc2) : 325s No weights or probabilities supplied, assuming equal probability 325s > 325s > (c1<-confint(s1,(1:5)*365)) 325s 0.025 0.975 325s 365 0.6446215 0.8594153 325s 730 0.5410938 0.7766848 325s 1095 0.2683127 0.5103356 325s 1460 0.1444731 0.3722001 325s 1825 0.1009672 0.3204713 325s > (c2<-confint(s2,(1:5)*365)) 325s 0.025 0.975 325s 365 0.6446215 0.8594153 325s 730 0.5410938 0.7766848 325s 1095 0.2683127 0.5103356 325s 1460 0.1444731 0.3722001 325s 1825 0.1009672 0.3204713 325s > all.equal(c1, c2) 325s [1] TRUE 325s > 325s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 325s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 325s > 325s > d<-data.frame(bili=c(5,10)) 325s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 325s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 327s > 327s > (pc1<-confint(p1[[1]],(1:5)*365)) 327s 0.025 0.975 327s 365 0.8410027 0.9266263 327s 730 0.7371114 0.8548312 327s 1095 0.5517779 0.7018583 327s 1460 0.4335073 0.5992819 328s 1825 0.3260899 0.5046241 328s > (pc2<-confint(p2[[1]],(1:5)*365)) 328s 0.025 0.975 328s 365 0.8409490 0.9267054 328s 730 0.7370152 0.8549432 328s 1095 0.5515848 0.7019513 328s 1460 0.4332252 0.5992968 328s 1825 0.3257172 0.5045795 328s > all.equal(pc1, pc2) 328s [1] "Mean relative difference: 0.0002070722" 328s > 328s > (q1<-quantile(p1[[2]])) 328s 0.75 0.5 0.25 328s 489 930 1492 328s > (q2<-quantile(p2[[2]])) 328s 0.75 0.5 0.25 328s 489 930 1492 328s > all.equal(q1,q2) 328s [1] TRUE 328s > 328s BEGIN TEST svyby-strings.R 328s 328s R version 4.4.3 (2025-02-28) -- "Trophy Case" 328s Copyright (C) 2025 The R Foundation for Statistical Computing 328s Platform: x86_64-pc-linux-gnu 328s 328s R is free software and comes with ABSOLUTELY NO WARRANTY. 328s You are welcome to redistribute it under certain conditions. 328s Type 'license()' or 'licence()' for distribution details. 328s 328s R is a collaborative project with many contributors. 328s Type 'contributors()' for more information and 328s 'citation()' on how to cite R or R packages in publications. 328s 328s Type 'demo()' for some demos, 'help()' for on-line help, or 328s 'help.start()' for an HTML browser interface to help. 328s Type 'q()' to quit R. 328s 328s > 328s > ## check that stringsAsFactors fixes the string levels problem 328s > data(api, package = "survey") 328s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 329s > est0 <- 329s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 329s > 329s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 329s > 329s BEGIN TEST svyby_bug.R 329s 329s R version 4.4.3 (2025-02-28) -- "Trophy Case" 329s Copyright (C) 2025 The R Foundation for Statistical Computing 329s Platform: x86_64-pc-linux-gnu 329s 329s R is free software and comes with ABSOLUTELY NO WARRANTY. 329s You are welcome to redistribute it under certain conditions. 329s Type 'license()' or 'licence()' for distribution details. 329s 329s R is a collaborative project with many contributors. 329s Type 'contributors()' for more information and 329s 'citation()' on how to cite R or R packages in publications. 329s 329s Type 'demo()' for some demos, 'help()' for on-line help, or 329s 'help.start()' for an HTML browser interface to help. 329s Type 'q()' to quit R. 329s 329s > library(survey) 329s Loading required package: grid 329s Loading required package: Matrix 330s Loading required package: survival 330s > options(warn=2) 330s > 330s Attaching package: 'survey' 330s 330s The following object is masked from 'package:graphics': 330s 330s dotchart 330s 330s 330s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 330s > data(api) 330s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 331s > svyby(~api99, ~stype, dclus1, svymean ) 331s stype api99 se 331s E E 607.7917 22.81660 331s H H 595.7143 41.76400 331s M M 608.6000 32.56064 331s > 331s > set.seed(123) 331s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 331s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 331s > 331s > # subsetting w/ na.rm = FALSE... 331s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 331s mean SE 331s api99 NA NA 331s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 331s mean SE 331s api99 595.71 41.764 331s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 331s mean SE 331s api99 NA NA 331s > 331s > # ... looks like this: 331s > svyby(~api99, ~stype, dclus1.na , svymean ) 331s stype api99 se 331s E E NA NA 331s H H 595.7143 41.764 331s M M NA NA 331s > 331s > # subsetting w/ na.rm = TRUE... 331s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 331s mean SE 331s api99 606.53 22.901 331s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 331s mean SE 331s api99 595.71 41.764 331s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 331s mean SE 331s api99 613.39 33.224 331s > 331s > # ... looks like this 331s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 331s stype api99 se 331s E E 606.5319 22.90084 331s H H 595.7143 41.76400 331s M M 613.3913 33.22358 331s > 331s > # Without missing values, this works: 331s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 331s stype api99 se 331s E E 607.7917 22.81660 331s H H 595.7143 41.76400 331s M M 608.6000 32.56064 331s > 331s > # ... but this breaks! 331s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 331s stype api99 se 331s E E 606.5319 22.90084 331s H H 595.7143 41.76400 331s M M 613.3913 33.22358 331s > 331s > # ... and i don't think this is the expected behavior 331s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 331s stype api99 se 331s E E NA NA 331s H H 595.7143 41.764 331s M M NA NA 331s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 331s stype api99 se 331s E E 606.5319 22.90084 331s H H 595.7143 41.76400 331s M M 613.3913 33.22358 331s > 331s > 331s > ## Now some more as tests 331s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 331s stype api99 se 331s E E 2894629.0 792809.8 331s H H 282283.9 101492.9 331s M M 477513.4 107555.5 331s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 331s stype api99/api00 se.api99/api00 331s E E 0.9367750 0.006365702 331s H H 0.9630485 0.010520785 331s M M 0.9682246 0.009390982 331s > 331s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 331s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 331s stype (Intercept) se.(Intercept) 331s E E 606.5319 22.90084 331s H H 595.7143 41.76400 331s M M 613.3913 33.22358 331s > 331s BEGIN TEST svyby_se.R 331s 331s R version 4.4.3 (2025-02-28) -- "Trophy Case" 331s Copyright (C) 2025 The R Foundation for Statistical Computing 331s Platform: x86_64-pc-linux-gnu 331s 331s R is free software and comes with ABSOLUTELY NO WARRANTY. 331s You are welcome to redistribute it under certain conditions. 331s Type 'license()' or 'licence()' for distribution details. 331s 331s R is a collaborative project with many contributors. 331s Type 'contributors()' for more information and 331s 'citation()' on how to cite R or R packages in publications. 331s 331s Type 'demo()' for some demos, 'help()' for on-line help, or 331s 'help.start()' for an HTML browser interface to help. 331s Type 'q()' to quit R. 331s 331s > library(survey) 331s Loading required package: grid 331s Loading required package: Matrix 332s Loading required package: survival 332s 332s Attaching package: 'survey' 332s 332s The following object is masked from 'package:graphics': 332s 332s dotchart 332s 332s > data(api) 332s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 332s > 332s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 332s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 332s > 332s > 332s > stopifnot(all.equal(SE(a),SE(b))) 332s > 332s BEGIN TEST svycontrast.R 332s 332s R version 4.4.3 (2025-02-28) -- "Trophy Case" 332s Copyright (C) 2025 The R Foundation for Statistical Computing 332s Platform: x86_64-pc-linux-gnu 332s 332s R is free software and comes with ABSOLUTELY NO WARRANTY. 332s You are welcome to redistribute it under certain conditions. 332s Type 'license()' or 'licence()' for distribution details. 332s 332s R is a collaborative project with many contributors. 332s Type 'contributors()' for more information and 332s 'citation()' on how to cite R or R packages in publications. 332s 332s Type 'demo()' for some demos, 'help()' for on-line help, or 332s 'help.start()' for an HTML browser interface to help. 332s Type 'q()' to quit R. 332s 332s > library(survey) 332s Loading required package: grid 333s Loading required package: Matrix 334s Loading required package: survival 334s 334s Attaching package: 'survey' 334s 334s > The following object is masked from 'package:graphics': 334s 334s dotchart 334s 334s data(api) 334s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 334s > rclus2<-as.svrepdesign(dclus2) 334s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 334s > svycontrast(model, c(ell=1,meals=0)) 334s contrast SE 334s contrast -2.0592 1.6177 334s > a<-svycontrast(model, c(0,1,0,0)) 334s > 334s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 334s > svycontrast(model2, c(ell=1,meals=0)) 334s contrast SE 334s contrast -2.0592 1.6177 334s > a2<-svycontrast(model2, c(0,1,0,0)) 334s > stopifnot(!is.null(a2$replicates)) 334s > 334s BEGIN TEST svyivreg-var.R 334s 334s R version 4.4.3 (2025-02-28) -- "Trophy Case" 334s Copyright (C) 2025 The R Foundation for Statistical Computing 334s Platform: x86_64-pc-linux-gnu 334s 334s R is free software and comes with ABSOLUTELY NO WARRANTY. 334s You are welcome to redistribute it under certain conditions. 334s Type 'license()' or 'licence()' for distribution details. 334s 334s R is a collaborative project with many contributors. 334s Type 'contributors()' for more information and 334s 'citation()' on how to cite R or R packages in publications. 334s 334s Type 'demo()' for some demos, 'help()' for on-line help, or 334s 'help.start()' for an HTML browser interface to help. 334s Type 'q()' to quit R. 334s 334s > 334s > library(survey) 334s Loading required package: grid 334s Loading required package: Matrix 335s Loading required package: survival 336s 336s Attaching package: 'survey' 336s 336s > data(api) 336s The following object is masked from 'package:graphics': 336s 336s dotchart 336s 336s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 336s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 336s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 336s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 336s > 336s BEGIN TEST svyivreg.R 336s 336s R version 4.4.3 (2025-02-28) -- "Trophy Case" 336s Copyright (C) 2025 The R Foundation for Statistical Computing 336s Platform: x86_64-pc-linux-gnu 336s 336s R is free software and comes with ABSOLUTELY NO WARRANTY. 336s You are welcome to redistribute it under certain conditions. 336s Type 'license()' or 'licence()' for distribution details. 336s 336s R is a collaborative project with many contributors. 336s Type 'contributors()' for more information and 336s 'citation()' on how to cite R or R packages in publications. 336s 336s Type 'demo()' for some demos, 'help()' for on-line help, or 336s 'help.start()' for an HTML browser interface to help. 336s Type 'q()' to quit R. 336s 336s > library(survey) 336s Loading required package: grid 336s Loading required package: Matrix 337s Loading required package: survival 337s 337s Attaching package: 'survey' 337s 337s The following object is masked from 'package:graphics': 337s 337s dotchart 337s 337s > library(AER) 337s Loading required package: car 337s Loading required package: carData 337s Loading required package: lmtest 337s Loading required package: zoo 337s 337s Attaching package: 'zoo' 337s 337s The following objects are masked from 'package:base': 337s 337s as.Date, as.Date.numeric 337s 337s Loading required package: sandwich 337s > 337s > load("cigsw.rda") 337s > 337s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 337s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 337s > 337s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 337s [1] TRUE 337s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 337s [1] TRUE 337s > 337s BEGIN TEST svyolr-rake-subset.R 337s 337s R version 4.4.3 (2025-02-28) -- "Trophy Case" 337s Copyright (C) 2025 The R Foundation for Statistical Computing 337s Platform: x86_64-pc-linux-gnu 337s 337s R is free software and comes with ABSOLUTELY NO WARRANTY. 337s You are welcome to redistribute it under certain conditions. 337s Type 'license()' or 'licence()' for distribution details. 337s 337s R is a collaborative project with many contributors. 337s Type 'contributors()' for more information and 337s 'citation()' on how to cite R or R packages in publications. 337s 337s Type 'demo()' for some demos, 'help()' for on-line help, or 337s 'help.start()' for an HTML browser interface to help. 337s Type 'q()' to quit R. 337s 337s > library(survey) 337s Loading required package: grid 337s Loading required package: Matrix 339s Loading required package: survival 339s 339s Attaching package: 'survey' 339s 339s > data(api) 339s The following object is masked from 'package:graphics': 339s 339s dotchart 339s 339s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 339s > 339s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 339s > 339s > ## population marginal totals for each stratum 339s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 339s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 339s > 339s > 339s > ## rake with the population totals 339s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 339s > 339s > # works 339s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 339s > 339s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 339s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 339s > 339s > # fails in 4.1 (should work because NA values are subsetted out) 339s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 339s > 339s BEGIN TEST svyolr.R 339s 339s R version 4.4.3 (2025-02-28) -- "Trophy Case" 339s Copyright (C) 2025 The R Foundation for Statistical Computing 339s Platform: x86_64-pc-linux-gnu 339s 339s R is free software and comes with ABSOLUTELY NO WARRANTY. 