0s autopkgtest [03:45:48]: starting date and time: 2026-02-10 03:45:48+0000 0s autopkgtest [03:45:48]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [03:45:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zxi2wj03/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-survey --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-5.secgroup --name adt-resolute-amd64-r-cran-survey-20260210-034548-juju-7f2275-prod-proposed-migration-environment-2-cd4dc104-e41e-4edb-a008-6345011de0c2 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-r-cran-survey-20260210-034548-juju-7f2275-prod-proposed-migration-environment-2-cd4dc104-e41e-4edb-a008-6345011de0c2 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 73s autopkgtest [03:47:01]: testbed dpkg architecture: amd64 73s autopkgtest [03:47:01]: testbed apt version: 3.1.14 74s autopkgtest [03:47:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 74s autopkgtest [03:47:02]: testbed release detected to be: None 74s autopkgtest [03:47:02]: updating testbed package index (apt update) 74s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 74s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 75s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 75s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 75s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [181 kB] 75s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB] 75s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 75s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB] 75s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [268 kB] 75s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5980 B] 75s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 75s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [768 kB] 75s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1791 kB] 75s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.6 kB] 75s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 75s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 75s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 76s Fetched 5189 kB in 1s (7973 kB/s) 76s Reading package lists... 77s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 77s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Reading package lists... 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Calculating upgrade... 78s The following package was automatically installed and is no longer required: 78s libpython3.13 78s Use 'sudo apt autoremove' to remove it. 78s The following NEW packages will be installed: 78s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 78s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 78s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 78s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 78s The following packages will be upgraded: 78s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 78s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 78s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 78s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 78s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0 78s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 78s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 78s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 78s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 78s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 78s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 78s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 78s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 78s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 78s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 78s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 78s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 237 MB of archives. 78s After this operation, 339 MB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 78s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 78s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 78s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 78s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 78s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 78s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 78s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 78s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 78s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 78s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 78s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 78s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 78s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 78s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 78s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 78s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 78s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 78s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 78s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 78s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 78s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 78s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 78s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 78s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 78s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 78s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 78s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 78s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 78s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 78s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 78s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 79s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 79s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 79s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 79s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 79s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 79s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 79s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 79s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 79s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 79s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 79s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 79s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 79s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 79s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 79s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 79s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 79s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 79s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 79s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 79s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 79s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 79s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 79s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 79s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 79s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 79s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 79s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 79s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 79s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 79s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 79s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 79s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 79s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 79s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 79s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 79s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 79s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 79s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 79s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 79s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 79s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 79s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 79s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 79s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 79s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 79s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 79s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 81s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 81s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 81s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 81s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 81s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 81s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 81s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 81s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 82s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 82s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 82s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 82s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 82s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 82s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 82s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 82s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 82s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 82s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 82s dpkg-preconfigure: unable to re-open stdin: No such file or directory 82s Fetched 237 MB in 4s (58.9 MB/s) 82s (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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 82s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 82s Setting up debianutils (5.23.2build1) ... 82s (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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 82s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 82s Setting up dash (0.5.12-12ubuntu3) ... 82s (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 ... 83957 files and directories currently installed.) 82s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 82s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 83s Setting up findutils (4.10.0-3build2) ... 83s (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 ... 83957 files and directories currently installed.) 83s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 83s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 83s Setting up sed (4.9-2build3) ... 83s (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 ... 83957 files and directories currently installed.) 83s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 83s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 83s Setting up tar (1.35+dfsg-3.1build2) ... 83s (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 ... 83957 files and directories currently installed.) 83s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 83s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 83s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 83s Selecting previously unselected package gcc-16-base:amd64. 83s (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 ... 83957 files and directories currently installed.) 83s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 83s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 83s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 83s (Reading database ... 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(7.7.0+6.19.0-3.3) ... 90s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 90s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 90s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 90s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 90s Setting up libsensors-config (1:3.6.2-2build1) ... 90s Setting up less (668-1build1) ... 90s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 90s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 90s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 90s amd64-microcode: microcode will be updated at next boot 90s Setting up man-db (2.13.1-1build1) ... 90s Updating database of manual pages ... 91s man-db.service is a disabled or a static unit not running, not starting it. 91s Setting up libjansson4:amd64 (2.14-2build4) ... 91s Setting up libglib2.0-data (2.87.2-2) ... 91s Setting up pollinate (4.33-4ubuntu5) ... 102s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 102s Setting up libwrap0:amd64 (7.6.q-36build2) ... 102s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 103s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 103s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 103s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 103s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 103s Setting up patch (2.8-2build1) ... 103s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 103s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 103s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 103s Setting up lsof (4.99.4+dfsg-2build2) ... 103s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 103s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 103s Setting up dracut-install (109-11ubuntu1) ... 103s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 103s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 103s Setting up pnp.ids (0.394-1build1) ... 103s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 103s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 103s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 103s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 103s Setting up mawk (1.3.4.20260129-1) ... 103s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 103s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 103s Setting up linux-image-virtual (6.19.0-3.3) ... 103s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 103s Setting up libbsd0:amd64 (0.12.2-2build2) ... 103s Setting up libdrm-common (2.4.131-1) ... 103s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 103s Setting up dbus-bin (1.16.2-2ubuntu3) ... 103s Setting up libonig5:amd64 (6.9.10-1build1) ... 103s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 103s Setting up ethtool (1:6.15-3build1) ... 103s Setting up python3-referencing (0.36.2-1ubuntu2) ... 103s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 103s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 103s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 103s Setting up tcpdump (4.99.5-2ubuntu3) ... 103s Setting up linux-image-generic (6.19.0-3.3) ... 103s Setting up wget (1.25.0-2ubuntu4) ... 103s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 103s Setting up iptables (1.8.11-2ubuntu3) ... 103s Setting up iproute2 (6.18.0-1ubuntu1) ... 104s Setting up linux-headers-generic (6.19.0-3.3) ... 104s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 104s Setting up hwdata (0.394-1build1) ... 104s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 104s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 104s No schema files found: doing nothing. 104s Setting up dbus (1.16.2-2ubuntu3) ... 104s A reboot is required to replace the running dbus-daemon. 104s Please reboot the system when convenient. 104s Setting up shared-mime-info (2.4-5build3) ... 104s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 104s Setting up pciutils (1:3.14.0-1build2) ... 104s Setting up python3-markdown-it (3.0.0-3build1) ... 105s Setting up libdrm2:amd64 (2.4.131-1) ... 105s Setting up libpython3.14:amd64 (3.14.2-1) ... 105s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 105s Setting up linux-tools-common (6.19.0-3.3) ... 105s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 105s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 105s Setting up apt (3.1.15) ... 105s Setting up linux-headers-virtual (6.19.0-3.3) ... 105s Setting up linux-generic (6.19.0-3.3) ... 105s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 105s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 105s Setting up ubuntu-standard (1.564) ... 105s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 105s Setting up linux-virtual (6.19.0-3.3) ... 105s Setting up linux-perf (6.19.0-3.3) ... 105s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 105s Processing triggers for debianutils (5.23.2build1) ... 105s Processing triggers for install-info (7.2-5) ... 105s Processing triggers for initramfs-tools (0.150ubuntu7) ... 105s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 109s Processing triggers for libc-bin (2.42-2ubuntu4) ... 109s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 109s /etc/kernel/postinst.d/initramfs-tools: 109s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 113s /etc/kernel/postinst.d/zz-update-grub: 113s Sourcing file `/etc/default/grub' 113s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 113s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 113s Generating grub configuration file ... 113s Found linux image: /boot/vmlinuz-6.19.0-3-generic 113s Found initrd image: /boot/initrd.img-6.19.0-3-generic 113s Found linux image: /boot/vmlinuz-6.18.0-9-generic 113s Found initrd image: /boot/initrd.img-6.18.0-9-generic 113s Warning: os-prober will not be executed to detect other bootable partitions. 113s Systems on them will not be added to the GRUB boot configuration. 113s Check GRUB_DISABLE_OS_PROBER documentation entry. 113s Adding boot menu entry for UEFI Firmware Settings ... 113s done 114s autopkgtest [03:47:42]: upgrading testbed (apt dist-upgrade and autopurge) 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s Calculating upgrade... 115s The following package was automatically installed and is no longer required: 115s libpython3.13 115s Use 'sudo apt autoremove' to remove it. 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Solving dependencies... 115s The following packages will be REMOVED: 115s libpython3.13* 115s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 115s After this operation, 7599 kB disk space will be freed. 115s (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 ... 125273 files and directories currently installed.) 115s Removing libpython3.13:amd64 (3.13.11-1) ... 115s Processing triggers for libc-bin (2.42-2ubuntu4) ... 115s autopkgtest [03:47:43]: rebooting testbed after setup commands that affected boot 144s autopkgtest [03:48:12]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 146s autopkgtest [03:48:14]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-survey 147s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (dsc) [2340 B] 147s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (tar) [2341 kB] 147s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-survey 4.4-2-2 (diff) [4580 B] 147s gpgv: Signature made Wed Oct 16 23:54:19 2024 UTC 147s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 147s gpgv: issuer "plessy@debian.org" 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./r-cran-survey_4.4-2-2.dsc: no acceptable signature found 147s autopkgtest [03:48:15]: testing package r-cran-survey version 4.4-2-2 148s autopkgtest [03:48:16]: build not needed 149s autopkgtest [03:48:17]: test run-unit-test: preparing testbed 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Solving dependencies... 149s The following NEW packages will be installed: 149s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 149s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 149s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 149s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 149s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 149s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 149s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 149s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 149s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css 149s r-base-core r-cran-abind r-cran-aer r-cran-backports r-cran-bit r-cran-bit64 149s r-cran-blob r-cran-boot r-cran-broom r-cran-cachem r-cran-car r-cran-cardata 149s r-cran-caret r-cran-class r-cran-cli r-cran-clock r-cran-codetools 149s r-cran-colorspace r-cran-conquer r-cran-cowplot r-cran-cpp11 r-cran-curl 149s r-cran-data.table r-cran-dbi r-cran-deriv r-cran-diagram r-cran-digest 149s r-cran-doby r-cran-dplyr r-cran-e1071 r-cran-evaluate r-cran-fansi 149s r-cran-farver r-cran-fastmap r-cran-foreach r-cran-forecast r-cran-foreign 149s r-cran-formula r-cran-fracdiff r-cran-future r-cran-future.apply 149s r-cran-generics r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gower 149s r-cran-gtable r-cran-hardhat r-cran-hexbin r-cran-highr r-cran-ipred 149s r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kernsmooth 149s r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava r-cran-lifecycle 149s r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest r-cran-lubridate 149s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixmodels 149s r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-microbenchmark 149s r-cran-minqa r-cran-mitools r-cran-modelmetrics r-cran-modelr r-cran-nlme 149s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-parallelly r-cran-pbkrtest 149s r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-plyr 149s r-cran-proc r-cran-prodlim r-cran-progressr r-cran-proxy r-cran-purrr 149s r-cran-quadprog r-cran-quantmod r-cran-quantreg r-cran-r.cache 149s r-cran-r.methodss3 r-cran-r.oo r-cran-r.rsp r-cran-r.utils r-cran-r6 149s r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo 149s r-cran-rcppeigen r-cran-rdpack r-cran-recipes r-cran-reformulas 149s r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-rsqlite r-cran-sandwich 149s r-cran-scales r-cran-shape r-cran-sparsem r-cran-sparsevctrs r-cran-squarem 149s r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey r-cran-survival 149s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-timechange 149s r-cran-timedate r-cran-tseries r-cran-ttr r-cran-tzdb r-cran-urca 149s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun 149s r-cran-xts r-cran-yaml r-cran-zoo tcl tcl8.6 unzip x11-common xdg-utils zip 149s 0 upgraded, 196 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 171 MB of archives. 149s After this operation, 340 MB of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 149s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 150s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 150s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 150s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 150s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 150s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 150s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 150s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 150s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 150s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 150s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 150s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 150s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 150s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 150s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 150s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 150s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 150s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 150s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 150s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 150s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 150s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 150s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 150s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 150s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 150s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 150s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 151s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 151s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 151s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 151s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 151s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 151s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 151s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 151s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 151s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 151s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 151s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 151s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 151s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 151s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 151s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 151s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 151s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 151s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 151s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 151s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 151s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 151s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 151s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 152s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1build1 [67.0 kB] 152s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cardata all 3.0.6-1 [1687 kB] 152s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formula all 1.2-5-1 [158 kB] 152s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 152s Get:56 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB] 152s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 153s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 153s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-4-1 [3556 kB] 153s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 153s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-boot all 1.3-32-1 [636 kB] 153s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 153s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 153s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 153s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 153s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnlopt0 amd64 2.7.1-7ubuntu1 [189 kB] 153s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nloptr amd64 2.2.1-2 [251 kB] 153s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 153s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rdpack all 2.6.3-1 [636 kB] 153s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reformulas all 0.4.4-1 [151 kB] 153s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 153s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 153s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 153s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lme4 amd64 1.1-38-1 [4197 kB] 153s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 153s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 153s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 153s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 153s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 153s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 153s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 153s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 153s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 154s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 154s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 154s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 154s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 154s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 154s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 154s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 154s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 154s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB] 154s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 154s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 154s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 154s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 154s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 154s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 154s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 154s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 154s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 154s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 154s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 154s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 154s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 154s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 154s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-deriv all 4.2.0-1 [154 kB] 154s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 154s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fracdiff amd64 1.5-3-1 [108 kB] 154s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-zoo amd64 1.8-15-1 [1025 kB] 154s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lmtest amd64 0.9.40-1build1 [400 kB] 154s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timedate amd64 4052.112-1 [1298 kB] 154s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quadprog amd64 1.5-8-1build2 [32.6 kB] 154s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xts amd64 0.14.1-1 [1198 kB] 155s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB] 155s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ttr amd64 0.24.4-1 [511 kB] 155s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 155s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quantmod all 0.4.28-1 [1037 kB] 155s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tseries amd64 0.10-59-3 [382 kB] 155s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-urca amd64 1.3-4-1build1 [1052 kB] 155s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB] 155s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-forecast amd64 8.23.0-1 [1569 kB] 155s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 155s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB] 155s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-doby all 4.7.1-3 [4741 kB] 155s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB] 155s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB] 155s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 155s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 155s Get:130 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 155s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 155s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 155s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sparsem amd64 1.84-2-1 [813 kB] 155s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixmodels all 0.5-4-1 [351 kB] 155s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-6-1 [8274 kB] 155s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB] 155s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-class amd64 7.3-23-1 [92.7 kB] 155s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] 156s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-e1071 amd64 1.7-17-1 [579 kB] 156s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1build1 [91.1 kB] 156s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-iterators all 1.0.14-1build1 [336 kB] 156s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreach all 1.5.2-1build1 [124 kB] 156s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 156s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelmetrics amd64 1.2.2.2-1build2 [155 kB] 156s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] 156s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-proc amd64 1.18.5-1 [966 kB] 156s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tzdb amd64 0.5.0-1 [538 kB] 156s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-clock amd64 0.7.2-1 [1903 kB] 156s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gower amd64 1.0.2-1 [210 kB] 156s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sparsevctrs amd64 0.2.0-2 [170 kB] 156s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hardhat all 1.4.2+dfsg-1 [596 kB] 156s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rpart amd64 4.1.24-1build1 [666 kB] 156s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shape all 1.4.6.1-1 [749 kB] 156s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diagram all 1.6.5-2 [656 kB] 156s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kernsmooth amd64 2.23-26-1build1 [93.6 kB] 156s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB] 156s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-globals all 0.19.0-1 [160 kB] 156s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 156s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-parallelly amd64 1.42.0-1 [540 kB] 156s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 156s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 156s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-progressr all 0.15.1-1 [353 kB] 156s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-squarem all 2021.1-1build1 [180 kB] 156s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lava all 1.8.2+dfsg-1 [2210 kB] 156s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-prodlim amd64 2024.06.25-1 [415 kB] 156s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ipred amd64 0.9-15-1 [386 kB] 156s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timechange amd64 0.3.0-2 [201 kB] 156s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1009 kB] 156s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 156s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reshape2 amd64 1.4.4-2build2 [123 kB] 156s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-caret amd64 7.0-1+dfsg-1 [3460 kB] 157s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-conquer amd64 1.3.3-1 [499 kB] 157s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quantreg amd64 6.1-1 [1455 kB] 157s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-car all 3.1-5-1 [1526 kB] 157s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sandwich all 3.1-1-1build1 [1483 kB] 157s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-aer all 1.2-15-1 [2607 kB] 157s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB] 157s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB] 157s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB] 157s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB] 157s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB] 157s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB] 157s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreign amd64 0.8.91-1 [245 kB] 157s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hexbin amd64 1.28.5-1 [1581 kB] 157s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB] 157s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mitools all 2.4-2build2 [266 kB] 157s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB] 157s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 157s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.oo all 1.27.1-1 [978 kB] 157s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.utils all 2.13.0-1 [1423 kB] 157s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.cache all 0.17.0-1 [117 kB] 157s Get:192 http://ftpmaster.internal/ubuntu resolute/main amd64 tcl8.6 amd64 8.6.17+dfsg-1build1 [14.9 kB] 157s Get:193 http://ftpmaster.internal/ubuntu resolute/main amd64 tcl amd64 8.6.16build1 [4200 B] 157s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.rsp all 0.46.0+ds-1 [1412 kB] 157s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB] 158s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survey amd64 4.4-2-2 [3453 kB] 158s Preconfiguring packages ... 158s Fetched 171 MB in 8s (20.2 MB/s) 158s Selecting previously unselected package fonts-dejavu-mono. 158s (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 ... 125269 files and directories currently installed.) 158s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8build1) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8build1) ... 158s Selecting previously unselected package fontconfig-config. 158s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 158s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 158s Selecting previously unselected package libfontconfig1:amd64. 158s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 158s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 158s Selecting previously unselected package fontconfig. 158s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 158s Unpacking fontconfig (2.17.1-3ubuntu1) ... 158s Selecting previously unselected package fonts-glyphicons-halflings. 158s Preparing to unpack .../005-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 158s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 158s Selecting previously unselected package fonts-mathjax. 158s Preparing to unpack .../006-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 158s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 158s Selecting previously unselected package libblas3:amd64. 158s Preparing to unpack .../007-libblas3_3.12.1-7ubuntu1_amd64.deb ... 158s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 158s Selecting previously unselected package libpixman-1-0:amd64. 158s Preparing to unpack .../008-libpixman-1-0_0.46.4-1_amd64.deb ... 158s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 158s Selecting previously unselected package libxcb-render0:amd64. 158s Preparing to unpack .../009-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 158s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 158s Selecting previously unselected package libxcb-shm0:amd64. 158s Preparing to unpack .../010-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 158s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 158s Selecting previously unselected package libxrender1:amd64. 158s Preparing to unpack .../011-libxrender1_1%3a0.9.12-1_amd64.deb ... 158s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 158s Selecting previously unselected package libcairo2:amd64. 158s Preparing to unpack .../012-libcairo2_1.18.4-3_amd64.deb ... 158s Unpacking libcairo2:amd64 (1.18.4-3) ... 158s Selecting previously unselected package libdatrie1:amd64. 158s Preparing to unpack .../013-libdatrie1_0.2.14-1_amd64.deb ... 158s Unpacking libdatrie1:amd64 (0.2.14-1) ... 159s Selecting previously unselected package libdeflate0:amd64. 159s Preparing to unpack .../014-libdeflate0_1.23-2build1_amd64.deb ... 159s Unpacking libdeflate0:amd64 (1.23-2build1) ... 159s Selecting previously unselected package libgfortran5:amd64. 159s Preparing to unpack .../015-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 159s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 159s Selecting previously unselected package libgomp1:amd64. 159s Preparing to unpack .../016-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 159s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 159s Selecting previously unselected package libgraphite2-3:amd64. 159s Preparing to unpack .../017-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 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to unpack .../055-r-cran-lattice_0.22-9-1_amd64.deb ... 159s Unpacking r-cran-lattice (0.22-9-1) ... 159s Selecting previously unselected package r-cran-nlme. 159s Preparing to unpack .../056-r-cran-nlme_3.1.168-1_amd64.deb ... 159s Unpacking r-cran-nlme (3.1.168-1) ... 159s Selecting previously unselected package r-cran-matrix. 159s Preparing to unpack .../057-r-cran-matrix_1.7-4-1_amd64.deb ... 159s Unpacking r-cran-matrix (1.7-4-1) ... 159s Selecting previously unselected package r-cran-mgcv. 159s Preparing to unpack .../058-r-cran-mgcv_1.9-4-1_amd64.deb ... 159s Unpacking r-cran-mgcv (1.9-4-1) ... 159s Selecting previously unselected package r-cran-nnet. 159s Preparing to unpack .../059-r-cran-nnet_7.3-20-1_amd64.deb ... 159s Unpacking r-cran-nnet (7.3-20-1) ... 159s Selecting previously unselected package r-cran-boot. 159s Preparing to unpack .../060-r-cran-boot_1.3-32-1_all.deb ... 159s Unpacking r-cran-boot (1.3-32-1) ... 159s Selecting previously unselected package r-cran-littler. 159s Preparing to unpack .../061-r-cran-littler_0.3.22-1_amd64.deb ... 159s Unpacking r-cran-littler (0.3.22-1) ... 159s Selecting previously unselected package r-cran-pkgkitten. 159s Preparing to unpack .../062-r-cran-pkgkitten_0.2.4-1_all.deb ... 159s Unpacking r-cran-pkgkitten (0.2.4-1) ... 159s Selecting previously unselected package r-cran-rcpp. 159s Preparing to unpack .../063-r-cran-rcpp_1.1.0-1_amd64.deb ... 159s Unpacking r-cran-rcpp (1.1.0-1) ... 159s Selecting previously unselected package r-cran-minqa. 159s Preparing to unpack .../064-r-cran-minqa_1.2.8-1_amd64.deb ... 159s Unpacking r-cran-minqa (1.2.8-1) ... 159s Selecting previously unselected package libnlopt0:amd64. 159s Preparing to unpack .../065-libnlopt0_2.7.1-7ubuntu1_amd64.deb ... 159s Unpacking libnlopt0:amd64 (2.7.1-7ubuntu1) ... 159s Selecting previously unselected package r-cran-nloptr. 159s Preparing to unpack .../066-r-cran-nloptr_2.2.1-2_amd64.deb ... 159s Unpacking r-cran-nloptr (2.2.1-2) 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r-cran-lifecycle. 160s Preparing to unpack .../078-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 160s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 160s Selecting previously unselected package r-cran-magrittr. 160s Preparing to unpack .../079-r-cran-magrittr_2.0.3-1_amd64.deb ... 160s Unpacking r-cran-magrittr (2.0.3-1) ... 160s Selecting previously unselected package r-cran-utf8. 160s Preparing to unpack .../080-r-cran-utf8_1.2.4-1_amd64.deb ... 160s Unpacking r-cran-utf8 (1.2.4-1) ... 160s Selecting previously unselected package r-cran-vctrs. 160s Preparing to unpack .../081-r-cran-vctrs_0.6.5-1_amd64.deb ... 160s Unpacking r-cran-vctrs (0.6.5-1) ... 160s Selecting previously unselected package r-cran-pillar. 160s Preparing to unpack .../082-r-cran-pillar_1.11.1+dfsg-1_all.deb ... 160s Unpacking r-cran-pillar (1.11.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-r6. 160s Preparing to unpack .../083-r-cran-r6_2.6.1-1_all.deb ... 160s Unpacking r-cran-r6 (2.6.1-1) ... 160s Selecting previously unselected package r-cran-fansi. 160s Preparing to unpack .../084-r-cran-fansi_1.0.6-2_amd64.deb ... 160s Unpacking r-cran-fansi (1.0.6-2) ... 160s Selecting previously unselected package r-cran-pkgconfig. 160s Preparing to unpack .../085-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 160s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 160s Selecting previously unselected package r-cran-tibble. 160s Preparing to unpack .../086-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 160s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 160s Selecting previously unselected package r-cran-withr. 160s Preparing to unpack .../087-r-cran-withr_3.0.2+dfsg-1_all.deb ... 160s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 160s Selecting previously unselected package r-cran-tidyselect. 160s Preparing to unpack .../088-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 160s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-dplyr. 160s Preparing to unpack .../089-r-cran-dplyr_1.1.4-4_amd64.deb ... 160s Unpacking r-cran-dplyr (1.1.4-4) ... 160s Selecting previously unselected package r-cran-purrr. 160s Preparing to unpack .../090-r-cran-purrr_1.0.4-1_amd64.deb ... 160s Unpacking r-cran-purrr (1.0.4-1) ... 160s Selecting previously unselected package r-cran-stringi. 160s Preparing to unpack .../091-r-cran-stringi_1.8.4-1build2_amd64.deb ... 160s Unpacking r-cran-stringi (1.8.4-1build2) ... 160s Selecting previously unselected package r-cran-stringr. 160s Preparing to unpack .../092-r-cran-stringr_1.5.1-1_all.deb ... 160s Unpacking r-cran-stringr (1.5.1-1) ... 160s Selecting previously unselected package r-cran-cpp11. 160s Preparing to unpack .../093-r-cran-cpp11_0.5.3-1_all.deb ... 160s Unpacking r-cran-cpp11 (0.5.3-1) ... 160s Selecting previously unselected package r-cran-tidyr. 160s Preparing to unpack .../094-r-cran-tidyr_1.3.1-1_amd64.deb ... 160s Unpacking r-cran-tidyr (1.3.1-1) ... 160s Selecting previously unselected package r-cran-broom. 160s Preparing to unpack .../095-r-cran-broom_1.0.12+dfsg-1_all.deb ... 160s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 160s Selecting previously unselected package r-cran-numderiv. 160s Preparing to unpack .../096-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 160s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 160s Selecting previously unselected package r-cran-gtable. 160s Preparing to unpack .../097-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 160s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 160s Selecting previously unselected package r-cran-isoband. 160s Preparing to unpack .../098-r-cran-isoband_0.2.7-1_amd64.deb ... 160s Unpacking r-cran-isoband (0.2.7-1) ... 160s Selecting previously unselected package r-cran-farver. 160s Preparing to unpack .../099-r-cran-farver_2.1.2-1_amd64.deb ... 160s Unpacking r-cran-farver (2.1.2-1) ... 160s Selecting previously unselected package r-cran-labeling. 160s Preparing to unpack .../100-r-cran-labeling_0.4.3-1_all.deb ... 160s Unpacking r-cran-labeling (0.4.3-1) ... 160s Selecting previously unselected package r-cran-rcolorbrewer. 160s Preparing to unpack .../101-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 160s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 160s Selecting previously unselected package r-cran-viridislite. 160s Preparing to unpack .../102-r-cran-viridislite_0.4.3-1_all.deb ... 160s Unpacking r-cran-viridislite (0.4.3-1) ... 160s Selecting previously unselected package r-cran-scales. 160s Preparing to unpack .../103-r-cran-scales_1.4.0-1_all.deb ... 160s Unpacking r-cran-scales (1.4.0-1) ... 160s Selecting previously unselected package r-cran-ggplot2. 160s Preparing to unpack .../104-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 160s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-cowplot. 160s Preparing to unpack .../105-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 160s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 160s Selecting previously unselected package r-cran-deriv. 160s Preparing to unpack .../106-r-cran-deriv_4.2.0-1_all.deb ... 160s Unpacking r-cran-deriv (4.2.0-1) ... 160s Selecting previously unselected package r-cran-colorspace. 160s Preparing to unpack .../107-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 160s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 160s Selecting previously unselected package r-cran-fracdiff. 160s Preparing to unpack .../108-r-cran-fracdiff_1.5-3-1_amd64.deb ... 160s Unpacking r-cran-fracdiff (1.5-3-1) ... 160s Selecting previously unselected package r-cran-zoo. 160s Preparing to unpack .../109-r-cran-zoo_1.8-15-1_amd64.deb ... 160s Unpacking r-cran-zoo (1.8-15-1) ... 160s Selecting previously unselected package r-cran-lmtest. 160s Preparing to unpack .../110-r-cran-lmtest_0.9.40-1build1_amd64.deb ... 160s Unpacking r-cran-lmtest (0.9.40-1build1) ... 160s Selecting previously unselected package r-cran-timedate. 160s Preparing to unpack .../111-r-cran-timedate_4052.112-1_amd64.deb ... 160s Unpacking r-cran-timedate (4052.112-1) ... 160s Selecting previously unselected package r-cran-quadprog. 160s Preparing to unpack .../112-r-cran-quadprog_1.5-8-1build2_amd64.deb ... 160s Unpacking r-cran-quadprog (1.5-8-1build2) ... 160s Selecting previously unselected package r-cran-xts. 160s Preparing to unpack .../113-r-cran-xts_0.14.1-1_amd64.deb ... 160s Unpacking r-cran-xts (0.14.1-1) ... 160s Selecting previously unselected package r-cran-curl. 160s Preparing to unpack .../114-r-cran-curl_7.0.0+dfsg-1_amd64.deb ... 160s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 160s Selecting previously unselected package r-cran-ttr. 160s Preparing to unpack .../115-r-cran-ttr_0.24.4-1_amd64.deb ... 160s Unpacking r-cran-ttr (0.24.4-1) ... 160s Selecting previously unselected package r-cran-jsonlite. 160s Preparing to unpack .../116-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ... 160s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 160s Selecting previously unselected package r-cran-quantmod. 160s Preparing to unpack .../117-r-cran-quantmod_0.4.28-1_all.deb ... 160s Unpacking r-cran-quantmod (0.4.28-1) ... 160s Selecting previously unselected package r-cran-tseries. 160s Preparing to unpack .../118-r-cran-tseries_0.10-59-3_amd64.deb ... 160s Unpacking r-cran-tseries (0.10-59-3) ... 160s Selecting previously unselected package r-cran-urca. 160s Preparing to unpack .../119-r-cran-urca_1.3-4-1build1_amd64.deb ... 160s Unpacking r-cran-urca (1.3-4-1build1) ... 161s Selecting previously unselected package r-cran-rcpparmadillo. 161s Preparing to unpack .../120-r-cran-rcpparmadillo_15.2.3-1-1_amd64.deb ... 161s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 161s Selecting previously unselected package r-cran-forecast. 161s Preparing to unpack .../121-r-cran-forecast_8.23.0-1_amd64.deb ... 161s Unpacking r-cran-forecast (8.23.0-1) ... 161s Selecting previously unselected package r-cran-modelr. 161s Preparing to unpack .../122-r-cran-modelr_0.1.11-1_all.deb ... 161s Unpacking r-cran-modelr (0.1.11-1) ... 161s Selecting previously unselected package r-cran-microbenchmark. 161s Preparing to unpack .../123-r-cran-microbenchmark_1.5.0-1_amd64.deb ... 161s Unpacking r-cran-microbenchmark (1.5.0-1) ... 161s Selecting previously unselected package r-cran-doby. 161s Preparing to unpack .../124-r-cran-doby_4.7.1-3_all.deb ... 161s Unpacking r-cran-doby (4.7.1-3) ... 161s Selecting previously unselected package r-cran-evaluate. 161s Preparing to unpack .../125-r-cran-evaluate_1.0.5-1_all.deb ... 161s Unpacking r-cran-evaluate (1.0.5-1) ... 161s Selecting previously unselected package r-cran-xfun. 161s Preparing to unpack .../126-r-cran-xfun_0.55+dfsg-1_amd64.deb ... 161s Unpacking r-cran-xfun (0.55+dfsg-1) ... 161s Selecting previously unselected package r-cran-highr. 161s Preparing to unpack .../127-r-cran-highr_0.11+dfsg-1_all.deb ... 161s Unpacking r-cran-highr (0.11+dfsg-1) ... 161s Selecting previously unselected package r-cran-yaml. 161s Preparing to unpack .../128-r-cran-yaml_2.3.10-1_amd64.deb ... 161s Unpacking r-cran-yaml (2.3.10-1) ... 161s Selecting previously unselected package libjs-mathjax. 161s Preparing to unpack .../129-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 161s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 161s Selecting previously unselected package r-cran-knitr. 161s Preparing to unpack .../130-r-cran-knitr_1.51+dfsg-1_all.deb ... 161s Unpacking r-cran-knitr (1.51+dfsg-1) ... 161s Selecting previously unselected package r-cran-pbkrtest. 161s Preparing to unpack .../131-r-cran-pbkrtest_0.5.5-1_all.deb ... 161s Unpacking r-cran-pbkrtest (0.5.5-1) ... 161s Selecting previously unselected package r-cran-sparsem. 161s Preparing to unpack .../132-r-cran-sparsem_1.84-2-1_amd64.deb ... 161s Unpacking r-cran-sparsem (1.84-2-1) ... 161s Selecting previously unselected package r-cran-matrixmodels. 161s Preparing to unpack .../133-r-cran-matrixmodels_0.5-4-1_all.deb ... 161s Unpacking r-cran-matrixmodels (0.5-4-1) ... 161s Selecting previously unselected package r-cran-survival. 161s Preparing to unpack .../134-r-cran-survival_3.8-6-1_amd64.deb ... 161s Unpacking r-cran-survival (3.8-6-1) ... 161s Selecting previously unselected package r-cran-matrixstats. 161s Preparing to unpack .../135-r-cran-matrixstats_1.5.0-1_amd64.deb ... 161s Unpacking r-cran-matrixstats (1.5.0-1) ... 161s Selecting previously unselected package r-cran-class. 161s Preparing to unpack .../136-r-cran-class_7.3-23-1_amd64.deb ... 161s Unpacking r-cran-class (7.3-23-1) ... 161s Selecting previously unselected package r-cran-proxy. 161s Preparing to unpack .../137-r-cran-proxy_0.4-27-1_amd64.deb ... 161s Unpacking r-cran-proxy (0.4-27-1) ... 161s Selecting previously unselected package r-cran-e1071. 161s Preparing to unpack .../138-r-cran-e1071_1.7-17-1_amd64.deb ... 161s Unpacking r-cran-e1071 (1.7-17-1) ... 161s Selecting previously unselected package r-cran-codetools. 161s Preparing to unpack .../139-r-cran-codetools_0.2-20-1build1_all.deb ... 161s Unpacking r-cran-codetools (0.2-20-1build1) ... 161s Selecting previously unselected package r-cran-iterators. 161s Preparing to unpack .../140-r-cran-iterators_1.0.14-1build1_all.deb ... 161s Unpacking r-cran-iterators (1.0.14-1build1) ... 161s Selecting previously unselected package r-cran-foreach. 161s Preparing to unpack .../141-r-cran-foreach_1.5.2-1build1_all.deb ... 161s Unpacking r-cran-foreach (1.5.2-1build1) ... 161s Selecting previously unselected package r-cran-data.table. 161s Preparing to unpack .../142-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ... 161s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 161s Selecting previously unselected package r-cran-modelmetrics. 161s Preparing to unpack .../143-r-cran-modelmetrics_1.2.2.2-1build2_amd64.deb ... 161s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ... 161s Selecting previously unselected package r-cran-plyr. 161s Preparing to unpack .../144-r-cran-plyr_1.8.9-1_amd64.deb ... 161s Unpacking r-cran-plyr (1.8.9-1) ... 161s Selecting previously unselected package r-cran-proc. 161s Preparing to unpack .../145-r-cran-proc_1.18.5-1_amd64.deb ... 161s Unpacking r-cran-proc (1.18.5-1) ... 161s Selecting previously unselected package r-cran-tzdb. 161s Preparing to unpack .../146-r-cran-tzdb_0.5.0-1_amd64.deb ... 161s Unpacking r-cran-tzdb (0.5.0-1) ... 161s Selecting previously unselected package r-cran-clock. 161s Preparing to unpack .../147-r-cran-clock_0.7.2-1_amd64.deb ... 161s Unpacking r-cran-clock (0.7.2-1) ... 161s Selecting previously unselected package r-cran-gower. 161s Preparing to unpack .../148-r-cran-gower_1.0.2-1_amd64.deb ... 161s Unpacking r-cran-gower (1.0.2-1) ... 161s Selecting previously unselected package r-cran-sparsevctrs. 161s Preparing to unpack .../149-r-cran-sparsevctrs_0.2.0-2_amd64.deb ... 161s Unpacking r-cran-sparsevctrs (0.2.0-2) ... 161s Selecting previously unselected package r-cran-hardhat. 161s Preparing to unpack .../150-r-cran-hardhat_1.4.2+dfsg-1_all.deb ... 161s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ... 161s Selecting previously unselected package r-cran-rpart. 161s Preparing to unpack .../151-r-cran-rpart_4.1.24-1build1_amd64.deb ... 161s Unpacking r-cran-rpart (4.1.24-1build1) ... 161s Selecting previously unselected package r-cran-shape. 161s Preparing to unpack .../152-r-cran-shape_1.4.6.1-1_all.deb ... 161s Unpacking r-cran-shape (1.4.6.1-1) ... 161s Selecting previously unselected package r-cran-diagram. 161s Preparing to unpack .../153-r-cran-diagram_1.6.5-2_all.deb ... 161s Unpacking r-cran-diagram (1.6.5-2) ... 161s Selecting previously unselected package r-cran-kernsmooth. 161s Preparing to unpack .../154-r-cran-kernsmooth_2.23-26-1build1_amd64.deb ... 161s Unpacking r-cran-kernsmooth (2.23-26-1build1) ... 161s Selecting previously unselected package r-cran-digest. 161s Preparing to unpack .../155-r-cran-digest_0.6.39-1_amd64.deb ... 161s Unpacking r-cran-digest (0.6.39-1) ... 161s Selecting previously unselected package r-cran-globals. 161s Preparing to unpack .../156-r-cran-globals_0.19.0-1_all.deb ... 161s Unpacking r-cran-globals (0.19.0-1) ... 161s Selecting previously unselected package r-cran-listenv. 161s Preparing to unpack .../157-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 161s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 161s Selecting previously unselected package r-cran-parallelly. 161s Preparing to unpack .../158-r-cran-parallelly_1.42.0-1_amd64.deb ... 161s Unpacking r-cran-parallelly (1.42.0-1) ... 161s Selecting previously unselected package r-cran-future. 161s Preparing to unpack .../159-r-cran-future_1.34.0+dfsg-1_all.deb ... 161s Unpacking r-cran-future (1.34.0+dfsg-1) ... 161s Selecting previously unselected package r-cran-future.apply. 161s Preparing to unpack .../160-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 161s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 161s Selecting previously unselected package r-cran-progressr. 161s Preparing to unpack .../161-r-cran-progressr_0.15.1-1_all.deb ... 161s Unpacking r-cran-progressr (0.15.1-1) ... 162s Selecting previously unselected package r-cran-squarem. 162s Preparing to unpack .../162-r-cran-squarem_2021.1-1build1_all.deb ... 162s Unpacking r-cran-squarem (2021.1-1build1) ... 162s Selecting previously unselected package r-cran-lava. 162s Preparing to unpack .../163-r-cran-lava_1.8.2+dfsg-1_all.deb ... 162s Unpacking r-cran-lava (1.8.2+dfsg-1) ... 162s Selecting previously unselected package r-cran-prodlim. 162s Preparing to unpack .../164-r-cran-prodlim_2024.06.25-1_amd64.deb ... 162s Unpacking r-cran-prodlim (2024.06.25-1) ... 162s Selecting previously unselected package r-cran-ipred. 162s Preparing to unpack .../165-r-cran-ipred_0.9-15-1_amd64.deb ... 162s Unpacking r-cran-ipred (0.9-15-1) ... 162s Selecting previously unselected package r-cran-timechange. 162s Preparing to unpack .../166-r-cran-timechange_0.3.0-2_amd64.deb ... 162s Unpacking r-cran-timechange (0.3.0-2) ... 162s Selecting previously unselected package r-cran-lubridate. 162s Preparing to unpack .../167-r-cran-lubridate_1.9.4+dfsg-1_amd64.deb ... 162s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 162s Selecting previously unselected package r-cran-recipes. 162s Preparing to unpack .../168-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 162s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 162s Selecting previously unselected package r-cran-reshape2. 162s Preparing to unpack .../169-r-cran-reshape2_1.4.4-2build2_amd64.deb ... 162s Unpacking r-cran-reshape2 (1.4.4-2build2) ... 162s Selecting previously unselected package r-cran-caret. 162s Preparing to unpack .../170-r-cran-caret_7.0-1+dfsg-1_amd64.deb ... 162s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 162s Selecting previously unselected package r-cran-conquer. 162s Preparing to unpack .../171-r-cran-conquer_1.3.3-1_amd64.deb ... 162s Unpacking r-cran-conquer (1.3.3-1) ... 162s Selecting previously unselected package r-cran-quantreg. 162s Preparing to unpack .../172-r-cran-quantreg_6.1-1_amd64.deb ... 162s Unpacking r-cran-quantreg (6.1-1) ... 162s Selecting previously unselected package r-cran-car. 162s Preparing to unpack .../173-r-cran-car_3.1-5-1_all.deb ... 162s Unpacking r-cran-car (3.1-5-1) ... 162s Selecting previously unselected package r-cran-sandwich. 162s Preparing to unpack .../174-r-cran-sandwich_3.1-1-1build1_all.deb ... 162s Unpacking r-cran-sandwich (3.1-1-1build1) ... 162s Selecting previously unselected package r-cran-aer. 162s Preparing to unpack .../175-r-cran-aer_1.2-15-1_all.deb ... 162s Unpacking r-cran-aer (1.2-15-1) ... 162s Selecting previously unselected package r-cran-bit. 162s Preparing to unpack .../176-r-cran-bit_4.6.0+dfsg-1_amd64.deb ... 162s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 162s Selecting previously unselected package r-cran-bit64. 162s Preparing to unpack .../177-r-cran-bit64_4.6.0-1-4_amd64.deb 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previously unselected package r-cran-r.utils. 162s Preparing to unpack .../189-r-cran-r.utils_2.13.0-1_all.deb ... 162s Unpacking r-cran-r.utils (2.13.0-1) ... 162s Selecting previously unselected package r-cran-r.cache. 162s Preparing to unpack .../190-r-cran-r.cache_0.17.0-1_all.deb ... 162s Unpacking r-cran-r.cache (0.17.0-1) ... 162s Selecting previously unselected package tcl8.6. 162s Preparing to unpack .../191-tcl8.6_8.6.17+dfsg-1build1_amd64.deb ... 162s Unpacking tcl8.6 (8.6.17+dfsg-1build1) ... 162s Selecting previously unselected package tcl. 162s Preparing to unpack .../192-tcl_8.6.16build1_amd64.deb ... 162s Unpacking tcl (8.6.16build1) ... 162s Selecting previously unselected package r-cran-r.rsp. 162s Preparing to unpack .../193-r-cran-r.rsp_0.46.0+ds-1_all.deb ... 162s Unpacking r-cran-r.rsp (0.46.0+ds-1) ... 162s Selecting previously unselected package r-cran-rsqlite. 162s Preparing to unpack .../194-r-cran-rsqlite_2.3.9-1_amd64.deb ... 162s Unpacking r-cran-rsqlite 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162s Setting up libgomp1:amd64 (16-20260208-1ubuntu1) ... 162s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 162s Setting up zip (3.0-15ubuntu3) ... 162s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 162s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 162s Setting up fonts-dejavu-mono (2.37-8build1) ... 162s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1build1) ... 162s Setting up fonts-dejavu-core (2.37-8build1) ... 162s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 162s Setting up libgfortran5:amd64 (16-20260208-1ubuntu1) ... 162s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 162s Setting up libjs-highlight.js (10.7.3+dfsg-2) ... 162s Setting up libharfbuzz0b:amd64 (12.3.2-1) ... 162s Setting up libthai-data (0.1.30-1) ... 162s Setting up libxss1:amd64 (1:1.2.3-1build4) ... 162s Setting up libpaper2:amd64 (2.2.5-0.3build1) ... 162s Setting up libjs-jquery 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r-cran-forecast (8.23.0-1) ... 165s Setting up r-cran-quantreg (6.1-1) ... 165s Setting up r-cran-modelr (0.1.11-1) ... 165s Setting up r-cran-doby (4.7.1-3) ... 165s Setting up r-cran-pbkrtest (0.5.5-1) ... 165s Setting up r-cran-car (3.1-5-1) ... 165s Setting up r-cran-aer (1.2-15-1) ... 165s Processing triggers for libc-bin (2.42-2ubuntu4) ... 165s Processing triggers for man-db (2.13.1-1build1) ... 166s Processing triggers for install-info (7.2-5) ... 166s autopkgtest [03:48:34]: test run-unit-test: [----------------------- 167s BEGIN TEST 3stage2phase.R 167s 167s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 167s Copyright (C) 2025 The R Foundation for Statistical Computing 167s Platform: x86_64-pc-linux-gnu 167s 167s R is free software and comes with ABSOLUTELY NO WARRANTY. 167s You are welcome to redistribute it under certain conditions. 167s Type 'license()' or 'licence()' for distribution details. 167s 167s R is a collaborative project with many contributors. 167s Type 'contributors()' for more information and 167s 'citation()' on how to cite R or R packages in publications. 167s 167s Type 'demo()' for some demos, 'help()' for on-line help, or 167s 'help.start()' for an HTML browser interface to help. 167s Type 'q()' to quit R. 167s 167s > ## simulated data with three-stage sample at phase 1, SRS at phase 2 167s > ## motivated by dietary biomarker substudy in HCHS 167s > 167s > library(survey) 167s Loading required package: grid 167s Loading required package: Matrix 167s Loading required package: survival 167s > 167s > load("simdata1.RData") 167s > 167s > twophase.full = twophase(id=list(~block+house+ind,~1), 167s + strata=list(~strat,NULL), 167s + probs=list(~P.block+P.house+P.ind,NULL), 167s + subset=~phase2, 167s + data=simdata1,method='full') 167s 167s Attaching package: 'survey' 167s 167s The following object is masked from 'package:graphics': 167s 167s dotchart 167s 168s > 168s > twophase.approx = twophase(id=list(~block+house+ind,~1), 168s + strata=list(~strat,NULL), 168s + probs=list(~P.block+P.house+P.ind,NULL), 168s + subset=~phase2, 168s + data=simdata1,method='approx') 168s > 168s > twophase.rep = twophase(id=list(~block,~1), 168s + strata=list(~strat,NULL), 168s + probs=list(~I(P.block*P.house*P.ind),NULL), 168s + subset=~phase2, 168s + data=simdata1,method='full') 168s > 168s > 168s > twophase.repapprox = twophase(id=list(~block,~1), 168s + strata=list(~strat,NULL), 168s + probs=list(~I(P.block*P.house*P.ind),NULL), 168s + subset=~phase2, 168s + data=simdata1,method='approx') 168s > 168s > 168s > svymean(~age, twophase.full) 168s mean SE 168s age 41.116 0.8114 168s > svymean(~age, twophase.approx) 168s mean SE 168s age 41.116 0.6693 168s > svymean(~age, twophase.rep) 168s mean SE 168s age 41.116 0.784 168s > svymean(~age, twophase.repapprox) 168s mean SE 168s age 41.116 0.6592 168s > 168s BEGIN TEST DBIcheck.R 168s 168s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 168s Copyright (C) 2025 The R Foundation for Statistical Computing 168s Platform: x86_64-pc-linux-gnu 168s 168s R is free software and comes with ABSOLUTELY NO WARRANTY. 168s You are welcome to redistribute it under certain conditions. 168s Type 'license()' or 'licence()' for distribution details. 168s 168s R is a collaborative project with many contributors. 168s Type 'contributors()' for more information and 168s 'citation()' on how to cite R or R packages in publications. 168s 168s Type 'demo()' for some demos, 'help()' for on-line help, or 168s 'help.start()' for an HTML browser interface to help. 168s Type 'q()' to quit R. 168s 168s > 168s > library(survey) 168s Loading required package: grid 168s Loading required package: Matrix 168s Loading required package: survival 169s > library(RSQLite) 169s 169s Attaching package: 'survey' 169s 169s The following object is masked from 'package:graphics': 169s 169s dotchart 169s 169s > 169s > data(api) 169s > apiclus1$api_stu<-apiclus1$api.stu 169s > apiclus1$comp_imp<-apiclus1$comp.imp 169s > dclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc,data=apiclus1) 169s > dbclus1<-svydesign(id=~dnum, weights=~pw, fpc=~fpc, 169s + data="apiclus1",dbtype="SQLite", dbname=system.file("api.db",package="survey")) 169s > 169s > m<-svymean(~api00+stype,dclus1) 169s > m.db<-svymean(~api00+stype, dbclus1) 169s > all.equal(coef(m),coef(m.db)) 169s [1] TRUE 169s > all.equal(vcov(m), vcov(m.db)) 169s [1] TRUE 169s > 169s > r<-svyratio(~api_stu, ~enroll, design=dclus1) 169s > r.db<-svyratio(~api_stu, ~enroll, design=dbclus1) 169s > all.equal(coef(r), coef(r.db)) 169s [1] TRUE 169s > all.equal(SE(r), SE(r.db)) 169s [1] TRUE 169s > 169s > b<-svyby(~api99+api00,~stype, design=dclus1, svymean, deff=TRUE) 169s > b.db<-svyby(~api99+api00,~stype, design=dbclus1,svymean, deff=TRUE) 169s > all.equal(coef(b), coef(b.db)) 169s [1] TRUE 169s > all.equal(SE(b), SE(b.db)) 169s [1] TRUE 169s > all.equal(deff(b), deff(b.db)) 169s [1] TRUE 169s > 169s > l<-svyglm(api00~api99+mobility, design=dclus1) 169s > l.db<-svyglm(api00~api99+mobility, design=dbclus1) 169s > all.equal(coef(l),coef(l.db)) 169s [1] TRUE 169s > all.equal(vcov(l), vcov(l.db)) 169s [1] TRUE 169s > 169s > dclus1<-update(dclus1, apidiff=api00-api99) 169s > dclus1<-update(dclus1, apipct= apidiff/api99) 169s > dbclus1<-update(dbclus1, apidiff=api00-api99) 169s > dbclus1<-update(dbclus1, apipct= apidiff/api99) 169s > 169s > u<-svymean(~api00+apidiff+apipct, dclus1) 169s > u.db<-svymean(~api00+apidiff+apipct, dbclus1) 169s > all.equal(u, u.db) 169s [1] TRUE 169s > 169s > all.equal(nrow(dclus1),nrow(dbclus1)) 169s [1] TRUE 169s > all.equal(nrow(subset(dclus1,stype=="E")), 169s + nrow(subset(dbclus1,stype=="E"))) 169s [1] "Mean relative difference: 0.2708333" 169s > 169s > ## replicate weights 169s > rclus1<-as.svrepdesign(dclus1) 169s > db_rclus1<-svrepdesign(weights=~pw, repweights="wt[1-9]+", type="JK1", scale=(1-15/757)*14/15, 169s + data="apiclus1rep",dbtype="SQLite", dbname=system.file("api.db",package="survey"),combined.weights=FALSE) 169s > m<-svymean(~api00+api99,rclus1) 169s > m.db<-svymean(~api00+api99,db_rclus1) 169s > all.equal(m,m.db) 169s [1] TRUE 169s > 169s > summary(db_rclus1) 169s DB-backed replicate weight design 169s Call: svrepdesign(weights = ~pw, repweights = "wt[1-9]+", type = "JK1", 169s scale = (1 - 15/757) * 14/15, data = "apiclus1rep", dbtype = "SQLite", 169s dbname = system.file("api.db", package = "survey"), combined.weights = FALSE) 169s Unstratified cluster jacknife (JK1) with 15 replicates. 169s Variables: 169s [1] "row_names" "cds" "stype" "name" "sname" 169s [6] "snum" "dname" "dnum" "cname" "cnum" 169s [11] "flag" "pcttest" "api00" "api99" "target" 169s [16] "growth" "sch_wide" "comp_imp" "both" "awards" 169s [21] "meals" "ell" "yr_rnd" "mobility" "acs_k3" 169s [26] "acs_46" "acs_core" "pct_resp" "not_hsg" "hsg" 169s [31] "some_col" "col_grad" "grad_sch" "avg_ed" "full__1" 169s [36] "emer" "enroll" "api_stu" "fpc" "pw" 169s [41] "row_names:1" "wt1" "wt2" "wt3" "wt4" 169s [46] "wt5" "wt6" "wt7" "wt8" "wt9" 169s [51] "wt10" "wt11" "wt12" "wt13" "wt14" 169s [56] "wt15" 169s > 169s > s<-svymean(~api00, subset(rclus1, comp_imp=="Yes")) 169s > s.db<-svymean(~api00, subset(db_rclus1, comp_imp=="Yes")) 169s > all.equal(s,s.db) 169s [1] TRUE 169s > 169s BEGIN TEST anova-svycoxph.R 169s 169s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 169s Copyright (C) 2025 The R Foundation for Statistical Computing 169s Platform: x86_64-pc-linux-gnu 169s 169s R is free software and comes with ABSOLUTELY NO WARRANTY. 169s You are welcome to redistribute it under certain conditions. 169s Type 'license()' or 'licence()' for distribution details. 169s 169s R is a collaborative project with many contributors. 169s Type 'contributors()' for more information and 169s 'citation()' on how to cite R or R packages in publications. 169s 169s Type 'demo()' for some demos, 'help()' for on-line help, or 169s 'help.start()' for an HTML browser interface to help. 169s Type 'q()' to quit R. 169s 169s Loading required package: grid 169s > 169s > library(survey) 169s Loading required package: Matrix 169s Loading required package: survival 170s 170s Attaching package: 'survey' 170s 170s > example(svycoxph, ask=FALSE) 170s The following object is masked from 'package:graphics': 170s 170s dotchart 170s 170s 170s svycxp> ## Somewhat unrealistic example of nonresponse bias. 170s svycxp> data(pbc, package="survival") 170s 170s svycxp> pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 170s 170s svycxp> biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 170s 170s svycxp> pbc$randprob<-fitted(biasmodel) 170s 170s svycxp> if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 170s 170s svycxp> dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 170s 170s svycxp> rpbc<-as.svrepdesign(dpbc) 170s 170s svycxp> (model<-svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=dpbc)) 170s Call: 170s svycoxph(formula = Surv(time, status > 0) ~ log(bili) + protime + 170s albumin, design = dpbc) 170s 170s coef exp(coef) se(coef) robust se z p 170s log(bili) 0.88592 2.42522 0.09140 0.09048 9.791 < 2e-16 170s protime 0.24487 1.27745 0.07825 0.08122 3.015 0.00257 170s albumin -1.04298 0.35240 0.21211 0.20454 -5.099 3.41e-07 170s 170s Likelihood ratio test= on 3 df, p= 170s n= 312, number of events= 144 170s 170s svycxp> svycoxph(Surv(time,status>0)~log(bili)+protime+albumin,design=rpbc) 170s Call: 170s svycoxph.svyrep.design(formula = Surv(time, status > 0) ~ log(bili) + 170s protime + albumin, design = rpbc) 170s 170s coef exp(coef) se(coef) z p 170s log(bili) 0.88592 2.42522 0.09838 9.005 < 2e-16 170s protime 0.24487 1.27745 0.09373 2.612 0.00899 170s albumin -1.04298 0.35240 0.21966 -4.748 2.05e-06 170s 170s Likelihood ratio test=NA on 3 df, p=NA 170s n= 312, number of events= 144 170s 170s svycxp> s<-predict(model,se=TRUE, type="curve", 170s svycxp+ newdata=data.frame(bili=c(3,9), protime=c(10,10), albumin=c(3.5,3.5))) 170s 170s svycxp> plot(s[[1]],ci=TRUE,col="sienna") 170s 170s svycxp> lines(s[[2]], ci=TRUE,col="royalblue") 170s 170s svycxp> quantile(s[[1]], ci=TRUE) 170s 0.75 0.5 0.25 170s 1435 2503 3574 170s attr(,"ci") 170s 0.025 0.975 170s 0.75 1217 1786 170s 0.5 2256 3170 170s 0.25 3222 Inf 170s 170s svycxp> confint(s[[2]], parm=365*(1:5)) 170s 0.025 0.975 170s 365 0.8375139 0.9453781 170s 730 0.7382750 0.8999016 170s 1095 0.4784105 0.7478460 170s 1460 0.3192009 0.6206764 170s 1825 0.2149475 0.5292978 170s > m<-update(model, .~.+I(protime^2)) 170s > a<-anova(m,model) 170s > b<-anova(m, model,force=TRUE) 170s > stopifnot(isTRUE(all.equal(b[2:6],a[c(3,4,6,7,8)]))) 170s > 170s BEGIN TEST api.R 170s 170s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 170s Copyright (C) 2025 The R Foundation for Statistical Computing 170s Platform: x86_64-pc-linux-gnu 170s 170s R is free software and comes with ABSOLUTELY NO WARRANTY. 170s You are welcome to redistribute it under certain conditions. 170s Type 'license()' or 'licence()' for distribution details. 170s 170s R is a collaborative project with many contributors. 170s Type 'contributors()' for more information and 170s 'citation()' on how to cite R or R packages in publications. 170s 170s Type 'demo()' for some demos, 'help()' for on-line help, or 170s 'help.start()' for an HTML browser interface to help. 170s Type 'q()' to quit R. 170s 170s > library(survey) 170s Loading required package: grid 170s Loading required package: Matrix 170s Loading required package: survival 171s 171s Attaching package: 'survey' 171s 171s > options(survey.replicates.mse=TRUE) 171s > example(api) 171s The following object is masked from 'package:graphics': 171s 171s dotchart 171s 171s 171s api> library(survey) 171s 171s api> data(api) 171s 171s api> mean(apipop$api00) 171s [1] 664.7126 171s 171s api> sum(apipop$enroll, na.rm=TRUE) 171s [1] 3811472 171s 171s api> #stratified sample 171s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 171s 171s api> summary(dstrat) 171s Stratified Independent Sampling design 171s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 171s Stratum Sizes: 171s E H M 171s obs 100 50 50 171s design.PSU 100 50 50 171s actual.PSU 100 50 50 171s Population stratum sizes (PSUs): 171s E H M 171s 4421 755 1018 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "pw" "fpc" 171s 171s api> svymean(~api00, dstrat) 171s mean SE 171s api00 662.29 9.4089 171s 171s api> svytotal(~enroll, dstrat, na.rm=TRUE) 171s total SE 171s enroll 3687178 114642 171s 171s api> # one-stage cluster sample 171s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 171s 171s api> summary(dclus1) 171s 1 - level Cluster Sampling design 171s With (15) clusters. 171s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 171s Population size (PSUs): 757 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> svymean(~api00, dclus1) 171s mean SE 171s api00 644.17 23.542 171s 171s api> svytotal(~enroll, dclus1, na.rm=TRUE) 171s total SE 171s enroll 3404940 932235 171s 171s api> # two-stage cluster sample 171s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 171s 171s api> summary(dclus2) 171s 2 - level Cluster Sampling design 171s With (40, 126) clusters. 171s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 171s Population size (PSUs): 757 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "pw" "fpc1" "fpc2" 171s 171s api> svymean(~api00, dclus2) 171s mean SE 171s api00 670.81 30.099 171s 171s api> svytotal(~enroll, dclus2, na.rm=TRUE) 171s total SE 171s enroll 2639273 799638 171s 171s api> # two-stage `with replacement' 171s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 171s 171s api> summary(dclus2wr) 171s 2 - level Cluster Sampling design (with replacement) 171s With (40, 126) clusters. 171s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "pw" "fpc1" "fpc2" 171s 171s api> svymean(~api00, dclus2wr) 171s mean SE 171s api00 670.81 30.712 171s 171s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 171s total SE 171s enroll 2639273 820261 171s 171s api> # convert to replicate weights 171s api> rclus1<-as.svrepdesign(dclus1) 171s 171s api> summary(rclus1) 171s Call: as.svrepdesign.default(dclus1) 171s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 171s Variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> svymean(~api00, rclus1) 171s mean SE 171s api00 644.17 26.335 171s 171s api> svytotal(~enroll, rclus1, na.rm=TRUE) 171s total SE 171s enroll 3404940 932235 171s 171s api> # post-stratify on school type 171s api> pop.types<-xtabs(~stype, data=apipop) 171s 171s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 171s 171s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 171s 171s api> summary(dclus1p) 171s 1 - level Cluster Sampling design 171s With (15) clusters. 171s dclus1p<-postStratify(dclus1, ~stype, pop.types) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 171s Population size (PSUs): 757 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> summary(rclus1p) 171s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 171s Unstratified cluster jacknife (JK1) with 15 replicates and MSE variances. 171s Variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> svymean(~api00, dclus1p) 171s mean SE 171s api00 642.31 23.921 171s 171s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 171s total SE 171s enroll 3680893 406293 171s 171s api> svymean(~api00, rclus1p) 171s mean SE 171s api00 642.31 26.936 171s 171s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 171s total SE 171s enroll 3680893 473434 171s > 171s > options(survey.replicates.mse=FALSE) 171s > example(api) 171s 171s api> library(survey) 171s 171s api> data(api) 171s 171s api> mean(apipop$api00) 171s [1] 664.7126 171s 171s api> sum(apipop$enroll, na.rm=TRUE) 171s [1] 3811472 171s 171s api> #stratified sample 171s api> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 171s 171s api> summary(dstrat) 171s Stratified Independent Sampling design 171s dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.02262 0.02262 0.03587 0.04014 0.05339 0.06623 171s Stratum Sizes: 171s E H M 171s obs 100 50 50 171s design.PSU 100 50 50 171s actual.PSU 100 50 50 171s Population stratum sizes (PSUs): 171s E H M 171s 4421 755 1018 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "pw" "fpc" 171s 171s api> svymean(~api00, dstrat) 171s mean SE 171s api00 662.29 9.4089 171s 171s api> svytotal(~enroll, dstrat, na.rm=TRUE) 171s total SE 171s enroll 3687178 114642 171s 171s api> # one-stage cluster sample 171s api> dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 171s 171s api> summary(dclus1) 171s 1 - level Cluster Sampling design 171s With (15) clusters. 171s dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 171s Population size (PSUs): 757 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> svymean(~api00, dclus1) 171s mean SE 171s api00 644.17 23.542 171s 171s api> svytotal(~enroll, dclus1, na.rm=TRUE) 171s total SE 171s enroll 3404940 932235 171s 171s api> # two-stage cluster sample 171s api> dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 171s 171s api> summary(dclus2) 171s 2 - level Cluster Sampling design 171s With (40, 126) clusters. 171s dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 171s Population size (PSUs): 757 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "pw" "fpc1" "fpc2" 171s 171s api> svymean(~api00, dclus2) 171s mean SE 171s api00 670.81 30.099 171s 171s api> svytotal(~enroll, dclus2, na.rm=TRUE) 171s total SE 171s enroll 2639273 799638 171s 171s api> # two-stage `with replacement' 171s api> dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 171s 171s api> summary(dclus2wr) 171s 2 - level Cluster Sampling design (with replacement) 171s With (40, 126) clusters. 171s dclus2wr<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.003669 0.037743 0.052840 0.042390 0.052840 0.052840 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "pw" "fpc1" "fpc2" 171s 171s api> svymean(~api00, dclus2wr) 171s mean SE 171s api00 670.81 30.712 171s 171s api> svytotal(~enroll, dclus2wr, na.rm=TRUE) 171s total SE 171s enroll 2639273 820261 171s 171s api> # convert to replicate weights 171s api> rclus1<-as.svrepdesign(dclus1) 171s 171s api> summary(rclus1) 171s Call: as.svrepdesign.default(dclus1) 171s Unstratified cluster jacknife (JK1) with 15 replicates. 171s Variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> svymean(~api00, rclus1) 171s mean SE 171s api00 644.17 26.329 171s 171s api> svytotal(~enroll, rclus1, na.rm=TRUE) 171s total SE 171s enroll 3404940 932235 171s 171s api> # post-stratify on school type 171s api> pop.types<-xtabs(~stype, data=apipop) 171s 171s api> rclus1p<-postStratify(rclus1, ~stype, pop.types) 171s 171s api> dclus1p<-postStratify(dclus1, ~stype, pop.types) 171s 171s api> summary(dclus1p) 171s 1 - level Cluster Sampling design 171s With (15) clusters. 171s dclus1p<-postStratify(dclus1, ~stype, pop.types) 171s Probabilities: 171s Min. 1st Qu. Median Mean 3rd Qu. Max. 171s 0.01854 0.03257 0.03257 0.03040 0.03257 0.03257 171s Population size (PSUs): 757 171s Data variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> summary(rclus1p) 171s Call: rclus1p<-postStratify(rclus1, ~stype, pop.types) 171s Unstratified cluster jacknife (JK1) with 15 replicates. 