339s You are welcome to redistribute it under certain conditions. 339s Type 'license()' or 'licence()' for distribution details. 339s 339s R is a collaborative project with many contributors. 339s Type 'contributors()' for more information and 339s 'citation()' on how to cite R or R packages in publications. 339s 339s Type 'demo()' for some demos, 'help()' for on-line help, or 339s 'help.start()' for an HTML browser interface to help. 339s Type 'q()' to quit R. 339s 339s > library(survey) 339s Loading required package: grid 339s Loading required package: Matrix 340s Loading required package: survival 340s 340s Attaching package: 'survey' 340s 340s The following object is masked from 'package:graphics': 340s 340s dotchart 340s 340s > 340s > ################################################################################ 340s > # Example from svyolr: runs OK 340s > data(api) 340s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 340s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 340s > 340s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 340s > m 340s Call: 340s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 340s 340s Coefficients: 340s avg.ed mobility stypeH stypeM 340s -2.6999217 0.0325042 -1.7574715 -0.6191463 340s 340s Intercepts: 340s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 340s -8.857919 -6.586464 -4.924938 340s > 340s > ## Use regTermTest for testing multiple parameters 340s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 340s > ################################################################################ 340s > 340s > ################################################################################ 340s > # If we wrap everything into a function: error b/c it looks for design variable 340s > # dclus1 in .GlobalEnv 340s > 340s > foo <- function(x){ 340s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 340s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 340s + 340s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 340s + ## Use regTermTest for testing multiple parameters 340s + regTermTest(m, ~avg.ed+stype, method="LRT") 340s + } 340s > 340s > # OK 340s > foo(apiclus1) 340s Working (Rao-Scott+F) LRT for avg.ed stype 340s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 340s Working 2logLR = 0.6580304 p= 0.73257 340s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 340s > 340s > # Clean-up everything but apiclus1 and foo 340s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 340s > 340s > # Error 340s > test2<-foo(apiclus1) 340s > ################################################################################ 340s > all.equal(test,test2) 340s [1] TRUE 340s > 340s > 340s BEGIN TEST toy_example_for_postStratify.R 341s 341s R version 4.4.3 (2025-02-28) -- "Trophy Case" 341s Copyright (C) 2025 The R Foundation for Statistical Computing 341s Platform: x86_64-pc-linux-gnu 341s 341s R is free software and comes with ABSOLUTELY NO WARRANTY. 341s You are welcome to redistribute it under certain conditions. 341s Type 'license()' or 'licence()' for distribution details. 341s 341s R is a collaborative project with many contributors. 341s Type 'contributors()' for more information and 341s 'citation()' on how to cite R or R packages in publications. 341s 341s Type 'demo()' for some demos, 'help()' for on-line help, or 341s 'help.start()' for an HTML browser interface to help. 341s Type 'q()' to quit R. 341s 341s > library(survey) 341s Loading required package: grid 341s Loading required package: Matrix 342s Loading required package: survival 342s > 342s > # Dummy data for testing nonresponse adjustments 342s > toy <- data.frame(id = 1:10, 342s + dummy = 1, 342s + class = c(rep("A", 5), rep("B", 5)), 342s + responded = c(rep(TRUE, 8), FALSE, FALSE), 342s + weight = rep(100, 10)) 342s > 342s 342s Attaching package: 'survey' 342s 342s The following object is masked from 'package:graphics': 342s 342s dotchart 342s 342s > # With jackknife replicate weights 342s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 342s > diag(toy_repweights) <- rep(0, 10) 342s > 342s > # Scramble up which person is in which jackknife group 342s > toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 342s > 342s > toy_design <- svrepdesign(variables = toy[, 1:4], 342s + weights = toy$weight, 342s + repweights = toy_repweights, 342s + type = "JK1", 342s + scale = 0.9) 342s > 342s > # Get the sum of the weights for the full sample 342s > poptotals <- as.data.frame(svyby(formula = ~dummy, 342s + by = ~class, 342s + design = toy_design, 342s + FUN = survey::svytotal)) 342s > 342s > poptotals$Freq <- poptotals$dummy 342s > poptotals$dummy <- NULL 342s > poptotals$se <- NULL 342s > 342s > # Adjust the weights of the responding sample to match to the full sample 342s > adjusted <- postStratify(design = subset(toy_design, responded), 342s + strata = ~class, 342s + population = poptotals) 342s > 342s > # This works for the weights... 342s > svyby(formula = ~dummy, 342s + by = ~class, 342s + design = adjusted, 342s + FUN = survey::svytotal) 342s class dummy se 342s A A 500 0 342s B B 500 0 342s > 342s > # ...and some, but not all, the replicate weights 342s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 342s > 342s > 342s > 342s BEGIN TEST twophase.R 342s 342s R version 4.4.3 (2025-02-28) -- "Trophy Case" 342s Copyright (C) 2025 The R Foundation for Statistical Computing 342s Platform: x86_64-pc-linux-gnu 342s 342s R is free software and comes with ABSOLUTELY NO WARRANTY. 342s You are welcome to redistribute it under certain conditions. 342s Type 'license()' or 'licence()' for distribution details. 342s 342s R is a collaborative project with many contributors. 342s Type 'contributors()' for more information and 342s 'citation()' on how to cite R or R packages in publications. 342s 342s Type 'demo()' for some demos, 'help()' for on-line help, or 342s 'help.start()' for an HTML browser interface to help. 342s Type 'q()' to quit R. 342s 342s > library(survey) 342s Loading required package: grid 342s Loading required package: Matrix 343s Loading required package: survival 343s > 343s > ## two-phase simple random sampling. 343s > data(pbc, package="survival") 343s 343s Attaching package: 'survey' 343s 343s The following object is masked from 'package:graphics': 343s 343s dotchart 343s 343s > pbc$id<-1:nrow(pbc) 343s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 343s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 343s Two-phase sparse-matrix design: 343s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 343s subset = subset, data = data, pps = pps) 343s Phase 1: 344s Independent Sampling design (with replacement) 344s svydesign(ids = ~id) 344s Phase 2: 344s Independent Sampling design 344s svydesign(ids = ~id, fpc = `*phase1*`) 344s > m<-svymean(~bili, d2pbc) 344s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 344s [1] TRUE 344s > all.equal(as.vector(SE(m)), 344s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 344s + tolerance=0.002) 344s [1] TRUE 344s > 344s > ## two-stage sampling as two-phase 344s > data(mu284) 344s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 344s > mu284.1<-mu284[ii,] 344s > mu284.1$id<-1:nrow(mu284.1) 344s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 344s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 344s > ## first phase cluster sample, second phase stratified within cluster 344s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 344s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 344s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 344s NULL), data = mu284.1, subset = ~sub, method = "approx") 344s Phase 1: 344s 1 - level Cluster Sampling design 344s With (5) clusters. 344s svydesign(ids = ~id1, fpc = ~n1) 344s Phase 2: 344s Stratified Independent Sampling design 344s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 344s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 344s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 344s Two-phase sparse-matrix design: 344s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 344s subset = subset, data = data, pps = pps) 344s Phase 1: 344s 1 - level Cluster Sampling design 344s With (5) clusters. 344s svydesign(ids = ~id1, fpc = ~n1) 344s Phase 2: 344s Stratified Independent Sampling design 344s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 344s > summary(d2mu284) 344s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 344s NULL), data = mu284.1, subset = ~sub, method = "approx") 344s Phase 1: 344s 1 - level Cluster Sampling design 344s With (5) clusters. 344s svydesign(ids = ~id1, fpc = ~n1) 344s Probabilities: 344s Min. 1st Qu. Median Mean 3rd Qu. Max. 344s 0.1 0.1 0.1 0.1 0.1 0.1 344s Population size (PSUs): 50 344s Phase 2: 344s Stratified Independent Sampling design 344s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 344s Probabilities: 344s Min. 1st Qu. Median Mean 3rd Qu. Max. 344s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 344s Stratum Sizes: 344s 19 31 45 47 50 344s obs 3 3 3 3 3 344s design.PSU 3 3 3 3 3 344s actual.PSU 3 3 3 3 3 344s Population stratum sizes (PSUs): 344s 19 31 45 47 50 344s 5 7 8 5 9 344s Data variables: 344s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 344s > t1<-svytotal(~y1, dmu284) 344s > t2<-svytotal(~y1, d2mu284) 344s > t22<-svytotal(~y1,d22mu284) 344s > m1<-svymean(~y1, dmu284) 344s > m2<-svymean(~y1, d2mu284) 344s > m22<-svymean(~y1, d22mu284) 344s > all.equal(coef(t1),coef(t2)) 344s [1] TRUE 344s > all.equal(coef(t1),coef(t22)) 344s [1] TRUE 344s > all.equal(coef(m1),coef(m2)) 344s [1] TRUE 344s > all.equal(coef(m1),coef(m22)) 344s [1] TRUE 344s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 344s [1] TRUE 344s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 344s [1] TRUE 344s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 344s [1] TRUE 344s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 344s [1] TRUE 344s > 344s > ## case-cohort design 344s > ##this example requires R 2.3.1 or later for cch and data. 344s > library("survival") 344s > data(nwtco, package="survival") 344s > ## unstratified, equivalent to Lin & Ying (1993) 344s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 344s + subset=~I(in.subcohort | rel), data=nwtco)) 344s Two-phase sparse-matrix design: 344s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 344s subset = subset, data = data, pps = pps) 344s Phase 1: 344s Independent Sampling design (with replacement) 344s svydesign(ids = ~seqno) 344s Phase 2: 344s Stratified Independent Sampling design 344s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 344s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 344s + design=dcchs) 344s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 344s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 344s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 344s + design=dcchs) 344s > all.equal(coef(cch1),coef(cch1.2)) 344s [1] TRUE 344s > all.equal(SE(cch1),SE(cch1.2)) 344s [1] TRUE 344s > ## Using survival::cch 344s > subcoh <- nwtco$in.subcohort 344s > selccoh <- with(nwtco, rel==1|subcoh==1) 344s > ccoh.data <- nwtco[selccoh,] 344s > ccoh.data$subcohort <- subcoh[selccoh] 344s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 344s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 344s + cohort.size=4028, method="LinYing", robust=TRUE) 344s > 344s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 344s [1] TRUE 344s > ## cch has smaller variances by a factor of 1.0005 because 344s > ## there is a (n/(n-1)) in the survey phase1 varianace 344s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 344s [1] TRUE 344s > 344s > 344s > ## bug report from Takahiro Tsuchiya for version 3.4 344s > ## We used to not match Sarndal exactly, because our old phase-one 344s > ## estimator had a small bias for finite populations 344s > rei<-read.table(tmp<-textConnection( 344s + " id N n.a h n.ah n.h sub y 344s + 1 1 300 20 1 12 5 TRUE 1 344s + 2 2 300 20 1 12 5 TRUE 2 344s + 3 3 300 20 1 12 5 TRUE 3 344s + 4 4 300 20 1 12 5 TRUE 4 344s + 5 5 300 20 1 12 5 TRUE 5 344s + 6 6 300 20 1 12 5 FALSE NA 344s + 7 7 300 20 1 12 5 FALSE NA 344s + 8 8 300 20 1 12 5 FALSE NA 344s + 9 9 300 20 1 12 5 FALSE NA 344s + 10 10 300 20 1 12 5 FALSE NA 344s + 11 11 300 20 1 12 5 FALSE NA 344s + 12 12 300 20 1 12 5 FALSE NA 344s + 13 13 300 20 2 8 3 TRUE 6 344s + 14 14 300 20 2 8 3 TRUE 7 344s + 15 15 300 20 2 8 3 TRUE 8 344s + 16 16 300 20 2 8 3 FALSE NA 344s + 17 17 300 20 2 8 3 FALSE NA 344s + 18 18 300 20 2 8 3 FALSE NA 344s + 19 19 300 20 2 8 3 FALSE NA 344s + 20 20 300 20 2 8 3 FALSE NA 344s + "), header=TRUE) 344s > close(tmp) 344s > 344s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 344s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 344s > tot<- svytotal(~y, des.rei) 344s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 344s + fpc=list(~N,NULL), subset=~sub, data=rei) 344s > tot2<- svytotal(~y, des.rei2) 344s > 344s > ## based on Sarndal et al (9.4.14) 344s > rei$w.ah <- rei$n.ah / rei$n.a 344s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 344s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 344s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 344s > 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)) 344s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 344s > 344s > a.rei$f.h<-with(a.rei, n.h/n.ah) 344s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 344s > 344s > a.rei$f<-with(a.rei, n.a/N) 344s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 344s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 344s > 344s > V 344s [1] 36522.63 344s > Vphase1 344s [1] 24072.63 344s > Vphase2 344s [1] 12450 344s > vcov(tot) 344s y 344s y 35911.05 344s attr(,"phases") 344s attr(,"phases")$phase1 344s [,1] 344s [1,] 23461.05 344s 344s attr(,"phases")$phase2 344s y 344s y 12450 344s 344s > vcov(tot2) 344s [,1] 344s [1,] 36522.63 344s attr(,"phases") 344s