171s Variables: 171s [1] "cds" "stype" "name" "sname" "snum" "dname" 171s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 171s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 171s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 171s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 171s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 171s [37] "api.stu" "fpc" "pw" 171s 171s api> svymean(~api00, dclus1p) 171s mean SE 171s api00 642.31 23.921 171s 171s api> svytotal(~enroll, dclus1p, na.rm=TRUE) 171s total SE 171s enroll 3680893 406293 171s 171s api> svymean(~api00, rclus1p) 171s mean SE 171s api00 642.31 26.934 171s 171s api> svytotal(~enroll, rclus1p, na.rm=TRUE) 171s total SE 171s enroll 3680893 473431 171s > 171s BEGIN TEST badcal.R 171s 171s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 171s Copyright (C) 2025 The R Foundation for Statistical Computing 171s Platform: x86_64-pc-linux-gnu 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > ## 171s > ## Calibration with badly-scaled initial weights (bug report by Takahiro Tsuchiya) 171s > ## 171s > library(survey) 171s Loading required package: grid 171s Loading required package: Matrix 171s Loading required package: survival 171s 171s Attaching package: 'survey' 171s 171s The following object is masked from 'package:graphics': 171s 171s dotchart 171s 171s > data <- data.frame(x=c(1,1,1,1,2,2,2,2,2,2), w=rep(10,10)) 171s > des <- svydesign(ids=~1, weights=~w, data=data) 171s > des.c <- calibrate(des, ~factor(x), c(10000, 5000)) 171s > des.r <- calibrate(des, ~factor(x), c(10000, 5000), calfun='raking') 172s > stopifnot(all.equal(svytotal(~factor(x), des.c), svytotal(~factor(x), des.r))) 172s > 172s BEGIN TEST brewer_cpp.R 172s 172s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > ## pps="brewer" can't use rcpp 172s > ## this checks that it doesn't 172s > library(survey) 172s Loading required package: grid 172s Loading required package: Matrix 172s Loading required package: survival 172s 172s Attaching package: 'survey' 172s 172s The following object is masked from 'package:graphics': 172s 172s dotchart 172s 172s > data(election) 172s > 172s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 172s > options(survey.use_rcpp=TRUE) 172s > a<-svytotal(~Bush+Kerry+Nader, dpps_br) 172s > options(survey.use_rcpp=FALSE) 172s > b<-svytotal(~Bush+Kerry+Nader, dpps_br) 172s > 172s > stopifnot(identical(a,b)) 172s > 172s BEGIN TEST bycovmat.R 172s 172s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s Loading required package: grid 172s Loading required package: Matrix 172s > 172s > library(survey) 173s Loading required package: survival 173s 173s Attaching package: 'survey' 173s 173s The following object is masked from 'package:graphics': 173s 173s dotchart 173s 173s > data(api) 173s > options(survey.replicates.mse=TRUE) 173s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 173s > rclus1<-as.svrepdesign(dclus1) 173s > 173s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 173s + covmat=TRUE,drop.empty.groups=FALSE) 173s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 173s + covmat=TRUE,drop.empty.groups=TRUE) 173s > 173s > stopifnot(all.equal( 173s + as.vector(as.matrix(SE(a))),as.vector(sqrt(diag(vcov(a)))) 173s + )) 173s > stopifnot(all.equal( 173s + as.vector(as.matrix(SE(b))),as.vector(sqrt(diag(vcov(b)))) 173s + )) 173s > 173s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 173s > all <- svytotal(~ell+mobility+meals, dclus1) 173s > 173s > stopifnot(all(abs(vcov(svycontrast(all, 173s + list(quote(ell/mobility), 173s + quote(mobility/mobility), 173s + quote(ell/meals),quote(mobility/meals)))) 173s + -vcov(rat))<1e-10)) 173s > 173s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 173s > 173s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 173s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 173s > 173s > con<-svycontrast(all, 173s + list(quote(ell/mobility), 173s + quote(mobility/mobility), 173s + quote(ell/meals),quote(mobility/meals))) 173s > 173s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 173s > 173s > options(survey.replicates.mse=FALSE) 173s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 173s > rclus1<-as.svrepdesign(dclus1) 173s > 173s > a<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 173s + covmat=TRUE,drop.empty.groups=FALSE) 173s > b<-svyby(~api00+api99, ~comp.imp+sch.wide,design=rclus1,svymean, 173s + covmat=TRUE,drop.empty.groups=TRUE) 173s > 173s > stopifnot(all.equal( 173s + as.vector(as.matrix(SE(a))), as.vector(sqrt(diag(vcov(a)))) 173s + )) 173s > stopifnot(all.equal( 173s + as.vector(as.matrix(SE(b))), as.vector(sqrt(diag(vcov(b)))) 173s + )) 173s > 173s > rat <- svyratio(~ell+mobility, ~mobility+meals, dclus1,covmat=TRUE) 173s > all <- svytotal(~ell+mobility+meals, dclus1) 173s > 173s > stopifnot(all(abs(vcov(svycontrast(all, 173s + list(quote(ell/mobility), 173s + quote(mobility/mobility), 173s + quote(ell/meals),quote(mobility/meals)))) 173s + -vcov(rat))<1e-10)) 173s > 173s > stopifnot(all(abs(SE(rat)-sqrt(diag(vcov(rat))))<1e-10)) 173s > 173s > rat <- svyratio(~ell+mobility, ~mobility+meals, rclus1,covmat=TRUE) 173s > all <- svytotal(~ell+mobility+meals, rclus1, return.replicates=TRUE) 173s > 173s > con<-svycontrast(all, 173s + list(quote(ell/mobility), 173s + quote(mobility/mobility), 173s + quote(ell/meals),quote(mobility/meals))) 173s > 173s > stopifnot(all(abs(survey:::svrVar(con$replicates, rclus1$scale,rclus1$rscales,mse=rclus1$mse, coef=coef(con))-vcov(rat))<1e-10)) 173s > 173s > 173s > 173s BEGIN TEST caleg.R 173s 173s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 173s Copyright (C) 2025 The R Foundation for Statistical Computing 173s Platform: x86_64-pc-linux-gnu 173s 173s R is free software and comes with ABSOLUTELY NO WARRANTY. 173s You are welcome to redistribute it under certain conditions. 173s Type 'license()' or 'licence()' for distribution details. 173s 173s R is a collaborative project with many contributors. 173s Type 'contributors()' for more information and 173s 'citation()' on how to cite R or R packages in publications. 173s 173s Type 'demo()' for some demos, 'help()' for on-line help, or 173s 'help.start()' for an HTML browser interface to help. 173s Type 'q()' to quit R. 173s 173s > ## 173s > ## Calibration examples 173s Loading required package: grid 173s > ## 173s > 173s > 173s > ## Example of calibration to first-stage clusters 173s > library(survey) 173s Loading required package: Matrix 174s Loading required package: survival 174s 174s Attaching package: 'survey' 174s 174s The following object is masked from 'package:graphics': 174s 174s dotchart 174s 174s > data(api) 174s > 174s > clusters<-table(apiclus2$dnum) 174s > clusters<-clusters[clusters>1 & names(clusters)!="639"] 174s > apiclus2a<-subset(apiclus2, dnum %in% as.numeric(names(clusters))) 174s > 174s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2a) 174s > 174s > popclusters<-subset(apipop, dnum %in% as.numeric(names(clusters))) 174s > 174s > pop<-lapply(as.numeric(names(clusters)), function(cluster) { 174s + colSums(model.matrix(~api99, model.frame(~api99, subset(popclusters, dnum %in% cluster))))}) 174s > 174s > names(pop)<-names(clusters) 174s > 174s > dclus2g<-calibrate(dclus2, ~api99, pop,stage=1) 174s > 174s > svymean(~api99, dclus2) 174s mean SE 174s api99 642.14 31.434 174s > svymean(~api99, dclus2g) 174s mean SE 174s api99 654.49 29.82 174s > 174s > round(svyby(~api99, ~dnum, design=dclus2, svymean),4) 174s dnum api99 se 174s 83 83 694.3333 0.0000 174s 132 132 505.0000 0.0000 174s 152 152 574.0000 0.0000 174s 173 173 894.7500 0.0000 174s 198 198 533.7500 0.0000 174s 200 200 589.8000 6.8335 174s 228 228 477.0000 0.0000 174s 295 295 646.4000 0.0000 174s 302 302 903.5000 0.0000 174s 403 403 852.4000 0.0000 174s 452 452 533.0000 0.0000 174s 480 480 614.2000 0.0000 174s 523 523 580.5000 0.0000 174s 534 534 564.6000 0.0000 174s 549 549 896.2000 0.0000 174s 552 552 730.0000 0.0000 174s 570 570 518.4000 7.5478 174s 575 575 800.8000 4.2513 174s 596 596 785.6000 2.4155 174s 620 620 591.6000 10.5869 174s 638 638 560.2000 4.0954 174s 674 674 760.0000 0.0000 174s 679 679 610.2500 0.0000 174s 687 687 718.6667 0.0000 174s 701 701 651.5000 0.0000 174s 711 711 690.5000 0.0000 174s 731 731 702.0000 2.1744 174s 768 768 562.5000 0.0000 174s 781 781 854.4000 0.7456 174s > 174s > round(svyby(~api99, ~dnum, design=dclus2g, svymean),4) 174s dnum api99 se 174s 83 83 694.3333 0 174s 132 132 505.0000 0 174s 152 152 574.0000 0 174s 173 173 894.7500 0 174s 198 198 533.7500 0 174s 200 200 567.5455 0 174s 228 228 477.0000 0 174s 295 295 646.4000 0 174s 302 302 903.5000 0 174s 403 403 852.4000 0 174s 452 452 533.0000 0 174s 480 480 614.2000 0 174s 523 523 580.5000 0 174s 534 534 564.6000 0 174s 549 549 896.2000 0 174s 552 552 730.0000 0 174s 570 570 548.9444 0 174s 575 575 824.5357 0 174s 596 596 787.5714 0 174s 620 620 609.3750 0 174s 638 638 585.6429 0 174s 674 674 760.0000 0 174s 679 679 610.2500 0 174s 687 687 718.6667 0 174s 701 701 651.5000 0 174s 711 711 690.5000 0 174s 731 731 700.6667 0 174s 768 768 562.5000 0 174s 781 781 851.0000 0 174s > 174s > ## Averaging to first stage 174s > 174s > dclus1<- svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 174s > pop<-colSums(cbind(1,apipop$enroll),na.rm=TRUE) 174s > 174s > dclus1g<-calibrate(dclus1, ~enroll, pop, aggregate=1) 174s > 174s > svytotal(~enroll,dclus1g) 174s total SE 174s enroll 3811472 0 174s > svytotal(~api.stu,dclus1g) 174s total SE 174s api.stu 3242857 38967 174s > 174s > #variation within clusters should be zero 174s > all.equal(0, max(ave(weights(dclus1g),dclus1g$cluster,FUN=var),na.rm=TRUE)) 174s [1] TRUE 174s > 174s > ##bounded weights 174s > dclus1g<-calibrate(dclus1, ~enroll, pop) 174s > range(weights(dclus1g)/weights(dclus1)) 174s [1] 0.7906782 1.7891164 174s > dclus1gb<-calibrate(dclus1, ~enroll, pop, bounds=c(.6,1.5)) 174s > range(weights(dclus1gb)/weights(dclus1)) 174s [1] 0.7198751 1.5000000 174s > 174s > ## Ratio estimators 174s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 174s > svytotal(~api.stu,dstrat) 174s total SE 174s api.stu 3086009 99477 174s > common<-svyratio(~api.stu, ~enroll, dstrat, separate=FALSE) 174s > total.enroll<-sum(apipop$enroll,na.rm=TRUE) 174s > predict(common, total=total.enroll) 174s $total 174s enroll 174s api.stu 3190038 174s 174s $se 174s enroll 174s api.stu 29565.98 174s 174s > dstratg<-calibrate(dstrat,~enroll-1, total.enroll, variance=1) 174s > svytotal(~api.stu, dstratg) 174s total SE 174s api.stu 3190038 29566 174s > 174s > ## postStratify vs calibrate in stratified sample (Ben French) 174s > set.seed(17) 174s > dat<-data.frame(y=rep(0:1,each=100),x=rnorm(200)+2*rep(0:1,each=100), 174s + z=rbinom(200,1,.2), fpc=rep(c(100,10000),each=100)) 174s > dat$w<-ifelse(dat$y,dat$z,1-dat$z) 174s > popw<-data.frame(w=c("0","1"), Freq=c(2000,8000)) 174s > des<-svydesign(id=~1,fpc=~fpc, data=dat,strata=~y) 174s > postStratify(des,~w,popw)->dps 174s > dcal<-calibrate(des,~factor(w), pop=c(10000,8000)) 174s > 174s > all.equal(SE(svymean(~x,dcal)),SE(svymean(~x,dps))) 174s [1] TRUE 174s > 174s > ## missing data in calibrated design 174s > dps$variables$z[1]<-NA 174s > summary(svyglm(y~z+x,design=dps,family=quasibinomial)) 174s 174s Call: 174s svyglm(formula = y ~ z + x, design = dps, family = quasibinomial) 174s 174s Survey design: 174s postStratify(des, ~w, popw) 174s 174s Coefficients: 174s Estimate Std. Error t value Pr(>|t|) 174s (Intercept) -0.1203 0.3380 -0.356 0.722 174s z 6.2118 0.6451 9.630 <2e-16 *** 174s x 2.2602 0.2514 8.992 <2e-16 *** 174s --- 174s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 174s 174s (Dispersion parameter for quasibinomial family taken to be 1.919987) 174s 174s Number of Fisher Scoring iterations: 9 174s 174s > 174s > ## Ratio estimator using the heteroskedasticity parameter (Daniel Oehm) 174s > # should match the ratio estmate above 174s > dstratgh <- calibrate(dstrat,~enroll-1, total.enroll, variance=apistrat$enroll) 174s > svytotal(~api.stu, dstratgh) 174s total SE 174s api.stu 3190038 29566 174s > 174s > ## individual boundary constraints as multiplicative values (Daniel Oehm) 174s > bnds <- list( 174s + lower = c(1, 1, rep(-Inf, nrow(apistrat)-2)), 174s + upper = c(1, 1, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged the others are free to move 174s > lapply(bnds, head) 174s $lower 174s [1] 1 1 -Inf -Inf -Inf -Inf 174s 174s $upper 174s [1] 1 1 Inf Inf Inf Inf 174s 174s > dstratg1<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, variance=apistrat$enroll) 174s > svytotal(~api.stu, dstratg1) 174s total SE 174s api.stu 3190133 29561 174s > head(weights(dstrat)) 174s 1 2 3 4 5 6 174s 44.21 44.21 44.21 44.21 44.21 44.21 174s > head(weights(dstratg1)) 174s 1 2 3 4 5 6 174s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 174s > all.equal(weights(dstrat)[1:2], weights(dstratg1)[1:2]) 174s [1] TRUE 174s > 174s > ## individual boundary constraints as constant values (Daniel Oehm) 174s > bnds <- list( 174s + lower = c(44.21, 44.21, rep(-Inf, nrow(apistrat)-2)), 174s + upper = c(44.21, 44.21, rep(Inf, nrow(apistrat)-2))) # the first two weights will remain unchanged 174s > lapply(bnds, head) 174s $lower 174s [1] 44.21 44.21 -Inf -Inf -Inf -Inf 174s 174s $upper 174s [1] 44.21 44.21 Inf Inf Inf Inf 174s 174s > dstratg2<-calibrate(dstrat, ~enroll-1, total.enroll, bounds = bnds, bounds.const = TRUE, variance=apistrat$enroll) 174s > svytotal(~api.stu, dstratg2) 174s total SE 174s api.stu 3190133 29561 174s > head(weights(dstrat)) 174s 1 2 3 4 5 6 174s 44.21 44.21 44.21 44.21 44.21 44.21 174s > head(weights(dstratg2)) 174s 1 2 3 4 5 6 174s 44.21000 44.21000 45.72055 45.72055 45.72055 45.72055 174s > all.equal(round(weights(dstrat)[1:2], 8), round(weights(dstratg2)[1:2]), 8) # minor rounding error but all good 174s [1] TRUE 174s > 174s > # sparse matrix support (Daniel Oehm) 174s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 174s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 174s > dclus1g<-calibrate(dclus1, ~stype, pop.totals) 174s > svymean(~api00, dclus1g) 174s mean SE 174s api00 642.31 23.921 174s > svytotal(~enroll, dclus1g) 174s total SE 174s enroll 3680893 406293 174s > 174s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 174s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE) 174s > svymean(~api00, dclus1g) 174s mean SE 174s api00 642.31 23.921 174s > svytotal(~enroll, dclus1g) 174s total SE 174s enroll 3680893 406293 174s > 174s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 174s > dclus1g<-calibrate(dclus1, ~stype, pop.totals, sparse = TRUE, calfun = "raking") 174s > svymean(~api00, dclus1g) 174s mean SE 174s api00 642.31 23.921 174s > svytotal(~enroll, dclus1g) 174s total SE 174s enroll 3680893 406293 174s > 174s BEGIN TEST check.R 174s 174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 174s Copyright (C) 2025 The R Foundation for Statistical Computing 174s Platform: x86_64-pc-linux-gnu 174s 174s R is free software and comes with ABSOLUTELY NO WARRANTY. 174s You are welcome to redistribute it under certain conditions. 174s Type 'license()' or 'licence()' for distribution details. 174s 174s R is a collaborative project with many contributors. 174s Type 'contributors()' for more information and 174s 'citation()' on how to cite R or R packages in publications. 174s 174s Type 'demo()' for some demos, 'help()' for on-line help, or 174s 'help.start()' for an HTML browser interface to help. 174s Type 'q()' to quit R. 174s 175s > library(survey) 175s Loading required package: grid 175s Loading required package: Matrix 175s Loading required package: survival 175s > data(fpc) 175s 175s Attaching package: 'survey' 175s 175s The following object is masked from 'package:graphics': 175s 175s dotchart 175s 175s > ## test various possibilities for svydesign 175s > a<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(weights = ~weight, ids = ~psuid, strata = ~stratid, 175s variables = ~x, data = fpc, nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7413 175s > a<-svydesign(weights=~weight, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(weights = ~weight, ids = ~0, strata = ~stratid, variables = ~x, 175s data = fpc, nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7413 175s > a<-svydesign(weights=1, ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(weights = 1, ids = ~0, strata = ~stratid, variables = ~x, 175s data = fpc, nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 44.2 6.237 175s > a<-svydesign(ids=~0, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(ids = ~0, strata = ~stratid, variables = ~x, data = fpc, 175s nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.525 0.7796 175s > a<-svydesign(ids=~0, strata=~stratid, prob=~I(1/weight),variables=~x, data=fpc, nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(ids = ~0, strata = ~stratid, prob = ~I(1/weight), variables = ~x, 175s data = fpc, nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7413 175s > a<-svydesign(ids=~psuid, strata=~stratid, variables=~x, data=fpc, nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(ids = ~psuid, strata = ~stratid, variables = ~x, data = fpc, 175s nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.525 0.7796 175s > a<-svydesign(ids=~psuid, variables=~x, data=fpc, nest=TRUE) 175s > a 175s 1 - level Cluster Sampling design (with replacement) 175s With (5) clusters. 175s svydesign(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.525 0.838 175s > a<-svydesign(ids=~psuid, weights=~weight, variables=~x, data=fpc, nest=TRUE) 175s > a 175s 1 - level Cluster Sampling design (with replacement) 175s With (5) clusters. 175s svydesign(ids = ~psuid, weights = ~weight, variables = ~x, data = fpc, 175s nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7938 175s > a<-svydesign(ids=~stratid+psuid, weights=~weight, variables=~x, data=fpc) 175s > a 175s 2 - level Cluster Sampling design (with replacement) 175s With (2, 8) clusters. 175s svydesign(ids = ~stratid + psuid, weights = ~weight, variables = ~x, 175s data = fpc) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.5465 175s > a<-svydesign(ids=~stratid+psuid, variables=~x, data=fpc) 175s > a 175s 2 - level Cluster Sampling design (with replacement) 175s With (2, 8) clusters. 175s svydesign(ids = ~stratid + psuid, variables = ~x, data = fpc) 175s > svymean(~x,a) 175s Warning message: 175s In svydesign.default(ids = ~0, strata = ~stratid, variables = ~x, : 175s No weights or probabilities supplied, assuming equal probability 175s Warning message: 175s In svydesign.default(ids = ~psuid, strata = ~stratid, variables = ~x, : 175s No weights or probabilities supplied, assuming equal probability 175s Warning message: 175s In svydesign.default(ids = ~psuid, variables = ~x, data = fpc, nest = TRUE) : 175s No weights or probabilities supplied, assuming equal probability 175s Warning message: 175s In svydesign.default(ids = ~stratid + psuid, variables = ~x, data = fpc) : 175s No weights or probabilities supplied, assuming equal probability 175s mean SE 175s x 5.525 0.5188 175s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,"x",drop=FALSE], nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 175s variables = fpc[, "x", drop = FALSE], nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7413 175s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, variables=fpc[,4:6], nest=TRUE) 175s > a 175s Stratified Independent Sampling design (with replacement) 175s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 175s variables = fpc[, 4:6], nest = TRUE) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7413 175s > 175s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, variables=fpc[,4:6], fpc=rep(27,8)) 175s > a 175s 1 - level Cluster Sampling design 175s With (5) clusters. 175s svydesign(weights = fpc$weight, ids = fpc$psuid, variables = fpc[, 175s 4:6], fpc = rep(27, 8)) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.7165 175s > 175s > a<-svydesign(weights=fpc$weight, ids=fpc$psuid, strata=fpc$stratid, nest=TRUE, variables=fpc[,4:6], fpc=fpc$Nh) 175s > a 175s Stratified Independent Sampling design 175s svydesign(weights = fpc$weight, ids = fpc$psuid, strata = fpc$stratid, 175s nest = TRUE, variables = fpc[, 4:6], fpc = fpc$Nh) 175s > svymean(~x,a) 175s mean SE 175s x 5.4481 0.616 175s > 175s BEGIN TEST confintrep.R 175s 175s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 175s Copyright (C) 2025 The R Foundation for Statistical Computing 175s Platform: x86_64-pc-linux-gnu 175s 175s R is free software and comes with ABSOLUTELY NO WARRANTY. 175s You are welcome to redistribute it under certain conditions. 175s Type 'license()' or 'licence()' for distribution details. 175s 175s R is a collaborative project with many contributors. 175s Type 'contributors()' for more information and 175s 'citation()' on how to cite R or R packages in publications. 175s 175s Type 'demo()' for some demos, 'help()' for on-line help, or 175s 'help.start()' for an HTML browser interface to help. 175s Type 'q()' to quit R. 175s 175s > library(survey) 175s Loading required package: grid 175s Loading required package: Matrix 176s Loading required package: survival 176s > data(api) 176s 176s Attaching package: 'survey' 176s 176s The following object is masked from 'package:graphics': 176s 176s dotchart 176s 176s > dclus2<-svydesign(id=~dnum+snum, fpc=~fpc1+fpc2, data=apiclus2) 176s > rclus2<-as.svrepdesign(dclus2) 176s Warning message: 176s In as.svrepdesign.default(dclus2) : 176s Finite population corrections after first stage have been dropped 176s > 176s > m<-svyglm(I(comp.imp=="Yes")~1, design=dclus2, family=quasibinomial) 176s > if(anyNA(confint(m, method="likelihood"))) stop("NA in confint") 176s > mrep<-svyglm(I(comp.imp=="Yes")~1, design=rclus2, family=quasibinomial) 176s > if(anyNA(confint(mrep))) stop("NA in confint") 176s > if(anyNA(confint(mrep, method="likelihood"))) stop("NA in confint") 176s > 176s BEGIN TEST contrast-replicates.R 176s 176s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 176s Copyright (C) 2025 The R Foundation for Statistical Computing 176s Platform: x86_64-pc-linux-gnu 176s 176s R is free software and comes with ABSOLUTELY NO WARRANTY. 176s You are welcome to redistribute it under certain conditions. 176s Type 'license()' or 'licence()' for distribution details. 176s 176s R is a collaborative project with many contributors. 176s Type 'contributors()' for more information and 176s 'citation()' on how to cite R or R packages in publications. 176s 176s Type 'demo()' for some demos, 'help()' for on-line help, or 176s 'help.start()' for an HTML browser interface to help. 176s Type 'q()' to quit R. 176s 176s > ## test use of replicates in svyby, svycontrast 176s > library(survey) 176s Loading required package: grid 176s Loading required package: Matrix 177s Loading required package: survival 177s 177s Attaching package: 'survey' 177s 177s > 177s > data(api) 177s The following object is masked from 'package:graphics': 177s 177s dotchart 177s 177s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 177s > rclus1<-as.svrepdesign(dclus1) 177s > 177s > meanlogs_without<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE) 177s > c_without<-svycontrast(meanlogs_without, quote(exp(E-H))) 177s > vcov(c_without) 177s contrast 177s contrast 0.06862947 177s > 177s > meanlogs_with<-svyby(~log(enroll),~stype,svymean, design=rclus1,covmat=TRUE,return.replicates=TRUE) 177s > 177s > c_with<-svycontrast(meanlogs_with, quote(exp(E-H))) 177s > 177s > v_with<- vcov(rclus1, c_with$replicates) 177s > 177s > r<- attr(meanlogs_with, "replicates") 177s > vr_with<-vcov(rclus1,exp(r[,1]-r[,2])) 177s > 177s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vr_with))) 177s > stopifnot(all.equal(as.numeric(v_with),as.numeric(vcov(c_with)))) 177s > 177s BEGIN TEST coxph-termtest.R 177s 177s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 177s Copyright (C) 2025 The R Foundation for Statistical Computing 177s Platform: x86_64-pc-linux-gnu 177s 177s R is free software and comes with ABSOLUTELY NO WARRANTY. 177s You are welcome to redistribute it under certain conditions. 177s Type 'license()' or 'licence()' for distribution details. 177s 177s R is a collaborative project with many contributors. 177s Type 'contributors()' for more information and 177s 'citation()' on how to cite R or R packages in publications. 177s 177s Type 'demo()' for some demos, 'help()' for on-line help, or 177s 'help.start()' for an HTML browser interface to help. 177s Type 'q()' to quit R. 177s 177s > library(survey) 177s Loading required package: grid 177s Loading required package: Matrix 178s Loading required package: survival 178s 178s Attaching package: 'survey' 178s 178s > library(survival) 178s > set.seed(2021-6-25) 178s The following object is masked from 'package:graphics': 178s 178s dotchart 178s 178s > test1 <- list(time=c(4,3,1,1,2,2,3), 178s + status=c(1,1,1,0,1,1,0), 178s + x1=as.factor(rbinom(7, 2, 0.5)), 178s + x=c(0,2,1,1,1,0,0)) 178s > # Fit a stratified model 178s > mod_c <- coxph(Surv(time, status) ~ x1 + x, test1) 178s > mod_d <- coxph(Surv(time, status) ~ x + x1, test1) 178s > stopifnot(all.equal(regTermTest(mod_c, ~x1, df = Inf)[c("chisq","df","test.terms","p")], 178s + regTermTest(mod_d, ~x1, df = Inf)[c("chisq","df","test.terms","p")])) 178s > 178s > data(pbc, package="survival") 178s > 178s > pbc$randomized<-with(pbc, !is.na(trt) & trt>0) 178s > biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial) 178s > pbc$randprob<-fitted(biasmodel) 178s > if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0 178s > 178s > dpbc<-svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized)) 178s > library(splines) 178s > model<-svycoxph(formula = Surv(time, status > 0) ~ bili + protime + albumin+ns(bili,4)[,1:3], design = dpbc) 178s > test<-regTermTest(model, ~ns(bili,4)[,1:3],method="LRT") 178s > stopifnot(all.equal(test$chisq, 47.314, tolerance=1e-4)) 178s > stopifnot(all.equal(test$lambda, c(1.4764260, 1.0109836, 0.6923415),tolerance=1e-4)) 178s > 178s BEGIN TEST deff.R 178s 178s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 178s Copyright (C) 2025 The R Foundation for Statistical Computing 178s Platform: x86_64-pc-linux-gnu 178s 178s R is free software and comes with ABSOLUTELY NO WARRANTY. 178s You are welcome to redistribute it under certain conditions. 178s Type 'license()' or 'licence()' for distribution details. 178s 178s R is a collaborative project with many contributors. 178s Type 'contributors()' for more information and 178s 'citation()' on how to cite R or R packages in publications. 178s 178s Type 'demo()' for some demos, 'help()' for on-line help, or 178s 'help.start()' for an HTML browser interface to help. 178s Type 'q()' to quit R. 178s 178s Loading required package: grid 178s > ## from Takahiro Tsuchiya 178s > library(survey) 178s Loading required package: Matrix 178s Loading required package: survival 178s 178s Attaching package: 'survey' 178s 178s > kigyo<-read.table(tmp<-textConnection(" obs uriage srs.w pps.w 178s + 1 1 15 100 20 178s + 2 2 143 100 200 178s + 3 3 21 100 11 178s + 4 4 51 100 25 178s + 5 5 337 100 550 178s + 6 6 50 100 30 178s + 7 7 274 100 250 178s + 8 8 145 100 100 178s + 9 9 15 100 10 178s + The following object is masked from 'package:graphics': 178s 178s dotchart 178s 178s 10 10 86 100 55 178s + ",open="r"),header=TRUE) 178s > close(tmp) 178s > des.srs <- svydesign(ids=~1, weights=~srs.w, data=kigyo) 178s > (res.srs <- svymean(~uriage, des.srs, deff=TRUE)) 178s mean SE DEff 178s uriage 113.700 35.626 1.0101 178s > (SE(res.srs)^2) / ((1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 178s uriage 178s uriage 1.010101 178s > 178s > (tres.srs <- svytotal(~uriage, des.srs, deff=TRUE)) 179s total SE DEff 179s uriage 113700 35626 1.0101 179s > (SE(tres.srs)^2) / (1000^2 * (1-10/1000) * coef(svyvar(~uriage, des.srs)) / 10) 179s uriage 179s uriage 1.010101 179s > 179s > 179s > des.pps <- svydesign(ids=~1, weights=~pps.w, data=kigyo) 179s > (res.pps <- svymean(~uriage, des.pps, deff='replace')) 179s mean SE DEff 179s uriage 243.914 48.752 1.9741 179s > (SE(res.pps)^2) / (coef(svyvar(~uriage, des.pps)) / 10) 179s uriage 179s uriage 1.974067 179s > (tres.pps <- svytotal(~uriage, des.pps, deff='replace')) 179s total SE DEff 179s uriage 305136 184965 18.157 179s > (N.hat <- sum(weights(des.pps))) 179s [1] 1251 179s > (SE(tres.pps)^2) / (N.hat^2 * coef(svyvar(~uriage, des.pps)) / 10) 179s uriage 179s uriage 18.15669 179s > 179s BEGIN TEST defftest.R 179s 179s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 179s Copyright (C) 2025 The R Foundation for Statistical Computing 179s Platform: x86_64-pc-linux-gnu 179s 179s R is free software and comes with ABSOLUTELY NO WARRANTY. 179s You are welcome to redistribute it under certain conditions. 179s Type 'license()' or 'licence()' for distribution details. 179s 179s R is a collaborative project with many contributors. 179s Type 'contributors()' for more information and 179s 'citation()' on how to cite R or R packages in publications. 179s 179s Type 'demo()' for some demos, 'help()' for on-line help, or 179s 'help.start()' for an HTML browser interface to help. 179s Type 'q()' to quit R. 179s 179s > library(survey) 179s Loading required package: grid 179s Loading required package: Matrix 179s Loading required package: survival 179s > 179s > data(api) 179s 179s Attaching package: 'survey' 179s 179s The following object is masked from 'package:graphics': 179s 179s dotchart 179s 179s > 179s > ## one-stage cluster sample 179s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 179s > 179s > # svyglm model 179s > mod <- svyglm(api99 ~ enroll + api.stu, design = dclus1, deff = TRUE) 179s > 179s > #deffs returned from svyglm model - implausibly high 179s > deff(mod) 179s (Intercept) enroll api.stu 179s 1.919945 2.500983 2.686102 179s > #> (Intercept) enroll api.stu 179s > #> 351.3500 457.6799 491.5567 179s > 179s > # run mod with same data and glm() 179s > srs_mod <- glm(api99 ~ enroll + api.stu, data = apiclus1) 179s > 179s > # manually calculate deffs 179s > 179s > clust_se <- summary(mod)$coefficients[,2] 179s > srs_se <- summary(srs_mod)$coefficients[,2] 179s > 179s > deffs <- clust_se^2 / srs_se^2 179s > stopifnot(all.equal(deffs, deff(mod))) 179s > 179s > 179s BEGIN TEST degf-svrepdesign.R 179s 179s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 179s Copyright (C) 2025 The R Foundation for Statistical Computing 179s Platform: x86_64-pc-linux-gnu 179s 179s R is free software and comes with ABSOLUTELY NO WARRANTY. 179s You are welcome to redistribute it under certain conditions. 179s Type 'license()' or 'licence()' for distribution details. 179s 179s R is a collaborative project with many contributors. 179s Type 'contributors()' for more information and 179s 'citation()' on how to cite R or R packages in publications. 179s 179s Type 'demo()' for some demos, 'help()' for on-line help, or 179s 'help.start()' for an HTML browser interface to help. 179s Type 'q()' to quit R. 179s 179s > library(survey) 179s Loading required package: grid 179s Loading required package: Matrix 180s Loading required package: survival 180s 180s Attaching package: 'survey' 180s 180s The following object is masked from 'package:graphics': 180s 180s dotchart 180s 180s > data(scd) 180s > 180s > repweights<-2*cbind(c(1,0,1,0,1,0), c(1,0,0,1,0,1), c(0,1,1,0,0,1), 180s + c(0,1,0,1,1,0)) 180s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights) 180s > 180s > stopifnot(degf(scdrep)==3) 180s > 180s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=4) 180s Warning message: 180s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights) : 180s No sampling weights provided: equal probability assumed 180s > stopifnot(degf(scdrep)==4) 180s > 180s > scdrep<-svrepdesign(data=scd, type="BRR", repweights=repweights, degf=2) 180s > stopifnot(degf(scdrep)==2) 180s > 180s > msg<-tryCatch(scdrep<-svrepdesign(data=scd, type="BRR",weights=~I(1000+0*ESA), repweights=repweights, combined.weights=FALSE,degf=10), 180s + warning=function(w) w) 180s > 180s > stopifnot(inherits(msg,"warning")) 180s > 180s > 180s > 180s > 180s BEGIN TEST domain.R 180s Warning message: 180s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 180s No sampling weights provided: equal probability assumed 180s Warning message: 180s In svrepdesign.default(data = scd, type = "BRR", repweights = repweights, : 180s No sampling weights provided: equal probability assumed 180s 180s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 180s Copyright (C) 2025 The R Foundation for Statistical Computing 180s Platform: x86_64-pc-linux-gnu 180s 180s R is free software and comes with ABSOLUTELY NO WARRANTY. 180s You are welcome to redistribute it under certain conditions. 180s Type 'license()' or 'licence()' for distribution details. 180s 180s R is a collaborative project with many contributors. 180s Type 'contributors()' for more information and 180s 'citation()' on how to cite R or R packages in publications. 180s 180s Type 'demo()' for some demos, 'help()' for on-line help, or 180s 'help.start()' for an HTML browser interface to help. 180s Type 'q()' to quit R. 180s 180s > ## 180s > ## Domain means can be written as ratio estimators or as regression coefficients 180s > ## 180s > ## This code checks that subsetting the design object gives the same results as 180s > ## these approaches. 180s > ## 180s > 180s > 180s > library(survey) 180s Loading required package: grid 180s Loading required package: Matrix 181s Loading required package: survival 181s 181s Attaching package: 'survey' 181s 181s > data(fpc) 181s The following object is masked from 'package:graphics': 181s 181s dotchart 181s 181s > dfpc<-svydesign(id=~psuid,strat=~stratid,weight=~weight,data=fpc,nest=TRUE) 181s > dsub<-subset(dfpc,x>4) 181s > (m1<-svymean(~x,design=dsub)) 181s mean SE 181s x 6.195 0.7555 181s > 181s > ## These should give the same domain estimates and standard errors 181s > (m2<-svyby(~x,~I(x>4),design=dfpc, svymean,keep.var=TRUE)) 181s I(x > 4) x se 181s FALSE FALSE 3.314286 0.3117042 181s TRUE TRUE 6.195000 0.7555129 181s > m3<-svyglm(x~I(x>4)+0,design=dfpc) 181s > summary(m3) 181s 181s Call: 181s svyglm(formula = x ~ I(x > 4) + 0, design = dfpc) 181s 181s Survey design: 181s svydesign(id = ~psuid, strat = ~stratid, weight = ~weight, data = fpc, 181s nest = TRUE) 181s 181s Coefficients: 181s Estimate Std. Error t value Pr(>|t|) 181s I(x > 4)FALSE 3.3143 0.3117 10.63 0.000127 *** 181s I(x > 4)TRUE 6.1950 0.7555 8.20 0.000439 *** 181s --- 181s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 181s 181s (Dispersion parameter for gaussian family taken to be 2.557379) 181s 181s Number of Fisher Scoring iterations: 2 181s 181s > (m4<-svyratio(~I(x*(x>4)),~as.numeric(x>4), dfpc)) 181s Ratio estimator: svyratio.survey.design2(~I(x * (x > 4)), ~as.numeric(x > 4), 181s dfpc) 181s Ratios= 181s as.numeric(x > 4) 181s I(x * (x > 4)) 6.195 181s SEs= 181s as.numeric(x > 4) 181s I(x * (x > 4)) 0.7555129 181s > stopifnot(isTRUE(all.equal(SE(m2), as.vector(SE(m3))))) 181s > stopifnot(isTRUE(all.equal(SE(m2)[2], as.vector(SE(m4))))) 181s > 181s > ## with strata 181s > data(api) 181s > dstrat<-svydesign(id=~1, strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 181s > m1<-svymean(~enroll, subset(dstrat, comp.imp=="Yes")) 181s > m2<-svyglm(enroll~comp.imp-1, dstrat) 181s > m3<- svyratio(~I(enroll*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dstrat) 181s > stopifnot(isTRUE(all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 181s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 181s > 181s > ## with calibration 181s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 181s > pop.totals<-c(`(Intercept)`=6194, stypeH=755, stypeM=1018) 181s > (dclus1g3 <- calibrate(dclus1, ~stype+api99, c(pop.totals, api99=3914069))) 181s 1 - level Cluster Sampling design 181s With (15) clusters. 181s calibrate(dclus1, ~stype + api99, c(pop.totals, api99 = 3914069)) 181s > 181s > m1<-svymean(~api00, subset(dclus1g3, comp.imp=="Yes")) 181s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1g3) 181s > m2<-svyglm(api00~comp.imp-1, dclus1g3) 181s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 181s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 181s > 181s > ## with raking 181s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 181s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 181s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 181s > m1<-svymean(~api00, subset(dclus1r, comp.imp=="Yes")) 181s > m2<-svyglm(api00~comp.imp-1, dclus1r) 181s > m3<-svyratio(~I(api00*(comp.imp=="Yes")), ~as.numeric(comp.imp=="Yes"), dclus1r) 181s > stopifnot(isTRUE( all.equal(as.vector(SE(m2)["comp.impYes"]), as.vector(SE(m1))))) 181s > stopifnot(isTRUE( all.equal(as.vector(SE(m1)), as.vector(drop(SE(m3)))))) 181s > 181s > 181s > 181s > ## 181s > ## based on bug report from Takahiro Tsuchiya for version 3.4 181s > ## 181s > rei<-read.table(tmp<-textConnection( 181s + " id N n.a h n.ah n.h sub y 181s + 1 1 300 20 1 12 5 TRUE 1 181s + 2 2 300 20 1 12 5 TRUE 2 181s + 3 3 300 20 1 12 5 TRUE 3 181s + 4 4 300 20 1 12 5 TRUE 4 181s + 5 5 300 20 1 12 5 TRUE 5 181s + 6 6 300 20 1 12 5 FALSE NA 181s + 7 7 300 20 1 12 5 FALSE NA 181s + 8 8 300 20 1 12 5 FALSE NA 181s + 9 9 300 20 1 12 5 FALSE NA 181s + 10 10 300 20 1 12 5 FALSE NA 181s + 11 11 300 20 1 12 5 FALSE NA 181s + 12 12 300 20 1 12 5 FALSE NA 181s + 13 13 300 20 2 8 3 TRUE 6 181s + 14 14 300 20 2 8 3 TRUE 7 181s + 15 15 300 20 2 8 3 TRUE 8 181s + 16 16 300 20 2 8 3 FALSE NA 181s + 17 17 300 20 2 8 3 FALSE NA 181s + 18 18 300 20 2 8 3 FALSE NA 181s + 19 19 300 20 2 8 3 FALSE NA 181s + 20 20 300 20 2 8 3 FALSE NA 181s + "), header=TRUE) 181s > close(tmp) 181s > 181s > 181s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 181s + fpc=list(~N,NULL), subset=~sub, data=rei, method="full") 181s > tot2<- svytotal(~y, subset(des.rei2, y>3)) 181s > 181s > rei$y<-rei$y*(rei$y>3) 181s > ## based on Sarndal et al (9.4.14) 181s > rei$w.ah <- rei$n.ah / rei$n.a 181s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 181s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 181s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 181s > V <- with(a.rei, sum(N * (N-1) * ((n.ah-1)/(n.a-1) - (n.h-1)/(N-1)) * w.ah * S.ysh / n.h)) 181s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 181s > 181s > a.rei$f.h<-with(a.rei, n.h/n.ah) 181s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 181s > 181s > a.rei$f<-with(a.rei, n.a/N) 181s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 181s > 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))) 181s > 181s > V 181s [1] 70761.47 181s > Vphase1 181s [1] 44325.47 181s > Vphase2 181s [1] 26436 181s > vcov(tot2) 181s [,1] 181s [1,] 70761.47 181s attr(,"phases") 181s attr(,"phases")$phase1 181s [,1] 181s [1,] 44325.47 181s 181s attr(,"phases")$phase2 181s [,1] 181s [1,] 26436 181s 181s > 181s > ## comparing to regression 181s > reg<-svyglm(y~I(y<4), design=des.rei2) 181s > mn<-svymean(~y, subset(des.rei2,y>3)) 181s > all.equal(as.vector(coef(reg))[1],as.vector(coef(mn))) 181s [1] TRUE 181s > all.equal(as.vector(SE(reg))[1],as.vector(SE(mn))) 181s [1] TRUE 181s > vcov(mn) 181s [,1] 181s [1,] 0.3292258 181s attr(,"phases") 181s attr(,"phases")$phase1 181s [,1] 181s [1,] 0.1599264 181s 181s attr(,"phases")$phase2 181s [,1] 181s [1,] 0.1692994 181s 181s > vcov(reg) 181s (Intercept) I(y < 4)TRUE 181s (Intercept) 0.3292258 -0.3292258 181s I(y < 4)TRUE -0.3292258 0.5901907 181s attr(,"phases") 181s attr(,"phases")$phase1 181s (Intercept) I(y < 4)TRUE 181s (Intercept) 0.1599264 -0.1599264 181s I(y < 4)TRUE -0.1599264 0.2588542 181s 181s attr(,"phases")$phase2 181s (Intercept) I(y < 4)TRUE 181s (Intercept) 0.1692994 -0.1692994 181s I(y < 4)TRUE -0.1692994 0.3313365 181s 181s > 181s > 181s BEGIN TEST fpc.R 181s 181s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 181s Copyright (C) 2025 The R Foundation for Statistical Computing 181s Platform: x86_64-pc-linux-gnu 181s 181s R is free software and comes with ABSOLUTELY NO WARRANTY. 181s You are welcome to redistribute it under certain conditions. 181s Type 'license()' or 'licence()' for distribution details. 181s 181s R is a collaborative project with many contributors. 181s Type 'contributors()' for more information and 181s 'citation()' on how to cite R or R packages in publications. 181s 181s Type 'demo()' for some demos, 'help()' for on-line help, or 181s 'help.start()' for an HTML browser interface to help. 181s Type 'q()' to quit R. 181s 181s > library(survey) 181s Loading required package: grid 181s Loading required package: Matrix 182s Loading required package: survival 182s 182s Attaching package: 'survey' 182s 182s > ## check many permutations of fpc specification 182s > example(fpc) 182s The following object is masked from 'package:graphics': 182s 182s dotchart 182s 182s 182s fpc> data(fpc) 182s 182s fpc> fpc 182s stratid psuid weight nh Nh x 182s 1 1 1 3 5 15 2.8 182s 2 1 2 3 5 15 4.1 182s 3 1 3 3 5 15 6.8 182s 4 1 4 3 5 15 6.8 182s 5 1 5 3 5 15 9.2 182s 6 2 1 4 3 12 3.7 182s 7 2 2 4 3 12 6.6 182s 8 2 3 4 3 12 4.2 182s 182s fpc> withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 182s fpc+ data=fpc, nest=TRUE) 182s 182s fpc> withoutfpc 182s Stratified Independent Sampling design (with replacement) 182s withoutfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, variables=~x, 182s data=fpc, nest=TRUE) 182s 182s fpc> svymean(~x, withoutfpc) 182s mean SE 182s x 5.4481 0.7413 182s 182s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 182s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 182s 182s fpc> withfpc 182s Stratified Independent Sampling design 182s withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 182s fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 182s 182s fpc> svymean(~x, withfpc) 182s mean SE 182s x 5.4481 0.616 182s 182s fpc> ## Other equivalent forms 182s fpc> withfpc<-svydesign(prob=~I(1/weight), ids=~psuid, strata=~stratid, 182s fpc+ fpc=~Nh, variables=~x, data=fpc, nest=TRUE) 182s 182s fpc> svymean(~x, withfpc) 182s mean SE 182s x 5.4481 0.616 182s 182s fpc> withfpc<-svydesign(weights=~weight, ids=~psuid, strata=~stratid, 182s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 182s 182s fpc> svymean(~x, withfpc) 182s mean SE 182s x 5.4481 0.616 182s 182s fpc> withfpc<-svydesign(weights=~weight, ids=~interaction(stratid,psuid), 182s fpc+ strata=~stratid, fpc=~I(nh/Nh), variables=~x, data=fpc) 182s 182s fpc> svymean(~x, withfpc) 182s mean SE 182s x 5.4481 0.616 182s 182s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, fpc=~Nh, 182s fpc+ variables=~x,data=fpc,nest=TRUE) 182s 182s fpc> svymean(~x, withfpc) 182s mean SE 182s x 5.4481 0.616 182s 182s fpc> withfpc<-svydesign(ids=~psuid, strata=~stratid, 182s fpc+ fpc=~I(nh/Nh), variables=~x, data=fpc, nest=TRUE) 182s 182s fpc> svymean(~x, withfpc) 182s mean SE 182s x 5.4481 0.616 182s > 182s > 182s BEGIN TEST glm-scoping.R 182s 182s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 182s Copyright (C) 2025 The R Foundation for Statistical Computing 182s Platform: x86_64-pc-linux-gnu 182s 182s R is free software and comes with ABSOLUTELY NO WARRANTY. 182s You are welcome to redistribute it under certain conditions. 182s Type 'license()' or 'licence()' for distribution details. 182s 182s R is a collaborative project with many contributors. 182s Type 'contributors()' for more information and 182s 'citation()' on how to cite R or R packages in publications. 182s 182s Type 'demo()' for some demos, 'help()' for on-line help, or 182s 'help.start()' for an HTML browser interface to help. 182s Type 'q()' to quit R. 182s 182s > ## bug report from Thomas Leeper, fixed in version 3.32-3 182s > 182s > library("survey") 182s Loading required package: grid 182s Loading required package: Matrix 182s Loading required package: survival 183s 183s Attaching package: 'survey' 183s 183s The following object is masked from 'package:graphics': 183s 183s dotchart 183s 183s > data(api) 183s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 183s > 183s > # pass `family` directly (WORKS!) 183s > svyglm(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 183s Stratified Independent Sampling design 183s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 183s fpc = ~fpc) 183s 183s Call: svyglm(formula = api00 ~ ell + meals + mobility, design = dstrat, 183s family = gaussian()) 183s 183s Coefficients: 183s (Intercept) ell meals mobility 183s 820.8873 -0.4806 -3.1415 0.2257 183s 183s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 183s Null Deviance: 3023000 183s Residual Deviance: 1029000 AIC: 2308 183s > 183s > # passing `family` via ... (WORKS!) 183s > myfun1 <- function(formula, design, ...) { 183s + svyglm(formula, design = design, ...) 183s + } 183s > myfun1(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 183s Stratified Independent Sampling design 183s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 183s fpc = ~fpc) 183s 183s Call: svyglm(formula = formula, design = design, family = ..1) 183s 183s Coefficients: 183s (Intercept) ell meals mobility 183s 820.8873 -0.4806 -3.1415 0.2257 183s 183s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 183s Null Deviance: 3023000 183s Residual Deviance: 1029000 AIC: 2308 183s > 183s > # passing `family` via default argument (DOES NOT WORK!) 183s > myfun2 <- function(formula, design, family = gaussian()) { 183s + svyglm(formula, design = design, family = family) 183s + } 183s > myfun2(api00~ell+meals+mobility, design=dstrat, family = gaussian()) 183s Stratified Independent Sampling design 183s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 183s fpc = ~fpc) 183s 183s Call: svyglm(formula = formula, design = design, family = family) 183s 183s Coefficients: 183s (Intercept) ell meals mobility 183s 820.8873 -0.4806 -3.1415 0.2257 183s 183s Degrees of Freedom: 199 Total (i.e. Null); 194 Residual 183s Null Deviance: 3023000 183s Residual Deviance: 1029000 AIC: 2308 183s > 183s BEGIN TEST kalton.R 183s 183s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 183s Copyright (C) 2025 The R Foundation for Statistical Computing 183s Platform: x86_64-pc-linux-gnu 183s 183s R is free software and comes with ABSOLUTELY NO WARRANTY. 183s You are welcome to redistribute it under certain conditions. 183s Type 'license()' or 'licence()' for distribution details. 183s 183s R is a collaborative project with many contributors. 183s Type 'contributors()' for more information and 183s 'citation()' on how to cite R or R packages in publications. 183s 183s Type 'demo()' for some demos, 'help()' for on-line help, or 183s 'help.start()' for an HTML browser interface to help. 183s Type 'q()' to quit R. 183s 183s > library(survey) 183s Loading required package: grid 183s Loading required package: Matrix 183s Loading required package: survival 183s 183s Attaching package: 'survey' 183s 183s The following object is masked from 'package:graphics': 183s 183s dotchart 183s 183s > 183s > ab<-expand.grid(a=factor(1:4),b=factor(1:3)) 183s > 183s > kaltonsample<-ab[rep(1:12,c(20,50,100,30,40,140,50,100,40,310,50,70)),] 183s > 183s > kaltonpop<-ab[rep(1:12,c(80,60,170,55,40,150,60,165,55,340,200,125)),] 183s > 183s > jointpop<-colSums(model.matrix(~a*b,kaltonpop)) 183s > marginalpop<-colSums(model.matrix(~a+b,kaltonpop)) 183s > gregpop<-colSums(model.matrix(~as.numeric(a)+as.numeric(b),kaltonpop)) 183s > 183s > dkalton<-svydesign(id=~1,data=kaltonsample) 183s Warning message: 183s In svydesign.default(id = ~1, data = kaltonsample) : 183s No weights or probabilities supplied, assuming equal probability 183s > 183s > dps<-postStratify(dkalton,~a+b,xtabs(~a+b,kaltonpop)) 183s > 183s > drake<-rake(dkalton, list(~a,~b),list(xtabs(~a,kaltonpop),xtabs(~b,kaltonpop)),control=list(epsilon=0.0001)) 183s > 183s > dcalps<-calibrate(dkalton, ~a*b, jointpop) 183s > dcalrake<-calibrate(dkalton,~a+b, marginalpop, calfun="raking") 183s > dlinear<-calibrate(dkalton, ~a+b, marginalpop) 183s > 183s > dtrunclinear<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2)) 183s > 183s > dlogit<-calibrate(dkalton, ~a+b, marginalpop,bounds=c(0.5,2.2),calfun="logit") 183s > 183s > dgreg<-calibrate(dkalton,~as.numeric(a)+as.numeric(b), gregpop) 183s > 183s > 183s > #table A 183s > round(svytable(~a+b,dps)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 4.00 1.00 1.38 183s 2 1.20 1.07 1.10 183s 3 1.70 1.20 4.00 183s 4 1.83 1.65 1.79 183s > round(svytable(~a+b,dcalps)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 4.00 1.00 1.37 183s 2 1.20 1.07 1.10 183s 3 1.70 1.20 4.00 183s 4 1.83 1.65 1.79 183s > 183s > #table B 183s > round(svytable(~a+b,drake)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 1.81 1.45 2.02 183s 2 1.08 0.87 1.21 183s 3 2.20 1.76 2.45 183s 4 1.83 1.47 2.04 183s > round(svytable(~a+b,dcalrake)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 1.81 1.45 2.02 183s 2 1.08 0.87 1.21 183s 3 2.20 1.76 2.45 183s 4 1.83 1.47 2.04 183s > 183s > #table C 183s > round(svytable(~a+b,dlinear)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 1.82 1.50 1.97 183s 2 1.09 0.78 1.24 183s 3 2.19 1.88 2.34 183s 4 1.83 1.52 1.98 183s > 183s > #table D 183s > round(svytable(~a+b,dgreg)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 1.21 1.17 1.14 183s 2 1.43 1.40 1.36 183s 3 1.66 1.62 1.59 183s 4 1.88 1.85 1.81 183s > 183s > #table G 183s > round(svytable(~a+b,dlogit)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 1.87 1.46 1.98 183s 2 1.08 0.74 1.27 183s 3 2.17 2.09 2.18 183s 4 1.89 1.49 1.99 183s > 183s > #table G 183s > round(svytable(~a+b,dtrunclinear)/xtabs(~a+b,kaltonsample),2) 183s b 183s a 1 2 3 183s 1 1.81 1.48 1.99 183s 2 1.08 0.75 1.26 183s 3 2.20 2.00 2.20 183s 4 1.83 1.50 2.00 183s > 184s BEGIN TEST logranktest.R 184s 184s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 184s Copyright (C) 2025 The R Foundation for Statistical Computing 184s Platform: x86_64-pc-linux-gnu 184s 184s R is free software and comes with ABSOLUTELY NO WARRANTY. 184s You are welcome to redistribute it under certain conditions. 184s Type 'license()' or 'licence()' for distribution details. 184s 184s R is a collaborative project with many contributors. 184s Type 'contributors()' for more information and 184s 'citation()' on how to cite R or R packages in publications. 184s 184s Type 'demo()' for some demos, 'help()' for on-line help, or 184s 'help.start()' for an HTML browser interface to help. 184s Type 'q()' to quit R. 184s 184s > ## StackOverflow 63333282 184s > 184s > library(survey) 184s Loading required package: grid 184s Loading required package: Matrix 184s Loading required package: survival 184s 184s Attaching package: 'survey' 184s 184s The following object is masked from 'package:graphics': 184s 184s dotchart 184s 184s > D = data.frame(unique_id = 1:135, 184s + 184s + weights = rep(1,135), 184s + 184s + 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 , 184s + 184s + 6.53631154, 6.31914568, 7.00146597, 9.67616088, 7.94212358, 9.70693890, 10.67575835, 10.06764688, 12.29175616, 13.60092871, 13.12508566, 14.66417522, 184s + 184s + 15.35250691, 0.93368707, 0.19087611, 3.15533767, 4.40821633, 17.54334957, 17.95177642, 15.50903946, 16.48376185, 20.87956697, 21.24571398, 22.34297263, 184s + 184s + 23.36042629, 21.01760215, 23.84785038, 26.06105822, 4.16866350, 1.96922485, 0.66199008, 6.76987830, 1.55617685, 0.19095871, 3.13291784, 5.43159409, 184s + 184s + 9.55805671, 4.31437322, 0.78259860, 5.26415156, 3.45095686, 1.69128712, 8.41942426, 3.33748695, 6.08516173, 2.72897404, 0.22789783, 0.86348009, 184s + 184s + 2.35707587, 2.97477615, 12.33273800, 0.58532123, 0.14586238, 10.67948547, 4.07655972, 3.94405136, 0.37226898, 1.42558725, 1.47680658, 4.22506540, 184s + 184s + 1.56703478, 8.37484756, 12.54015087, 1.80994787, 3.66453633, 1.02834532, 1.99065652, 1.23577436, 16.21981618, 14.35039798, 4.15321606, 2.79740679, 184s + 184s + 0.35538726, 7.46823358, 1.66329088, 7.46525382, 2.62734831, 3.19057957, 0.33317193, 0.09122886, 9.14616245, 2.48542578, 2.37569263, 5.48499630, 184s + 184s + 2.22749399, 2.64816296, 0.97101545, 1.42468625, 1.27668904, 0.03692447, 1.98783210, 5.47692729, 3.88316178, 0.32921277, 1.77225345, 9.33268901, 184s + 184s + 2.44517775, 1.49813702, 2.56059172, 3.43194832, 1.22955630, 3.56263947, 9.07060099, 3.58312362, 2.22755370, 4.24783776, 3.46364804, 1.61671354, 184s + 184s + 11.10973565, 7.18764270, 1.80400046, 6.39833474, 6.72825192, 6.46063344, 5.76855531, 5.27157807, 4.66154734, 3.50019718, 2.27156678, 3.28531594, 184s + 184s + 2.35699896, 2.94956000, 8.85381736), 184s + 184s + 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, 184s + 184s + 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, 184s + 184s + 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), 184s + 184s + group = c(rep("group1", 40), rep("group2", 95))) 184s > 184s > 184s > 184s > svykm_formula = as.formula("Surv(event_time, event_flag) ~ group") 184s > 184s > svy_design = svydesign( ids = ~unique_id , weights = ~weights, data = D ) 184s > 184s > a<-svylogrank(formula = svykm_formula, design = svy_design) 184s > 184s > ii<-with(D, order(event_time, event_flag)) 184s > 184s > svy_design2 = svydesign( ids = ~unique_id , weights = ~weights, data = D[ii,] ) 184s > 184s > b<-svylogrank(formula = svykm_formula, design = svy_design2) 184s > d<-svylogrank(formula = svykm_formula, design = svy_design, method = "large") 184s > 184s > f<- svylogrank(formula = svykm_formula, design = svy_design, method = "score") 184s > 184s > 184s > stopifnot(all.equal(a[[2]],b[[2]])) 184s > 184s > stopifnot(all.equal(a[[2]],d[[2]])) 184s > 184s > stopifnot(all.equal(a[[2]],f[-1])) 184s > 184s > 184s BEGIN TEST lonely.psu.R 184s 184s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 184s Copyright (C) 2025 The R Foundation for Statistical Computing 184s Platform: x86_64-pc-linux-gnu 184s 184s R is free software and comes with ABSOLUTELY NO WARRANTY. 184s You are welcome to redistribute it under certain conditions. 184s Type 'license()' or 'licence()' for distribution details. 184s 184s R is a collaborative project with many contributors. 184s Type 'contributors()' for more information and 184s 'citation()' on how to cite R or R packages in publications. 184s 184s Type 'demo()' for some demos, 'help()' for on-line help, or 184s 'help.start()' for an HTML browser interface to help. 184s Type 'q()' to quit R. 184s 184s > 184s > ## lonely PSUs by design 184s > library(survey) 184s Loading required package: grid 184s Loading required package: Matrix 185s Loading required package: survival 185s > data(api) 185s 185s Attaching package: 'survey' 185s 185s The following object is masked from 'package:graphics': 185s 185s dotchart 185s 185s > ## not certainty PSUs by fpc 185s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 185s > summary(ds) 185s Stratified Independent Sampling design (with replacement) 185s Error in onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 185s Stratum (413) has only one PSU at stage 1 185s Error in jknweights(design$strata[, 1], design$cluster[, 1], fpc = fpc, : 185s Stratum413has only one PSU 185s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1) 185s Probabilities: 185s Min. 1st Qu. Median Mean 3rd Qu. Max. 185s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 185s Stratum Sizes: 185s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 185s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 185s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 185s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 185s Data variables: 185s [1] "cds" "stype" "name" "sname" "snum" "dname" 185s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 185s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 185s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 185s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 185s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 185s [37] "api.stu" "fpc" "pw" 185s > 185s > options(survey.lonely.psu="fail") 185s > try(svymean(~api00,ds)) 185s > try(svymean(~api00, as.svrepdesign(ds))) 185s > options(survey.lonely.psu="remove") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.8058 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.8058 185s > options(survey.lonely.psu="certainty") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.8058 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.8058 185s > options(survey.lonely.psu="adjust") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.8281 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.8267 185s > options(survey.lonely.psu="average") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 6.0096 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.8217 185s > 185s > ## fpc specified 185s > fpc<-ifelse(apiclus1$dnum==413, 1,1000) 185s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1,fpc=fpc) 185s > summary(ds) 185s Stratified Independent Sampling design 185s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = apiclus1, 185s fpc = fpc) 185s Probabilities: 185s Min. 1st Qu. Median Mean 3rd Qu. Max. 185s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 185s Stratum Sizes: 185s 61 135 178 197 255 406 413 437 448 510 568 637 716 778 815 185s obs 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 185s design.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 185s actual.PSU 13 34 4 13 16 2 1 4 12 21 9 11 37 2 4 185s Population stratum sizes (PSUs): 185s 135 178 197 255 406 413 437 448 510 568 61 637 716 778 815 185s 1000 1000 1000 1000 1000 1 1000 1000 1000 1000 1000 1000 1000 1000 1000 185s Data variables: 185s [1] "cds" "stype" "name" "sname" "snum" "dname" 185s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 185s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 185s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 185s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 185s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 185s [37] "api.stu" "fpc" "pw" 185s > 185s > options(survey.lonely.psu="fail") 185s > try(svymean(~api00,ds)) 185s mean SE 185s api00 644.17 5.7344 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.7344 185s > options(survey.lonely.psu="remove") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.7344 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.7344 185s > options(survey.lonely.psu="certainty") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.7344 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.7344 185s > options(survey.lonely.psu="adjust") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.7344 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.7344 185s > options(survey.lonely.psu="average") 185s > svymean(~api00,ds) 185s mean SE 185s api00 644.17 5.7344 185s > svymean(~api00, as.svrepdesign(ds)) 185s mean SE 185s api00 644.17 5.7501 185s > 185s > rs<-as.svrepdesign(ds) 185s > svytotal(~api00,rs) 185s total SE 185s api00 3989986 35616 185s > SE(svytotal(~api00,subset(rs, dnum==413)))==0 185s [1] TRUE 185s > 185s > ## lonely PSUs after subsetting 185s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 185s > ds1<-ds[-31,] 185s > summary(ds1) 185s Stratified Independent Sampling design (with replacement) 185s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 185s dnum != 413)) 185s Probabilities: 185s Min. 1st Qu. Median Mean 3rd Qu. Max. 185s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 185s Stratum Sizes: 185s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 185s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 185s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 185s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 185s Data variables: 185s [1] "cds" "stype" "name" "sname" "snum" "dname" 185s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 185s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 185s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 185s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 185s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 185s [37] "api.stu" "fpc" "pw" 185s > 185s > options(survey.lonely.psu="fail") 185s > svymean(~api00,ds1) 185s mean SE 185s api00 645.14 5.8909 185s > options(survey.lonely.psu="remove") 185s > svymean(~api00,ds1) 185s mean SE 185s api00 645.14 5.8909 185s > options(survey.lonely.psu="certainty") 185s > svymean(~api00,ds1) 185s mean SE 185s api00 645.14 5.8909 185s > options(survey.lonely.psu="adjust") 185s > svymean(~api00,ds1) 185s mean SE 185s api00 645.14 5.8909 185s > options(survey.lonely.psu="average") 185s > svymean(~api00,ds1) 185s mean SE 185s api00 645.14 5.8909 185s > 185s > ## with adjustment 185s > options(survey.adjust.domain.lonely=TRUE) 185s > ds<-svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1,dnum !=413)) 185s Warning message: 185s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 185s Stratum (406) has only one PSU at stage 1 185s > ds1<-ds[-31,] 185s > summary(ds1) 185s Stratified Independent Sampling design (with replacement) 185s svydesign(id = ~1, weights = ~pw, strata = ~dnum, data = subset(apiclus1, 185s dnum != 413)) 185s Probabilities: 185s Min. 1st Qu. Median Mean 3rd Qu. Max. 185s 0.02954 0.02954 0.02954 0.02954 0.02954 0.02954 185s Stratum Sizes: 185s 61 135 178 197 255 406 437 448 510 568 637 716 778 815 185s obs 13 34 4 13 16 1 4 12 21 9 11 37 2 4 185s design.PSU 13 34 4 13 16 2 4 12 21 9 11 37 2 4 185s actual.PSU 13 34 4 13 16 1 4 12 21 9 11 37 2 4 185s Data variables: 185s [1] "cds" "stype" "name" "sname" "snum" "dname" 185s [7] "dnum" "cname" "cnum" "flag" "pcttest" "api00" 185s [13] "api99" "target" "growth" "sch.wide" "comp.imp" "both" 185s [19] "awards" "meals" "ell" "yr.rnd" "mobility" "acs.k3" 185s [25] "acs.46" "acs.core" "pct.resp" "not.hsg" "hsg" "some.col" 185s [31] "col.grad" "grad.sch" "avg.ed" "full" "emer" "enroll" 185s [37] "api.stu" "fpc" "pw" 185s > 185s > options(survey.lonely.psu="fail") 185s > try(svymean(~api00,ds1)) 185s mean SE 185s api00 645.14 5.8909 185s > options(survey.lonely.psu="remove") 185s > svymean(~api00,ds1) 185s mean SE 185s api00 645.14 5.8909 185s Warning message: 185s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 185s Stratum (406) has only one PSU at stage 1 185s > options(survey.lonely.psu="certainty") 185s > svymean(~api00,ds1) 185s Warning message: 185s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 185s Stratum (406) has only one PSU at stage 1 185s mean SE 185s api00 645.14 5.8909 185s > options(survey.lonely.psu="adjust") 185s > svymean(~api00,ds1) 185s Warning message: 185s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : 185s Stratum (406) has only one PSU at stage 1 185s mean SE 185s api00 645.14 5.9119 185s > options(survey.lonely.psu="average") 185s > svymean(~api00,ds1) 185s Warning message: 185s In onestrat(`attr<-`(x[index, , drop = FALSE], "recentering", recentering), : mean SE 185s api00 645.14 6.0914 185s > 185s > ## checks for `svytotal()` 185s > 185s > df_w_singleton <- data.frame( 185s + Stratum = c(1, 1, 2, 2, 3), 185s + PSU = c(1, 2, 3, 4, 5), 185s + Design_Weight = c(10.5, 10.5, 20, 20, 15), 185s + Sex = c("M", "F", "F", "M", "M"), 185s + Age = c(30.5, 40.5, 35, 52, 44), 185s + Height = c(6.2, 5.0, 5.3, 5.7, 5.5) 185s + ) 185s 185s Stratum (406) has only one PSU at stage 1 185s > 185s > design_w_singleton <- survey::svydesign( 185s + data = df_w_singleton, 185s + ids = ~ PSU, strata = ~ Stratum, 185s + weights = ~ Design_Weight 185s + ) 185s > 185s > options("survey.lonely.psu" = "remove") 185s > 185s > stopifnot(all.equal( 185s + target = 126625, 185s + current = as.numeric( 185s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 185s + ) 185s + )) 185s > 185s > options("survey.lonely.psu" = "certainty") 185s > 185s > stopifnot(all.equal( 185s + target = 126625, 185s + current = as.numeric( 185s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 185s + ) 185s + )) 185s > 185s > options("survey.lonely.psu" = "adjust") 185s > 185s > stopifnot(all.equal( 185s + target = 127579.8, 185s + current = as.numeric( 185s + vcov(svytotal(x = ~ Age, design = design_w_singleton)) 185s + ), 185s + scale = 127579.8, tolerance = 0.000001 185s + )) 185s > 185s BEGIN TEST mtcars-var.R 185s 185s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 185s Copyright (C) 2025 The R Foundation for Statistical Computing 185s Platform: x86_64-pc-linux-gnu 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 185s > library(survey) 185s Loading required package: grid 185s Loading required package: Matrix 186s Loading required package: survival 186s 186s Attaching package: 'survey' 186s 186s The following object is masked from 'package:graphics': 186s 186s dotchart 186s 186s > 186s > # don't throw an error on domains of size 1, just return NA 186s > input <- mtcars 186s > input$carb <- factor(input$carb) 186s > design <- svydesign(ids = ~0, weights = NULL, data = input) 186s > svyby( 186s + ~mpg, 186s + ~carb, 186s + design, 186s + svyvar 186s + ) 186s carb mpg se 186s 1 1 36.01619 11.2823286 186s 2 2 29.94444 9.0030898 186s 3 3 1.11000 0.4604066 186s 4 4 15.29656 4.3174617 186s 6 6 NA NA 186s 8 8 NA NA 186s > 186s > 186s > ## same n with na.rm=TRUE as subset(, !is.na) 186s > input$mpg[1]<-NA 186s > design <- svydesign(ids = ~0, weights = NULL, data = input) 186s > stopifnot(all.equal(svyvar(~mpg, design, na.rm=TRUE), 186s + svyvar(~mpg, subset(design, !is.na(mpg))))) 186s > 186s BEGIN TEST multistage-rcpp.R 186s 186s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 186s Copyright (C) 2025 The R Foundation for Statistical Computing 186s Platform: x86_64-pc-linux-gnu 186s 186s R is free software and comes with ABSOLUTELY NO WARRANTY. 186s You are welcome to redistribute it under certain conditions. 186s Type 'license()' or 'licence()' for distribution details. 186s 186s R is a collaborative project with many contributors. 186s Type 'contributors()' for more information and 186s 'citation()' on how to cite R or R packages in publications. 186s 186s Type 'demo()' for some demos, 'help()' for on-line help, or 186s 'help.start()' for an HTML browser interface to help. 186s Type 'q()' to quit R. 186s 186s Loading required package: grid 186s > ## temporarily disable while it's being fixed 186s > ## q("no") 186s > 186s > ## 186s > ## Check that multistage() and multistage_rcpp() give same results 186s > ## for different options. 186s > ## 186s > library(survey) 186s Loading required package: Matrix 187s Loading required package: survival 187s 187s Attaching package: 'survey' 187s 187s > 187s > # Check for a simple random sample ---- 187s > 187s > data('api', package = 'survey') 187s The following object is masked from 'package:graphics': 187s 187s dotchart 187s 187s > api_srs_design <- svydesign( 187s + data = apisrs, 187s + ids = ~ 1, 187s + weights = ~ 1 187s + ) 187s > 187s > x <- as.matrix(api_srs_design$variables[,c('api00','api99')] / api_srs_design$prob) 187s > 187s > base_r_result <- survey:::multistage(x = x, 187s + clusters = api_srs_design$cluster, 187s + stratas = api_srs_design$strata, 187s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=TRUE, stage = 1, cal = NULL) 187s > 187s > rcpp_result <- survey:::multistage_rcpp(x = x, 187s + clusters = api_srs_design$cluster, 187s + stratas = api_srs_design$strata, 187s + nPSUs = api_srs_design$fpc$sampsize, fpcs = api_srs_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=TRUE, stage = 1, cal = NULL) 187s > 187s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 187s + stop("Differences between `multistage()` and `multistage_rcpp()` for SRS") 187s + } 187s > 187s > # Check for a stratified simple random sample ---- 187s > 187s > apistrat_design <- svydesign( 187s + data = apistrat, 187s + id =~ 1, 187s + strata =~ stype, 187s + weights =~ pw, 187s + fpc =~ fpc 187s + ) 187s > 187s > x <- as.matrix(apistrat_design$variables[,c('api00','api99')] / apistrat_design$prob) 187s > 187s > base_r_result <- survey:::multistage(x = x, 187s + clusters = apistrat_design$cluster, 187s + stratas = apistrat_design$strata, 187s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=TRUE, stage = 1, cal = NULL) 187s > 187s > rcpp_result <- survey:::multistage_rcpp(x = x, 187s + clusters = apistrat_design$cluster, 187s + stratas = apistrat_design$strata, 187s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=TRUE, stage = 1, cal = NULL) 187s > 187s > if (!isTRUE(all.equal(base_r_result, rcpp_result))) { 187s + stop("Differences between `multistage()` and `multistage_rcpp()` for stratified sample") 187s + } 187s > 187s > ##_ Check whether expected true zeroes are actually computed as zeroes ---- 187s > 187s > x <- as.matrix(model.matrix(~ -1 + stype, data = apistrat_design$variables) / (sum(apistrat_design$prob)/apistrat_design$prob)) 187s > 187s > base_r_result <- survey:::multistage(x = x, 187s + clusters = apistrat_design$cluster, 187s + stratas = apistrat_design$strata, 187s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=TRUE, stage = 1, cal = NULL) 187s > 187s > rcpp_result <- survey:::multistage_rcpp(x = x, 187s + clusters = apistrat_design$cluster, 187s + stratas = apistrat_design$strata, 187s + nPSUs = apistrat_design$fpc$sampsize, fpcs = apistrat_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=TRUE, stage = 1, cal = NULL) 187s > 187s > if (!all(rcpp_result == 0) | !all(diag(rcpp_result) >= 0)) { 187s + stop("Computations which should equal zero do not.") 187s + } 187s > 187s > # Create a stratified, multistage design ---- 187s > 187s > data(mu284) 187s > 187s > ## Create three strata, the third of which has only one PSU 187s > mu284_stratified <- rbind( 187s + transform(mu284, stratum = 1, 187s + y2 = y1 + c(0, 2, 1, 0, -1, 2, 0, 3, 0, 0, -1, -1, 1, -1, 0)), 187s + transform(mu284, stratum = 2, 187s + y2 = y1 + c(-1, 0, -1, 0, -1, 0, 0, 1, 2, -1, 1, 1, 0, 1, 0)), 187s + transform(mu284[1,], stratum = 3, 187s + y2 = y1 + 2) 187s + ) 187s > 187s > ## Create domain variables which yield a lonely PSU or a lonely SSU 187s > mu284_stratified[['DOMAIN_W_LONELY_PSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19) 187s > mu284_stratified[['DOMAIN_W_LONELY_SSU']] <- mu284_stratified$stratum == 1 | (mu284_stratified$stratum == 2 & mu284_stratified$id1 == 19 & mu284_stratified$id2 == 1) 187s > 187s > ## Create a survey design object with no lonely PSUs 187s > dmu284_strat <- svydesign(data = subset(mu284_stratified, stratum != 3), 187s + strata = ~ stratum, nest = TRUE, 187s + id = ~ id1 + id2, fpc = ~ n1 + n2) 187s > ## Create a survey design with one lonely PSU 187s > dmu284_strat_w_lonely <- svydesign(data = mu284_stratified, 187s + strata = ~ stratum, nest = TRUE, 187s + id = ~ id1 + id2, fpc = ~ n1 + n2) 187s > ## Create subsetted design objects, subsetted to domain with a lonely PSU or SSU 187s > dmu284_strat_domain_lonely_psu <- subset(dmu284_strat, DOMAIN_W_LONELY_PSU) 187s > dmu284_strat_domain_lonely_ssu <- subset(dmu284_strat, DOMAIN_W_LONELY_SSU) 187s > 187s > 187s > # Check same results for different values of 'lonely PSU' options ---- 187s > 187s > lonely_psu_options <- c(certainty = 'certainty', 187s + remove = 'remove', 187s + average = 'average', 187s + adjust = 'adjust') 187s > one_stage_options <- c(TRUE, FALSE) 187s > 187s > design_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 187s + 'one.stage' = one_stage_options, 187s + stringsAsFactors = FALSE) 187s > design_lonely_psu_comparisons[['results_match']] <- NA 187s > 187s > ##_ Check for lonely PSUs caused by design ---- 187s > for (i in seq_len(nrow(design_lonely_psu_comparisons))) { 187s + survey.lonely.psu <- design_lonely_psu_comparisons[['survey.lonely.psu']][i] 187s + one.stage <- design_lonely_psu_comparisons[['one.stage']][i] 187s + options('survey.lonely.psu' = survey.lonely.psu) 187s + 187s + x <- as.matrix(dmu284_strat_w_lonely$variables[,c('y1','y2')] / dmu284_strat_w_lonely$prob) 187s + 187s + base_r_result <- survey:::multistage(x = x, 187s + clusters = dmu284_strat_w_lonely$cluster, 187s + stratas = dmu284_strat_w_lonely$strata, 187s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=one.stage, stage = 1, cal = NULL) 187s + 187s + rcpp_result <- survey:::multistage_rcpp(x = x, 187s + clusters = dmu284_strat_w_lonely$cluster, 187s + stratas = dmu284_strat_w_lonely$strata, 187s + nPSUs = dmu284_strat_w_lonely$fpc$sampsize, fpcs = dmu284_strat_w_lonely$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=one.stage, stage = 1, cal = NULL) 187s + 187s + design_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 187s + } 187s > 187s > print(design_lonely_psu_comparisons) 187s survey.lonely.psu one.stage results_match 187s 1 certainty TRUE TRUE 187s 2 remove TRUE TRUE 187s 3 average TRUE TRUE 187s 4 adjust TRUE TRUE 187s 5 certainty FALSE TRUE 187s 6 remove FALSE TRUE 187s 7 average FALSE TRUE 187s 8 adjust FALSE TRUE 187s > if (!all(design_lonely_psu_comparisons$results_match)) { 187s + stop("Results for design lonely PSUs differ between base R and Rcpp implementations.") 187s + } 187s > 187s > ##_ Check for domain lonely PSUs caused by subsetting ---- 187s > 187s > domain_lonely_psu_comparisons <- expand.grid('survey.lonely.psu' = lonely_psu_options, 187s + 'survey.adjust.domain.lonely' = c(FALSE, TRUE), 187s + 'one.stage' = one_stage_options, 187s + stringsAsFactors = FALSE) 187s > domain_lonely_psu_comparisons[['results_match']] <- NA 187s > 187s > for (i in seq_len(nrow(domain_lonely_psu_comparisons))) { 187s + 187s + options('survey.lonely.psu' = domain_lonely_psu_comparisons[['survey.lonely.psu']][i]) 187s + options('survey.adjust.domain.lonely' = domain_lonely_psu_comparisons[['survey.adjust.domain.lonely']][i]) 187s + one.stage <- domain_lonely_psu_comparisons[['one.stage']][i] 187s + 187s + 187s + x <- as.matrix(dmu284_strat_domain_lonely_psu$variables[,c('y1','y2')] / dmu284_strat_domain_lonely_psu$prob) 187s + suppressWarnings({ 187s + base_r_result <- survey:::multistage(x = x, 187s + clusters = dmu284_strat_domain_lonely_psu$cluster, 187s + stratas = dmu284_strat_domain_lonely_psu$strata, 187s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 187s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=one.stage, stage = 1, cal = NULL) 187s + }) 187s + 187s + rcpp_result <- survey:::multistage_rcpp(x = x, 187s + clusters = dmu284_strat_domain_lonely_psu$cluster, 187s + stratas = dmu284_strat_domain_lonely_psu$strata, 187s + nPSUs = dmu284_strat_domain_lonely_psu$fpc$sampsize, 187s + fpcs = dmu284_strat_domain_lonely_psu$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=one.stage, stage = 1, cal = NULL) 187s + 187s + domain_lonely_psu_comparisons[['results_match']][i] <- isTRUE(all.equal(base_r_result, rcpp_result)) 187s + } 187s Warning messages: 187s 1: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s 2: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s 3: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s 4: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s 5: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s 6: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, :> 187s > print(domain_lonely_psu_comparisons) 187s 187s At least one stratum contains only one PSU at stage 1 187s 7: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s 8: In arma_multistage(Y = as.matrix(x), samp_unit_ids = clusters, strata_ids = stratas, : 187s At least one stratum contains only one PSU at stage 1 187s survey.lonely.psu survey.adjust.domain.lonely one.stage results_match 187s 1 certainty FALSE TRUE TRUE 187s 2 remove FALSE TRUE TRUE 187s 3 average FALSE TRUE TRUE 187s 4 adjust FALSE TRUE TRUE 187s 5 certainty TRUE TRUE TRUE 187s 6 remove TRUE TRUE TRUE 187s 7 average TRUE TRUE TRUE 187s 8 adjust TRUE TRUE TRUE 187s 9 certainty FALSE FALSE TRUE 187s 10 remove FALSE FALSE TRUE 187s 11 average FALSE FALSE TRUE 187s 12 adjust FALSE FALSE TRUE 187s 13 certainty TRUE FALSE TRUE 187s 14 remove TRUE FALSE TRUE 187s 15 average TRUE FALSE TRUE 187s 16 adjust TRUE FALSE TRUE 187s > if (!all(domain_lonely_psu_comparisons$results_match)) { 187s + stop("Results for domain lonely PSUs differ between base R and Rcpp implementations.") 187s + } 187s > 187s > # Checks for edge cases ---- 187s > 187s > ## Zero records ---- 187s > 187s > zero_row_design <- dmu284_strat |> subset(id1 == "Nonexistent") 187s > 187s > zero_row_result <- survey:::multistage_rcpp( 187s + x = as.matrix(zero_row_design$variables[,c('y1', 'y2')]), 187s + clusters = zero_row_design$cluster, 187s + stratas = zero_row_design$strata, 187s + nPSUs = zero_row_design$fpc$sampsize, 187s + fpcs = zero_row_design$fpc$popsize, 187s + lonely.psu=getOption("survey.lonely.psu"), 187s + one.stage=one.stage, stage = 1, cal = NULL 187s + ) 187s > 187s > if (any(is.na(zero_row_result)) || any(zero_row_result != 0)) { 187s + stop("`multistage_rcpp()` should return zeros for zero-row inputs.") 187s + } 187s > 187s > 187s BEGIN TEST multistage.R 187s 187s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 187s Copyright (C) 2025 The R Foundation for Statistical Computing 187s Platform: x86_64-pc-linux-gnu 187s 187s R is free software and comes with ABSOLUTELY NO WARRANTY. 187s You are welcome to redistribute it under certain conditions. 187s Type 'license()' or 'licence()' for distribution details. 187s 187s R is a collaborative project with many contributors. 187s Type 'contributors()' for more information and 187s 'citation()' on how to cite R or R packages in publications. 187s 187s Type 'demo()' for some demos, 'help()' for on-line help, or 187s 'help.start()' for an HTML browser interface to help. 187s Type 'q()' to quit R. 187s 187s > ## 187s > ## Check that multistage samples still work 187s > ## 187s > library(survey) 187s Loading required package: grid 187s Loading required package: Matrix 188s Loading required package: survival 188s 188s Attaching package: 'survey' 188s 188s The following object is masked from 'package:graphics': 188s 188s dotchart 188s 188s > example(mu284) 188s 188s mu284> data(mu284) 188s 188s mu284> (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 188s 2 - level Cluster Sampling design 188s With (5, 15) clusters. 188s (dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284)) 188s 188s mu284> (ytotal<-svytotal(~y1, dmu284)) 188s total SE 188s y1 15080 2274.3 188s 188s mu284> vcov(ytotal) 188s y1 188s y1 5172234 188s > 188s > 188s BEGIN TEST na_action.R 188s 188s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 188s Copyright (C) 2025 The R Foundation for Statistical Computing 188s Platform: x86_64-pc-linux-gnu 188s 188s R is free software and comes with ABSOLUTELY NO WARRANTY. 188s You are welcome to redistribute it under certain conditions. 188s Type 'license()' or 'licence()' for distribution details. 188s 188s R is a collaborative project with many contributors. 188s Type 'contributors()' for more information and 188s 'citation()' on how to cite R or R packages in publications. 188s 188s Type 'demo()' for some demos, 'help()' for on-line help, or 188s 'help.start()' for an HTML browser interface to help. 188s Type 'q()' to quit R. 188s 188s > ## from Terry Therneau 188s > library(survey) 188s Loading required package: grid 188s Loading required package: Matrix 188s Loading required package: survival 189s > load("naa.rda") 189s 189s Attaching package: 'survey' 189s 189s The following object is masked from 'package:graphics': 189s 189s dotchart 189s 189s > 189s > fit1e <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s,na.action=na.exclude) 189s > fit1o <- svyglm( pseudo ~ age34 + ccr5 + factor(times), design= adata.s) 189s > all.equal(coef(fit1e),coef(fit1o)) 189s [1] TRUE 189s > all.equal(vcov(fit1e),vcov(fit1o)) 189s [1] TRUE 189s > 189s BEGIN TEST newquantile.R 189s 189s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 189s Copyright (C) 2025 The R Foundation for Statistical Computing 189s Platform: x86_64-pc-linux-gnu 189s 189s R is free software and comes with ABSOLUTELY NO WARRANTY. 189s You are welcome to redistribute it under certain conditions. 189s Type 'license()' or 'licence()' for distribution details. 189s 189s R is a collaborative project with many contributors. 189s Type 'contributors()' for more information and 189s 'citation()' on how to cite R or R packages in publications. 189s 189s Type 'demo()' for some demos, 'help()' for on-line help, or 189s 'help.start()' for an HTML browser interface to help. 189s Type 'q()' to quit R. 189s 189s > ## quantiles with equal weights 189s > 189s > library(survey) 189s Loading required package: grid 189s Loading required package: Matrix 189s Loading required package: survival 189s > data(api) 189s 189s Attaching package: 'survey' 189s 189s The following object is masked from 'package:graphics': 189s 189s dotchart 189s 189s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 189s > 189s > 189s > for(i in 1:9){ 189s + print(i) 189s + all.equal( 189s + as.vector(coef(svyquantile(~ell, dclus1, c(0.2,0.5,0.9), qrule=paste0("hf",i)))), 189s + as.vector(quantile(apiclus1$ell, c(0.2,0.5,0.9), type=i)) 189s + ) 189s + 189s + } 189s [1] 1 189s [1] 2 189s [1] 3 189s [1] 4 189s [1] 5 189s [1] 6 189s [1] 7 189s [1] 8 189s [1] 9 189s > 189s BEGIN TEST nwts-cch.R 189s 189s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 189s Copyright (C) 2025 The R Foundation for Statistical Computing 189s Platform: x86_64-pc-linux-gnu 189s 189s R is free software and comes with ABSOLUTELY NO WARRANTY. 189s You are welcome to redistribute it under certain conditions. 189s Type 'license()' or 'licence()' for distribution details. 189s 189s R is a collaborative project with many contributors. 