attr(,"phases")$phase1 344s [,1] 344s [1,] 24072.63 344s 344s attr(,"phases")$phase2 344s [,1] 344s [1,] 12450 344s 344s > ## phase 2 identical 344s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 344s [1] TRUE 344s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 344s [1] TRUE 344s > ## phase 1 differs by 2.6% for old twophase estimator 344s > Vphase1/attr(vcov(tot),"phases")$phase1 344s [,1] 344s [1,] 1.026068 344s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 344s [1] TRUE 344s > 344s > 345s autopkgtest [22:42:27]: test run-unit-test: -----------------------] 345s autopkgtest [22:42:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 345s run-unit-test PASS 346s autopkgtest [22:42:28]: test pkg-r-autopkgtest: preparing testbed 420s autopkgtest [22:43:42]: testbed dpkg architecture: amd64 421s autopkgtest [22:43:43]: testbed apt version: 2.9.31ubuntu1 421s autopkgtest [22:43:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 421s autopkgtest [22:43:43]: testbed release detected to be: plucky 422s autopkgtest [22:43:44]: updating testbed package index (apt update) 423s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 423s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 423s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 423s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 423s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 423s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 423s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 423s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 423s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 423s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 423s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 423s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 423s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 423s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 423s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 424s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 424s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 424s Fetched 1265 kB in 1s (1358 kB/s) 425s Reading package lists... 425s Reading package lists... 426s Building dependency tree... 426s Reading state information... 426s Calculating upgrade... 426s Calculating upgrade... 426s The following package was automatically installed and is no longer required: 426s libnl-genl-3-200 426s Use 'sudo apt autoremove' to remove it. 426s The following NEW packages will be installed: 426s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 426s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 426s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 426s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 426s The following packages will be upgraded: 426s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 426s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 426s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 426s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 426s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 426s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 427s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 427s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 427s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 427s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 427s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 427s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 427s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 427s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 427s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 427s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 427s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 427s parted pci.ids pciutils pinentry-curses python-apt-common python3 427s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 427s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 427s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 427s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 427s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 427s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 427s xz-utils 427s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 427s Need to get 829 MB of archives. 427s After this operation, 325 MB of additional disk space will be used. 427s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 427s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 427s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 427s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 427s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 428s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 428s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 428s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 428s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 428s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 428s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 428s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 428s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 428s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 428s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 428s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 428s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 428s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 428s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 428s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 428s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 428s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 428s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 428s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 428s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 428s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 428s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 428s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 428s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 428s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 428s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 428s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 428s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 428s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 428s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 428s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 428s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 428s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 428s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 428s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 428s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 428s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 428s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 428s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 428s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 429s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 429s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 429s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 429s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 429s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 429s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 429s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 429s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 429s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 429s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 429s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 429s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 429s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 429s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 429s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 429s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 429s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 429s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 429s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 429s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 429s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 429s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 429s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 429s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 429s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 429s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 429s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 429s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 429s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 429s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 429s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 429s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 429s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 429s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 429s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 429s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 429s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 429s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 429s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 429s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 429s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 429s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 429s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 429s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 429s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 429s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 429s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 429s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 429s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 429s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 429s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 429s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 429s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 429s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 429s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 429s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 430s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 430s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 430s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 430s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 430s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 430s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 430s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 430s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 458s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 458s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 458s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 458s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 458s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 458s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 458s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 458s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 461s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 462s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 471s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 471s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 471s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 471s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 471s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 471s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 474s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 474s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 474s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 475s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 475s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 475s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 475s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 475s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 475s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 475s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 475s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 476s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 476s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 476s Preconfiguring packages ... 476s Fetched 829 MB in 49s (16.9 MB/s) 477s (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 ... 109140 files and directories currently installed.) 477s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 477s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 477s Setting up ncurses-bin (6.5+20250216-2) ... 477s (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 ... 109140 files and directories currently installed.) 477s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 477s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 477s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 477s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 477s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 477s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 477s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 477s Checking for services that may need to be restarted... 477s Checking init scripts... 477s Checking for services that may need to be restarted... 477s Checking init scripts... 478s Stopping some services possibly affected by the upgrade (will be restarted later): 478s cron: stopping...done. 478s 478s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 478s Setting up libc6:amd64 (2.41-1ubuntu1) ... 478s Checking for services that may need to be restarted... 478s Checking init scripts... 478s Restarting services possibly affected by the upgrade: 478s cron: restarting...done. 478s 478s Services restarted successfully. 478s (Reading database ... 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.../23-parted_3.6-5_amd64.deb ... 488s Unpacking parted (3.6-5) over (3.6-4build1) ... 488s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 488s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 488s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 488s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 488s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 488s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 488s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 488s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 488s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 488s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 488s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 488s Unpacking strace 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.../56-initramfs-tools_0.146ubuntu1_all.deb ... 494s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 494s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 494s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 494s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 494s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 494s Selecting previously unselected package libdebuginfod1t64:amd64. 494s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 494s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 494s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 494s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 494s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 494s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 494s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 494s Unpacking 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new version of config file /etc/mime.types ... 502s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 502s Setting up ubuntu-kernel-accessories (1.549) ... 502s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 502s Setting up pci.ids (0.0~2025.03.09-1) ... 502s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 502s Setting up apt-utils (2.9.33) ... 502s Setting up libdebuginfod-common (0.192-4) ... 502s Setting up exfatprogs (1.2.8-1) ... 502s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 502s Setting up bpftool (7.6.0+6.14.0-10.10) ... 502s Setting up libestr0:amd64 (0.1.11-2) ... 502s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 502s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 502s Setting up dosfstools (4.2-1.2) ... 502s Setting up rsyslog (8.2412.0-2ubuntu2) ... 502s info: The user `syslog' is already a member of `adm'. 503s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 503s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 503s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 503s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 503s Setting up systemd (257.3-1ubuntu3) ... 503s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 503s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 504s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 504s Setting up libparted2t64:amd64 (3.6-5) ... 504s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 504s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 504s Setting up linux-headers-generic (6.14.0-10.10) ... 504s Setting up libjemalloc2:amd64 (5.3.0-3) ... 504s Setting up locales (2.41-1ubuntu1) ... 504s Installing new version of config file /etc/locale.alias ... 505s Generating locales (this might take a while)... 507s en_US.UTF-8... done 507s Generation complete. 507s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 507s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 507s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 507s Installing new version of config file /etc/apparmor.d/fusermount3 ... 507s Installing new version of config file /etc/apparmor.d/lsusb ... 507s Installing new version of config file /etc/apparmor.d/openvpn ... 508s Reloading AppArmor profiles 509s Setting up libftdi1-2:amd64 (1.5-8build1) ... 509s Setting up libglib2.0-data (2.84.0-1) ... 509s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 509s Setting up libncurses6:amd64 (6.5+20250216-2) ... 509s Setting up strace (6.13+ds-1ubuntu1) ... 509s Setting up xz-utils (5.6.4-1) ... 509s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 509s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 510s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 510s Setting up udev (257.3-1ubuntu3) ... 510s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 513s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 513s Setting up libpci3:amd64 (1:3.13.0-2) ... 513s Setting up whiptail (0.52.24-4ubuntu2) ... 513s Setting up python-apt-common (2.9.9build1) ... 513s Setting up pnp.ids (0.393-3) ... 513s Setting up libnl-3-200:amd64 (3.7.0-1) ... 513s Setting up python3.13-minimal (3.13.2-2) ... 514s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 514s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 514s Setting up libc-dev-bin (2.41-1ubuntu1) ... 514s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 514s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 514s Setting up rsync (3.4.1+ds1-3) ... 515s rsync.service is a disabled or a static unit not running, not starting it. 515s Setting up python3.13-gdbm (3.13.2-2) ... 515s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 515s Setting up systemd-resolved (257.3-1ubuntu3) ... 515s Setting up initramfs-tools-bin (0.146ubuntu1) ... 515s Setting up ncurses-term (6.5+20250216-2) ... 515s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 515s Setting up libpython3.13:amd64 (3.13.2-2) ... 515s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 515s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 515s Setting up systemd-sysv (257.3-1ubuntu3) ... 515s Setting up linux-headers-virtual (6.14.0-10.10) ... 515s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 515s Setting up python3.13 (3.13.2-2) ... 516s Setting up htop (3.4.0-2) ... 516s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 518s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 518s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 518s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 518s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 518s Setting up parted (3.6-5) ... 518s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 518s Setting up python3 (3.13.2-2) ... 518s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 518s Setting up python3-markupsafe (2.1.5-1build4) ... 518s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 521s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 521s Setting up hwdata (0.393-3) ... 521s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 521s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 521s No schema files found: doing nothing. 521s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 521s Setting up linux-perf (6.14.0-10.10) ... 521s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 521s Setting up pciutils (1:3.13.0-2) ... 521s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 521s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 521s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 521s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 521s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 521s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 521s Setting up curl (8.12.1-3ubuntu1) ... 521s Setting up linux-image-virtual (6.14.0-10.10) ... 521s Setting up initramfs-tools-core (0.146ubuntu1) ... 521s Setting up linux-tools-common (6.14.0-10.10) ... 521s Setting up python3-systemd (235-1build6) ... 521s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 521s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 521s Setting up linux-image-generic (6.14.0-10.10) ... 521s Setting up python3-dbus (1.3.2-5build5) ... 522s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 522s Setting up initramfs-tools (0.146ubuntu1) ... 522s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 522s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 522s update-initramfs: deferring update (trigger activated) 522s Setting up linux-generic (6.14.0-10.10) ... 522s Setting up ubuntu-minimal (1.549) ... 522s Setting up python3-apt (2.9.9build1) ... 522s Setting up python3-bcrypt (4.2.0-2.1build1) ... 522s Setting up python3-yaml (6.0.2-1build2) ... 522s Setting up libfwupd3:amd64 (2.0.6-4) ... 522s Setting up python3-lazr.uri (1.0.6-6) ... 522s Setting up binutils (2.44-3ubuntu1) ... 522s Setting up ubuntu-standard (1.549) ... 522s Setting up cloud-init-base (25.1-0ubuntu3) ... 524s Setting up linux-virtual (6.14.0-10.10) ... 524s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 524s Setting up python3-gi (3.50.0-4build1) ... 524s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 524s Setting up fwupd (2.0.6-4) ... 524s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 524s fwupd.service is a disabled or a static unit not running, not starting it. 524s Setting up cloud-init (25.1-0ubuntu3) ... 524s Processing triggers for man-db (2.13.0-1) ... 526s Processing triggers for dbus (1.16.2-1ubuntu1) ... 526s Processing triggers for shared-mime-info (2.4-5) ... 526s Warning: program compiled against libxml 212 using older 209 526s Processing triggers for libc-bin (2.41-1ubuntu1) ... 526s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 526s /etc/kernel/postinst.d/initramfs-tools: 526s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 526s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 537s /etc/kernel/postinst.d/zz-update-grub: 537s Sourcing file `/etc/default/grub' 537s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 537s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 537s Generating grub configuration file ... 537s Found linux image: /boot/vmlinuz-6.14.0-10-generic 537s Found initrd image: /boot/initrd.img-6.14.0-10-generic 538s Found linux image: /boot/vmlinuz-6.12.0-16-generic 538s Found initrd image: /boot/initrd.img-6.12.0-16-generic 538s Found linux image: /boot/vmlinuz-6.11.0-8-generic 538s Found initrd image: /boot/initrd.img-6.11.0-8-generic 538s Warning: os-prober will not be executed to detect other bootable partitions. 538s Systems on them will not be added to the GRUB boot configuration. 538s Check GRUB_DISABLE_OS_PROBER documentation entry. 538s Adding boot menu entry for UEFI Firmware Settings ... 538s done 538s Processing triggers for initramfs-tools (0.146ubuntu1) ... 538s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 538s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 550s Reading package lists... 550s Building dependency tree... 550s Reading state information... 550s Solving dependencies... 550s The following packages will be REMOVED: 550s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 550s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 550s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 550s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 550s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 550s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 550s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 550s linux-tools-6.12.0-16-generic* 551s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 551s After this operation, 545 MB disk space will be freed. 551s (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 ... 148643 files and directories currently installed.) 551s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 551s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 551s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 551s Removing libpython3.12t64:amd64 (3.12.9-1) ... 551s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 551s Removing libnsl2:amd64 (1.3.0-3build3) ... 551s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 551s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 552s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 554s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 554s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 557s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 557s /etc/kernel/postrm.d/initramfs-tools: 557s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 557s /etc/kernel/postrm.d/zz-update-grub: 557s Sourcing file `/etc/default/grub' 557s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 557s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 557s Generating grub configuration file ... 557s Found linux image: /boot/vmlinuz-6.14.0-10-generic 557s Found initrd image: /boot/initrd.img-6.14.0-10-generic 558s Found linux image: /boot/vmlinuz-6.12.0-16-generic 558s Found initrd image: /boot/initrd.img-6.12.0-16-generic 558s Warning: os-prober will not be executed to detect other bootable partitions. 558s Systems on them will not be added to the GRUB boot configuration. 558s Check GRUB_DISABLE_OS_PROBER documentation entry. 558s Adding boot menu entry for UEFI Firmware Settings ... 558s done 558s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 558s W: Removing the running kernel 558s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 558s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 558s /etc/kernel/postrm.d/initramfs-tools: 558s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 558s /etc/kernel/postrm.d/zz-update-grub: 558s Sourcing file `/etc/default/grub' 558s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 558s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 558s Generating grub configuration file ... 558s Found linux image: /boot/vmlinuz-6.14.0-10-generic 558s Found initrd image: /boot/initrd.img-6.14.0-10-generic 559s Warning: os-prober will not be executed to detect other bootable partitions. 559s Systems on them will not be added to the GRUB boot configuration. 559s Check GRUB_DISABLE_OS_PROBER documentation entry. 559s Adding boot menu entry for UEFI Firmware Settings ... 559s done 559s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 559s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 561s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 561s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 561s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 561s Processing triggers for libc-bin (2.41-1ubuntu1) ... 