189s Type 'contributors()' for more information and 189s 'citation()' on how to cite R or R packages in publications. 189s 189s Type 'demo()' for some demos, 'help()' for on-line help, or 189s 'help.start()' for an HTML browser interface to help. 189s Type 'q()' to quit R. 189s 190s > library(survey) 190s Loading required package: grid 190s Loading required package: Matrix 190s Loading required package: survival 190s 190s Attaching package: 'survey' 190s 190s The following object is masked from 'package:graphics': 190s 190s dotchart 190s 190s > library(survival) 190s > data(nwtco) 190s > 190s > ntwco<-subset(nwtco, !is.na(edrel)) 190s > 190s > load("nwtco-subcohort.rda") 190s > nwtco$subcohort<-subcohort 190s > 190s > d_BorganII <- twophase(id=list(~seqno,~seqno), 190s + strata=list(NULL,~interaction(instit,rel)), 190s + data=nwtco, subset=~I(rel |subcohort)) 191s > 191s > ##Coefficient results same as Splus with code from 191s > ## http://faculty.washington.edu/norm/software.html 191s > ## SE slightly larger due to using sandwich variance. 191s > 191s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganII) 191s Call: 191s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 191s I(age/12), design = d_BorganII) 191s 191s coef exp(coef) se(coef) robust se z p 191s factor(stage)2 0.46286 1.58861 0.23762 0.18087 2.559 0.01049 191s factor(stage)3 0.58309 1.79156 0.23965 0.17848 3.267 0.00109 191s factor(stage)4 1.05967 2.88541 0.26182 0.20524 5.163 2.43e-07 191s factor(histol)2 1.59744 4.94035 0.17688 0.13342 11.973 < 2e-16 191s I(age/12) 0.02994 1.03039 0.02942 0.03337 0.897 0.36972 191s 191s Likelihood ratio test= on 5 df, p= 191s n= 1062, number of events= 571 191s > 191s > ## 191s > ## This gives higher standard errors. calibrate() does not recompute the 191s > ## finite population correction if a calibration variable happens to predict 191s > ## sampling perfectly. It probably should. 191s > ## 191s > d_BorganIIps<-calibrate(twophase(id=list(~seqno,~seqno), 191s + strata=list(NULL,~rel), 191s + data=nwtco, subset=~I(rel |subcohort)), 191s + phase=2, formula=~interaction(instit,rel), 191s + epsilon=1e-10) 191s > 191s > svycoxph(Surv(edrel, rel)~factor(stage)+factor(histol)+I(age/12), design=d_BorganIIps) 191s Call: 191s svycoxph(formula = Surv(edrel, rel) ~ factor(stage) + factor(histol) + 191s I(age/12), design = d_BorganIIps) 191s 191s coef exp(coef) se(coef) robust se z p 191s factor(stage)2 0.46286 1.58861 0.23762 0.18076 2.561 0.01045 191s factor(stage)3 0.58309 1.79156 0.23965 0.17838 3.269 0.00108 191s factor(stage)4 1.05967 2.88541 0.26182 0.20513 5.166 2.39e-07 191s factor(histol)2 1.59744 4.94035 0.17688 0.13044 12.246 < 2e-16 191s I(age/12) 0.02994 1.03039 0.02942 0.03331 0.899 0.36876 191s 191s Likelihood ratio test= on 5 df, p= 191s n= 1062, number of events= 571 191s > 191s BEGIN TEST nwts.R 191s 191s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 191s Copyright (C) 2025 The R Foundation for Statistical Computing 191s Platform: x86_64-pc-linux-gnu 191s 191s R is free software and comes with ABSOLUTELY NO WARRANTY. 191s You are welcome to redistribute it under certain conditions. 191s Type 'license()' or 'licence()' for distribution details. 191s 191s R is a collaborative project with many contributors. 191s Type 'contributors()' for more information and 191s 'citation()' on how to cite R or R packages in publications. 191s 191s Type 'demo()' for some demos, 'help()' for on-line help, or 191s 'help.start()' for an HTML browser interface to help. 191s Type 'q()' to quit R. 191s 191s > 191s > ## examples from Breslow & Chatterjee: Applied Statistics 1999 No. 4, p458 191s > ## data from Norman Breslow's web page. 191s > library(survey) 191s Loading required package: grid 191s Loading required package: Matrix 191s Loading required package: survival 192s 192s Attaching package: 'survey' 192s 192s The following object is masked from 'package:graphics': 192s 192s dotchart 192s 192s > load("nwts.rda") 192s > nwtsnb<-nwts 192s > nwtsnb$case<-nwts$case-nwtsb$case 192s > nwtsnb$control<-nwts$control-nwtsb$control 192s > 192s > a<-rbind(nwtsb,nwtsnb) 192s > a$in.ccs<-rep(c(TRUE,FALSE),each=16) 192s > 192s > b<-rbind(a,a) 192s > b$rel<-rep(c(1,0),each=32) 192s > b$n<-ifelse(b$rel,b$case,b$control) 192s > 192s > index<-rep(1:64,b$n) 192s > 192s > nwt.exp<-b[index,c(1:3,6,7)] 192s > nwt.exp$id<-1:4088 192s > 192s > dccs2<-twophase(id=list(~id,~id),subset=~in.ccs, 192s + strata=list(NULL,~interaction(instit,rel)),data=nwt.exp) 192s > 192s > dccs8<-twophase(id=list(~id,~id),subset=~in.ccs, 192s + strata=list(NULL,~interaction(instit,stage,rel)),data=nwt.exp) 192s > 192s > gccs8<-calibrate(dccs2,phase=2,formula=~interaction(instit,stage,rel)) 192s > 192s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs2)) 192s 192s Call: 192s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs2, 192s family = quasibinomial) 192s 192s Survey design: 192s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 192s subset = subset, data = data, pps = pps) 192s 192s Coefficients: 192s Estimate Std. Error t value Pr(>|t|) 192s (Intercept) -2.5701 0.1288 -19.955 < 2e-16 *** 192s factor(stage)2 0.5482 0.1979 2.769 0.005708 ** 192s factor(stage)3 0.4791 0.2032 2.359 0.018515 * 192s factor(stage)4 1.0037 0.2592 3.872 0.000114 *** 192s factor(histol)2 1.3505 0.3107 4.346 1.51e-05 *** 192s factor(stage)2:factor(histol)2 0.1152 0.4410 0.261 0.793876 192s factor(stage)3:factor(histol)2 0.5066 0.4241 1.194 0.232548 192s factor(stage)4:factor(histol)2 0.9785 0.6214 1.575 0.115615 192s --- 192s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 192s 192s (Dispersion parameter for quasibinomial family taken to be 1.000876) 192s 192s Number of Fisher Scoring iterations: 4 192s 192s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=dccs8)) 192s 192s Call: 192s svyglm(formula = rel ~ factor(stage) * factor(histol), design = dccs8, 192s family = quasibinomial) 192s 192s Survey design: 192s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 192s subset = subset, data = data, pps = pps) 192s 192s Coefficients: 192s Estimate Std. Error t value Pr(>|t|) 192s (Intercept) -2.71604 0.10827 -25.085 < 2e-16 *** 192s factor(stage)2 0.78141 0.14726 5.306 1.35e-07 *** 192s factor(stage)3 0.80093 0.15250 5.252 1.80e-07 *** 192s factor(stage)4 1.07293 0.17817 6.022 2.33e-09 *** 192s factor(histol)2 1.45836 0.31780 4.589 4.96e-06 *** 192s factor(stage)2:factor(histol)2 -0.04743 0.43495 -0.109 0.913 192s factor(stage)3:factor(histol)2 0.28064 0.41298 0.680 0.497 192s factor(stage)4:factor(histol)2 0.90983 0.63774 1.427 0.154 192s --- 192s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 192s 192s (Dispersion parameter for quasibinomial family taken to be 1.000876) 192s 192s Number of Fisher Scoring iterations: 4 192s 192s > summary(svyglm(rel~factor(stage)*factor(histol),family=quasibinomial,design=gccs8)) 192s 192s Call: 192s svyglm(formula = rel ~ factor(stage) * factor(histol), design = gccs8, 192s family = quasibinomial) 192s 192s Survey design: 192s calibrate(dccs2, phase = 2, formula = ~interaction(instit, stage, 192s rel)) 192s 192s Coefficients: 192s Estimate Std. Error t value Pr(>|t|) 192s (Intercept) -2.71604 0.10878 -24.968 < 2e-16 *** 192s factor(stage)2 0.78141 0.14729 5.305 1.35e-07 *** 192s factor(stage)3 0.80093 0.15212 5.265 1.68e-07 *** 192s factor(stage)4 1.07293 0.17905 5.993 2.77e-09 *** 192s factor(histol)2 1.45836 0.31757 4.592 4.88e-06 *** 192s factor(stage)2:factor(histol)2 -0.04743 0.43432 -0.109 0.913 192s factor(stage)3:factor(histol)2 0.28064 0.41231 0.681 0.496 192s factor(stage)4:factor(histol)2 0.90983 0.63187 1.440 0.150 192s --- 192s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 192s 192s (Dispersion parameter for quasibinomial family taken to be 1.000876) 192s 192s Number of Fisher Scoring iterations: 4 192s 192s > 192s > ## check subsets of calibrated designs. 192s > summary(svyglm(rel~factor(stage), 192s + family=quasibinomial,design=subset(dccs8,histol==1))) 192s Warning messages: 192s 1: In `[.twophase2`(x, r, ) : 1 strata have only one PSU in this subset. 192s 192s Call: 192s svyglm(formula = rel ~ factor(stage), design = subset(dccs8, 192s histol == 1), family = quasibinomial) 192s 192s Survey design: 192s subset(dccs8, histol == 1) 192s 192s Coefficients: 192s Estimate Std. Error t value Pr(>|t|) 192s (Intercept) -2.7160 0.1083 -25.085 < 2e-16 *** 192s factor(stage)2 0.7814 0.1473 5.306 1.48e-07 *** 192s factor(stage)3 0.8009 0.1525 5.252 1.97e-07 *** 192s factor(stage)4 1.0729 0.1782 6.022 2.73e-09 *** 192s --- 192s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 192s 192s (Dispersion parameter for quasibinomial family taken to be 1.001333) 192s 192s Number of Fisher Scoring iterations: 4 192s 192s 2: In summary.glm(g) : 192s observations with zero weight not used for calculating dispersion 192s 3: In summary.glm(glm.object) : 192s observations with zero weight not used for calculating dispersion 192s 4: In `[.twophase2`(design, nas == 0, ) : 192s 1 strata have only one PSU in this subset. 192s 5: In `[.twophase2`(design, nas == 0, ) : 192s 1 strata have only one PSU in this subset. 192s > summary(svyglm(rel~factor(stage), 192s + family=quasibinomial,design=subset(gccs8,histol==1))) 192s 192s Call: 192s svyglm(formula = rel ~ factor(stage), design = subset(gccs8, 192s histol == 1), family = quasibinomial) 192s 192s Survey design: 192s subset(gccs8, histol == 1) 192s 192s Coefficients: 192s Warning messages: 192s 1: In summary.glm(g) : 192s observations with zero weight not used for calculating dispersion 192s 2: In summary.glm(glm.object) : 192s observations with zero weight not used for calculating dispersion 192s Estimate Std. Error t value Pr(>|t|) 192s (Intercept) -2.7160 0.1082 -25.105 < 2e-16 *** 192s factor(stage)2 0.7814 0.1457 5.363 1.10e-07 *** 192s factor(stage)3 0.8009 0.1504 5.324 1.34e-07 *** 192s factor(stage)4 1.0729 0.1759 6.101 1.70e-09 *** 192s --- 192s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 192s 192s (Dispersion parameter for quasibinomial family taken to be 1.001333) 192s 192s Number of Fisher Scoring iterations: 4 192s 192s > 192s > 192s BEGIN TEST poisson.R 192s 192s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 192s Copyright (C) 2025 The R Foundation for Statistical Computing 192s Platform: x86_64-pc-linux-gnu 192s 192s R is free software and comes with ABSOLUTELY NO WARRANTY. 192s You are welcome to redistribute it under certain conditions. 192s Type 'license()' or 'licence()' for distribution details. 192s 192s R is a collaborative project with many contributors. 192s Type 'contributors()' for more information and 192s 'citation()' on how to cite R or R packages in publications. 192s 192s Type 'demo()' for some demos, 'help()' for on-line help, or 192s 'help.start()' for an HTML browser interface to help. 192s Type 'q()' to quit R. 192s 192s > ## check poisson sampling 192s > library(survey) 192s Loading required package: grid 192s Loading required package: Matrix 193s Loading required package: survival 193s 193s Attaching package: 'survey' 193s 193s The following object is masked from 'package:graphics': 193s 193s dotchart 193s 193s > data(api) 193s > set.seed(2021-7-15) 193s > apipop$prob<-apipop$api00/1000 193s > insample<-rbinom(nrow(apipop),1,apipop$prob) 193s > apipois<-apipop[insample,] 193s > des<-svydesign(id=~1, prob=~prob, pps=poisson_sampling(apipois$prob), data=apipois) 193s > 193s > stopifnot(isTRUE(all.equal( 193s + as.vector(SE(svytotal(~api00,design=des))), 193s + as.vector(sqrt(sum( (apipois$api00*weights(des))^2*(1-apipois$prob)))) 193s + ))) 193s > 193s > 193s BEGIN TEST pps.R 193s 193s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 193s Copyright (C) 2025 The R Foundation for Statistical Computing 193s Platform: x86_64-pc-linux-gnu 193s 193s R is free software and comes with ABSOLUTELY NO WARRANTY. 193s You are welcome to redistribute it under certain conditions. 193s Type 'license()' or 'licence()' for distribution details. 193s 193s R is a collaborative project with many contributors. 193s Type 'contributors()' for more information and 193s 'citation()' on how to cite R or R packages in publications. 193s 193s Type 'demo()' for some demos, 'help()' for on-line help, or 193s 'help.start()' for an HTML browser interface to help. 193s Type 'q()' to quit R. 193s 193s > library(survey) 193s Loading required package: grid 193s Loading required package: Matrix 194s Loading required package: survival 194s 194s Attaching package: 'survey' 194s 194s The following object is masked from 'package:graphics': 194s 194s dotchart 194s 194s > data(election) 194s > 194s > dpps<- svydesign(id=~1, weights=~wt, fpc=~p, data=election_pps, pps="brewer") 194s > dppswr <-svydesign(id=~1, weights=~wt, data=election_pps) 194s > svytotal(~Bush+Kerry+Nader, dpps) 194s total SE 194s Bush 64518472 2447629 194s Kerry 51202102 2450787 194s Nader 478530 102420 194s > svytotal(~Bush+Kerry+Nader, dppswr) 194s total SE 194s Bush 64518472 2671455 194s Kerry 51202102 2679433 194s Nader 478530 105303 194s > 194s > ##subsets 194s > svytotal(~Bush+Kerry+Nader, subset(dpps, Nader>0)) 194s total SE 194s Bush 34944285 5399833 194s Kerry 25581714 4028434 194s Nader 478530 102420 194s > 194s > ##multistage: should agree with STRS analysis 194s > data(api) 194s > dclus2<-svydesign(id = ~dnum + snum, fpc = ~fpc1 + fpc2, data = apiclus2) 194s > dclus2pps<-svydesign(id = ~dnum + snum, fpc = ~I(40/fpc1) + I(pmin(1,5/fpc2)), data = apiclus2) 194s > 194s > all.equal(svytotal(~sch.wide,dclus2), svytotal(~sch.wide,dclus2pps)) 194s [1] TRUE 194s > all.equal(svymean(~sch.wide,dclus2), svymean(~sch.wide,dclus2pps)) 194s [1] TRUE 194s > all.equal(svytotal(~enroll,dclus2), svytotal(~enroll,dclus2pps)) 194s [1] TRUE 194s > 194s > ## the new without-replacement methods 194s > data(election) 194s > dpps_br<- svydesign(id=~1, fpc=~p, data=election_pps, pps="brewer") 194s > dpps_ov<- svydesign(id=~1, fpc=~p, data=election_pps, pps="overton") 194s > dpps_hr<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40)) 194s > dpps_hr1<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR()) 194s > dpps_ht<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob)) 194s > ## Yates-Grundy type 194s > dpps_yg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=ppsmat(election_jointprob),variance="YG") 194s > dpps_hryg<- svydesign(id=~1, fpc=~p, data=election_pps, pps=HR(sum(election$p^2)/40),variance="YG") 194s > 194s > ## The with-replacement approximation 194s > svytotal(~Bush+Kerry+Nader, dpps_ht) 194s total SE 194s Bush 64518472 2604404 194s Kerry 51202102 2523712 194s Nader 478530 102326 194s > svytotal(~Bush+Kerry+Nader, dpps_yg) 194s total SE 194s Bush 64518472 2406526 194s Kerry 51202102 2408091 194s Nader 478530 101664 194s > svytotal(~Bush+Kerry+Nader, dpps_hr) 194s total SE 194s Bush 64518472 2624662 194s Kerry 51202102 2525222 194s Nader 478530 102793 194s > svytotal(~Bush+Kerry+Nader, dpps_hryg) 194s total SE 194s Bush 64518472 2436738 194s Kerry 51202102 2439845 194s Nader 478530 102016 194s > svytotal(~Bush+Kerry+Nader, dpps_hr1) 194s total SE 194s Bush 64518472 2472753 194s Kerry 51202102 2426842 194s Nader 478530 102595 194s > svytotal(~Bush+Kerry+Nader, dpps_br) 194s total SE 194s Bush 64518472 2447629 194s Kerry 51202102 2450787 194s Nader 478530 102420 194s > svytotal(~Bush+Kerry+Nader, dpps_ov) 194s total SE 194s Bush 64518472 2939608 194s Kerry 51202102 1964632 194s Nader 478530 104373 194s > 194s > ## subsets 194s > svytotal(~Bush+Kerry+Nader, subset(dpps_ht, Nader>0)) 194s total SE 194s Bush 34944285 5406348 194s Kerry 25581714 4047741 194s Nader 478530 102326 194s > svytotal(~Bush+Kerry+Nader, subset(dpps_hryg, Nader>0)) 194s total SE 194s Bush 34944285 5377659 194s Kerry 25581714 4010908 194s Nader 478530 102016 194s > 194s > ## counts 194s > svyby(~Bush+Kerry+Nader,~I(Nader>0), unwtd.count,design=dpps_ht) 194s I(Nader > 0) counts se 194s FALSE FALSE 19 0 194s TRUE TRUE 21 0 194s > 194s BEGIN TEST qrule-swiss.R 194s 194s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 194s Copyright (C) 2025 The R Foundation for Statistical Computing 194s Platform: x86_64-pc-linux-gnu 194s 194s R is free software and comes with ABSOLUTELY NO WARRANTY. 194s You are welcome to redistribute it under certain conditions. 194s Type 'license()' or 'licence()' for distribution details. 194s 194s R is a collaborative project with many contributors. 194s Type 'contributors()' for more information and 194s 'citation()' on how to cite R or R packages in publications. 194s 194s Type 'demo()' for some demos, 'help()' for on-line help, or 194s 'help.start()' for an HTML browser interface to help. 194s Type 'q()' to quit R. 194s 194s > library(survey) 194s Loading required package: grid 194s Loading required package: Matrix 195s Loading required package: survival 195s 195s Attaching package: 'survey' 195s 195s The following object is masked from 'package:graphics': 195s 195s dotchart 195s 195s > 195s > data_no_strat <- data.frame(x = 1:10, id = 1:10, fpc = 10, probs = 1) 195s > 195s > design_no_strat <- svydesign(id = ~id, 195s + probs = ~probs, 195s + data = data_no_strat, 195s + fpc = ~fpc) 195s > 195s > quantiles <- c(0.01, 0.05, 0.1, 0.15, seq(21, 81, 10)*0.01, 0.85, 0.9, 0.95, 0.99) 195s > 195s > res <- svyquantile(~x, design_no_strat, quantiles, ci = TRUE, 195s + interval.type = "mean", qrule = "hf1") 195s > 195s > stopifnot(all(diff(res$x[,"quantile"])>=0)) 195s > 195s > 195s > 195s BEGIN TEST quantile.R 195s 195s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 195s Copyright (C) 2025 The R Foundation for Statistical Computing 195s Platform: x86_64-pc-linux-gnu 195s 195s R is free software and comes with ABSOLUTELY NO WARRANTY. 195s You are welcome to redistribute it under certain conditions. 195s Type 'license()' or 'licence()' for distribution details. 195s 195s R is a collaborative project with many contributors. 195s Type 'contributors()' for more information and 195s 'citation()' on how to cite R or R packages in publications. 195s 195s Type 'demo()' for some demos, 'help()' for on-line help, or 195s 'help.start()' for an HTML browser interface to help. 195s Type 'q()' to quit R. 195s 195s > library(survey) 195s Loading required package: grid 195s Loading required package: Matrix 195s Loading required package: survival 196s 196s Attaching package: 'survey' 196s 196s > set.seed(42) 196s > 196s > df<-data.frame(x=exp(rnorm(1000))) 196s The following object is masked from 'package:graphics': 196s 196s dotchart 196s 196s > df$y<-round(df$x,1) 196s > ddf<-svydesign(id=~1,data=df) 196s > rdf<-as.svrepdesign(ddf) 196s Warning message: 196s In svydesign.default(id = ~1, data = df) : 196s No weights or probabilities supplied, assuming equal probability 196s > 196s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 196s 0.01 0.1 0.5 0.9 0.99 196s 0.01543792 0.01264453 0.03386225 0.16131948 2.10605799 196s > 196s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 196s x 196s q0.01 0.01554946 196s q0.1 0.01425828 196s q0.5 0.03428012 196s q0.9 0.16457488 196s q0.99 1.88672412 196s > 196s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 196s 0.01 0.1 0.5 0.9 0.99 196s 0.01545209 0.01265608 0.03388011 0.16145776 2.10061576 196s > 196s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 196s x 196s q0.01 0.01556240 196s q0.1 0.01420086 196s q0.5 0.03430175 196s q0.9 0.16461019 196s q0.99 1.88818131 196s > 196s > 196s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 196s $quantiles 196s 0.01 0.1 0.5 0.9 0.99 196s y 0.02352941 0.2230769 0.9340909 3.55 9.4 196s 196s $CIs 196s , , y 196s 196s 0.01 0.1 0.5 0.9 0.99 196s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 196s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 196s 196s 196s > 196s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 196s Statistic: 196s y 196s q0.01 0.1 196s q0.1 0.3 196s q0.5 1.0 196s q0.9 3.6 196s q0.99 9.4 196s SE: 196s y 196s q0.01 0.02547977 196s q0.1 0.02547977 196s q0.5 0.02547977 196s q0.9 0.15287859 196s q0.99 1.88302540 196s > 196s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 196s $quantiles 196s 0.01 0.1 0.5 0.9 0.99 196s y 0.02352941 0.2230769 0.9340909 3.55 9.4 196s 196s $CIs 196s , , y 196s 196s 0.01 0.1 0.5 0.9 0.99 196s (lower 0.01594200 0.2020115 0.8578143 3.207543 7.568142 196s upper) 0.03287947 0.2467045 1.0059815 3.862241 14.978632 196s 196s 196s > 196s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 196s Statistic: 196s y 196s q0.01 0.1 196s q0.1 0.3 196s q0.5 1.0 196s q0.9 3.6 196s q0.99 9.4 196s SE: 196s y 196s q0.01 0.02551067 196s q0.1 0.02551067 196s q0.5 0.02551067 196s q0.9 0.15306404 196s q0.99 1.88450896 196s > 196s > 196s > 196s > df<-data.frame(x=exp(rnorm(20))) 196s > Warning message: 196s In svydesign.default(id = ~1, data = df) : 196s No weights or probabilities supplied, assuming equal probability 196s df$y<-round(df$x,1) 196s > ddf<-svydesign(id=~1,data=df) 196s > rdf<-as.svrepdesign(ddf) 196s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 196s 0.01 0.1 0.5 0.9 0.99 196s 0.03576771 0.07329496 0.30149917 2.03440784 1.88468597 196s > 196s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE)) 196s x 196s q0.01 0.00000000 196s q0.1 0.04598541 196s q0.5 0.25943731 196s q0.9 2.12343073 196s q0.99 1.91998924 196s > 196s > SE(oldsvyquantile(~x,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 196s 0.01 0.1 0.5 0.9 0.99 196s 0.03637398 0.07470310 0.29938115 2.16381289 2.00708994 196s > 196s > SE(oldsvyquantile(~x,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,df=Inf)) 196s x 196s q0.01 0.00000000 196s q0.1 0.04732818 196s q0.5 0.24957966 196s q0.9 2.25211815 196s q0.99 2.04043154 196s > 196s > 196s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald") 196s $quantiles 196s 0.01 0.1 0.5 0.9 0.99 196s y 0.1 0.15 0.75 2.4 8.68 196s 196s $CIs 196s , , y 196s 196s 0.01 0.1 0.5 0.9 0.99 196s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 196s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 196s 196s 196s > 196s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE) 196s Statistic: 196s y 196s q0.01 0.10 196s q0.1 0.20 196s q0.5 0.80 196s q0.9 2.40 196s q0.99 8.68 196s SE: 196s y 196s q0.01 0.00000000 196s q0.1 0.02611112 196s q0.5 0.26542051 196s q0.9 2.10908603 196s q0.99 1.91777710 196s > 196s > oldsvyquantile(~y,ddf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE,ties="rounded",interval.type="betaWald",df=Inf) 196s $quantiles 196s 0.01 0.1 0.5 0.9 0.99 196s y 0.1 0.15 0.75 2.4 8.68 196s 196s $CIs 196s , , y 196s 196s 0.01 0.1 0.5 0.9 0.99 196s (lower 0.100000 0.1000000 0.3674054 1.352279 0.5674674 196s upper) 1.132533 0.3464541 1.6303784 8.473337 10.2000000 196s 196s 196s > 196s > oldsvyquantile(~y,rdf, c(0.01,0.1,0.5,0.9,0.99),ci=TRUE, df=Inf) 196s Statistic: 196s y 196s q0.01 0.10 196s q0.1 0.20 196s q0.5 0.80 196s q0.9 2.40 196s q0.99 8.68 196s SE: 196s y 196s q0.01 0.00000000 196s q0.1 0.02551067 196s q0.5 0.25244616 196s q0.9 2.23558589 196s q0.99 2.03881114 196s > 196s BEGIN TEST quantiles-chile.R 196s 196s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 196s Copyright (C) 2025 The R Foundation for Statistical Computing 196s Platform: x86_64-pc-linux-gnu 196s 196s R is free software and comes with ABSOLUTELY NO WARRANTY. 196s You are welcome to redistribute it under certain conditions. 196s Type 'license()' or 'licence()' for distribution details. 196s 196s R is a collaborative project with many contributors. 196s Type 'contributors()' for more information and 196s 'citation()' on how to cite R or R packages in publications. 196s 196s Type 'demo()' for some demos, 'help()' for on-line help, or 196s 'help.start()' for an HTML browser interface to help. 196s Type 'q()' to quit R. 196s 196s Loading required package: grid 196s > library(survey) 196s Loading required package: Matrix 197s Loading required package: survival 197s > datos <- readRDS("datos_ejemplo.rds") 197s > 197s > design <- svydesign(id = ~id_directorio, strata = ~estrato, weights = ~f_pers, check.strata = TRUE, data = datos) 197s 197s Attaching package: 'survey' 197s 197s The following object is masked from 'package:graphics': 197s 197s dotchart 197s 197s > set.seed(234262762) 197s > repdesign <- as.svrepdesign(design, type = "subbootstrap", replicates=20) 197s > options(survey.lonely.psu="remove") 197s > 197s > values<-datos$ing_t_p[datos$CL_GRUPO_OCU_08=="ISCO08_6"] 197s > 197s > suppressWarnings({ 197s + f0<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 197s + f0.5<-coef(svyquantile(~ing_t_p, subset(design,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 197s + }) 197s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 197s [1] TRUE 197s > 197s > suppressWarnings({ 197s + f0<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="math")) 197s + f0.5<-coef(svyquantile(~ing_t_p, subset(repdesign,CL_GRUPO_OCU_08=="ISCO08_6"),quantiles=c(0.5), qrule="school")) 197s + }) 197s > all.equal(c(values[1],mean(values)), as.vector(c(f0,f0.5))) 197s [1] TRUE 197s > 197s BEGIN TEST rakecheck.R 197s 197s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 197s Copyright (C) 2025 The R Foundation for Statistical Computing 197s Platform: x86_64-pc-linux-gnu 197s 197s R is free software and comes with ABSOLUTELY NO WARRANTY. 197s You are welcome to redistribute it under certain conditions. 197s Type 'license()' or 'licence()' for distribution details. 197s 197s R is a collaborative project with many contributors. 197s Type 'contributors()' for more information and 197s 'citation()' on how to cite R or R packages in publications. 197s 197s Type 'demo()' for some demos, 'help()' for on-line help, or 197s 'help.start()' for an HTML browser interface to help. 197s Type 'q()' to quit R. 197s 197s > library(survey) 197s Loading required package: grid 197s Loading required package: Matrix 198s Loading required package: survival 198s 198s Attaching package: 'survey' 198s 198s The following object is masked from 'package:graphics': 198s 198s dotchart 198s 198s > 198s > data(api) 198s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 198s > rclus1 <- as.svrepdesign(dclus1) 198s > 198s > ## population marginal totals for each stratum 198s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 198s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 198s > 198s > rclus1r <- rake(rclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 198s > 198s > svymean(~api00, rclus1r) 198s mean SE 198s api00 641.23 26.873 198s > svytotal(~enroll, rclus1r) 198s total SE 198s enroll 3647300 463511 198s > 198s > ff<-~stype+sch.wide 198s > poptotals<-colSums(model.matrix(ff,model.frame(ff,apipop))) 198s > rclus1g<-calibrate(rclus1, ~stype+sch.wide, poptotals,calfun="raking") 198s > 198s > svymean(~api00,rclus1g) 198s mean SE 198s api00 641.23 26.874 198s > svytotal(~enroll,rclus1g) 198s total SE 198s enroll 3647280 463582 198s > 198s > summary(weights(rclus1g)/weights(rclus1r)) 198s V1 V2 V3 V4 V5 V6 198s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 198s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 198s Median :1 Median :1 Median :1 Median :1 Median :1 Median :1 198s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 198s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 198s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 198s NA's :11 NA's :4 NA's :2 NA's :13 NA's :2 NA's :4 198s V7 V8 V9 V10 V11 198s Min. :1 Min. :1 Min. :1 Min. :1 Min. :1 198s 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 1st Qu.:1 198s Median :1 Median :1 Median :1 Median :1 Median :1 198s Mean :1 Mean :1 Mean :1 Mean :1 Mean :1 198s 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 198s Max. :1 Max. :1 Max. :1 Max. :1 Max. :1 198s NA's :4 NA's :16 NA's :9 NA's :34 NA's :21 198s V12 V13 V14 V15 198s Min. :0.9997 Min. :1 Min. :1 Min. :1 198s 1st Qu.:1.0001 1st Qu.:1 1st Qu.:1 1st Qu.:1 198s Median :1.0001 Median :1 Median :1 Median :1 198s Mean :1.0000 Mean :1 Mean :1 Mean :1 198s 3rd Qu.:1.0001 3rd Qu.:1 3rd Qu.:1 3rd Qu.:1 198s Max. :1.0002 Max. :1 Max. :1 Max. :1 198s NA's :37 NA's :13 NA's :1 NA's :12 198s > 198s > 198s > ## Do it for a design without replicate weights 198s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 198s > 198s > svymean(~api00, dclus1r) 198s mean SE 198s api00 641.23 23.704 198s > svytotal(~enroll, dclus1r) 198s total SE 198s enroll 3647300 400603 198s > 198s > dclus1g<-calibrate(dclus1, ~stype+sch.wide, poptotals,calfun="raking") 198s > 198s > svymean(~api00,dclus1g) 198s mean SE 198s api00 641.23 23.704 198s > svytotal(~enroll,dclus1g) 198s total SE 198s enroll 3647280 400603 198s > 198s > summary(weights(dclus1g)/weights(dclus1r)) 198s Min. 1st Qu. Median Mean 3rd Qu. Max. 198s 1 1 1 1 1 1 198s > 198s > 198s > 198s > ## Example of raking with partial joint distributions 198s > pop.table <- xtabs(~stype+sch.wide,apipop) 198s > pop.imp<-data.frame(comp.imp=c("No","Yes"),Freq=c(1712,4482)) 198s > dclus1r2<-rake(dclus1, list(~stype+sch.wide, ~comp.imp), 198s + list(pop.table, pop.imp)) 198s > svymean(~api00, dclus1r2) 198s mean SE 198s api00 642.62 22.732 198s > 198s > ff1 <-~stype*sch.wide+comp.imp 198s > 198s > poptotals1<-colSums(model.matrix(ff1,model.frame(ff1,apipop))) 198s > dclus1g2<-calibrate(dclus1, ~stype*sch.wide+comp.imp, poptotals1, calfun="raking") 198s > 198s > svymean(~api00, dclus1g2) 198s mean SE 198s api00 642.61 22.731 198s > 198s > summary(weights(dclus1r2)/weights(dclus1g2)) 198s Min. 1st Qu. Median Mean 3rd Qu. Max. 198s 0.999 1.000 1.000 1.000 1.000 1.002 198s > 198s BEGIN TEST raowuboot.R 198s 198s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 198s Copyright (C) 2025 The R Foundation for Statistical Computing 198s Platform: x86_64-pc-linux-gnu 198s 198s R is free software and comes with ABSOLUTELY NO WARRANTY. 198s You are welcome to redistribute it under certain conditions. 198s Type 'license()' or 'licence()' for distribution details. 198s 198s R is a collaborative project with many contributors. 198s Type 'contributors()' for more information and 198s 'citation()' on how to cite R or R packages in publications. 198s 198s Type 'demo()' for some demos, 'help()' for on-line help, or 198s 'help.start()' for an HTML browser interface to help. 198s Type 'q()' to quit R. 198s 198s > ## regression test for bug reported by Richard Valliant 198s > library(survey) 198s Loading required package: grid 198s Loading required package: Matrix 199s Loading required package: survival 199s > s<-subbootweights(c(1,1),1:2, 50) 199s 199s Attaching package: 'survey' 199s 199s The following object is masked from 'package:graphics': 199s 199s dotchart 199s 199s > stopifnot(all(s$repweights$weights %in% c(0,2))) 199s > 199s BEGIN TEST regTermTest-missing.R 199s 199s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 199s Copyright (C) 2025 The R Foundation for Statistical Computing 199s Platform: x86_64-pc-linux-gnu 199s 199s R is free software and comes with ABSOLUTELY NO WARRANTY. 199s You are welcome to redistribute it under certain conditions. 199s Type 'license()' or 'licence()' for distribution details. 199s 199s R is a collaborative project with many contributors. 199s Type 'contributors()' for more information and 199s 'citation()' on how to cite R or R packages in publications. 199s 199s Type 'demo()' for some demos, 'help()' for on-line help, or 199s 'help.start()' for an HTML browser interface to help. 199s Type 'q()' to quit R. 199s 199s > library(survey) 199s Loading required package: grid 199s Loading required package: Matrix 199s Loading required package: survival 199s 199s Attaching package: 'survey' 199s 199s The following object is masked from 'package:graphics': 199s 199s dotchart 199s 199s > data(nhanes) 199s > design <- svydesign(id=~SDMVPSU, strata=~SDMVSTRA, weights=~WTMEC2YR, nest=TRUE,data=nhanes) 199s > 199s > a<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design = subset(design,!is.na(HI_CHOL)), family=quasibinomial) 200s > b<-svyglm(formula = I(race == 1) ~ HI_CHOL + agecat + RIAGENDR, design =design , family=quasibinomial) 200s > 200s > ta<-regTermTest(a, ~HI_CHOL) 200s > tb<-regTermTest(b, ~HI_CHOL) 200s > 200s > stopifnot(isTRUE(all.equal(ta$chisq, tb$chisq))) 200s > stopifnot(isTRUE(all.equal(ta$lambda, tb$lambda))) 200s > 200s BEGIN TEST regpredict.R 200s 200s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 200s Copyright (C) 2025 The R Foundation for Statistical Computing 200s Platform: x86_64-pc-linux-gnu 200s 200s R is free software and comes with ABSOLUTELY NO WARRANTY. 200s You are welcome to redistribute it under certain conditions. 200s Type 'license()' or 'licence()' for distribution details. 200s 200s R is a collaborative project with many contributors. 200s Type 'contributors()' for more information and 200s 'citation()' on how to cite R or R packages in publications. 200s 200s Type 'demo()' for some demos, 'help()' for on-line help, or 200s 'help.start()' for an HTML browser interface to help. 200s Type 'q()' to quit R. 200s 200s > library(survey) 200s Loading required package: grid 200s Loading required package: Matrix 200s Loading required package: survival 200s > data(api) 200s 200s Attaching package: 'survey' 200s 200s The following object is masked from 'package:graphics': 200s 200s dotchart 200s 200s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 200s > 200s > 200s > ## regression estimator of total, three ways 200s > pop<-data.frame(enroll=sum(apipop$enroll, na.rm=TRUE)) 200s > npop <- sum(!is.na(apipop$enroll)) 200s > 200s > api.reg <- svyglm(api.stu~enroll, design=dstrat) 200s > a <- predict(api.reg, newdata=pop, total=npop) 200s > b <- svytotal(~api.stu, calibrate(dstrat, ~enroll, pop=c(npop, pop$enroll))) 200s > 200s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 200s [1] TRUE 200s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 200s [1] TRUE 200s > if(!is.null(getOption("DEBUG"))){ ## uses 6194x6194 matrix 200s + d <- predict(api.reg, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 200s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 200s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 200s + } 200s > 200s > ## classical ratio estimator, four ways. 200s > api.reg2 <- svyglm(api.stu~enroll-1, design=dstrat, 200s + family=quasi(link="identity", var="mu")) 200s > 200s > a <- predict(api.reg2, newdata=pop, total=npop) 200s > b <- svytotal(~api.stu, 200s + calibrate(dstrat, ~enroll-1, pop= pop$enroll, variance=2)) 200s > e <- predict(svyratio(~api.stu, ~enroll, dstrat),total=pop$enroll) 200s > 200s > all.equal(as.vector(coef(a)),as.vector(coef(b))) 200s [1] TRUE 200s > all.equal(as.vector(SE(a)), as.vector(SE(b))) 200s [1] TRUE 200s > all.equal(as.vector(coef(a)),as.vector(e$total)) 200s [1] TRUE 200s > all.equal(as.vector(SE(a)), as.vector(e$se)) 200s [1] TRUE 200s > if(!is.null(getOption("DEBUG"))){## uses 6194x6194 matrix 200s + d <- predict(api.reg2, newdata=na.omit(apipop[,"enroll",drop=FALSE])) 200s + all.equal(as.vector(coef(a)), as.vector(sum(coef(d)))) 200s + all.equal(as.vector(SE(a)), as.vector(sqrt(sum(vcov(d))))) 200s + } 200s > 200s BEGIN TEST rss_scores.R 200s 200s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 200s Copyright (C) 2025 The R Foundation for Statistical Computing 200s Platform: x86_64-pc-linux-gnu 200s 200s R is free software and comes with ABSOLUTELY NO WARRANTY. 200s You are welcome to redistribute it under certain conditions. 200s Type 'license()' or 'licence()' for distribution details. 200s 200s R is a collaborative project with many contributors. 200s Type 'contributors()' for more information and 200s 'citation()' on how to cite R or R packages in publications. 200s 200s Type 'demo()' for some demos, 'help()' for on-line help, or 200s 'help.start()' for an HTML browser interface to help. 200s Type 'q()' to quit R. 200s 200s > ## Example from Rao, Scott, and Skinner 1998 Statistica Sinica 200s > library(survey) 200s Loading required package: grid 200s Loading required package: Matrix 201s Loading required package: survival 201s 201s Attaching package: 'survey' 201s 201s > data(myco) 201s The following object is masked from 'package:graphics': 201s 201s dotchart 201s 201s > dmyco<-svydesign(id=~1, strata=~interaction(Age,leprosy),weights=~wt,data=myco) 201s > m_full<-svyglm(leprosy~I((Age+7.5)^-2)+Scar, family=quasibinomial, design=dmyco) 201s > m_null<-svyglm(leprosy~I((Age+7.5)^-2), family=quasibinomial, design=dmyco) 201s > 201s > stopifnot(isTRUE(all.equal(coef(m_null), c(`(Intercept)`=-4.6, `I((Age + 7.5)^-2)`=-427),tol=1e-2))) 201s > 201s > s<-svyscoretest(m_full, ~Scar) 201s > stopifnot(abs(s[1]-10.73)<0.05) 201s > 201s > t<-svyscoretest(m_full,~Scar,method="individual") 201s > stopifnot(abs(coef(t)- -32.61)<0.1) 201s > stopifnot(abs(vcov(t)-99.1)<0.1) 201s > 201s > 201s BEGIN TEST scoping.R 201s 201s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 201s Copyright (C) 2025 The R Foundation for Statistical Computing 201s Platform: x86_64-pc-linux-gnu 201s 201s R is free software and comes with ABSOLUTELY NO WARRANTY. 201s You are welcome to redistribute it under certain conditions. 201s Type 'license()' or 'licence()' for distribution details. 201s 201s R is a collaborative project with many contributors. 201s Type 'contributors()' for more information and 201s 'citation()' on how to cite R or R packages in publications. 201s 201s Type 'demo()' for some demos, 'help()' for on-line help, or 201s 'help.start()' for an HTML browser interface to help. 201s Type 'q()' to quit R. 201s 201s > 201s > ## regression test for testing regression 201s > 201s > library(survey) 201s Loading required package: grid 201s Loading required package: Matrix 202s Loading required package: survival 202s 202s Attaching package: 'survey' 202s 202s > data(api) 202s The following object is masked from 'package:graphics': 202s 202s dotchart 202s 202s > 202s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 202s > 202s > 202s > f<-function(){ 202s + form<-acs.46~stype 202s + svyglm(formula=form, design = dstrat) 202s + } 202s > 202s > g<-function(form){ 202s + svyglm(formula=form, design = dstrat) 202s + } 202s > f() 202s Stratified Independent Sampling design 202s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 202s fpc = ~fpc) 202s 202s Call: svyglm(formula = form, design = dstrat) 202s 202s Coefficients: 202s (Intercept) stypeH stypeM 202s 28.7449 0.7551 0.4022 202s 202s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 202s (66 observations deleted due to missingness) 202s Null Deviance: 1838 202s Residual Deviance: 1835 AIC: 719.8 202s > g(acs.46~stype) 202s Stratified Independent Sampling design 202s svydesign(id = ~1, strata = ~stype, weights = ~pw, data = apistrat, 202s fpc = ~fpc) 202s 202s Call: svyglm(formula = form, design = dstrat) 202s 202s Coefficients: 202s (Intercept) stypeH stypeM 202s 28.7449 0.7551 0.4022 202s 202s Degrees of Freedom: 133 Total (i.e. Null); 129 Residual 202s (66 observations deleted due to missingness) 202s Null Deviance: 1838 202s Residual Deviance: 1835 AIC: 719.8 202s > 202s > f<-function(){ 202s + form<-Surv(acs.46)~stype 202s + svycoxph(formula=form, design = dstrat) 202s + } 202s > 202s > g<-function(form){ 202s + svycoxph(formula=form, design = dstrat) 202s + } 202s > 202s > f() 202s Call: 202s svycoxph(formula = form, design = dstrat) 202s 202s coef exp(coef) se(coef) robust se z p 202s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 202s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 202s 202s Likelihood ratio test= on 2 df, p= 202s n= 134, number of events= 134 202s (66 observations deleted due to missingness) 202s > g(Surv(acs.46)~stype) 202s Call: 202s svycoxph(formula = form, design = dstrat) 202s 202s coef exp(coef) se(coef) robust se z p 202s stypeH -0.6766 0.5083 1.0208 0.6652 -1.017 0.309 202s stypeM -0.2509 0.7781 0.2308 0.2089 -1.201 0.230 202s 202s Likelihood ratio test= on 2 df, p= 202s n= 134, number of events= 134 202s (66 observations deleted due to missingness) 202s > 202s > ## check coxph for a single predictor 202s > svycoxph(Surv(acs.46)~api00,design=dstrat) 202s Call: 202s svycoxph(formula = Surv(acs.46) ~ api00, design = dstrat) 202s 202s coef exp(coef) se(coef) robust se z p 202s api00 6.060e-06 1.000e+00 6.244e-04 7.492e-04 0.008 0.994 202s 202s Likelihood ratio test= on 1 df, p= 202s n= 134, number of events= 134 202s (66 observations deleted due to missingness) 202s > 202s BEGIN TEST survcurve.R 202s 202s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 202s Copyright (C) 2025 The R Foundation for Statistical Computing 202s Platform: x86_64-pc-linux-gnu 202s 202s R is free software and comes with ABSOLUTELY NO WARRANTY. 