561s (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 ... 76972 files and directories currently installed.) 561s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 561s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 561s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 561s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 561s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 561s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 561s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 561s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 561s autopkgtest [22:46:03]: upgrading testbed (apt dist-upgrade and autopurge) 561s Reading package lists... 562s Building dependency tree... 562s Reading state information... 562s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 562s Starting 2 pkgProblemResolver with broken count: 0 562s Done 563s Entering ResolveByKeep 563s 563s Calculating upgrade... 563s The following packages will be upgraded: 563s libc-bin libc-dev-bin libc6 libc6-dev locales 564s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 564s Need to get 10.5 MB of archives. 564s After this operation, 1024 B of additional disk space will be used. 564s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 564s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 564s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 565s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 565s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 566s Preconfiguring packages ... 566s Fetched 10.5 MB in 3s (4048 kB/s) 566s (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 ... 76968 files and directories currently installed.) 566s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 566s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 567s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 567s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 567s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 567s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 567s Setting up libc6:amd64 (2.41-1ubuntu2) ... 567s (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 ... 76968 files and directories currently installed.) 567s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 567s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 567s Setting up libc-bin (2.41-1ubuntu2) ... 567s (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 ... 76968 files and directories currently installed.) 567s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 567s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 568s Setting up locales (2.41-1ubuntu2) ... 569s Generating locales (this might take a while)... 570s en_US.UTF-8... done 570s Generation complete. 570s Setting up libc-dev-bin (2.41-1ubuntu2) ... 570s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 570s Processing triggers for man-db (2.13.0-1) ... 571s Processing triggers for systemd (257.3-1ubuntu3) ... 572s Reading package lists... 572s Building dependency tree... 572s Reading state information... 572s Starting pkgProblemResolver with broken count: 0 572s Starting 2 pkgProblemResolver with broken count: 0 572s Done 573s Solving dependencies... 573s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 573s autopkgtest [22:46:15]: rebooting testbed after setup commands that affected boot 600s Reading package lists... 600s Building dependency tree... 600s Reading state information... 600s Starting pkgProblemResolver with broken count: 0 600s Starting 2 pkgProblemResolver with broken count: 0 600s Done 601s The following NEW packages will be installed: 601s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 601s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 601s fonts-glyphicons-halflings fonts-mathjax g++ g++-14 g++-14-x86-64-linux-gnu 601s g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 601s gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu 601s icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 601s libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev 601s libgfortran-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 601s libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev 601s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap 601s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 601s liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 601s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 601s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 601s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 601s libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 601s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 601s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 601s littler node-normalize.css pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core 601s r-base-dev r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 601s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 601s r-cran-caret r-cran-cellranger r-cran-class r-cran-cli r-cran-clipr 601s r-cran-clock r-cran-codetools r-cran-colorspace r-cran-conquer 601s r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table 601s r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest r-cran-doby 601s r-cran-dplyr r-cran-e1071 r-cran-ellipsis r-cran-evaluate r-cran-fansi 601s r-cran-farver r-cran-fastmap r-cran-forcats r-cran-foreach r-cran-foreign 601s r-cran-formula r-cran-future r-cran-future.apply r-cran-generics 601s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower r-cran-gtable 601s r-cran-hardhat r-cran-haven r-cran-hexbin r-cran-highr r-cran-hms 601s r-cran-ipred r-cran-isoband r-cran-iterators r-cran-kernsmooth r-cran-knitr 601s r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle r-cran-listenv 601s r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate r-cran-magrittr 601s r-cran-mass r-cran-matrix r-cran-matrixmodels r-cran-matrixstats 601s r-cran-memoise r-cran-mgcv r-cran-microbenchmark r-cran-minqa r-cran-mitools 601s r-cran-modelmetrics r-cran-modelr r-cran-munsell r-cran-nlme r-cran-nloptr 601s r-cran-nnet r-cran-numderiv r-cran-openxlsx r-cran-parallelly 601s r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 601s r-cran-plyr r-cran-prettyunits r-cran-proc r-cran-prodlim r-cran-progress 601s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quantreg 601s r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rbibutils 601s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen 601s r-cran-rdpack r-cran-readr r-cran-readxl r-cran-recipes r-cran-reformulas 601s r-cran-rematch r-cran-reshape2 r-cran-rio r-cran-rlang r-cran-rpart 601s r-cran-rsqlite r-cran-sandwich r-cran-scales r-cran-shape r-cran-sparsem 601s r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey 601s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 601s r-cran-timechange r-cran-timedate r-cran-tzdb r-cran-utf8 r-cran-vctrs 601s r-cran-viridislite r-cran-vroom r-cran-withr r-cran-writexl r-cran-xfun 601s r-cran-yaml r-cran-zip r-cran-zoo unzip x11-common xdg-utils zip zlib1g-dev 601s 0 upgraded, 256 newly installed, 0 to remove and 0 not upgraded. 601s Need to get 273 MB of archives. 601s After this operation, 707 MB of additional disk space will be used. 601s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 602s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 602s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 603s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 603s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 603s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 603s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 603s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 603s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 603s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 604s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 604s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 604s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 604s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 604s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 604s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 604s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 605s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 605s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 605s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 605s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 605s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 606s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 606s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 606s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 606s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 606s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 606s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 606s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 606s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 606s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 606s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 606s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 606s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 606s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 606s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 606s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 607s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 607s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 607s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 607s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 607s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 607s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 607s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 607s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 607s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 607s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 607s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 607s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 607s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 607s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 607s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 607s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 607s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 607s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 607s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 607s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 607s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 607s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 607s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 607s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 607s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 607s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 607s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 607s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 607s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 607s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 607s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 608s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 608s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 608s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 608s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 608s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 608s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 608s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 608s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 608s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 608s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 608s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 608s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 608s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 608s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 608s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 608s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 608s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 608s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 608s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 608s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 608s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 608s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 608s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 608s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 608s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 608s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 608s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 608s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 608s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 608s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 608s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 610s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 610s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B] 610s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 610s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB] 610s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 610s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 610s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 610s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 610s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 610s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB] 610s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cardata all 3.0.5-1 [1819 kB] 610s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-formula all 1.2-5-1 [158 kB] 610s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 610s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 610s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 610s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 611s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 611s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 611s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-boot all 1.3-31-1 [635 kB] 611s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 611s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 611s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 611s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB] 611s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nloptr amd64 2.1.1-1 [251 kB] 611s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 611s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 611s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reformulas all 0.4.0-1 [91.5 kB] 611s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 611s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 611s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lme4 amd64 1.1-36-1 [4135 kB] 611s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 611s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 611s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 611s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 611s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 612s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 612s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 612s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 612s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 612s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] 612s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 612s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 612s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 612s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 612s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 612s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 612s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 612s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 612s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringi amd64 1.8.4-1build1 [927 kB] 612s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 612s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB] 612s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 612s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-broom all 1.0.7+dfsg-1 [1802 kB] 612s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 612s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 612s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 612s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 612s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 612s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 612s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-munsell all 0.5.1-1 [213 kB] 612s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 612s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 612s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 612s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 613s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 613s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-deriv all 4.1.6-1 [151 kB] 613s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 613s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB] 613s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-doby all 4.6.25-1 [4772 kB] 613s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 613s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.51+dfsg-1 [574 kB] 613s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 613s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 613s Get:173 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 613s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 613s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pbkrtest all 0.5.3-1 [178 kB] 613s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sparsem amd64 1.84-2-1 [813 kB] 613s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixmodels all 0.5-3-1 [361 kB] 613s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB] 614s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB] 614s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpparmadillo amd64 14.2.3-1-1 [864 kB] 614s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-class amd64 7.3-23-1 [92.7 kB] 614s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] 614s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-e1071 amd64 1.7-16-1 [565 kB] 614s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB] 614s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-iterators all 1.0.14-1 [336 kB] 614s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-foreach all 1.5.2-1 [124 kB] 614s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 614s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-modelmetrics amd64 1.2.2.2-1build1 [128 kB] 614s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] 614s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-proc amd64 1.18.5-1 [966 kB] 614s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tzdb amd64 0.4.0-2 [521 kB] 614s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clock amd64 0.7.2-1 [1903 kB] 614s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gower amd64 1.0.2-1 [210 kB] 614s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hardhat all 1.4.0+dfsg-1 [565 kB] 614s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rpart amd64 4.1.24-1 [670 kB] 614s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-shape all 1.4.6.1-1 [749 kB] 614s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-diagram all 1.6.5-2 [656 kB] 614s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-kernsmooth amd64 2.23-26-1 [94.5 kB] 614s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB] 614s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-globals all 0.16.3-1 [120 kB] 614s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-listenv all 0.9.1+dfsg-1 [112 kB] 614s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-parallelly amd64 1.42.0-1 [540 kB] 615s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 615s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 615s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progressr all 0.15.1-1 [353 kB] 615s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-squarem all 2021.1-1 [179 kB] 615s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lava all 1.8.1+dfsg-1 [2191 kB] 615s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prodlim amd64 2024.06.25-1 [415 kB] 615s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ipred amd64 0.9-15-1 [386 kB] 615s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timechange amd64 0.3.0-1 [178 kB] 615s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1009 kB] 616s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-timedate amd64 4041.110-1 [1208 kB] 616s Get:213 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 616s Get:214 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reshape2 amd64 1.4.4-2build1 [114 kB] 616s Get:215 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-caret amd64 7.0-1+dfsg-1 [3460 kB] 616s Get:216 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-conquer amd64 1.3.3-1 [499 kB] 616s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-quantreg amd64 6.00-1 [1454 kB] 616s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-foreign amd64 0.8.88-1 [250 kB] 616s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 616s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-forcats all 1.0.0-1 [369 kB] 616s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB] 616s Get:222 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-clipr all 0.8.0-1 [53.5 kB] 616s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB] 616s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB] 616s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit64 amd64 4.6.0-1-1ubuntu2 [501 kB] 616s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] 616s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB] 616s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vroom amd64 1.6.5-1 [848 kB] 616s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readr amd64 2.1.5-1 [766 kB] 616s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-haven amd64 2.5.4-1 [346 kB] 616s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-curl amd64 6.2.1+dfsg-1ubuntu1 [197 kB] 616s Get:232 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rematch all 2.0.0-1 [18.3 kB] 616s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cellranger all 1.1.0-3 [102 kB] 616s Get:234 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-readxl amd64 1.4.4-1 [360 kB] 616s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-writexl amd64 1.5.1-1 [158 kB] 616s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 616s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.oo all 1.27.0-1 [979 kB] 616s Get:238 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r.utils all 2.13.0-1 [1423 kB] 617s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-zip amd64 2.3.2-1 [156 kB] 617s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-openxlsx amd64 4.2.8-1 [2056 kB] 617s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rio all 1.2.3-1 [546 kB] 617s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-car all 3.1-3-1 [1525 kB] 617s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-zoo amd64 1.8-13-1 [999 kB] 617s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lmtest amd64 0.9.40-1 [396 kB] 617s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sandwich all 3.1-1-1 [1483 kB] 617s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-aer all 1.2-14-1 [2597 kB] 617s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB] 617s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB] 617s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB] 617s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB] 617s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hexbin amd64 1.28.5-1 [1581 kB] 617s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB] 617s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mitools all 2.4-2build1 [265 kB] 617s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 617s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB] 617s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survey amd64 4.4-2-2 [3453 kB] 618s Preconfiguring packages ... 618s Fetched 273 MB in 16s (16.7 MB/s) 618s Selecting previously unselected package libisl23:amd64. 619s (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 ... 76968 files and directories currently installed.) 619s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ... 619s Unpacking libisl23:amd64 (0.27-1) ... 619s Selecting previously unselected package libmpc3:amd64. 619s Preparing to unpack .../001-libmpc3_1.3.1-1build2_amd64.deb ... 619s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 619s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 619s Preparing to unpack .../002-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 619s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 619s Selecting previously unselected package cpp-14. 619s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 619s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 619s Selecting previously unselected package cpp-x86-64-linux-gnu. 619s Preparing to unpack .../004-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 619s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 619s Selecting previously unselected package cpp. 619s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 619s Unpacking cpp (4:14.2.0-1ubuntu1) ... 619s Selecting previously unselected package libcc1-0:amd64. 619s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package libgomp1:amd64. 619s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package libitm1:amd64. 619s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package libasan8:amd64. 619s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package liblsan0:amd64. 619s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package libtsan2:amd64. 619s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package libubsan1:amd64. 619s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ... 619s Selecting previously unselected package libhwasan0:amd64. 619s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_amd64.deb ... 619s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ... 620s Selecting previously unselected package libquadmath0:amd64. 620s Preparing to unpack .../014-libquadmath0_15-20250222-0ubuntu1_amd64.deb ... 620s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ... 620s Selecting previously unselected package libgcc-14-dev:amd64. 620s Preparing to unpack .../015-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 620s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 620s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 620s Preparing to unpack .../016-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 620s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 620s Selecting previously unselected package gcc-14. 620s Preparing to unpack .../017-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 620s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 620s Selecting previously unselected package gcc-x86-64-linux-gnu. 620s Preparing to unpack .../018-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 620s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 620s Selecting previously unselected package gcc. 620s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 620s Unpacking gcc (4:14.2.0-1ubuntu1) ... 620s Selecting previously unselected package libstdc++-14-dev:amd64. 620s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 620s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 620s Selecting previously unselected package g++-14-x86-64-linux-gnu. 620s Preparing to unpack .../021-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 620s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 621s Selecting previously unselected package g++-14. 