202s You are welcome to redistribute it under certain conditions. 202s Type 'license()' or 'licence()' for distribution details. 202s 202s R is a collaborative project with many contributors. 202s Type 'contributors()' for more information and 202s 'citation()' on how to cite R or R packages in publications. 202s 202s Type 'demo()' for some demos, 'help()' for on-line help, or 202s 'help.start()' for an HTML browser interface to help. 202s Type 'q()' to quit R. 202s 202s > library(survey) 202s Loading required package: grid 202s Loading required package: Matrix 203s Loading required package: survival 203s > library(survival) 203s > 203s > pbc2<-rbind(pbc,pbc) 203s 203s Attaching package: 'survey' 203s 203s The following object is masked from 'package:graphics': 203s 203s dotchart 203s 203s > pbc2$id<-rep(1:418,2) 203s > 203s > dpbc1<-svydesign(id=~1, data=pbc) 203s Warning message: 203s In svydesign.default(id = ~1, data = pbc) : 203s No weights or probabilities supplied, assuming equal probability 203s Warning message: 203s In svydesign.default(id = ~id, data = pbc2) : 203s No weights or probabilities supplied, assuming equal probability 203s > dpbc2<-svydesign(id=~id, data=pbc2) 203s > 203s > s1<-svykm(Surv(time,status>0)~1, subset(dpbc1, bili>6), se=TRUE) 203s > s2<-svykm(Surv(time,status>0)~1, subset(dpbc2, bili>6), se=TRUE) 203s > 203s > (c1<-confint(s1,(1:5)*365)) 203s 0.025 0.975 203s 365 0.6446215 0.8594153 203s 730 0.5410938 0.7766848 203s 1095 0.2683127 0.5103356 203s 1460 0.1444731 0.3722001 203s 1825 0.1009672 0.3204713 203s > (c2<-confint(s2,(1:5)*365)) 203s 0.025 0.975 203s 365 0.6446215 0.8594153 203s 730 0.5410938 0.7766848 203s 1095 0.2683127 0.5103356 203s 1460 0.1444731 0.3722001 203s 1825 0.1009672 0.3204713 203s > all.equal(c1, c2) 203s [1] TRUE 203s > 203s > m1<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc1) 203s > m2<-svycoxph(Surv(time,status>0)~log(bili), design=dpbc2) 203s > 203s > d<-data.frame(bili=c(5,10)) 203s > p1<-predict(m1, se=TRUE, newdata=d,type="curve") 203s > p2<-predict(m2, se=TRUE, newdata=d,type="curve") 204s > 204s > (pc1<-confint(p1[[1]],(1:5)*365)) 204s 0.025 0.975 204s 365 0.8410027 0.9266263 204s 730 0.7371114 0.8548312 204s 1095 0.5517779 0.7018583 204s 1460 0.4335073 0.5992819 204s 1825 0.3260899 0.5046241 204s > (pc2<-confint(p2[[1]],(1:5)*365)) 204s 0.025 0.975 204s 365 0.8409490 0.9267054 204s 730 0.7370152 0.8549432 204s 1095 0.5515848 0.7019513 204s 1460 0.4332252 0.5992968 204s 1825 0.3257172 0.5045795 204s > all.equal(pc1, pc2) 204s [1] "Mean relative difference: 0.0002070722" 204s > 204s > (q1<-quantile(p1[[2]])) 204s 0.75 0.5 0.25 204s 489 930 1492 204s > (q2<-quantile(p2[[2]])) 204s 0.75 0.5 0.25 204s 489 930 1492 204s > all.equal(q1,q2) 204s [1] TRUE 204s > 204s BEGIN TEST svyby-strings.R 204s 204s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 204s Copyright (C) 2025 The R Foundation for Statistical Computing 204s Platform: x86_64-pc-linux-gnu 204s 204s R is free software and comes with ABSOLUTELY NO WARRANTY. 204s You are welcome to redistribute it under certain conditions. 204s Type 'license()' or 'licence()' for distribution details. 204s 204s R is a collaborative project with many contributors. 204s Type 'contributors()' for more information and 204s 'citation()' on how to cite R or R packages in publications. 204s 204s Type 'demo()' for some demos, 'help()' for on-line help, or 204s 'help.start()' for an HTML browser interface to help. 204s Type 'q()' to quit R. 204s 204s > 204s > ## check that stringsAsFactors fixes the string levels problem 204s > data(api, package = "survey") 204s > des <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) 205s > est0 <- 205s + survey::svyby(design=des, formula=~cname, by=~both, FUN=survey::svymean, keep.var=TRUE, stringsAsFactors=TRUE) 205s > 205s > stopifnot(isTRUE(all(dim(est0)==c(2,23)))) 205s > 205s BEGIN TEST svyby_bug.R 205s 205s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 205s Copyright (C) 2025 The R Foundation for Statistical Computing 205s Platform: x86_64-pc-linux-gnu 205s 205s R is free software and comes with ABSOLUTELY NO WARRANTY. 205s You are welcome to redistribute it under certain conditions. 205s Type 'license()' or 'licence()' for distribution details. 205s 205s R is a collaborative project with many contributors. 205s Type 'contributors()' for more information and 205s 'citation()' on how to cite R or R packages in publications. 205s 205s Type 'demo()' for some demos, 'help()' for on-line help, or 205s 'help.start()' for an HTML browser interface to help. 205s Type 'q()' to quit R. 205s 205s > library(survey) 205s Loading required package: grid 205s Loading required package: Matrix 206s Loading required package: survival 206s > options(warn=2) 206s > 206s > ## Caused warnings and unhelpful results in 4.1_1 (Guilherme Jacob) 206s > data(api) 206s 206s Attaching package: 'survey' 206s 206s The following object is masked from 'package:graphics': 206s 206s dotchart 206s 206s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 206s > svyby(~api99, ~stype, dclus1, svymean ) 206s stype api99 se 206s E E 607.7917 22.81660 206s H H 595.7143 41.76400 206s M M 608.6000 32.56064 206s > 206s > set.seed(123) 206s > apiclus1$api99[ sample.int( nrow(apiclus1) , 5 ) ] <- NA 206s > dclus1.na <-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 206s > 206s > # subsetting w/ na.rm = FALSE... 206s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = FALSE ) 206s mean SE 206s api99 NA NA 206s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = FALSE ) 206s mean SE 206s api99 595.71 41.764 206s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = FALSE ) 206s mean SE 206s api99 NA NA 206s > 206s > # ... looks like this: 206s > svyby(~api99, ~stype, dclus1.na , svymean ) 206s stype api99 se 206s E E NA NA 206s H H 595.7143 41.764 206s M M NA NA 206s > 206s > # subsetting w/ na.rm = TRUE... 206s > svymean( ~api99 , subset( dclus1.na , stype == "E" ) , na.rm = TRUE ) 206s mean SE 206s api99 606.53 22.901 206s > svymean( ~api99 , subset( dclus1.na , stype == "H" ) , na.rm = TRUE ) 206s mean SE 206s api99 595.71 41.764 206s > svymean( ~api99 , subset( dclus1.na , stype == "M" ) , na.rm = TRUE ) 206s mean SE 206s api99 613.39 33.224 206s > 206s > # ... looks like this 206s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE ) 206s stype api99 se 206s E E 606.5319 22.90084 206s H H 595.7143 41.76400 206s M M 613.3913 33.22358 206s > 206s > # Without missing values, this works: 206s > svyby(~api99, ~stype, dclus1 , svymean , na.rm = TRUE , covmat = TRUE ) 206s stype api99 se 206s E E 607.7917 22.81660 206s H H 595.7143 41.76400 206s M M 608.6000 32.56064 206s > 206s > # ... but this breaks! 206s > svyby(~api99, ~stype, dclus1.na , svymean , na.rm = TRUE , covmat = TRUE ) 206s stype api99 se 206s E E 606.5319 22.90084 206s H H 595.7143 41.76400 206s M M 613.3913 33.22358 206s > 206s > # ... and i don't think this is the expected behavior 206s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , covmat = TRUE ) 206s stype api99 se 206s E E NA NA 206s H H 595.7143 41.764 206s M M NA NA 206s > svyby( ~api99, ~stype, dclus1.na , svymean , na.rm.all = TRUE , na.rm = TRUE , covmat = TRUE ) 206s stype api99 se 206s E E 606.5319 22.90084 206s H H 595.7143 41.76400 206s M M 613.3913 33.22358 206s > 206s > 206s > ## Now some more as tests 206s > svyby(~api99, ~stype, dclus1.na , svytotal , na.rm = TRUE , covmat = TRUE ) 206s stype api99 se 206s E E 2894629.0 792809.8 206s H H 282283.9 101492.9 206s M M 477513.4 107555.5 206s > svyby(~api99, ~stype, dclus1.na , svyratio , na.rm = TRUE , denominator=~api00, covmat = TRUE ) 206s stype api99/api00 se.api99/api00 206s E E 0.9367750 0.006365702 206s H H 0.9630485 0.010520785 206s M M 0.9682246 0.009390982 206s > 206s > ff<-function(f,d,...,na.rm=TRUE) svyglm(f,d,...) 206s > svyby(api99~1, ~stype, dclus1.na , ff , na.rm = TRUE , covmat = TRUE ) 206s stype (Intercept) se.(Intercept) 206s E E 606.5319 22.90084 206s H H 595.7143 41.76400 206s M M 613.3913 33.22358 206s > 206s BEGIN TEST svyby_se.R 206s 206s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 206s Copyright (C) 2025 The R Foundation for Statistical Computing 206s Platform: x86_64-pc-linux-gnu 206s 206s R is free software and comes with ABSOLUTELY NO WARRANTY. 206s You are welcome to redistribute it under certain conditions. 206s Type 'license()' or 'licence()' for distribution details. 206s 206s R is a collaborative project with many contributors. 206s Type 'contributors()' for more information and 206s 'citation()' on how to cite R or R packages in publications. 206s 206s Type 'demo()' for some demos, 'help()' for on-line help, or 206s 'help.start()' for an HTML browser interface to help. 206s Type 'q()' to quit R. 206s 206s Loading required package: grid 206s Loading required package: Matrix 206s > library(survey) 206s Loading required package: survival 207s > data(api) 207s 207s Attaching package: 'survey' 207s 207s The following object is masked from 'package:graphics': 207s 207s dotchart 207s 207s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 207s > 207s > a<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("ci","se")) 207s > b<-svyby(~enroll,~stype,design=dstrat,svytotal,vartype=c("se","ci")) 207s > 207s > 207s > stopifnot(all.equal(SE(a),SE(b))) 207s > 207s BEGIN TEST svycontrast.R 207s 207s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 207s Copyright (C) 2025 The R Foundation for Statistical Computing 207s Platform: x86_64-pc-linux-gnu 207s 207s R is free software and comes with ABSOLUTELY NO WARRANTY. 207s You are welcome to redistribute it under certain conditions. 207s Type 'license()' or 'licence()' for distribution details. 207s 207s R is a collaborative project with many contributors. 207s Type 'contributors()' for more information and 207s 'citation()' on how to cite R or R packages in publications. 207s 207s Type 'demo()' for some demos, 'help()' for on-line help, or 207s 'help.start()' for an HTML browser interface to help. 207s Type 'q()' to quit R. 207s 207s Loading required package: grid 207s > library(survey) 207s Loading required package: Matrix 207s Loading required package: survival 207s 207s Attaching package: 'survey' 207s 207s The following object is masked from 'package:graphics': 207s 207s dotchart 207s 207s > data(api) 207s > dclus2<-svydesign(id=~dnum+snum, weights=~pw, data=apiclus2) 207s > rclus2<-as.svrepdesign(dclus2) 207s > model<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2) 207s > svycontrast(model, c(ell=1,meals=0)) 207s contrast SE 207s contrast -2.0592 1.6177 207s > a<-svycontrast(model, c(0,1,0,0)) 207s > 207s > model2<-svyglm(formula = api00 ~ ell + meals + mobility, design = rclus2,return.replicates=TRUE) 207s > svycontrast(model2, c(ell=1,meals=0)) 207s contrast SE 207s contrast -2.0592 1.6177 207s > a2<-svycontrast(model2, c(0,1,0,0)) 207s > stopifnot(!is.null(a2$replicates)) 207s > 207s BEGIN TEST svyivreg-var.R 207s 207s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 207s Copyright (C) 2025 The R Foundation for Statistical Computing 207s Platform: x86_64-pc-linux-gnu 207s 207s R is free software and comes with ABSOLUTELY NO WARRANTY. 207s You are welcome to redistribute it under certain conditions. 207s Type 'license()' or 'licence()' for distribution details. 207s 207s R is a collaborative project with many contributors. 207s Type 'contributors()' for more information and 207s 'citation()' on how to cite R or R packages in publications. 207s 207s Type 'demo()' for some demos, 'help()' for on-line help, or 207s 'help.start()' for an HTML browser interface to help. 207s Type 'q()' to quit R. 207s 208s > 208s > library(survey) 208s Loading required package: grid 208s Loading required package: Matrix 208s Loading required package: survival 208s 208s Attaching package: 'survey' 208s 208s The following object is masked from 'package:graphics': 208s 208s dotchart 208s 208s > data(api) 208s > dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc) 208s > a<-summary(svyglm(api00~ell+meals+mobility, design=dstrat)) 208s > b<- summary(svyivreg(api00~ell+meals+mobility, design=dstrat)) 208s > stopifnot(isTRUE(all.equal(a$cov.scaled, b$vcov))) 208s > 208s BEGIN TEST svyivreg.R 208s 208s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 208s Copyright (C) 2025 The R Foundation for Statistical Computing 208s Platform: x86_64-pc-linux-gnu 208s 208s R is free software and comes with ABSOLUTELY NO WARRANTY. 208s You are welcome to redistribute it under certain conditions. 208s Type 'license()' or 'licence()' for distribution details. 208s 208s R is a collaborative project with many contributors. 208s Type 'contributors()' for more information and 208s 'citation()' on how to cite R or R packages in publications. 208s 208s Type 'demo()' for some demos, 'help()' for on-line help, or 208s 'help.start()' for an HTML browser interface to help. 208s Type 'q()' to quit R. 208s 208s > library(survey) 208s Loading required package: grid 208s Loading required package: Matrix 209s Loading required package: survival 209s 209s Attaching package: 'survey' 209s 209s The following object is masked from 'package:graphics': 209s 209s dotchart 209s 209s > library(AER) 209s Loading required package: car 209s Loading required package: carData 209s Loading required package: lmtest 209s Loading required package: zoo 209s 209s Attaching package: 'zoo' 209s 209s The following objects are masked from 'package:base': 209s 209s as.Date, as.Date.numeric 209s 209s Loading required package: sandwich 209s > 209s > load("cigsw.rda") 209s > 209s > des<-svydesign(id=~1, weights=~wt, data=cigsw) 209s > m<-svyivreg(log(packs) ~ log(rprice) + log(rincome) | log(rincome) + tdiff + I(tax/cpi), design=des) 209s > 209s > all.equal(as.vector(coef(m)), c(10.42009 , -1.588135, 0.6140887),tolerance=1e-6) 209s [1] TRUE 209s > all.equal(as.vector(SE(m)), c( 1.047699, .3394232, .3614382 ),tolerance=1e-6) 209s [1] TRUE 209s > 209s BEGIN TEST svyolr-rake-subset.R 209s 209s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 209s Copyright (C) 2025 The R Foundation for Statistical Computing 209s Platform: x86_64-pc-linux-gnu 209s 209s R is free software and comes with ABSOLUTELY NO WARRANTY. 209s You are welcome to redistribute it under certain conditions. 209s Type 'license()' or 'licence()' for distribution details. 209s 209s R is a collaborative project with many contributors. 209s Type 'contributors()' for more information and 209s 'citation()' on how to cite R or R packages in publications. 209s 209s Type 'demo()' for some demos, 'help()' for on-line help, or 209s 'help.start()' for an HTML browser interface to help. 209s Type 'q()' to quit R. 209s 209s > library(survey) 209s Loading required package: grid 209s Loading required package: Matrix 210s Loading required package: survival 210s > data(api) 210s 210s Attaching package: 'survey' 210s 210s The following object is masked from 'package:graphics': 210s 210s dotchart 210s 210s > dclus1 <- svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 210s > 210s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 210s > 210s > ## population marginal totals for each stratum 210s > pop.types <- data.frame(stype=c("E","H","M"), Freq=c(4421,755,1018)) 210s > pop.schwide <- data.frame(sch.wide=c("No","Yes"), Freq=c(1072,5122)) 210s > 210s > 210s > ## rake with the population totals 210s > dclus1r<-rake(dclus1, list(~stype,~sch.wide), list(pop.types, pop.schwide)) 210s > 210s > # works 210s > m <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 210s > 210s > # fails in 4.1 (should work because svyolr's default na.action is na.omit) 210s > m2 <- svyolr(mealcat~avg.ed+mobility+stype, design=dclus1r) 210s > 210s > # fails in 4.1 (should work because NA values are subsetted out) 210s > m3 <- svyolr(mealcat~avg.ed+mobility+stype, design=subset( dclus1r , !is.na( avg.ed ) ) ) 210s > 210s BEGIN TEST svyolr.R 210s 210s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 210s Copyright (C) 2025 The R Foundation for Statistical Computing 210s Platform: x86_64-pc-linux-gnu 210s 210s R is free software and comes with ABSOLUTELY NO WARRANTY. 210s You are welcome to redistribute it under certain conditions. 210s Type 'license()' or 'licence()' for distribution details. 210s 210s R is a collaborative project with many contributors. 210s Type 'contributors()' for more information and 210s 'citation()' on how to cite R or R packages in publications. 210s 210s Type 'demo()' for some demos, 'help()' for on-line help, or 210s 'help.start()' for an HTML browser interface to help. 210s Type 'q()' to quit R. 210s 210s > library(survey) 210s Loading required package: grid 210s Loading required package: Matrix 211s Loading required package: survival 211s > 211s > ################################################################################ 211s > # Example from svyolr: runs OK 211s > data(api) 211s 211s Attaching package: 'survey' 211s 211s The following object is masked from 'package:graphics': 211s 211s dotchart 211s 211s > dclus1<-svydesign(id=~dnum, weights=~pw, data=apiclus1, fpc=~fpc) 211s > dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 211s > 211s > m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 211s > m 211s Call: 211s svyolr(mealcat ~ avg.ed + mobility + stype, design = dclus1) 211s 211s Coefficients: 211s avg.ed mobility stypeH stypeM 211s -2.6999217 0.0325042 -1.7574715 -0.6191463 211s 211s Intercepts: 211s (0,25]|(25,50] (25,50]|(50,75] (50,75]|(75,100] 211s -8.857919 -6.586464 -4.924938 211s > 211s > ## Use regTermTest for testing multiple parameters 211s > test<-regTermTest(m, ~avg.ed+stype, method="LRT") 211s > ################################################################################ 211s > 211s > ################################################################################ 211s > # If we wrap everything into a function: error b/c it looks for design variable 211s > # dclus1 in .GlobalEnv 211s > 211s > foo <- function(x){ 211s + dclus1<-svydesign(id=~dnum, weights=~pw, data=x, fpc=~fpc) 211s + dclus1<-update(dclus1, mealcat=cut(meals,c(0,25,50,75,100))) 211s + 211s + m<-svyolr(mealcat~avg.ed+mobility+stype, design=dclus1) 211s + ## Use regTermTest for testing multiple parameters 211s + regTermTest(m, ~avg.ed+stype, method="LRT") 211s + } 211s > 211s > # OK 211s > foo(apiclus1) 211s Working (Rao-Scott+F) LRT for avg.ed stype 211s in svyolr(formula = mealcat ~ avg.ed + mobility + stype, design = dclus1) 211s Working 2logLR = 0.6580304 p= 0.73257 211s (scale factors: 2.7 0.22 0.11 ); denominator df= 10 211s > 211s > # Clean-up everything but apiclus1 and foo 211s > rm(list = setdiff(ls(),c('apiclus1','foo','test'))) 211s > 211s > # Error 211s > test2<-foo(apiclus1) 211s > ################################################################################ 211s > all.equal(test,test2) 211s [1] TRUE 211s > 211s > 211s BEGIN TEST toy_example_for_postStratify.R 211s 211s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 211s Copyright (C) 2025 The R Foundation for Statistical Computing 211s Platform: x86_64-pc-linux-gnu 211s 211s R is free software and comes with ABSOLUTELY NO WARRANTY. 211s You are welcome to redistribute it under certain conditions. 211s Type 'license()' or 'licence()' for distribution details. 211s 211s R is a collaborative project with many contributors. 211s Type 'contributors()' for more information and 211s 'citation()' on how to cite R or R packages in publications. 211s 211s Type 'demo()' for some demos, 'help()' for on-line help, or 211s 'help.start()' for an HTML browser interface to help. 211s Type 'q()' to quit R. 211s 211s > library(survey) 211s Loading required package: grid 211s Loading required package: Matrix 211s Loading required package: survival 212s > 212s > # Dummy data for testing nonresponse adjustments 212s > toy <- data.frame(id = 1:10, 212s + dummy = 1, 212s + class = c(rep("A", 5), rep("B", 5)), 212s + responded = c(rep(TRUE, 8), FALSE, FALSE), 212s + weight = rep(100, 10)) 212s > 212s > # With jackknife replicate weights 212s > toy_repweights <- matrix(rep(1000/9, 100), nrow = 10) 212s > diag(toy_repweights) <- rep(0, 10) 212s > 212s > # Scramble up which person is in which jackknife group 212s > 212s Attaching package: 'survey' 212s 212s The following object is masked from 'package:graphics': 212s 212s dotchart 212s 212s toy_repweights <- toy_repweights[sample(1:10, size = 10), ] 212s > 212s > toy_design <- svrepdesign(variables = toy[, 1:4], 212s + weights = toy$weight, 212s + repweights = toy_repweights, 212s + type = "JK1", 212s + scale = 0.9) 212s > 212s > # Get the sum of the weights for the full sample 212s > poptotals <- as.data.frame(svyby(formula = ~dummy, 212s + by = ~class, 212s + design = toy_design, 212s + FUN = survey::svytotal)) 212s > 212s > poptotals$Freq <- poptotals$dummy 212s > poptotals$dummy <- NULL 212s > poptotals$se <- NULL 212s > 212s > # Adjust the weights of the responding sample to match to the full sample 212s > adjusted <- postStratify(design = subset(toy_design, responded), 212s + strata = ~class, 212s + population = poptotals) 212s > 212s > # This works for the weights... 212s > svyby(formula = ~dummy, 212s + by = ~class, 212s + design = adjusted, 212s + FUN = survey::svytotal) 212s class dummy se 212s A A 500 0 212s B B 500 0 212s > 212s > # ...and some, but not all, the replicate weights 212s > stopifnot(all.equal(colSums(toy_design$repweights), colSums(adjusted$repweights))) 212s > 212s > 212s > 212s BEGIN TEST twophase.R 212s 212s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 212s Copyright (C) 2025 The R Foundation for Statistical Computing 212s Platform: x86_64-pc-linux-gnu 212s 212s R is free software and comes with ABSOLUTELY NO WARRANTY. 212s You are welcome to redistribute it under certain conditions. 212s Type 'license()' or 'licence()' for distribution details. 212s 212s R is a collaborative project with many contributors. 212s Type 'contributors()' for more information and 212s 'citation()' on how to cite R or R packages in publications. 212s 212s Type 'demo()' for some demos, 'help()' for on-line help, or 212s 'help.start()' for an HTML browser interface to help. 212s Type 'q()' to quit R. 212s 212s > library(survey) 212s Loading required package: grid 212s Loading required package: Matrix 212s Loading required package: survival 212s 212s Attaching package: 'survey' 212s 212s The following object is masked from 'package:graphics': 212s 212s dotchart 212s 212s > 212s > ## two-phase simple random sampling. 212s > data(pbc, package="survival") 212s > pbc$id<-1:nrow(pbc) 212s > pbc$randomized<-with(pbc, !is.na(trt) & trt>-9) 212s > (d2pbc<-twophase(id=list(~id,~id), data=pbc, subset=~I(!randomized))) 212s Two-phase sparse-matrix design: 212s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 212s subset = subset, data = data, pps = pps) 212s Phase 1: 212s Independent Sampling design (with replacement) 212s svydesign(ids = ~id) 212s Phase 2: 212s Independent Sampling design 212s svydesign(ids = ~id, fpc = `*phase1*`) 212s > m<-svymean(~bili, d2pbc) 212s > all.equal(as.vector(coef(m)),with(pbc, mean(bili[!randomized]))) 212s [1] TRUE 212s > all.equal(as.vector(SE(m)), 212s + with(pbc, sd(bili[!randomized])/sqrt(sum(!randomized))), 212s + tolerance=0.002) 212s [1] TRUE 212s > 212s > ## two-stage sampling as two-phase 212s > data(mu284) 212s > ii<-with(mu284, c(1:15, rep(1:5,n2[1:5]-3))) 212s > mu284.1<-mu284[ii,] 212s > mu284.1$id<-1:nrow(mu284.1) 212s > mu284.1$sub<-rep(c(TRUE,FALSE),c(15,34-15)) 212s > dmu284<-svydesign(id=~id1+id2,fpc=~n1+n2, data=mu284) 212s > ## first phase cluster sample, second phase stratified within cluster 212s > (d2mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 212s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="approx")) 212s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 212s NULL), data = mu284.1, subset = ~sub, method = "approx") 212s Phase 1: 212s 1 - level Cluster Sampling design 212s With (5) clusters. 212s svydesign(ids = ~id1, fpc = ~n1) 212s Phase 2: 212s Stratified Independent Sampling design 212s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 212s > (d22mu284<-twophase(id=list(~id1,~id),strata=list(NULL,~id1), 212s + fpc=list(~n1,NULL),data=mu284.1,subset=~sub,method="full")) 212s Two-phase sparse-matrix design: 212s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 212s subset = subset, data = data, pps = pps) 212s Phase 1: 212s 1 - level Cluster Sampling design 212s With (5) clusters. 212s svydesign(ids = ~id1, fpc = ~n1) 212s Phase 2: 212s Stratified Independent Sampling design 212s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 212s > summary(d2mu284) 212s Two-phase design: twophase(id = list(~id1, ~id), strata = list(NULL, ~id1), fpc = list(~n1, 212s NULL), data = mu284.1, subset = ~sub, method = "approx") 212s Phase 1: 212s 1 - level Cluster Sampling design 212s With (5) clusters. 212s svydesign(ids = ~id1, fpc = ~n1) 212s Probabilities: 212s Min. 1st Qu. Median Mean 3rd Qu. Max. 212s 0.1 0.1 0.1 0.1 0.1 0.1 212s Population size (PSUs): 50 212s Phase 2: 212s Stratified Independent Sampling design 212s svydesign(ids = ~id, strata = ~id1, fpc = `*phase1*`) 212s Probabilities: 212s Min. 1st Qu. Median Mean 3rd Qu. Max. 212s 0.3333 0.3750 0.4286 0.4674 0.6000 0.6000 212s Stratum Sizes: 212s 19 31 45 47 50 212s obs 3 3 3 3 3 212s design.PSU 3 3 3 3 3 212s actual.PSU 3 3 3 3 3 212s Population stratum sizes (PSUs): 212s 19 31 45 47 50 212s 5 7 8 5 9 212s Data variables: 212s [1] "id1" "n1" "id2" "y1" "n2" "id" "sub" 212s > t1<-svytotal(~y1, dmu284) 212s > t2<-svytotal(~y1, d2mu284) 212s > t22<-svytotal(~y1,d22mu284) 212s > m1<-svymean(~y1, dmu284) 212s > m2<-svymean(~y1, d2mu284) 212s > m22<-svymean(~y1, d22mu284) 212s > all.equal(coef(t1),coef(t2)) 212s [1] TRUE 212s > all.equal(coef(t1),coef(t22)) 212s [1] TRUE 212s > all.equal(coef(m1),coef(m2)) 212s [1] TRUE 212s > all.equal(coef(m1),coef(m22)) 212s [1] TRUE 212s > all.equal(as.vector(SE(m1)),as.vector(SE(m2))) 212s [1] TRUE 212s > all.equal(as.vector(SE(m1)),as.vector(SE(m22))) 212s [1] TRUE 212s > all.equal(as.vector(SE(t1)),as.vector(SE(t2))) 212s [1] TRUE 212s > all.equal(as.vector(SE(t1)),as.vector(SE(t22))) 212s [1] TRUE 212s > 212s > ## case-cohort design 212s > ##this example requires R 2.3.1 or later for cch and data. 212s > library("survival") 212s > data(nwtco, package="survival") 212s > ## unstratified, equivalent to Lin & Ying (1993) 212s > print(dcchs<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 212s + subset=~I(in.subcohort | rel), data=nwtco)) 213s Two-phase sparse-matrix design: 213s twophase2(id = id, strata = strata, probs = probs, fpc = fpc, 213s subset = subset, data = data, pps = pps) 213s Phase 1: 213s Independent Sampling design (with replacement) 213s svydesign(ids = ~seqno) 213s Phase 2: 213s Stratified Independent Sampling design 213s svydesign(ids = ~seqno, strata = ~rel, fpc = `*phase1*`) 213s > cch1<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 213s + design=dcchs) 213s > dcchs2<-twophase(id=list(~seqno,~seqno), strata=list(NULL,~rel), 213s + subset=~I(in.subcohort | rel), data=nwtco,method="approx") 213s > cch1.2<-svycoxph(Surv(edrel,rel)~factor(stage)+factor(histol)+I(age/12), 213s + design=dcchs) 213s > all.equal(coef(cch1),coef(cch1.2)) 213s [1] TRUE 213s > all.equal(SE(cch1),SE(cch1.2)) 213s [1] TRUE 213s > ## Using survival::cch 213s > subcoh <- nwtco$in.subcohort 213s > selccoh <- with(nwtco, rel==1|subcoh==1) 213s > ccoh.data <- nwtco[selccoh,] 213s > ccoh.data$subcohort <- subcoh[selccoh] 213s > cch2<-cch(Surv(edrel, rel) ~ factor(stage) + factor(histol) + I(age/12), 213s + data =ccoh.data, subcoh = ~subcohort, id=~seqno, 213s + cohort.size=4028, method="LinYing", robust=TRUE) 213s > 213s > print(all.equal(as.vector(coef(cch1)),as.vector(coef(cch2)))) 213s [1] TRUE 213s > ## cch has smaller variances by a factor of 1.0005 because 213s > ## there is a (n/(n-1)) in the survey phase1 varianace 213s > print(all.equal(as.vector(SE(cch1)), as.vector(SE(cch2)),tolerance=0.0006)) 213s [1] TRUE 213s > 213s > 213s > ## bug report from Takahiro Tsuchiya for version 3.4 213s > ## We used to not match Sarndal exactly, because our old phase-one 213s > ## estimator had a small bias for finite populations 213s > rei<-read.table(tmp<-textConnection( 213s + " id N n.a h n.ah n.h sub y 213s + 1 1 300 20 1 12 5 TRUE 1 213s + 2 2 300 20 1 12 5 TRUE 2 213s + 3 3 300 20 1 12 5 TRUE 3 213s + 4 4 300 20 1 12 5 TRUE 4 213s + 5 5 300 20 1 12 5 TRUE 5 213s + 6 6 300 20 1 12 5 FALSE NA 213s + 7 7 300 20 1 12 5 FALSE NA 213s + 8 8 300 20 1 12 5 FALSE NA 213s + 9 9 300 20 1 12 5 FALSE NA 213s + 10 10 300 20 1 12 5 FALSE NA 213s + 11 11 300 20 1 12 5 FALSE NA 213s + 12 12 300 20 1 12 5 FALSE NA 213s + 13 13 300 20 2 8 3 TRUE 6 213s + 14 14 300 20 2 8 3 TRUE 7 213s + 15 15 300 20 2 8 3 TRUE 8 213s + 16 16 300 20 2 8 3 FALSE NA 213s + 17 17 300 20 2 8 3 FALSE NA 213s + 18 18 300 20 2 8 3 FALSE NA 213s + 19 19 300 20 2 8 3 FALSE NA 213s + 20 20 300 20 2 8 3 FALSE NA 213s + "), header=TRUE) 213s > close(tmp) 213s > 213s > des.rei <- twophase(id=list(~id,~id), strata=list(NULL,~h), 213s + fpc=list(~N,NULL), subset=~sub, data=rei, method="approx") 213s > tot<- svytotal(~y, des.rei) 213s > des.rei2 <- twophase(id=list(~id,~id), strata=list(NULL,~h), 213s + fpc=list(~N,NULL), subset=~sub, data=rei) 213s > tot2<- svytotal(~y, des.rei2) 213s > 213s > ## based on Sarndal et al (9.4.14) 213s > rei$w.ah <- rei$n.ah / rei$n.a 213s > a.rei <- aggregate(rei, by=list(rei$h), mean, na.rm=TRUE) 213s > a.rei$S.ysh <- tapply(rei$y, rei$h, var, na.rm=TRUE) 213s > a.rei$y.u <- sum(a.rei$w.ah * a.rei$y) 213s > 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)) 213s > V <- V + with(a.rei, sum(N * (N-n.a) * w.ah * (y - y.u)^2 / (n.a-1))) 213s > 213s > a.rei$f.h<-with(a.rei, n.h/n.ah) 213s > Vphase2<-with(a.rei, sum(N*N*w.ah^2* ((1-f.h)/n.h) *S.ysh)) 213s > 213s > a.rei$f<-with(a.rei, n.a/N) 213s > a.rei$delta.h<-with(a.rei, (1/n.h)*(n.a-n.ah)/(n.a-1)) 213s > Vphase1<-with(a.rei, sum(N*N*((1-f)/n.a)*( w.ah*(1-delta.h)*S.ysh+ ((n.a)/(n.a-1))*w.ah*(y-y.u)^2))) 213s > 213s > V 213s [1] 36522.63 213s > Vphase1 213s [1] 24072.63 213s > Vphase2 213s [1] 12450 213s > vcov(tot) 213s y 213s y 35911.05 213s attr(,"phases") 213s attr(,"phases")$phase1 213s [,1] 213s [1,] 23461.05 213s 213s attr(,"phases")$phase2 213s y 213s y 12450 213s 213s > vcov(tot2) 213s [,1] 213s [1,] 36522.63 213s attr(,"phases") 213s attr(,"phases")$phase1 213s [,1] 213s [1,] 24072.63 213s 213s attr(,"phases")$phase2 213s [,1] 213s [1,] 12450 213s 213s > ## phase 2 identical 213s > all.equal(Vphase2,drop(attr(vcov(tot),"phases")$phase2)) 213s [1] TRUE 213s > all.equal(Vphase2,drop(attr(vcov(tot2),"phases")$phase2)) 213s [1] TRUE 213s > ## phase 1 differs by 2.6% for old twophase estimator 213s > Vphase1/attr(vcov(tot),"phases")$phase1 213s [,1] 213s [1,] 1.026068 213s > all.equal(Vphase1,as.vector(attr(vcov(tot2),"phases")$phase1)) 213s [1] TRUE 213s > 213s > 213s autopkgtest [03:49:21]: test run-unit-test: -----------------------] 214s run-unit-test PASS 214s autopkgtest [03:49:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 214s autopkgtest [03:49:22]: test pkg-r-autopkgtest: preparing testbed 221s Creating nova instance adt-resolute-amd64-r-cran-survey-20260210-034548-juju-7f2275-prod-proposed-migration-environment-2-cd4dc104-e41e-4edb-a008-6345011de0c2 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 289s autopkgtest [03:50:37]: testbed dpkg architecture: amd64 289s autopkgtest [03:50:37]: testbed apt version: 3.1.14 289s autopkgtest [03:50:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 290s autopkgtest [03:50:38]: testbed release detected to be: resolute 290s autopkgtest [03:50:38]: updating testbed package index (apt update) 291s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 291s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 291s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 291s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 291s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [181 kB] 291s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB] 291s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 291s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB] 291s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [268 kB] 291s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5980 B] 291s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 291s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [768 kB] 291s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1791 kB] 291s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.6 kB] 291s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 291s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 291s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 292s Fetched 5189 kB in 1s (6379 kB/s) 293s Reading package lists... 293s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 293s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 293s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 293s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 294s Reading package lists... 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 295s Calculating upgrade... 295s The following package was automatically installed and is no longer required: 295s libpython3.13 295s Use 'sudo apt autoremove' to remove it. 295s The following NEW packages will be installed: 295s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 295s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 295s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 295s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 295s The following packages will be upgraded: 295s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 295s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 295s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 295s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 295s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0 295s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 295s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 295s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 295s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 295s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 295s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 295s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 295s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 295s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 295s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 295s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 295s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 295s Need to get 237 MB of archives. 295s After this operation, 339 MB of additional disk space will be used. 295s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 295s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 295s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 295s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 295s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 295s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 295s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 295s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 295s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 295s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 295s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 295s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 295s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 295s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 295s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 295s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 295s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 295s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 295s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 295s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 295s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 295s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 295s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 295s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 295s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 295s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 295s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 295s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 295s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 295s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 295s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 295s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 295s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 295s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 295s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 295s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 295s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 295s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 295s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 295s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 295s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 295s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 295s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 295s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 295s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 295s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 295s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 295s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 295s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 295s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 295s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 295s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 295s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 295s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 295s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 295s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 295s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 295s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 295s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 295s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 295s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 295s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 295s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 296s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 296s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 296s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 296s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 296s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 296s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 296s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 296s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 296s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 296s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 296s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 296s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 296s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 296s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 296s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 296s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 296s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 296s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 296s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 299s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 299s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 299s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 299s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 299s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 299s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 299s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 299s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 299s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 299s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 299s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 299s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 299s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 299s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 299s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 299s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 299s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 299s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 300s dpkg-preconfigure: unable to re-open stdin: No such file or directory 300s Fetched 237 MB in 5s (49.7 MB/s) 300s (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 ... 