621s Preparing to unpack .../022-g++-14_14.2.0-17ubuntu3_amd64.deb ... 621s Unpacking g++-14 (14.2.0-17ubuntu3) ... 621s Selecting previously unselected package g++-x86-64-linux-gnu. 621s Preparing to unpack .../023-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 621s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 621s Selecting previously unselected package g++. 621s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 621s Unpacking g++ (4:14.2.0-1ubuntu1) ... 621s Selecting previously unselected package build-essential. 621s Preparing to unpack .../025-build-essential_12.10ubuntu1_amd64.deb ... 621s Unpacking build-essential (12.10ubuntu1) ... 621s Selecting previously unselected package dctrl-tools. 621s Preparing to unpack .../026-dctrl-tools_2.24-3build3_amd64.deb ... 621s Unpacking dctrl-tools (2.24-3build3) ... 621s Selecting previously unselected package fonts-dejavu-mono. 621s Preparing to unpack .../027-fonts-dejavu-mono_2.37-8_all.deb ... 621s Unpacking fonts-dejavu-mono (2.37-8) ... 621s Selecting previously unselected package fonts-dejavu-core. 621s Preparing to unpack .../028-fonts-dejavu-core_2.37-8_all.deb ... 621s Unpacking fonts-dejavu-core (2.37-8) ... 621s Selecting previously unselected package fontconfig-config. 621s Preparing to unpack .../029-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 621s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 621s Selecting previously unselected package libfontconfig1:amd64. 621s Preparing to unpack .../030-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 621s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 621s Selecting previously unselected package fontconfig. 621s Preparing to unpack .../031-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 621s Unpacking fontconfig (2.15.0-2ubuntu1) ... 621s Selecting previously unselected package fonts-glyphicons-halflings. 621s Preparing to unpack .../032-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 621s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 621s Selecting previously unselected package fonts-mathjax. 621s Preparing to unpack .../033-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 621s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 621s Selecting previously unselected package libgfortran5:amd64. 621s Preparing to unpack .../034-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 621s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 621s Selecting previously unselected package libgfortran-14-dev:amd64. 621s Preparing to unpack .../035-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ... 621s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 622s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 622s Preparing to unpack .../036-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 622s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 622s Selecting previously unselected package gfortran-14. 622s Preparing to unpack .../037-gfortran-14_14.2.0-17ubuntu3_amd64.deb ... 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previously unselected package libsharpyuv0:amd64. 624s Preparing to unpack .../085-libsharpyuv0_1.5.0-0.1_amd64.deb ... 624s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 624s Selecting previously unselected package libsm6:amd64. 624s Preparing to unpack .../086-libsm6_2%3a1.2.4-1_amd64.deb ... 624s Unpacking libsm6:amd64 (2:1.2.4-1) ... 624s Selecting previously unselected package libtcl8.6:amd64. 624s Preparing to unpack .../087-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 624s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 624s Selecting previously unselected package libjbig0:amd64. 624s Preparing to unpack .../088-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 624s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 624s Selecting previously unselected package libwebp7:amd64. 624s Preparing to unpack .../089-libwebp7_1.5.0-0.1_amd64.deb ... 624s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 624s Selecting previously unselected package libtiff6:amd64. 624s Preparing to unpack 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... 626s Unpacking r-cran-rdpack (2.6.2-1syncable1) ... 626s Selecting previously unselected package r-cran-reformulas. 626s Preparing to unpack .../125-r-cran-reformulas_0.4.0-1_all.deb ... 626s Unpacking r-cran-reformulas (0.4.0-1) ... 626s Selecting previously unselected package r-cran-rcppeigen. 626s Preparing to unpack .../126-r-cran-rcppeigen_0.3.4.0.2-1_amd64.deb ... 626s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 626s Selecting previously unselected package r-cran-statmod. 626s Preparing to unpack .../127-r-cran-statmod_1.5.0-1_amd64.deb ... 626s Unpacking r-cran-statmod (1.5.0-1) ... 626s Selecting previously unselected package r-cran-lme4. 626s Preparing to unpack .../128-r-cran-lme4_1.1-36-1_amd64.deb ... 626s Unpacking r-cran-lme4 (1.1-36-1) ... 626s Selecting previously unselected package r-cran-backports. 627s Preparing to unpack .../129-r-cran-backports_1.5.0-2_amd64.deb ... 627s Unpacking r-cran-backports (1.5.0-2) ... 627s Selecting previously unselected package r-cran-cli. 627s Preparing to unpack .../130-r-cran-cli_3.6.4-1_amd64.deb ... 627s Unpacking r-cran-cli (3.6.4-1) ... 627s Selecting previously unselected package r-cran-generics. 627s Preparing to unpack .../131-r-cran-generics_0.1.3-1_all.deb ... 627s Unpacking r-cran-generics (0.1.3-1) ... 627s Selecting previously unselected package r-cran-glue. 627s Preparing to unpack .../132-r-cran-glue_1.8.0-1_amd64.deb ... 627s Unpacking r-cran-glue (1.8.0-1) ... 627s Selecting previously unselected package r-cran-rlang. 627s Preparing to unpack .../133-r-cran-rlang_1.1.5-1_amd64.deb ... 627s Unpacking r-cran-rlang (1.1.5-1) ... 627s Selecting previously unselected package r-cran-lifecycle. 627s Preparing to unpack .../134-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 627s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 627s Selecting previously unselected package r-cran-magrittr. 627s Preparing to unpack .../135-r-cran-magrittr_2.0.3-1_amd64.deb ... 627s Unpacking r-cran-magrittr (2.0.3-1) ... 627s Selecting previously unselected package r-cran-utf8. 627s Preparing to unpack .../136-r-cran-utf8_1.2.4-1_amd64.deb ... 627s Unpacking r-cran-utf8 (1.2.4-1) ... 627s Selecting previously unselected package r-cran-vctrs. 627s Preparing to unpack .../137-r-cran-vctrs_0.6.5-1_amd64.deb ... 627s Unpacking r-cran-vctrs (0.6.5-1) ... 627s Selecting previously unselected package r-cran-pillar. 627s Preparing to unpack .../138-r-cran-pillar_1.10.1+dfsg-1_all.deb ... 627s Unpacking r-cran-pillar (1.10.1+dfsg-1) ... 627s Selecting previously unselected package r-cran-r6. 627s Preparing to unpack .../139-r-cran-r6_2.6.1-1_all.deb ... 627s Unpacking r-cran-r6 (2.6.1-1) ... 627s Selecting previously unselected package r-cran-fansi. 627s Preparing to unpack .../140-r-cran-fansi_1.0.5-1_amd64.deb ... 627s Unpacking r-cran-fansi (1.0.5-1) ... 627s Selecting previously unselected package r-cran-pkgconfig. 627s Preparing to unpack .../141-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 627s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 627s Selecting previously unselected package r-cran-tibble. 627s Preparing to unpack .../142-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 627s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 627s Selecting previously unselected package r-cran-withr. 627s Preparing to unpack .../143-r-cran-withr_3.0.2+dfsg-1_all.deb ... 627s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 627s Selecting previously unselected package r-cran-tidyselect. 627s Preparing to unpack .../144-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 627s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 627s Selecting previously unselected package r-cran-dplyr. 627s Preparing to unpack .../145-r-cran-dplyr_1.1.4-4_amd64.deb ... 627s Unpacking r-cran-dplyr (1.1.4-4) ... 627s Selecting previously unselected package r-cran-purrr. 627s Preparing to unpack .../146-r-cran-purrr_1.0.4-1_amd64.deb ... 627s Unpacking r-cran-purrr (1.0.4-1) ... 627s Selecting previously unselected package r-cran-stringi. 627s Preparing to unpack .../147-r-cran-stringi_1.8.4-1build1_amd64.deb ... 627s Unpacking r-cran-stringi (1.8.4-1build1) ... 627s Selecting previously unselected package r-cran-stringr. 627s Preparing to unpack .../148-r-cran-stringr_1.5.1-1_all.deb ... 627s Unpacking r-cran-stringr (1.5.1-1) ... 627s Selecting previously unselected package r-cran-cpp11. 627s Preparing to unpack .../149-r-cran-cpp11_0.5.2-1_all.deb ... 627s Unpacking r-cran-cpp11 (0.5.2-1) ... 627s Selecting previously unselected package r-cran-tidyr. 627s Preparing to unpack .../150-r-cran-tidyr_1.3.1-1_amd64.deb ... 627s Unpacking r-cran-tidyr (1.3.1-1) ... 627s Selecting previously unselected package r-cran-broom. 628s Preparing to unpack .../151-r-cran-broom_1.0.7+dfsg-1_all.deb ... 628s Unpacking r-cran-broom (1.0.7+dfsg-1) ... 628s Selecting previously unselected package r-cran-numderiv. 628s Preparing to unpack .../152-r-cran-numderiv_2016.8-1.1-3_all.deb ... 628s Unpacking r-cran-numderiv (2016.8-1.1-3) ... 628s Selecting previously unselected package r-cran-gtable. 628s Preparing to unpack .../153-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 628s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 628s Selecting previously unselected package r-cran-isoband. 628s Preparing to unpack .../154-r-cran-isoband_0.2.7-1_amd64.deb ... 628s Unpacking r-cran-isoband (0.2.7-1) ... 628s Selecting previously unselected package r-cran-farver. 628s Preparing to unpack .../155-r-cran-farver_2.1.2-1_amd64.deb ... 628s Unpacking r-cran-farver (2.1.2-1) ... 628s Selecting previously unselected package r-cran-labeling. 628s Preparing to unpack .../156-r-cran-labeling_0.4.3-1_all.deb ... 628s Unpacking r-cran-labeling (0.4.3-1) ... 628s Selecting previously unselected package r-cran-colorspace. 628s Preparing to unpack .../157-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 628s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 628s Selecting previously unselected package r-cran-munsell. 628s Preparing to unpack .../158-r-cran-munsell_0.5.1-1_all.deb ... 628s Unpacking r-cran-munsell (0.5.1-1) ... 628s Selecting previously unselected package r-cran-rcolorbrewer. 628s Preparing to unpack .../159-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 628s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 628s Selecting previously unselected package r-cran-viridislite. 628s Preparing to unpack .../160-r-cran-viridislite_0.4.2-2_all.deb ... 628s Unpacking r-cran-viridislite (0.4.2-2) ... 628s Selecting previously unselected package r-cran-scales. 628s Preparing to unpack .../161-r-cran-scales_1.3.0-1_all.deb ... 628s Unpacking r-cran-scales (1.3.0-1) ... 628s Selecting previously unselected package r-cran-ggplot2. 628s Preparing to unpack .../162-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 628s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 628s Selecting previously unselected package r-cran-cowplot. 628s Preparing to unpack .../163-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 628s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 628s Selecting previously unselected package r-cran-deriv. 628s Preparing to unpack .../164-r-cran-deriv_4.1.6-1_all.deb ... 628s Unpacking r-cran-deriv (4.1.6-1) ... 628s Selecting previously unselected package r-cran-modelr. 628s Preparing to unpack .../165-r-cran-modelr_0.1.11-1_all.deb ... 628s Unpacking r-cran-modelr (0.1.11-1) ... 628s Selecting previously unselected package r-cran-microbenchmark. 628s Preparing to unpack .../166-r-cran-microbenchmark_1.5.0-1_amd64.deb ... 628s Unpacking r-cran-microbenchmark (1.5.0-1) ... 628s Selecting previously unselected package r-cran-doby. 628s Preparing to unpack .../167-r-cran-doby_4.6.25-1_all.deb ... 628s Unpacking r-cran-doby (4.6.25-1) ... 628s Selecting previously unselected package r-cran-evaluate. 628s Preparing to unpack .../168-r-cran-evaluate_1.0.3-1_all.deb ... 628s Unpacking r-cran-evaluate (1.0.3-1) ... 628s Selecting previously unselected package r-cran-xfun. 628s Preparing to unpack .../169-r-cran-xfun_0.51+dfsg-1_amd64.deb ... 628s Unpacking r-cran-xfun (0.51+dfsg-1) ... 628s Selecting previously unselected package r-cran-highr. 628s Preparing to unpack .../170-r-cran-highr_0.11+dfsg-1_all.deb ... 628s Unpacking r-cran-highr (0.11+dfsg-1) ... 628s Selecting previously unselected package r-cran-yaml. 628s Preparing to unpack .../171-r-cran-yaml_2.3.10-1_amd64.deb ... 628s Unpacking r-cran-yaml (2.3.10-1) ... 628s Selecting previously unselected package libjs-mathjax. 628s Preparing to unpack .../172-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 628s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 629s Selecting previously unselected package r-cran-knitr. 629s Preparing to unpack .../173-r-cran-knitr_1.49+dfsg-1_all.deb ... 629s Unpacking r-cran-knitr (1.49+dfsg-1) ... 629s Selecting previously unselected package r-cran-pbkrtest. 629s Preparing to unpack .../174-r-cran-pbkrtest_0.5.3-1_all.deb ... 629s Unpacking r-cran-pbkrtest (0.5.3-1) ... 629s Selecting previously unselected package r-cran-sparsem. 629s Preparing to unpack .../175-r-cran-sparsem_1.84-2-1_amd64.deb ... 629s Unpacking r-cran-sparsem (1.84-2-1) ... 629s Selecting previously unselected package r-cran-matrixmodels. 629s Preparing to unpack .../176-r-cran-matrixmodels_0.5-3-1_all.deb ... 629s Unpacking r-cran-matrixmodels (0.5-3-1) ... 629s Selecting previously unselected package r-cran-survival. 629s Preparing to unpack .../177-r-cran-survival_3.8-3-1_amd64.deb ... 629s Unpacking r-cran-survival (3.8-3-1) ... 630s Selecting previously unselected package r-cran-matrixstats. 630s Preparing to unpack .../178-r-cran-matrixstats_1.5.0-1_amd64.deb ... 630s Unpacking r-cran-matrixstats (1.5.0-1) ... 