83957 files and directories currently installed.) 300s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 300s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 300s Setting up debianutils (5.23.2build1) ... 300s (Reading database ... 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Selecting previously unselected package linux-headers-6.19.0-3-generic. 307s Preparing to unpack .../82-linux-headers-6.19.0-3-generic_6.19.0-3.3_amd64.deb ... 307s Unpacking linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 308s Preparing to unpack .../83-linux-headers-generic_6.19.0-3.3_amd64.deb ... 308s Unpacking linux-headers-generic (6.19.0-3.3) over (6.18.0-9.9+1) ... 308s Preparing to unpack .../84-linux-perf_6.19.0-3.3_amd64.deb ... 308s Unpacking linux-perf (6.19.0-3.3) over (6.18.0-9.9) ... 308s Preparing to unpack .../85-linux-tools-common_6.19.0-3.3_all.deb ... 308s Unpacking linux-tools-common (6.19.0-3.3) over (6.18.0-9.9) ... 308s Selecting previously unselected package linux-tools-6.19.0-3. 308s Preparing to unpack .../86-linux-tools-6.19.0-3_6.19.0-3.3_amd64.deb ... 308s Unpacking linux-tools-6.19.0-3 (6.19.0-3.3) ... 308s Selecting previously unselected package linux-tools-6.19.0-3-generic. 308s Preparing to unpack .../87-linux-tools-6.19.0-3-generic_6.19.0-3.3_amd64.deb ... 308s Unpacking linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 308s Preparing to unpack .../88-patch_2.8-2build1_amd64.deb ... 308s Unpacking patch (2.8-2build1) over (2.8-2) ... 308s Preparing to unpack .../89-pollinate_4.33-4ubuntu5_all.deb ... 308s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 308s Preparing to unpack .../90-python3-referencing_0.36.2-1ubuntu2_all.deb ... 308s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 308s Preparing to unpack .../91-ubuntu-kernel-accessories_1.564_amd64.deb ... 308s Unpacking ubuntu-kernel-accessories (1.564) over (1.563) ... 308s Setting up libip4tc2:amd64 (1.8.11-2ubuntu3) ... 308s Setting up 3cpio (0.14.0-1ubuntu1) ... 308s Setting up libxau6:amd64 (1:1.0.11-1build2) ... 308s Setting up libnpth0t64:amd64 (1.8-3build1) ... 308s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ... 308s Setting up ubuntu-kernel-accessories (1.564) ... 308s Setting up libgpm2:amd64 (1.20.7-12build1) ... 308s Setting up libgdbm6t64:amd64 (1.26-1build1) ... 308s Setting up linux-modules-6.19.0-3-generic (6.19.0-3.3) ... 310s Setting up libgdbm-compat4t64:amd64 (1.26-1build1) ... 310s Setting up bpftool (7.7.0+6.19.0-3.3) ... 310s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 310s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 310s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 310s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 310s Setting up libsensors-config (1:3.6.2-2build1) ... 310s Setting up less (668-1build1) ... 310s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 310s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 310s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 310s amd64-microcode: microcode will be updated at next boot 310s Setting up man-db (2.13.1-1build1) ... 310s Updating database of manual pages ... 311s man-db.service is a disabled or a static unit not running, not starting it. 311s Setting up libjansson4:amd64 (2.14-2build4) ... 311s Setting up libglib2.0-data (2.87.2-2) ... 311s Setting up pollinate (4.33-4ubuntu5) ... 322s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 322s Setting up libwrap0:amd64 (7.6.q-36build2) ... 322s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 323s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 323s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 323s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 323s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 323s Setting up patch (2.8-2build1) ... 323s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 323s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 323s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 323s Setting up lsof (4.99.4+dfsg-2build2) ... 323s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 323s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 323s Setting up dracut-install (109-11ubuntu1) ... 323s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 323s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 323s Setting up pnp.ids (0.394-1build1) ... 323s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 323s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 323s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 323s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 323s Setting up mawk (1.3.4.20260129-1) ... 323s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 323s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 323s Setting up linux-image-virtual (6.19.0-3.3) ... 323s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 323s Setting up libbsd0:amd64 (0.12.2-2build2) ... 323s Setting up libdrm-common (2.4.131-1) ... 323s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 323s Setting up dbus-bin (1.16.2-2ubuntu3) ... 323s Setting up libonig5:amd64 (6.9.10-1build1) ... 323s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 323s Setting up ethtool (1:6.15-3build1) ... 323s Setting up python3-referencing (0.36.2-1ubuntu2) ... 323s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 323s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 323s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 323s Setting up tcpdump (4.99.5-2ubuntu3) ... 323s Setting up linux-image-generic (6.19.0-3.3) ... 323s Setting up wget (1.25.0-2ubuntu4) ... 323s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 323s Setting up iptables (1.8.11-2ubuntu3) ... 323s Setting up iproute2 (6.18.0-1ubuntu1) ... 324s Setting up linux-headers-generic (6.19.0-3.3) ... 324s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 324s Setting up hwdata (0.394-1build1) ... 324s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 324s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 324s No schema files found: doing nothing. 324s Setting up dbus (1.16.2-2ubuntu3) ... 324s A reboot is required to replace the running dbus-daemon. 324s Please reboot the system when convenient. 324s Setting up shared-mime-info (2.4-5build3) ... 325s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 325s Setting up pciutils (1:3.14.0-1build2) ... 325s Setting up python3-markdown-it (3.0.0-3build1) ... 325s Setting up libdrm2:amd64 (2.4.131-1) ... 325s Setting up libpython3.14:amd64 (3.14.2-1) ... 325s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 325s Setting up linux-tools-common (6.19.0-3.3) ... 325s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 325s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 325s Setting up apt (3.1.15) ... 325s Setting up linux-headers-virtual (6.19.0-3.3) ... 325s Setting up linux-generic (6.19.0-3.3) ... 325s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 325s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 325s Setting up ubuntu-standard (1.564) ... 325s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 325s Setting up linux-virtual (6.19.0-3.3) ... 325s Setting up linux-perf (6.19.0-3.3) ... 325s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 325s Processing triggers for debianutils (5.23.2build1) ... 325s Processing triggers for install-info (7.2-5) ... 325s Processing triggers for initramfs-tools (0.150ubuntu7) ... 325s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 330s Processing triggers for libc-bin (2.42-2ubuntu4) ... 331s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 331s /etc/kernel/postinst.d/initramfs-tools: 331s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 335s /etc/kernel/postinst.d/zz-update-grub: 335s Sourcing file `/etc/default/grub' 335s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 335s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 335s Generating grub configuration file ... 335s Found linux image: /boot/vmlinuz-6.19.0-3-generic 335s Found initrd image: /boot/initrd.img-6.19.0-3-generic 335s Found linux image: /boot/vmlinuz-6.18.0-9-generic 335s Found initrd image: /boot/initrd.img-6.18.0-9-generic 335s Warning: os-prober will not be executed to detect other bootable partitions. 335s Systems on them will not be added to the GRUB boot configuration. 335s Check GRUB_DISABLE_OS_PROBER documentation entry. 335s Adding boot menu entry for UEFI Firmware Settings ... 335s done 335s autopkgtest [03:51:23]: upgrading testbed (apt dist-upgrade and autopurge) 336s Reading package lists... 336s Building dependency tree... 336s Reading state information... 336s Calculating upgrade... 336s The following package was automatically installed and is no longer required: 336s libpython3.13 336s Use 'sudo apt autoremove' to remove it. 336s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 337s Reading package lists... 337s Building dependency tree... 337s Reading state information... 337s Solving dependencies... 337s The following packages will be REMOVED: 337s libpython3.13* 337s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 337s After this operation, 7599 kB disk space will be freed. 337s (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 ... 125273 files and directories currently installed.) 337s Removing libpython3.13:amd64 (3.13.11-1) ... 337s Processing triggers for libc-bin (2.42-2ubuntu4) ... 338s autopkgtest [03:51:26]: rebooting testbed after setup commands that affected boot 368s Reading package lists... 369s Building dependency tree... 369s Reading state information... 369s Solving dependencies... 369s The following NEW packages will be installed: 369s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 369s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 369s fonts-glyphicons-halflings fonts-mathjax g++ g++-15 g++-15-x86-64-linux-gnu 369s g++-x86-64-linux-gnu gcc gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu 369s gfortran gfortran-15 gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu 369s icu-devtools libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev 369s libcairo2 libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 369s libfontconfig1 libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 369s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1 369s libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 369s libjs-bootstrap libjs-highlight.js libjs-jquery libjs-jquery-datatables 369s libjs-mathjax liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 369s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 369s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 369s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 369s libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libtcl8.6 369s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 369s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 369s libzstd-dev linux-libc-dev node-normalize.css pkg-r-autopkgtest pkgconf 369s pkgconf-bin r-base-core r-base-dev r-cran-abind r-cran-aer r-cran-backports 369s r-cran-bit r-cran-bit64 r-cran-blob r-cran-boot r-cran-broom r-cran-cachem 369s r-cran-car r-cran-cardata r-cran-caret r-cran-class r-cran-cli r-cran-clock 369s r-cran-codetools r-cran-colorspace r-cran-conquer r-cran-cowplot 369s r-cran-cpp11 r-cran-curl r-cran-data.table r-cran-dbi r-cran-deriv 369s r-cran-diagram r-cran-digest r-cran-doby r-cran-dplyr r-cran-e1071 369s r-cran-evaluate r-cran-fansi r-cran-farver r-cran-fastmap r-cran-foreach 369s r-cran-forecast r-cran-foreign r-cran-formula r-cran-fracdiff r-cran-future 369s r-cran-future.apply r-cran-generics r-cran-ggplot2 r-cran-globals 369s r-cran-glue r-cran-gower r-cran-gtable r-cran-hardhat r-cran-hexbin 369s r-cran-highr r-cran-ipred r-cran-isoband r-cran-iterators r-cran-jsonlite 369s r-cran-kernsmooth r-cran-knitr r-cran-labeling r-cran-lattice r-cran-lava 369s r-cran-lifecycle r-cran-listenv r-cran-littler r-cran-lme4 r-cran-lmtest 369s r-cran-lubridate r-cran-magrittr r-cran-mass r-cran-matrix 369s r-cran-matrixmodels r-cran-matrixstats r-cran-memoise r-cran-mgcv 369s r-cran-microbenchmark r-cran-minqa r-cran-mitools r-cran-modelmetrics 369s r-cran-modelr r-cran-nlme r-cran-nloptr r-cran-nnet r-cran-numderiv 369s r-cran-parallelly r-cran-pbkrtest r-cran-pillar r-cran-pkgconfig 369s r-cran-pkgkitten r-cran-plogr r-cran-plyr r-cran-proc r-cran-prodlim 369s r-cran-progressr r-cran-proxy r-cran-purrr r-cran-quadprog r-cran-quantmod 369s r-cran-quantreg r-cran-r6 r-cran-rbibutils r-cran-rcolorbrewer r-cran-rcpp 369s r-cran-rcpparmadillo r-cran-rcppeigen r-cran-rdpack r-cran-recipes 369s r-cran-reformulas r-cran-reshape2 r-cran-rlang r-cran-rpart r-cran-rsqlite 369s r-cran-sandwich r-cran-scales r-cran-shape r-cran-sparsem r-cran-sparsevctrs 369s r-cran-squarem r-cran-statmod r-cran-stringi r-cran-stringr r-cran-survey 369s r-cran-survival r-cran-tibble r-cran-tidyr r-cran-tidyselect 369s r-cran-timechange r-cran-timedate r-cran-tseries r-cran-ttr r-cran-tzdb 369s r-cran-urca r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 369s r-cran-xfun r-cran-xts r-cran-yaml r-cran-zoo rpcsvc-proto unzip x11-common 369s xdg-utils zip zlib1g-dev 369s 0 upgraded, 250 newly installed, 0 to remove and 0 not upgraded. 369s Need to get 279 MB of archives. 369s After this operation, 736 MB of additional disk space will be used. 369s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 369s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 371s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 371s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 371s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 372s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 372s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 372s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 373s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 373s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 373s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 373s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 373s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 373s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 373s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 373s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 373s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 373s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 373s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 374s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 374s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 374s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 375s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 375s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 375s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 375s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 375s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 375s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 375s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 375s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 375s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 375s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 375s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 375s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 375s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 375s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 375s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 375s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 375s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 375s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 375s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 375s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 376s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 376s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 376s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 376s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 376s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 376s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 376s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 376s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 376s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 376s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 376s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 376s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 376s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 376s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 376s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 376s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 376s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 376s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 376s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 376s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 376s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 376s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 376s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 376s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 376s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 376s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 376s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 376s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 376s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 376s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 376s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 376s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 376s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 376s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 376s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 376s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 376s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 376s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 376s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 376s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 376s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 376s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 376s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 376s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 377s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 377s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 377s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 377s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 377s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 377s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 377s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 377s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 377s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 377s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 377s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 377s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 377s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 377s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 377s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 377s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 377s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 377s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 377s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 377s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 378s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 378s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 378s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 378s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 378s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 378s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 378s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1build1 [67.0 kB] 378s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cardata all 3.0.6-1 [1687 kB] 378s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formula all 1.2-5-1 [158 kB] 378s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 378s Get:117 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB] 378s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 378s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 378s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-4-1 [3556 kB] 378s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 378s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-boot all 1.3-32-1 [636 kB] 378s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 378s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 378s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 378s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 378s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnlopt0 amd64 2.7.1-7ubuntu1 [189 kB] 378s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nloptr amd64 2.2.1-2 [251 kB] 378s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 379s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rdpack all 2.6.3-1 [636 kB] 379s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reformulas all 0.4.4-1 [151 kB] 379s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 379s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 379s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 379s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lme4 amd64 1.1-38-1 [4197 kB] 379s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-backports amd64 1.5.0-2 [121 kB] 379s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 379s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 379s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 379s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 379s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 379s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 379s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 379s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB] 379s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 379s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB] 379s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 379s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB] 379s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 379s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB] 379s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB] 379s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB] 379s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB] 379s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 379s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 379s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 379s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-broom all 1.0.12+dfsg-1 [1708 kB] 379s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-numderiv all 2016.8-1.1-3build1 [116 kB] 379s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 379s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 379s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 379s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 379s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 379s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 379s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 379s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB] 380s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB] 380s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-deriv all 4.2.0-1 [154 kB] 380s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB] 380s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fracdiff amd64 1.5-3-1 [108 kB] 380s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-zoo amd64 1.8-15-1 [1025 kB] 380s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lmtest amd64 0.9.40-1build1 [400 kB] 380s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timedate amd64 4052.112-1 [1298 kB] 380s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quadprog amd64 1.5-8-1build2 [32.6 kB] 380s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xts amd64 0.14.1-1 [1198 kB] 380s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB] 380s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ttr amd64 0.24.4-1 [511 kB] 380s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 380s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quantmod all 0.4.28-1 [1037 kB] 380s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tseries amd64 0.10-59-3 [382 kB] 380s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-urca amd64 1.3-4-1build1 [1052 kB] 380s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB] 380s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-forecast amd64 8.23.0-1 [1569 kB] 380s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelr all 0.1.11-1 [195 kB] 380s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-microbenchmark amd64 1.5.0-1 [67.4 kB] 380s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-doby all 4.7.1-3 [4741 kB] 380s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB] 380s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB] 380s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 380s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 380s Get:191 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 380s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 380s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pbkrtest all 0.5.5-1 [217 kB] 380s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sparsem amd64 1.84-2-1 [813 kB] 381s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixmodels all 0.5-4-1 [351 kB] 381s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-6-1 [8274 kB] 381s Get:197 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB] 381s Get:198 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-class amd64 7.3-23-1 [92.7 kB] 381s Get:199 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-proxy amd64 0.4-27-1 [182 kB] 381s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-e1071 amd64 1.7-17-1 [579 kB] 381s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1build1 [91.1 kB] 381s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-iterators all 1.0.14-1build1 [336 kB] 381s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreach all 1.5.2-1build1 [124 kB] 381s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 381s Get:205 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-modelmetrics amd64 1.2.2.2-1build2 [155 kB] 381s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] 381s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-proc amd64 1.18.5-1 [966 kB] 381s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tzdb amd64 0.5.0-1 [538 kB] 381s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-clock amd64 0.7.2-1 [1903 kB] 381s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gower amd64 1.0.2-1 [210 kB] 381s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sparsevctrs amd64 0.2.0-2 [170 kB] 381s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hardhat all 1.4.2+dfsg-1 [596 kB] 381s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rpart amd64 4.1.24-1build1 [666 kB] 381s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shape all 1.4.6.1-1 [749 kB] 381s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diagram all 1.6.5-2 [656 kB] 381s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kernsmooth amd64 2.23-26-1build1 [93.6 kB] 381s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB] 381s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-globals all 0.19.0-1 [160 kB] 381s Get:219 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 381s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-parallelly amd64 1.42.0-1 [540 kB] 381s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 381s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-future.apply all 1.11.3+dfsg-1 [175 kB] 381s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-progressr all 0.15.1-1 [353 kB] 381s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-squarem all 2021.1-1build1 [180 kB] 381s Get:225 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lava all 1.8.2+dfsg-1 [2210 kB] 382s Get:226 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-prodlim amd64 2024.06.25-1 [415 kB] 382s Get:227 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ipred amd64 0.9-15-1 [386 kB] 382s Get:228 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-timechange amd64 0.3.0-2 [201 kB] 382s Get:229 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lubridate amd64 1.9.4+dfsg-1 [1009 kB] 382s Get:230 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-recipes all 1.1.0+dfsg-1 [2035 kB] 382s Get:231 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reshape2 amd64 1.4.4-2build2 [123 kB] 382s Get:232 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-caret amd64 7.0-1+dfsg-1 [3460 kB] 382s Get:233 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-conquer amd64 1.3.3-1 [499 kB] 382s Get:234 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quantreg amd64 6.1-1 [1455 kB] 382s Get:235 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-car all 3.1-5-1 [1526 kB] 382s Get:236 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sandwich all 3.1-1-1build1 [1483 kB] 382s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-aer all 1.2-15-1 [2607 kB] 382s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB] 382s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB] 382s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB] 382s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB] 382s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB] 382s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB] 382s Get:244 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreign amd64 0.8.91-1 [245 kB] 382s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hexbin amd64 1.28.5-1 [1581 kB] 382s Get:246 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB] 382s Get:247 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mitools all 2.4-2build2 [266 kB] 382s Get:248 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB] 382s Get:249 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB] 382s Get:250 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survey amd64 4.4-2-2 [3453 kB] 383s Preconfiguring packages ... 383s Fetched 279 MB in 13s (20.7 MB/s) 383s Selecting previously unselected package libc-dev-bin. 383s (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 ... 125269 files and directories currently installed.) 383s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 383s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 383s Selecting previously unselected package linux-libc-dev:amd64. 383s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ... 383s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 383s Selecting previously unselected package libcrypt-dev:amd64. 383s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 383s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 383s Selecting previously unselected package rpcsvc-proto. 383s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 383s Unpacking rpcsvc-proto (1.4.3-1build1) ... 383s Selecting previously unselected package libc6-dev:amd64. 383s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ... 383s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 383s Selecting previously unselected package libisl23:amd64. 383s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ... 383s Unpacking libisl23:amd64 (0.27-1build1) ... 383s Selecting previously unselected package libmpc3:amd64. 383s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ... 383s Unpacking libmpc3:amd64 (1.3.1-2) ... 383s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 383s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 383s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 383s Selecting previously unselected package cpp-15. 383s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 383s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 383s Selecting previously unselected package cpp-x86-64-linux-gnu. 383s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 383s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 383s Selecting previously unselected package cpp. 383s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 383s Unpacking cpp (4:15.2.0-4ubuntu1) ... 383s Selecting previously unselected package libcc1-0:amd64. 383s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 383s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 383s Selecting previously unselected package libgomp1:amd64. 383s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 383s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 383s Selecting previously unselected package libitm1:amd64. 383s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ... 383s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 383s Selecting previously unselected package libasan8:amd64. 383s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ... 383s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 383s Selecting previously unselected package liblsan0:amd64. 383s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 383s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 383s Selecting previously unselected package libtsan2:amd64. 383s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 383s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 384s Selecting previously unselected package libubsan1:amd64. 384s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 384s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 384s Selecting previously unselected package libhwasan0:amd64. 384s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 384s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 384s Selecting previously unselected package libquadmath0:amd64. 384s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ... 384s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ... 384s Selecting previously unselected package libgcc-15-dev:amd64. 384s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 384s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 384s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 384s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 384s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 384s Selecting previously unselected package gcc-15. 384s Preparing to unpack .../022-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 384s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 384s Selecting previously unselected package gcc-x86-64-linux-gnu. 384s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 384s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 384s Selecting previously unselected package gcc. 384s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 384s Unpacking gcc (4:15.2.0-4ubuntu1) ... 384s Selecting previously unselected package libstdc++-15-dev:amd64. 384s Preparing to unpack .../025-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 384s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 384s Selecting previously unselected package g++-15-x86-64-linux-gnu. 384s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 384s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 384s Selecting previously unselected package g++-15. 384s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ... 384s Unpacking g++-15 (15.2.0-12ubuntu1) ... 384s Selecting previously unselected package g++-x86-64-linux-gnu. 384s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 384s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 384s Selecting previously unselected package g++. 384s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 384s Unpacking g++ (4:15.2.0-4ubuntu1) ... 384s Selecting previously unselected package build-essential. 384s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ... 384s Unpacking build-essential (12.12ubuntu2) ... 384s Selecting previously unselected package dctrl-tools. 384s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ... 384s Unpacking dctrl-tools (2.24-3build4) ... 384s Selecting previously unselected package fonts-dejavu-mono. 384s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ... 384s Unpacking fonts-dejavu-mono (2.37-8build1) ... 384s Selecting previously unselected package fonts-dejavu-core. 384s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ... 384s Unpacking fonts-dejavu-core (2.37-8build1) ... 384s Selecting previously unselected package fontconfig-config. 384s Preparing to unpack .../034-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 385s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 385s Selecting previously unselected package libfontconfig1:amd64. 385s Preparing to unpack .../035-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 385s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 385s Selecting previously unselected package fontconfig. 385s Preparing to unpack .../036-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 385s Unpacking fontconfig (2.17.1-3ubuntu1) ... 385s Selecting previously unselected package fonts-glyphicons-halflings. 385s Preparing to unpack .../037-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 385s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 385s Selecting previously unselected package fonts-mathjax. 385s Preparing to unpack .../038-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 385s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 385s Selecting previously unselected package libgfortran5:amd64. 385s Preparing to unpack .../039-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 385s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 385s Selecting previously unselected package libgfortran-15-dev:amd64. 385s Preparing to unpack .../040-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ... 385s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 385s Selecting previously unselected package gfortran-15-x86-64-linux-gnu. 385s Preparing to unpack .../041-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 385s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 385s Selecting previously unselected package gfortran-15. 385s Preparing to unpack .../042-gfortran-15_15.2.0-12ubuntu1_amd64.deb ... 385s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 385s Selecting previously unselected package gfortran-x86-64-linux-gnu. 385s Preparing to unpack .../043-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 385s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 385s Selecting previously unselected package gfortran. 385s Preparing to unpack .../044-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 385s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 385s Selecting previously unselected package icu-devtools. 385s Preparing to unpack .../045-icu-devtools_78.2-1ubuntu1_amd64.deb ... 385s Unpacking icu-devtools (78.2-1ubuntu1) ... 385s Selecting previously unselected package libblas3:amd64. 385s Preparing to unpack .../046-libblas3_3.12.1-7ubuntu1_amd64.deb ... 385s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 385s Selecting previously unselected package libblas-dev:amd64. 385s Preparing to unpack .../047-libblas-dev_3.12.1-7ubuntu1_amd64.deb ... 385s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ... 385s Selecting previously unselected package libbz2-dev:amd64. 385s Preparing to unpack .../048-libbz2-dev_1.0.8-6build2_amd64.deb ... 385s Unpacking libbz2-dev:amd64 (1.0.8-6build2) ... 385s Selecting previously unselected package libpixman-1-0:amd64. 385s Preparing to unpack .../049-libpixman-1-0_0.46.4-1_amd64.deb ... 385s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 385s Selecting previously unselected package libxcb-render0:amd64. 385s Preparing to unpack .../050-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 385s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 385s Selecting previously unselected package libxcb-shm0:amd64. 385s Preparing to unpack .../051-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 385s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 385s Selecting previously unselected package libxrender1:amd64. 385s Preparing to unpack .../052-libxrender1_1%3a0.9.12-1_amd64.deb ... 385s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 385s Selecting previously unselected package libcairo2:amd64. 385s Preparing to unpack .../053-libcairo2_1.18.4-3_amd64.deb ... 385s Unpacking libcairo2:amd64 (1.18.4-3) ... 385s Selecting previously unselected package libdatrie1:amd64. 385s Preparing to unpack .../054-libdatrie1_0.2.14-1_amd64.deb ... 385s Unpacking libdatrie1:amd64 (0.2.14-1) ... 385s Selecting previously unselected package libdeflate0:amd64. 385s Preparing to unpack .../055-libdeflate0_1.23-2build1_amd64.deb ... 385s Unpacking libdeflate0:amd64 (1.23-2build1) ... 385s Selecting previously unselected package libdeflate-dev:amd64. 385s Preparing to unpack .../056-libdeflate-dev_1.23-2build1_amd64.deb ... 385s Unpacking libdeflate-dev:amd64 (1.23-2build1) ... 385s Selecting previously unselected package libgraphite2-3:amd64. 385s Preparing to unpack .../057-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 385s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 385s Selecting previously unselected package libharfbuzz0b:amd64. 385s Preparing to unpack .../058-libharfbuzz0b_12.3.2-1_amd64.deb ... 385s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 385s Selecting previously unselected package x11-common. 385s Preparing to unpack .../059-x11-common_1%3a7.7+24ubuntu1_all.deb ... 385s Unpacking x11-common (1:7.7+24ubuntu1) ... 385s Selecting previously unselected package libice6:amd64. 385s Preparing to unpack .../060-libice6_2%3a1.1.1-1build1_amd64.deb ... 385s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 385s Selecting previously unselected package libicu-dev:amd64. 385s Preparing to unpack .../061-libicu-dev_78.2-1ubuntu1_amd64.deb ... 385s Unpacking libicu-dev:amd64 (78.2-1ubuntu1) ... 385s Selecting previously unselected package libjpeg-turbo8:amd64. 385s Preparing to unpack .../062-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 385s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 385s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 385s Preparing to unpack .../063-libjpeg-turbo8-dev_2.1.5-4ubuntu3_amd64.deb ... 385s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ... 385s Selecting previously unselected package libjpeg8:amd64. 385s Preparing to unpack .../064-libjpeg8_8c-2ubuntu12_amd64.deb ... 385s Unpacking libjpeg8:amd64 (8c-2ubuntu12) ... 385s Selecting previously unselected package libjpeg8-dev:amd64. 385s Preparing to unpack .../065-libjpeg8-dev_8c-2ubuntu12_amd64.deb ... 385s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu12) ... 385s Selecting previously unselected package libjpeg-dev:amd64. 385s Preparing to unpack .../066-libjpeg-dev_8c-2ubuntu12_amd64.deb ... 385s Unpacking libjpeg-dev:amd64 (8c-2ubuntu12) ... 385s Selecting previously unselected package libjs-bootstrap. 386s Preparing to unpack .../067-libjs-bootstrap_3.4.1+dfsg-6_all.deb ... 386s Unpacking libjs-bootstrap (3.4.1+dfsg-6) ... 386s Selecting previously unselected package libjs-highlight.js. 386s Preparing to unpack .../068-libjs-highlight.js_10.7.3+dfsg-2_all.deb ... 386s Unpacking libjs-highlight.js (10.7.3+dfsg-2) ... 386s Selecting previously unselected package libjs-jquery. 386s Preparing to unpack .../069-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 386s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 386s Selecting previously unselected package libjs-jquery-datatables. 386s Preparing to unpack .../070-libjs-jquery-datatables_1.11.5+dfsg-2build1_all.deb ... 386s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 386s Selecting previously unselected package liblapack3:amd64. 386s Preparing to unpack .../071-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 386s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 386s Selecting previously unselected package liblapack-dev:amd64. 386s Preparing to unpack .../072-liblapack-dev_3.12.1-7ubuntu1_amd64.deb ... 386s Unpacking liblapack-dev:amd64 (3.12.1-7ubuntu1) ... 386s Selecting previously unselected package liblerc4:amd64. 386s Preparing to unpack .../073-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 386s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 386s Selecting previously unselected package libncurses-dev:amd64. 386s Preparing to unpack .../074-libncurses-dev_6.6+20251231-1_amd64.deb ... 386s Unpacking libncurses-dev:amd64 (6.6+20251231-1) ... 386s Selecting previously unselected package libthai-data. 386s Preparing to unpack .../075-libthai-data_0.1.30-1_all.deb ... 386s Unpacking libthai-data (0.1.30-1) ... 386s Selecting previously unselected package libthai0:amd64. 386s Preparing to unpack .../076-libthai0_0.1.30-1_amd64.deb ... 386s Unpacking libthai0:amd64 (0.1.30-1) ... 386s Selecting previously unselected package libpango-1.0-0:amd64. 386s Preparing to unpack .../077-libpango-1.0-0_1.57.0-1_amd64.deb ... 386s Unpacking libpango-1.0-0:amd64 (1.57.0-1) ... 386s Selecting previously unselected package libpangoft2-1.0-0:amd64. 386s Preparing to unpack .../078-libpangoft2-1.0-0_1.57.0-1_amd64.deb ... 386s Unpacking libpangoft2-1.0-0:amd64 (1.57.0-1) ... 386s Selecting previously unselected package libpangocairo-1.0-0:amd64. 386s Preparing to unpack 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libtiff6:amd64. 386s Preparing to unpack .../095-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 386s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 386s Selecting previously unselected package libxft2:amd64. 386s Preparing to unpack .../096-libxft2_2.3.6-1build2_amd64.deb ... 386s Unpacking libxft2:amd64 (2.3.6-1build2) ... 386s Selecting previously unselected package libxss1:amd64. 386s Preparing to unpack .../097-libxss1_1%3a1.2.3-1build4_amd64.deb ... 386s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 386s Selecting previously unselected package libtk8.6:amd64. 386s Preparing to unpack .../098-libtk8.6_8.6.17-1_amd64.deb ... 386s Unpacking libtk8.6:amd64 (8.6.17-1) ... 386s Selecting previously unselected package libxt6t64:amd64. 386s Preparing to unpack .../099-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 386s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 386s Selecting previously unselected package libzstd-dev:amd64. 386s Preparing to unpack .../100-libzstd-dev_1.5.7+dfsg-3_amd64.deb ... 386s Unpacking libzstd-dev:amd64 (1.5.7+dfsg-3) ... 386s Selecting previously unselected package node-normalize.css. 386s Preparing to unpack .../101-node-normalize.css_8.0.1-5.1_all.deb ... 386s Unpacking node-normalize.css (8.0.1-5.1) ... 386s Selecting previously unselected package zip. 386s Preparing to unpack .../102-zip_3.0-15ubuntu3_amd64.deb ... 386s Unpacking zip (3.0-15ubuntu3) ... 386s Selecting previously unselected package unzip. 386s Preparing to unpack .../103-unzip_6.0-29ubuntu1_amd64.deb ... 386s Unpacking unzip (6.0-29ubuntu1) ... 386s Selecting previously unselected package xdg-utils. 386s Preparing to unpack .../104-xdg-utils_1.2.1-2ubuntu2_all.deb ... 386s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 386s Selecting previously unselected package r-base-core. 386s Preparing to unpack .../105-r-base-core_4.5.2-1ubuntu2_amd64.deb ... 386s Unpacking r-base-core (4.5.2-1ubuntu2) ... 387s Selecting previously unselected package liblzma-dev:amd64. 387s Preparing to unpack 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Selecting previously unselected package r-cran-abind. 387s Preparing to unpack .../112-r-cran-abind_1.4-8-1build1_all.deb ... 387s Unpacking r-cran-abind (1.4-8-1build1) ... 387s Selecting previously unselected package r-cran-cardata. 387s Preparing to unpack .../113-r-cran-cardata_3.0.6-1_all.deb ... 387s Unpacking r-cran-cardata (3.0.6-1) ... 387s Selecting previously unselected package r-cran-formula. 387s Preparing to unpack .../114-r-cran-formula_1.2-5-1_all.deb ... 387s Unpacking r-cran-formula (1.2-5-1) ... 387s Selecting previously unselected package r-cran-mass. 387s Preparing to unpack .../115-r-cran-mass_7.3-65-1_amd64.deb ... 387s Unpacking r-cran-mass (7.3-65-1) ... 387s Selecting previously unselected package r-cran-lattice. 387s Preparing to unpack .../116-r-cran-lattice_0.22-9-1_amd64.deb ... 387s Unpacking r-cran-lattice (0.22-9-1) ... 387s Selecting previously unselected package r-cran-nlme. 387s Preparing to unpack .../117-r-cran-nlme_3.1.168-1_amd64.deb ... 387s Unpacking r-cran-nlme (3.1.168-1) ... 387s Selecting previously unselected package r-cran-matrix. 387s Preparing to unpack .../118-r-cran-matrix_1.7-4-1_amd64.deb ... 387s Unpacking r-cran-matrix (1.7-4-1) ... 387s Selecting previously unselected package r-cran-mgcv. 387s Preparing to unpack .../119-r-cran-mgcv_1.9-4-1_amd64.deb ... 387s Unpacking r-cran-mgcv (1.9-4-1) ... 387s Selecting previously unselected package r-cran-nnet. 387s Preparing to unpack .../120-r-cran-nnet_7.3-20-1_amd64.deb ... 387s Unpacking r-cran-nnet (7.3-20-1) ... 387s Selecting previously unselected package r-cran-boot. 387s Preparing to unpack .../121-r-cran-boot_1.3-32-1_all.deb ... 387s Unpacking r-cran-boot (1.3-32-1) ... 387s Selecting previously unselected package r-cran-littler. 387s Preparing to unpack .../122-r-cran-littler_0.3.22-1_amd64.deb ... 387s Unpacking r-cran-littler (0.3.22-1) ... 387s Selecting previously unselected package r-cran-pkgkitten. 387s Preparing to unpack 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package r-cran-rdpack. 387s Preparing to unpack .../129-r-cran-rdpack_2.6.3-1_all.deb ... 387s Unpacking r-cran-rdpack (2.6.3-1) ... 387s Selecting previously unselected package r-cran-reformulas. 387s Preparing to unpack .../130-r-cran-reformulas_0.4.4-1_all.deb ... 387s Unpacking r-cran-reformulas (0.4.4-1) ... 387s Selecting previously unselected package r-cran-rlang. 387s Preparing to unpack .../131-r-cran-rlang_1.1.5-3_amd64.deb ... 387s Unpacking r-cran-rlang (1.1.5-3) ... 387s Selecting previously unselected package r-cran-rcppeigen. 387s Preparing to unpack .../132-r-cran-rcppeigen_0.3.4.0.2-1_amd64.deb ... 387s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 387s Selecting previously unselected package r-cran-statmod. 387s Preparing to unpack .../133-r-cran-statmod_1.5.0-1_amd64.deb ... 387s Unpacking r-cran-statmod (1.5.0-1) ... 387s Selecting previously unselected package r-cran-lme4. 387s Preparing to unpack .../134-r-cran-lme4_1.1-38-1_amd64.deb ... 387s Unpacking r-cran-lme4 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388s Preparing to unpack .../146-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 388s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 388s Selecting previously unselected package r-cran-tibble. 388s Preparing to unpack .../147-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ... 388s Unpacking r-cran-tibble (3.2.1+dfsg-3) ... 388s Selecting previously unselected package r-cran-withr. 388s Preparing to unpack .../148-r-cran-withr_3.0.2+dfsg-1_all.deb ... 388s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 388s Selecting previously unselected package r-cran-tidyselect. 388s Preparing to unpack .../149-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ... 388s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ... 388s Selecting previously unselected package r-cran-dplyr. 388s Preparing to unpack .../150-r-cran-dplyr_1.1.4-4_amd64.deb ... 388s Unpacking r-cran-dplyr (1.1.4-4) ... 388s Selecting previously unselected package r-cran-purrr. 388s Preparing to unpack .../151-r-cran-purrr_1.0.4-1_amd64.deb ... 388s Unpacking r-cran-purrr (1.0.4-1) ... 388s Selecting previously unselected package r-cran-stringi. 388s Preparing to unpack .../152-r-cran-stringi_1.8.4-1build2_amd64.deb ... 388s Unpacking r-cran-stringi (1.8.4-1build2) ... 388s Selecting previously unselected package r-cran-stringr. 388s Preparing to unpack .../153-r-cran-stringr_1.5.1-1_all.deb ... 388s Unpacking r-cran-stringr (1.5.1-1) ... 388s Selecting previously unselected package r-cran-cpp11. 388s Preparing to unpack .../154-r-cran-cpp11_0.5.3-1_all.deb ... 388s Unpacking r-cran-cpp11 (0.5.3-1) ... 388s Selecting previously unselected package r-cran-tidyr. 388s Preparing to unpack .../155-r-cran-tidyr_1.3.1-1_amd64.deb ... 388s Unpacking r-cran-tidyr (1.3.1-1) ... 388s Selecting previously unselected package r-cran-broom. 388s Preparing to unpack .../156-r-cran-broom_1.0.12+dfsg-1_all.deb ... 388s Unpacking r-cran-broom (1.0.12+dfsg-1) ... 388s Selecting previously unselected package r-cran-numderiv. 388s Preparing to unpack .../157-r-cran-numderiv_2016.8-1.1-3build1_all.deb ... 388s Unpacking r-cran-numderiv (2016.8-1.1-3build1) ... 388s Selecting previously unselected package r-cran-gtable. 388s Preparing to unpack .../158-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 388s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 388s Selecting previously unselected package r-cran-isoband. 388s Preparing to unpack .../159-r-cran-isoband_0.2.7-1_amd64.deb ... 388s Unpacking r-cran-isoband (0.2.7-1) ... 388s Selecting previously unselected package r-cran-farver. 388s Preparing to unpack .../160-r-cran-farver_2.1.2-1_amd64.deb ... 388s Unpacking r-cran-farver (2.1.2-1) ... 388s Selecting previously unselected package r-cran-labeling. 388s Preparing to unpack .../161-r-cran-labeling_0.4.3-1_all.deb ... 388s Unpacking r-cran-labeling (0.4.3-1) ... 388s Selecting previously unselected package r-cran-rcolorbrewer. 388s Preparing to unpack .../162-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 388s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 388s Selecting previously unselected package r-cran-viridislite. 388s Preparing to unpack .../163-r-cran-viridislite_0.4.3-1_all.deb ... 388s Unpacking r-cran-viridislite (0.4.3-1) ... 388s Selecting previously unselected package r-cran-scales. 388s Preparing to unpack .../164-r-cran-scales_1.4.0-1_all.deb ... 388s Unpacking r-cran-scales (1.4.0-1) ... 388s Selecting previously unselected package r-cran-ggplot2. 388s Preparing to unpack .../165-r-cran-ggplot2_3.5.1+dfsg-1_all.deb ... 388s Unpacking r-cran-ggplot2 (3.5.1+dfsg-1) ... 388s Selecting previously unselected package r-cran-cowplot. 388s Preparing to unpack .../166-r-cran-cowplot_1.1.3+dfsg-1_all.deb ... 388s Unpacking r-cran-cowplot (1.1.3+dfsg-1) ... 388s Selecting previously unselected package r-cran-deriv. 388s Preparing to unpack .../167-r-cran-deriv_4.2.0-1_all.deb ... 388s Unpacking r-cran-deriv (4.2.0-1) ... 388s Selecting previously unselected package r-cran-colorspace. 388s Preparing to unpack .../168-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... 388s Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... 388s Selecting previously unselected package r-cran-fracdiff. 388s Preparing to unpack .../169-r-cran-fracdiff_1.5-3-1_amd64.deb ... 388s Unpacking r-cran-fracdiff (1.5-3-1) ... 388s Selecting previously unselected package r-cran-zoo. 388s Preparing to unpack .../170-r-cran-zoo_1.8-15-1_amd64.deb ... 388s Unpacking r-cran-zoo (1.8-15-1) ... 388s Selecting previously unselected package r-cran-lmtest. 388s Preparing to unpack .../171-r-cran-lmtest_0.9.40-1build1_amd64.deb ... 388s Unpacking r-cran-lmtest (0.9.40-1build1) ... 388s Selecting previously unselected package r-cran-timedate. 388s Preparing to unpack .../172-r-cran-timedate_4052.112-1_amd64.deb ... 388s Unpacking r-cran-timedate (4052.112-1) ... 388s Selecting previously unselected package r-cran-quadprog. 388s Preparing to unpack .../173-r-cran-quadprog_1.5-8-1build2_amd64.deb ... 388s Unpacking r-cran-quadprog (1.5-8-1build2) ... 388s Selecting previously unselected package r-cran-xts. 388s Preparing to unpack .../174-r-cran-xts_0.14.1-1_amd64.deb ... 388s Unpacking r-cran-xts (0.14.1-1) ... 388s Selecting previously unselected package r-cran-curl. 388s Preparing to unpack .../175-r-cran-curl_7.0.0+dfsg-1_amd64.deb ... 388s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 388s Selecting previously unselected package r-cran-ttr. 388s Preparing to unpack .../176-r-cran-ttr_0.24.4-1_amd64.deb ... 388s Unpacking r-cran-ttr (0.24.4-1) ... 388s Selecting previously unselected package r-cran-jsonlite. 388s Preparing to unpack .../177-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ... 388s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 388s Selecting previously unselected package r-cran-quantmod. 388s Preparing to unpack .../178-r-cran-quantmod_0.4.28-1_all.deb ... 388s Unpacking r-cran-quantmod (0.4.28-1) ... 388s Selecting previously unselected package r-cran-tseries. 388s Preparing to unpack .../179-r-cran-tseries_0.10-59-3_amd64.deb ... 388s Unpacking r-cran-tseries (0.10-59-3) ... 388s Selecting previously unselected package r-cran-urca. 388s Preparing to unpack .../180-r-cran-urca_1.3-4-1build1_amd64.deb ... 388s Unpacking r-cran-urca (1.3-4-1build1) ... 388s Selecting previously unselected package r-cran-rcpparmadillo. 388s Preparing to unpack .../181-r-cran-rcpparmadillo_15.2.3-1-1_amd64.deb ... 388s Unpacking r-cran-rcpparmadillo (15.2.3-1-1) ... 388s Selecting previously unselected package r-cran-forecast. 388s Preparing to unpack .../182-r-cran-forecast_8.23.0-1_amd64.deb ... 388s Unpacking r-cran-forecast (8.23.0-1) ... 388s Selecting previously unselected package r-cran-modelr. 388s Preparing to unpack .../183-r-cran-modelr_0.1.11-1_all.deb ... 388s Unpacking r-cran-modelr (0.1.11-1) ... 388s Selecting previously unselected package r-cran-microbenchmark. 389s Preparing to unpack .../184-r-cran-microbenchmark_1.5.0-1_amd64.deb ... 389s Unpacking r-cran-microbenchmark (1.5.0-1) ... 389s Selecting previously unselected package r-cran-doby. 389s Preparing to unpack .../185-r-cran-doby_4.7.1-3_all.deb ... 389s Unpacking r-cran-doby (4.7.1-3) ... 389s Selecting previously unselected package r-cran-evaluate. 389s Preparing to unpack .../186-r-cran-evaluate_1.0.5-1_all.deb ... 389s Unpacking r-cran-evaluate (1.0.5-1) ... 389s Selecting previously unselected package r-cran-xfun. 389s Preparing to unpack .../187-r-cran-xfun_0.55+dfsg-1_amd64.deb ... 389s Unpacking r-cran-xfun (0.55+dfsg-1) ... 389s Selecting previously unselected package r-cran-highr. 389s Preparing to unpack .../188-r-cran-highr_0.11+dfsg-1_all.deb ... 389s Unpacking r-cran-highr (0.11+dfsg-1) ... 389s Selecting previously unselected package r-cran-yaml. 389s Preparing to unpack .../189-r-cran-yaml_2.3.10-1_amd64.deb ... 389s Unpacking r-cran-yaml (2.3.10-1) ... 389s Selecting previously unselected package libjs-mathjax. 389s Preparing to unpack .../190-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 389s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 389s Selecting previously unselected package r-cran-knitr. 389s Preparing to unpack .../191-r-cran-knitr_1.51+dfsg-1_all.deb ... 389s Unpacking r-cran-knitr (1.51+dfsg-1) ... 389s Selecting previously unselected package r-cran-pbkrtest. 389s Preparing to unpack .../192-r-cran-pbkrtest_0.5.5-1_all.deb ... 389s Unpacking r-cran-pbkrtest (0.5.5-1) ... 389s Selecting previously unselected package r-cran-sparsem. 389s Preparing to unpack .../193-r-cran-sparsem_1.84-2-1_amd64.deb ... 389s Unpacking r-cran-sparsem (1.84-2-1) ... 389s Selecting previously unselected package r-cran-matrixmodels. 389s Preparing to unpack .../194-r-cran-matrixmodels_0.5-4-1_all.deb ... 389s Unpacking r-cran-matrixmodels (0.5-4-1) ... 389s Selecting previously unselected package r-cran-survival. 389s Preparing to unpack .../195-r-cran-survival_3.8-6-1_amd64.deb ... 389s Unpacking r-cran-survival (3.8-6-1) ... 389s Selecting previously unselected package r-cran-matrixstats. 389s Preparing to unpack .../196-r-cran-matrixstats_1.5.0-1_amd64.deb ... 389s Unpacking r-cran-matrixstats (1.5.0-1) ... 389s Selecting previously unselected package r-cran-class. 389s Preparing to unpack .../197-r-cran-class_7.3-23-1_amd64.deb ... 389s Unpacking r-cran-class (7.3-23-1) ... 389s Selecting previously unselected package r-cran-proxy. 389s Preparing to unpack .../198-r-cran-proxy_0.4-27-1_amd64.deb ... 389s Unpacking r-cran-proxy (0.4-27-1) ... 389s Selecting previously unselected package r-cran-e1071. 389s Preparing to unpack .../199-r-cran-e1071_1.7-17-1_amd64.deb ... 389s Unpacking r-cran-e1071 (1.7-17-1) ... 389s Selecting previously unselected package r-cran-codetools. 389s Preparing to unpack .../200-r-cran-codetools_0.2-20-1build1_all.deb ... 389s Unpacking r-cran-codetools (0.2-20-1build1) ... 389s Selecting previously unselected package r-cran-iterators. 389s Preparing to unpack .../201-r-cran-iterators_1.0.14-1build1_all.deb ... 389s Unpacking r-cran-iterators (1.0.14-1build1) ... 389s Selecting previously unselected package r-cran-foreach. 389s Preparing to unpack .../202-r-cran-foreach_1.5.2-1build1_all.deb ... 389s Unpacking r-cran-foreach (1.5.2-1build1) ... 389s Selecting previously unselected package r-cran-data.table. 389s Preparing to unpack .../203-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ... 389s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 389s Selecting previously unselected package r-cran-modelmetrics. 389s Preparing to unpack .../204-r-cran-modelmetrics_1.2.2.2-1build2_amd64.deb ... 389s Unpacking r-cran-modelmetrics (1.2.2.2-1build2) ... 389s Selecting previously unselected package r-cran-plyr. 389s Preparing to unpack .../205-r-cran-plyr_1.8.9-1_amd64.deb ... 389s Unpacking r-cran-plyr (1.8.9-1) ... 389s Selecting previously unselected package r-cran-proc. 389s Preparing to unpack .../206-r-cran-proc_1.18.5-1_amd64.deb ... 389s Unpacking r-cran-proc (1.18.5-1) ... 389s Selecting previously unselected package r-cran-tzdb. 389s Preparing to unpack .../207-r-cran-tzdb_0.5.0-1_amd64.deb ... 389s Unpacking r-cran-tzdb (0.5.0-1) ... 389s Selecting previously unselected package r-cran-clock. 389s Preparing to unpack .../208-r-cran-clock_0.7.2-1_amd64.deb ... 389s Unpacking r-cran-clock (0.7.2-1) ... 389s Selecting previously unselected package r-cran-gower. 389s Preparing to unpack .../209-r-cran-gower_1.0.2-1_amd64.deb ... 389s Unpacking r-cran-gower (1.0.2-1) ... 389s Selecting previously unselected package r-cran-sparsevctrs. 389s Preparing to unpack .../210-r-cran-sparsevctrs_0.2.0-2_amd64.deb ... 389s Unpacking r-cran-sparsevctrs (0.2.0-2) ... 389s Selecting previously unselected package r-cran-hardhat. 389s Preparing to unpack .../211-r-cran-hardhat_1.4.2+dfsg-1_all.deb ... 389s Unpacking r-cran-hardhat (1.4.2+dfsg-1) ... 389s Selecting previously unselected package r-cran-rpart. 389s Preparing to unpack .../212-r-cran-rpart_4.1.24-1build1_amd64.deb ... 389s Unpacking r-cran-rpart (4.1.24-1build1) ... 389s Selecting previously unselected package r-cran-shape. 389s Preparing to unpack .../213-r-cran-shape_1.4.6.1-1_all.deb ... 389s Unpacking r-cran-shape (1.4.6.1-1) ... 389s Selecting previously unselected package r-cran-diagram. 389s Preparing to unpack .../214-r-cran-diagram_1.6.5-2_all.deb ... 389s Unpacking r-cran-diagram (1.6.5-2) ... 389s Selecting previously unselected package r-cran-kernsmooth. 389s Preparing to unpack .../215-r-cran-kernsmooth_2.23-26-1build1_amd64.deb ... 389s Unpacking r-cran-kernsmooth (2.23-26-1build1) ... 389s Selecting previously unselected package r-cran-digest. 389s Preparing to unpack .../216-r-cran-digest_0.6.39-1_amd64.deb ... 389s Unpacking r-cran-digest (0.6.39-1) ... 389s Selecting previously unselected package r-cran-globals. 389s Preparing to unpack .../217-r-cran-globals_0.19.0-1_all.deb ... 389s Unpacking r-cran-globals (0.19.0-1) ... 389s Selecting previously unselected package r-cran-listenv. 389s Preparing to unpack .../218-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 389s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 389s Selecting previously unselected package r-cran-parallelly. 389s Preparing to unpack .../219-r-cran-parallelly_1.42.0-1_amd64.deb ... 389s Unpacking r-cran-parallelly (1.42.0-1) ... 389s Selecting previously unselected package r-cran-future. 389s Preparing to unpack .../220-r-cran-future_1.34.0+dfsg-1_all.deb ... 389s Unpacking r-cran-future (1.34.0+dfsg-1) ... 390s Selecting previously unselected package r-cran-future.apply. 390s Preparing to unpack .../221-r-cran-future.apply_1.11.3+dfsg-1_all.deb ... 390s Unpacking r-cran-future.apply (1.11.3+dfsg-1) ... 390s Selecting previously unselected package r-cran-progressr. 390s Preparing to unpack .../222-r-cran-progressr_0.15.1-1_all.deb ... 390s Unpacking r-cran-progressr (0.15.1-1) ... 390s Selecting previously unselected package r-cran-squarem. 390s Preparing to unpack .../223-r-cran-squarem_2021.1-1build1_all.deb ... 390s Unpacking r-cran-squarem (2021.1-1build1) ... 390s Selecting previously unselected package r-cran-lava. 390s Preparing to unpack .../224-r-cran-lava_1.8.2+dfsg-1_all.deb ... 390s Unpacking r-cran-lava (1.8.2+dfsg-1) ... 390s Selecting previously unselected package r-cran-prodlim. 390s Preparing to unpack .../225-r-cran-prodlim_2024.06.25-1_amd64.deb ... 390s Unpacking r-cran-prodlim (2024.06.25-1) ... 390s Selecting previously unselected package r-cran-ipred. 390s Preparing to unpack .../226-r-cran-ipred_0.9-15-1_amd64.deb ... 390s Unpacking r-cran-ipred (0.9-15-1) ... 390s Selecting previously unselected package r-cran-timechange. 390s Preparing to unpack .../227-r-cran-timechange_0.3.0-2_amd64.deb ... 390s Unpacking r-cran-timechange (0.3.0-2) ... 390s Selecting previously unselected package r-cran-lubridate. 390s Preparing to unpack .../228-r-cran-lubridate_1.9.4+dfsg-1_amd64.deb ... 390s Unpacking r-cran-lubridate (1.9.4+dfsg-1) ... 390s Selecting previously unselected package r-cran-recipes. 390s Preparing to unpack .../229-r-cran-recipes_1.1.0+dfsg-1_all.deb ... 390s Unpacking r-cran-recipes (1.1.0+dfsg-1) ... 390s Selecting previously unselected package r-cran-reshape2. 390s Preparing to unpack .../230-r-cran-reshape2_1.4.4-2build2_amd64.deb ... 390s Unpacking r-cran-reshape2 (1.4.4-2build2) ... 390s Selecting previously unselected package r-cran-caret. 390s Preparing to unpack .../231-r-cran-caret_7.0-1+dfsg-1_amd64.deb ... 390s Unpacking r-cran-caret (7.0-1+dfsg-1) ... 390s Selecting previously unselected package r-cran-conquer. 390s Preparing to unpack .../232-r-cran-conquer_1.3.3-1_amd64.deb ... 390s Unpacking r-cran-conquer (1.3.3-1) ... 390s Selecting previously unselected package r-cran-quantreg. 390s Preparing to unpack .../233-r-cran-quantreg_6.1-1_amd64.deb ... 390s Unpacking r-cran-quantreg (6.1-1) ... 390s Selecting previously unselected package r-cran-car. 390s Preparing to unpack .../234-r-cran-car_3.1-5-1_all.deb ... 390s Unpacking r-cran-car (3.1-5-1) ... 390s Selecting previously unselected package r-cran-sandwich. 390s Preparing to unpack .../235-r-cran-sandwich_3.1-1-1build1_all.deb ... 390s Unpacking r-cran-sandwich (3.1-1-1build1) ... 390s Selecting previously unselected package r-cran-aer. 390s Preparing to unpack .../236-r-cran-aer_1.2-15-1_all.deb ... 390s Unpacking r-cran-aer (1.2-15-1) ... 390s Selecting previously unselected package r-cran-bit. 390s Preparing to unpack .../237-r-cran-bit_4.6.0+dfsg-1_amd64.deb ... 390s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 390s Selecting previously unselected package r-cran-bit64. 390s Preparing to unpack .../238-r-cran-bit64_4.6.0-1-4_amd64.deb ... 390s Unpacking r-cran-bit64 (4.6.0-1-4) ... 390s Selecting previously unselected package r-cran-blob. 390s Preparing to unpack .../239-r-cran-blob_1.3.0-1_all.deb ... 390s Unpacking r-cran-blob (1.3.0-1) ... 390s Selecting previously unselected package r-cran-fastmap. 390s Preparing to unpack .../240-r-cran-fastmap_1.2.0-1_amd64.deb ... 390s Unpacking r-cran-fastmap (1.2.0-1) ... 390s Selecting previously unselected package r-cran-cachem. 390s Preparing to unpack .../241-r-cran-cachem_1.1.0-1_amd64.deb ... 390s Unpacking r-cran-cachem (1.1.0-1) ... 390s Selecting previously unselected package r-cran-dbi. 390s Preparing to unpack .../242-r-cran-dbi_1.2.3-1build1_all.deb ... 390s Unpacking r-cran-dbi (1.2.3-1build1) ... 390s Selecting previously unselected package r-cran-foreign. 390s Preparing to unpack .../243-r-cran-foreign_0.8.91-1_amd64.deb ... 390s Unpacking r-cran-foreign (0.8.91-1) ... 390s Selecting previously unselected package r-cran-hexbin. 390s Preparing to unpack .../244-r-cran-hexbin_1.28.5-1_amd64.deb ... 390s Unpacking r-cran-hexbin (1.28.5-1) ... 390s Selecting previously unselected package r-cran-memoise. 390s Preparing to unpack .../245-r-cran-memoise_2.0.1-1build1_all.deb ... 390s Unpacking r-cran-memoise 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... 391s Setting up libblas-dev:amd64 (3.12.1-7ubuntu1) ... 391s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 391s Setting up dctrl-tools (2.24-3build4) ... 391s Setting up libjs-bootstrap (3.4.1+dfsg-6) ... 391s Setting up libitm1:amd64 (16-20260208-1ubuntu1) ... 391s Setting up libjpeg8:amd64 (8c-2ubuntu12) ... 391s Setting up libice6:amd64 (2:1.1.1-1build1) ... 391s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 391s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 391s Setting up libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 391s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 391s Setting up libpaper-utils (2.2.5-0.3build1) ... 391s Setting up cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 391s Setting up libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 391s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ... 391s Setting up pkgconf:amd64 (1.8.1-4build1) ... 391s Setting up gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 391s Setting up libthai0:amd64 (0.1.30-1) ... 391s Setting up liblapack-dev:amd64 (3.12.1-7ubuntu1) ... 391s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 391s Setting up cpp-15 (15.2.0-12ubuntu1) ... 391s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 391s Setting up libc6-dev:amd64 (2.42-2ubuntu4) ... 391s Setting up libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 391s Setting up libsm6:amd64 (2:1.2.6-1build1) ... 391s Setting up libicu-dev:amd64 (78.2-1ubuntu1) ... 391s Setting up libbz2-dev:amd64 (1.0.8-6build2) ... 391s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 391s Setting up gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 391s Setting up fontconfig (2.17.1-3ubuntu1) ... 393s Regenerating fonts cache... done. 393s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ... 393s Setting up libxft2:amd64 (2.3.6-1build2) ... 393s Setting up libncurses-dev:amd64 (6.6+20251231-1) ... 393s Setting up libpcre2-dev:amd64 (10.46-1) ... 393s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 393s Setting up libtk8.6:amd64 (8.6.17-1) ... 393s Setting up libpango-1.0-0:amd64 (1.57.0-1) ... 393s Setting up libreadline-dev:amd64 (8.3-3) ... 393s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 393s Setting up libcairo2:amd64 (1.18.4-3) ... 393s Setting up gcc-15 (15.2.0-12ubuntu1) ... 393s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 393s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 393s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 393s Setting up cpp (4:15.2.0-4ubuntu1) ... 393s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ... 393s Setting up libjpeg8-dev:amd64 (8c-2ubuntu12) ... 393s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 393s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ... 393s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 393s Setting up libpng-dev:amd64 (1.6.54-1) ... 393s Setting up libjpeg-dev:amd64 (8c-2ubuntu12) ... 393s Setting up gcc (4:15.2.0-4ubuntu1) ... 393s Setting up r-base-core (4.5.2-1ubuntu2) ... 393s Creating config file /etc/R/Renviron with new version 393s Setting up r-cran-squarem (2021.1-1build1) ... 393s Setting up r-cran-labeling (0.4.3-1) ... 393s Setting up r-cran-lattice (0.22-9-1) ... 393s Setting up r-cran-nlme (3.1.168-1) ... 393s Setting up r-cran-farver (2.1.2-1) ... 393s Setting up r-cran-formula (1.2-5-1) ... 393s Setting up r-cran-hexbin (1.28.5-1) ... 393s Setting up r-cran-viridislite (0.4.3-1) ... 393s Setting up r-cran-sparsem (1.84-2-1) ... 393s Setting up r-cran-statmod (1.5.0-1) ... 393s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 393s Setting up r-cran-nnet (7.3-20-1) ... 393s Setting up r-cran-proxy (0.4-27-1) ... 393s Setting up r-cran-r6 (2.6.1-1) ... 393s Setting up r-cran-pkgkitten (0.2.4-1) ... 393s Setting up r-cran-numderiv (2016.8-1.1-3build1) ... 393s Setting up g++-15 (15.2.0-12ubuntu1) ... 393s Setting up r-cran-magrittr (2.0.3-1) ... 393s Setting up r-cran-microbenchmark (1.5.0-1) ... 393s Setting up r-cran-quadprog (1.5-8-1build2) ... 393s Setting up r-cran-littler (0.3.22-1) ... 393s Setting up r-cran-rcpp (1.1.0-1) ... 393s Setting up r-cran-curl (7.0.0+dfsg-1) ... 393s Setting up r-cran-codetools (0.2-20-1build1) ... 393s Setting up r-cran-nloptr (2.2.1-2) ... 393s Setting up r-cran-boot (1.3-32-1) ... 393s Setting up r-cran-rlang (1.1.5-3) ... 393s Setting up r-cran-matrixstats (1.5.0-1) ... 393s Setting up r-cran-listenv (0.10.0+dfsg-1) ... 393s Setting up r-cran-xfun (0.55+dfsg-1) ... 393s Setting up r-cran-urca (1.3-4-1build1) ... 393s Setting up r-cran-plogr (0.2.0-3build2) ... 393s Setting up r-cran-withr (3.0.2+dfsg-1) ... 393s Setting up r-cran-backports (1.5.0-2) ... 393s Setting up r-cran-deriv (4.2.0-1) ... 393s Setting up r-cran-generics (0.1.4-1) ... 393s Setting up r-cran-iterators (1.0.14-1build1) ... 393s Setting up r-cran-abind (1.4-8-1build1) ... 393s Setting up r-cran-digest (0.6.39-1) ... 393s Setting up r-cran-yaml (2.3.10-1) ... 393s Setting up r-cran-gower (1.0.2-1) ... 393s Setting up r-cran-evaluate (1.0.5-1) ... 393s Setting up r-cran-dbi (1.2.3-1build1) ... 393s Setting up r-cran-timedate (4052.112-1) ... 393s Setting up r-cran-highr (0.11+dfsg-1) ... 393s Setting up r-cran-foreach (1.5.2-1build1) ... 393s Setting up r-cran-fansi (1.0.6-2) ... 393s Setting up r-cran-cardata (3.0.6-1) ... 393s Setting up r-cran-mass (7.3-65-1) ... 393s Setting up r-cran-data.table (1.17.0+dfsg-1) ... 393s Setting up r-cran-glue (1.8.0-1) ... 393s Setting up r-cran-foreign (0.8.91-1) ... 393s Setting up r-cran-fracdiff (1.5-3-1) ... 393s Setting up r-cran-bit (4.6.0+dfsg-1) ... 393s Setting up r-cran-cli (3.6.4-1) ... 393s Setting up gfortran (4:15.2.0-4ubuntu1) ... 393s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 393s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 393s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 393s 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 393s Setting up r-cran-rbibutils (2.3-1) ... 393s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 393s Setting up r-cran-bit64 (4.6.0-1-4) ... 393s Setting up r-cran-progressr (0.15.1-1) ... 393s Setting up r-cran-shape (1.4.6.1-1) ... 393s Setting up r-cran-fastmap (1.2.0-1) ... 393s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... 393s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 393s Setting up r-cran-utf8 (1.2.4-1) ... 393s Setting up r-cran-colorspace (2.1-1+dfsg-1) ... 393s Setting up r-cran-parallelly (1.42.0-1) ... 393s Setting up r-cran-stringi (1.8.4-1build2) ... 393s Setting up r-cran-cpp11 (0.5.3-1) ... 393s Setting up r-cran-plyr (1.8.9-1) ... 393s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ... 393s Setting up r-cran-isoband (0.2.7-1) ... 393s Setting up r-cran-diagram (1.6.5-2) ... 393s Setting up r-cran-scales (1.4.0-1) ... 393s Setting up r-cran-gtable (0.3.6+dfsg-1) ... 393s Setting up r-cran-zoo (1.8-15-1) ... 393s Setting up r-cran-matrix (1.7-4-1) ... 393s Setting up r-cran-kernsmooth (2.23-26-1build1) ... 393s Setting up r-cran-knitr (1.51+dfsg-1) ... 393s Setting up r-cran-mgcv (1.9-4-1) ... 393s Setting up g++ (4:15.2.0-4ubuntu1) ... 393s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 393s Setting up r-cran-cachem (1.1.0-1) ... 393s Setting up r-cran-lmtest (0.9.40-1build1) ... 393s Setting up build-essential (12.12ubuntu2) ... 393s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... 393s Setting up r-cran-tzdb (0.5.0-1) ... 393s Setting up r-cran-globals (0.19.0-1) ... 393s Setting up r-cran-vctrs (0.6.5-1) ... 393s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 393s Setting up r-cran-mitools (2.4-2build2) ... 393s Setting up r-cran-pillar (1.11.1+dfsg-1) ... 393s Setting up r-cran-minqa (1.2.8-1) ... 393s Setting up r-base-dev (4.5.2-1ubuntu2) ... 393s Setting up r-cran-stringr (1.5.1-1) ... 393s Setting up r-cran-class (7.3-23-1) ... 393s Setting up r-cran-modelmetrics (1.2.2.2-1build2) ... 393s Setting up r-cran-matrixmodels (0.5-4-1) ... 393s Setting up r-cran-sparsevctrs (0.2.0-2) ... 393s Setting up r-cran-tibble (3.2.1+dfsg-3) ... 393s Setting up r-cran-clock (0.7.2-1) ... 393s Setting up r-cran-sandwich (3.1-1-1build1) ... 393s Setting up r-cran-proc (1.18.5-1) ... 393s Setting up r-cran-survival (3.8-6-1) ... 393s Setting up r-cran-xts (0.14.1-1) ... 393s Setting up r-cran-survey (4.4-2-2) ... 393s Setting up r-cran-rdpack (2.6.3-1) ... 393s Setting up r-cran-future (1.34.0+dfsg-1) ... 393s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... 393s Setting up r-cran-reshape2 (1.4.4-2build2) ... 393s Setting up r-cran-future.apply (1.11.3+dfsg-1) ... 393s Setting up r-cran-timechange (0.3.0-2) ... 393s Setting up r-cran-memoise (2.0.1-1build1) ... 393s Setting up r-cran-lava (1.8.2+dfsg-1) ... 393s Setting up r-cran-purrr (1.0.4-1) ... 393s Setting up r-cran-e1071 (1.7-17-1) ... 393s Setting up r-cran-blob (1.3.0-1) ... 393s Setting up pkg-r-autopkgtest (20250812) ... 393s Setting up r-cran-hardhat (1.4.2+dfsg-1) ... 393s Setting up r-cran-dplyr (1.1.4-4) ... 393s Setting up r-cran-reformulas (0.4.4-1) ... 393s Setting up r-cran-rsqlite (2.3.9-1) ... 393s Setting up r-cran-ttr (0.24.4-1) ... 393s Setting up r-cran-lubridate (1.9.4+dfsg-1) ... 393s Setting up r-cran-prodlim (2024.06.25-1) ... 393s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... 393s Setting up r-cran-rpart (4.1.24-1build1) ... 393s Setting up r-cran-ipred (0.9-15-1) ... 393s Setting up r-cran-lme4 (1.1-38-1) ... 393s Setting up r-cran-tidyr (1.3.1-1) ... 393s Setting up r-cran-recipes (1.1.0+dfsg-1) ... 393s Setting up r-cran-quantmod (0.4.28-1) ... 393s Setting up r-cran-cowplot (1.1.3+dfsg-1) ... 393s Setting up r-cran-caret (7.0-1+dfsg-1) ... 393s Setting up r-cran-tseries (0.10-59-3) ... 393s Setting up r-cran-broom (1.0.12+dfsg-1) ... 393s Setting up r-cran-conquer (1.3.3-1) ... 393s Setting up r-cran-forecast (8.23.0-1) ... 393s Setting up r-cran-quantreg (6.1-1) ... 393s Setting up r-cran-modelr (0.1.11-1) ... 393s Setting up r-cran-doby (4.7.1-3) ... 393s Setting up r-cran-pbkrtest (0.5.5-1) ... 393s Setting up r-cran-car (3.1-5-1) ... 393s Setting up r-cran-aer (1.2-15-1) ... 393s Processing triggers for libc-bin (2.42-2ubuntu4) ... 393s Processing triggers for man-db (2.13.1-1build1) ... 394s Processing triggers for install-info (7.2-5) ... 396s autopkgtest [03:52:24]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 396s autopkgtest [03:52:24]: test pkg-r-autopkgtest: [----------------------- 396s Test: Try to load the R library survey 396s 396s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 396s Copyright (C) 2025 The R Foundation for Statistical Computing 396s Platform: x86_64-pc-linux-gnu 396s 396s R is free software and comes with ABSOLUTELY NO WARRANTY. 396s You are welcome to redistribute it under certain conditions. 396s Type 'license()' or 'licence()' for distribution details. 396s 396s R is a collaborative project with many contributors. 396s Type 'contributors()' for more information and 396s 'citation()' on how to cite R or R packages in publications. 396s 396s Type 'demo()' for some demos, 'help()' for on-line help, or 396s 'help.start()' for an HTML browser interface to help. 396s Type 'q()' to quit R. 396s 396s > library('survey') 396s Loading required package: grid 396s Loading required package: Matrix 397s Loading required package: survival 397s > 397s 397s Attaching package: ‘survey’ 397s 397s The following object is masked from ‘package:graphics’: 397s 397s dotchart 397s 397s autopkgtest [03:52:25]: test pkg-r-autopkgtest: -----------------------] 398s pkg-r-autopkgtest PASS 398s autopkgtest [03:52:26]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 398s autopkgtest [03:52:26]: @@@@@@@@@@@@@@@@@@@@ summary 398s run-unit-test PASS 398s pkg-r-autopkgtest PASS