630s Selecting previously unselected package r-cran-rcpparmadillo. 630s Preparing to unpack .../179-r-cran-rcpparmadillo_14.2.3-1-1_amd64.deb ... 630s Unpacking r-cran-rcpparmadillo (14.2.3-1-1) ... 630s Selecting previously unselected package r-cran-class. 630s Preparing to unpack .../180-r-cran-class_7.3-23-1_amd64.deb ... 630s Unpacking r-cran-class (7.3-23-1) ... 630s Selecting previously unselected package r-cran-proxy. 630s Preparing to unpack .../181-r-cran-proxy_0.4-27-1_amd64.deb ... 630s Unpacking r-cran-proxy (0.4-27-1) ... 630s Selecting previously unselected package r-cran-e1071. 630s Preparing to unpack .../182-r-cran-e1071_1.7-16-1_amd64.deb ... 630s Unpacking r-cran-e1071 (1.7-16-1) ... 630s Selecting previously unselected package r-cran-codetools. 630s Preparing to unpack .../183-r-cran-codetools_0.2-20-1_all.deb ... 630s Unpacking r-cran-codetools (0.2-20-1) ... 630s Selecting previously unselected package r-cran-iterators. 630s Preparing to unpack .../184-r-cran-iterators_1.0.14-1_all.deb ... 630s Unpacking r-cran-iterators (1.0.14-1) ... 630s Selecting previously unselected package r-cran-foreach. 630s Preparing to unpack .../185-r-cran-foreach_1.5.2-1_all.deb ... 630s Unpacking r-cran-foreach (1.5.2-1) ... 630s Selecting previously unselected package r-cran-data.table. 630s Preparing to unpack .../186-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ... 630s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 630s Selecting previously unselected package r-cran-modelmetrics. 630s Preparing to unpack .../187-r-cran-modelmetrics_1.2.2.2-1build1_amd64.deb ... 630s Unpacking r-cran-modelmetrics (1.2.2.2-1build1) ... 630s Selecting previously unselected package r-cran-plyr. 630s Preparing to unpack .../188-r-cran-plyr_1.8.9-1_amd64.deb ... 630s Unpacking r-cran-plyr (1.8.9-1) ... 630s Selecting previously unselected package r-cran-proc. 630s Preparing to unpack .../189-r-cran-proc_1.18.5-1_amd64.deb ... 630s Unpacking r-cran-proc (1.18.5-1) ... 630s Selecting previously unselected package r-cran-tzdb. 630s Preparing to unpack .../190-r-cran-tzdb_0.4.0-2_amd64.deb ... 630s Unpacking r-cran-tzdb (0.4.0-2) ... 630s Selecting previously unselected package r-cran-clock. 630s Preparing to unpack .../191-r-cran-clock_0.7.2-1_amd64.deb ... 630s Unpacking r-cran-clock (0.7.2-1) ... 630s Selecting previously unselected package r-cran-gower. 630s Preparing to unpack .../192-r-cran-gower_1.0.2-1_amd64.deb ... 630s Unpacking r-cran-gower (1.0.2-1) ... 630s Selecting previously unselected package r-cran-hardhat. 630s Preparing to unpack .../193-r-cran-hardhat_1.4.0+dfsg-1_all.deb ... 630s Unpacking r-cran-hardhat (1.4.0+dfsg-1) ... 631s Selecting previously unselected package r-cran-rpart. 631s Preparing to unpack .../194-r-cran-rpart_4.1.24-1_amd64.deb ... 631s Unpacking r-cran-rpart (4.1.24-1) ... 631s Selecting previously unselected package r-cran-shape. 631s Preparing to unpack .../195-r-cran-shape_1.4.6.1-1_all.deb ... 631s Unpacking r-cran-shape (1.4.6.1-1) ... 631s Selecting previously unselected package r-cran-diagram. 631s Preparing to unpack .../196-r-cran-diagram_1.6.5-2_all.deb ... 631s Unpacking r-cran-diagram (1.6.5-2) ... 631s Selecting previously unselected package r-cran-kernsmooth. 631s Preparing to unpack .../197-r-cran-kernsmooth_2.23-26-1_amd64.deb ... 631s Unpacking r-cran-kernsmooth (2.23-26-1) ... 631s Selecting previously unselected package r-cran-digest. 631s Preparing to unpack .../198-r-cran-digest_0.6.37-1_amd64.deb ... 631s Unpacking r-cran-digest (0.6.37-1) ... 631s Selecting previously unselected package r-cran-globals. 631s Preparing to unpack .../199-r-cran-globals_0.16.3-1_all.deb ... 631s Unpacking r-cran-globals (0.16.3-1) ... 631s Selecting previously unselected package r-cran-listenv. 631s Preparing to unpack .../200-r-cran-listenv_0.9.1+dfsg-1_all.deb ... 631s Unpacking r-cran-listenv (0.9.1+dfsg-1) ... 631s Selecting previously unselected package r-cran-parallelly. 631s Preparing to unpack .../201-r-cran-parallelly_1.42.0-1_amd64.deb ... 631s Unpacking r-cran-parallelly (1.42.0-1) ... 631s Selecting previously unselected package r-cran-future. 631s Preparing to unpack .../202-r-cran-future_1.34.0+dfsg-1_all.deb ... 631s Unpacking r-cran-future (1.34.0+dfsg-1) ... 631s Selecting previously unselected package r-cran-future.apply. 631s Preparing to unpack .../203-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 631s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 631s Selecting previously unselected package r-cran-progressr. 631s Preparing to unpack .../204-r-cran-progressr_0.15.1-1_all.deb ... 631s Unpacking r-cran-progressr (0.15.1-1) ... 631s Selecting previously unselected package r-cran-squarem. 631s Preparing to unpack .../205-r-cran-squarem_2021.1-1_all.deb ... 631s Unpacking r-cran-squarem (2021.1-1) ... 631s Selecting previously unselected package r-cran-lava. 631s Preparing to unpack .../206-r-cran-lava_1.8.1+dfsg-1_all.deb ... 631s Unpacking r-cran-lava (1.8.1+dfsg-1) ... 631s Selecting previously unselected package r-cran-prodlim. 631s Preparing to unpack .../207-r-cran-prodlim_2024.06.25-1_amd64.deb ... 631s Unpacking r-cran-prodlim (2024.06.25-1) ... 631s Selecting previously unselected package r-cran-ipred. 631s Preparing to unpack .../208-r-cran-ipred_0.9-15-1_amd64.deb ... 631s Unpacking r-cran-ipred (0.9-15-1) ... 631s Selecting previously unselected package r-cran-timechange. 631s Preparing to unpack .../209-r-cran-timechange_0.3.0-1_amd64.deb ... 631s Unpacking r-cran-timechange (0.3.0-1) ... 631s Selecting previously unselected package r-cran-lubridate. 631s Preparing to unpack .../210-r-cran-lubridate_1.9.4+dfsg-1_amd64.deb ... 631s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 631s Selecting previously unselected package r-cran-timedate. 631s Preparing to unpack .../211-r-cran-timedate_4041.110-1_amd64.deb ... 631s Unpacking r-cran-timedate (4041.110-1) ... 631s Selecting previously unselected package r-cran-recipes. 631s Preparing to unpack .../212-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 631s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 631s Selecting previously unselected package r-cran-reshape2. 631s Preparing to unpack .../213-r-cran-reshape2_1.4.4-2build1_amd64.deb ... 631s Unpacking r-cran-reshape2 (1.4.4-2build1) ... 631s Selecting previously unselected package r-cran-caret. 631s Preparing to unpack .../214-r-cran-caret_7.0-1+dfsg-1_amd64.deb ... 631s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 632s Selecting previously unselected package r-cran-conquer. 632s Preparing to unpack .../215-r-cran-conquer_1.3.3-1_amd64.deb ... 632s Unpacking r-cran-conquer (1.3.3-1) ... 632s Selecting previously unselected package r-cran-quantreg. 632s Preparing to unpack .../216-r-cran-quantreg_6.00-1_amd64.deb ... 632s Unpacking r-cran-quantreg (6.00-1) ... 632s Selecting previously unselected package r-cran-foreign. 632s Preparing to unpack .../217-r-cran-foreign_0.8.88-1_amd64.deb ... 632s Unpacking r-cran-foreign (0.8.88-1) ... 632s Selecting previously unselected package r-cran-ellipsis. 632s Preparing to unpack .../218-r-cran-ellipsis_0.3.2-2_amd64.deb ... 632s Unpacking r-cran-ellipsis (0.3.2-2) ... 632s Selecting previously unselected package r-cran-forcats. 632s Preparing to unpack .../219-r-cran-forcats_1.0.0-1_all.deb ... 632s Unpacking r-cran-forcats (1.0.0-1) ... 632s Selecting previously unselected package r-cran-hms. 632s Preparing to unpack .../220-r-cran-hms_1.1.3-1_all.deb ... 632s Unpacking r-cran-hms (1.1.3-1) ... 632s Selecting previously unselected package r-cran-clipr. 632s Preparing to unpack .../221-r-cran-clipr_0.8.0-1_all.deb ... 632s Unpacking r-cran-clipr (0.8.0-1) ... 632s Selecting previously unselected package r-cran-crayon. 632s Preparing to unpack .../222-r-cran-crayon_1.5.3-1_all.deb ... 632s Unpacking r-cran-crayon (1.5.3-1) ... 632s Selecting previously unselected package r-cran-bit. 632s Preparing to unpack .../223-r-cran-bit_4.6.0+dfsg-1_amd64.deb ... 632s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 632s Selecting previously unselected package r-cran-bit64. 632s Preparing to unpack .../224-r-cran-bit64_4.6.0-1-1ubuntu2_amd64.deb ... 632s Unpacking r-cran-bit64 (4.6.0-1-1ubuntu2) ... 632s Selecting previously unselected package r-cran-prettyunits. 632s Preparing to unpack .../225-r-cran-prettyunits_1.2.0-1_all.deb ... 632s Unpacking r-cran-prettyunits (1.2.0-1) ... 632s Selecting previously unselected package r-cran-progress. 632s Preparing to unpack .../226-r-cran-progress_1.2.3-1_all.deb ... 632s Unpacking r-cran-progress (1.2.3-1) ... 632s Selecting previously unselected package r-cran-vroom. 632s Preparing to unpack .../227-r-cran-vroom_1.6.5-1_amd64.deb ... 632s Unpacking r-cran-vroom (1.6.5-1) ... 632s Selecting previously unselected package r-cran-readr. 632s Preparing to unpack .../228-r-cran-readr_2.1.5-1_amd64.deb ... 632s Unpacking r-cran-readr (2.1.5-1) ... 632s Selecting previously unselected package r-cran-haven. 632s Preparing to unpack .../229-r-cran-haven_2.5.4-1_amd64.deb ... 632s Unpacking r-cran-haven (2.5.4-1) ... 632s Selecting previously unselected package r-cran-curl. 632s Preparing to unpack .../230-r-cran-curl_6.2.1+dfsg-1ubuntu1_amd64.deb ... 632s Unpacking r-cran-curl 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creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 637s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 637s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 637s Setting up r-cran-forcats (1.0.0-1) ... 637s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 637s Setting up r-cran-reshape2 (1.4.4-2build1) ... 637s Setting up r-cran-future.apply (1.11.3+dfsg-1) ... 637s Setting up r-cran-timechange (0.3.0-1) ... 637s Setting up r-cran-hms (1.1.3-1) ... 637s Setting up r-cran-scales (1.3.0-1) ... 637s Setting up r-cran-memoise (2.0.1-1) ... 637s Setting up r-cran-lava (1.8.1+dfsg-1) ... 637s Setting up r-cran-purrr (1.0.4-1) ... 637s Setting up r-cran-e1071 (1.7-16-1) ... 637s Setting up r-cran-blob (1.2.4-1) ... 637s Setting up r-cran-hardhat (1.4.0+dfsg-1) ... 637s Setting up r-cran-dplyr (1.1.4-4) ... 637s Setting up r-cran-reformulas (0.4.0-1) ... 637s Setting up r-cran-rsqlite (2.3.9-1) ... 637s Setting up r-cran-progress (1.2.3-1) ... 637s Setting up r-cran-lubridate (1.9.4+dfsg-1) ... 637s Setting up r-cran-r.utils (2.13.0-1) ... 637s Setting up r-cran-vroom (1.6.5-1) ... 637s Setting up r-base-dev (4.4.3-1) ... 637s Setting up r-cran-prodlim (2024.06.25-1) ... 637s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 637s Setting up r-cran-cellranger (1.1.0-3) ... 637s Setting up r-cran-rpart (4.1.24-1) ... 637s Setting up r-cran-ipred (0.9-15-1) ... 637s Setting up r-cran-lme4 (1.1-36-1) ... 637s Setting up r-cran-readr (2.1.5-1) ... 637s Setting up r-cran-tidyr (1.3.1-1) ... 637s Setting up r-cran-recipes (1.1.0+dfsg-1) ... 637s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 637s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 637s Setting up r-cran-readxl (1.4.4-1) ... 637s Setting up r-cran-haven (2.5.4-1) ... 637s Setting up r-cran-caret (7.0-1+dfsg-1) ... 637s Setting up r-cran-broom (1.0.7+dfsg-1) ... 637s Setting up r-cran-conquer (1.3.3-1) ... 637s Setting up r-cran-rio (1.2.3-1) ... 637s Setting up r-cran-quantreg (6.00-1) ... 637s Setting up r-cran-modelr (0.1.11-1) ... 637s Setting up r-cran-doby (4.6.25-1) ... 637s Setting up r-cran-pbkrtest (0.5.3-1) ... 637s Setting up r-cran-car (3.1-3-1) ... 637s Setting up r-cran-aer (1.2-14-1) ... 637s Processing triggers for libc-bin (2.41-1ubuntu2) ... 637s Processing triggers for man-db (2.13.0-1) ... 639s Processing triggers for install-info (7.1.1-1) ... 645s autopkgtest [22:47:27]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 645s autopkgtest [22:47:27]: test pkg-r-autopkgtest: [----------------------- 645s Test: Try to load the R library survey 645s 645s R version 4.4.3 (2025-02-28) -- "Trophy Case" 645s Copyright (C) 2025 The R Foundation for Statistical Computing 645s Platform: x86_64-pc-linux-gnu 645s 645s R is free software and comes with ABSOLUTELY NO WARRANTY. 645s You are welcome to redistribute it under certain conditions. 645s Type 'license()' or 'licence()' for distribution details. 645s 645s R is a collaborative project with many contributors. 645s Type 'contributors()' for more information and 645s 'citation()' on how to cite R or R packages in publications. 645s 645s Type 'demo()' for some demos, 'help()' for on-line help, or 645s 'help.start()' for an HTML browser interface to help. 645s Type 'q()' to quit R. 645s 646s > library('survey') 646s Loading required package: grid 646s Loading required package: Matrix 646s Loading required package: survival 647s 647s Attaching package: ‘survey’ 647s 647s The following object is masked from ‘package:graphics’: 647s 647s dotchart 647s 647s > 647s > 647s Other tests are currently unsupported! 647s They will be progressively added. 647s autopkgtest [22:47:29]: test pkg-r-autopkgtest: -----------------------] 648s autopkgtest [22:47:30]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 648s pkg-r-autopkgtest PASS 648s autopkgtest [22:47:30]: @@@@@@@@@@@@@@@@@@@@ summary 648s run-unit-test PASS 648s pkg-r-autopkgtest PASS 666s nova [W] Skipping flock for amd64 666s Creating nova instance adt-plucky-amd64-r-cran-survey-20250315-223641-juju-7f2275-prod-proposed-migration-environment-2-9cfdce76-ee4e-49d2-b03d-fd8c64f2317b from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 666s nova [W] Timed out waiting for 6a29068c-a633-4b93-9eab-68bb5571410d to get deleted. 666s nova [W] Skipping flock for amd64 666s Creating nova instance adt-plucky-amd64-r-cran-survey-20250315-223641-juju-7f2275-prod-proposed-migration-environment-2-9cfdce76-ee4e-49d2-b03d-fd8c64f2317b from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 666s nova [W] Timed out waiting for 2ef20022-6b08-46f8-833f-2b3cb6221db7 to get deleted.