0s autopkgtest [22:19:29]: starting date and time: 2025-03-15 22:19:29+0000 0s autopkgtest [22:19:29]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:19:29]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gkys16cs/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-ordinal --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-8.secgroup --name adt-plucky-amd64-r-cran-ordinal-20250315-221929-juju-7f2275-prod-proposed-migration-environment-20-6e349ed0-2ecf-4c61-bd04-fd6c043b3ff9 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 47s autopkgtest [22:20:16]: testbed dpkg architecture: amd64 47s autopkgtest [22:20:16]: testbed apt version: 2.9.31ubuntu1 47s autopkgtest [22:20:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [22:20:16]: testbed release detected to be: None 48s autopkgtest [22:20:17]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 49s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 49s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 49s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 49s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 49s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 49s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 49s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 49s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 49s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 50s Fetched 1265 kB in 1s (1281 kB/s) 50s Reading package lists... 51s Reading package lists... 51s Building dependency tree... 51s Reading state information... 52s Calculating upgrade... 52s Calculating upgrade... 52s The following package was automatically installed and is no longer required: 52s libnl-genl-3-200 52s Use 'sudo apt autoremove' to remove it. 52s The following NEW packages will be installed: 52s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 52s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 52s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 52s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 52s The following packages will be upgraded: 52s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 52s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 52s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 52s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 52s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 52s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 52s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 52s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 52s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 52s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 52s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 52s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 52s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 52s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 52s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 52s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 52s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 52s parted pci.ids pciutils pinentry-curses python-apt-common python3 52s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 52s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 52s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 52s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 52s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 52s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 52s xz-utils 52s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 829 MB of archives. 52s After this operation, 325 MB of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 52s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 52s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 53s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 53s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 53s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 53s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 53s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 53s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 53s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 53s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 53s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 53s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 53s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 53s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 54s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 54s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 54s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 54s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 54s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 54s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 54s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 54s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 54s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 54s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 54s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 54s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 54s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 54s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 54s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 54s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 54s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 54s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 54s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 54s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 54s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 54s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 54s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 54s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 54s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 54s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 55s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 55s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 55s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 55s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 55s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 55s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 55s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 55s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 55s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 55s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 55s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 55s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 55s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 55s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 55s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 55s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 55s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 55s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 55s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 55s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 55s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 55s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 55s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 55s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 55s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 55s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 55s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 55s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 55s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 55s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 55s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 55s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 55s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 55s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 55s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 55s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 55s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 55s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 55s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 55s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 55s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 55s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 55s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 55s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 55s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 55s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 55s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 55s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 55s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 55s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 55s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 55s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 55s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 55s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 56s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 56s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 56s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 56s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 56s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 56s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 56s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 56s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 79s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 79s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 79s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 79s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 79s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 79s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 79s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 79s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 80s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 81s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 87s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 87s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 87s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 87s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 87s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 87s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 87s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 87s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 87s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 88s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 88s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 88s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 88s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 88s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 88s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 88s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 88s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 88s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 88s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 88s Preconfiguring packages ... 88s Fetched 829 MB in 36s (23.1 MB/s) 89s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 93s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 93s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 93s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 93s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 94s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 94s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 94s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 94s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 94s Setting up python3-minimal (3.13.2-2) ... 95s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 95s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 95s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 95s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 95s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 95s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 95s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 96s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 96s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 96s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 96s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 96s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 96s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 96s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 96s Selecting previously unselected package libdebuginfod-common. 96s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 96s Unpacking libdebuginfod-common (0.192-4) ... 96s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 96s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 96s Setting up libsemanage-common (3.7-2.1build1) ... 96s (Reading database ... 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over (0.21.0-2ubuntu1) ... 110s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 110s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 110s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 110s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 110s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 110s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 110s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 110s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 110s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 110s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 110s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 110s Setting up media-types (13.0.0) ... 110s Installing new version of config file /etc/mime.types ... 110s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 110s Setting up ubuntu-kernel-accessories (1.549) ... 110s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 110s Setting up pci.ids (0.0~2025.03.09-1) ... 110s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 110s Setting up apt-utils (2.9.33) ... 110s Setting up libdebuginfod-common (0.192-4) ... 110s Setting up exfatprogs (1.2.8-1) ... 110s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 110s Setting up bpftool (7.6.0+6.14.0-10.10) ... 110s Setting up libestr0:amd64 (0.1.11-2) ... 110s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 110s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 110s Setting up dosfstools (4.2-1.2) ... 110s Setting up rsyslog (8.2412.0-2ubuntu2) ... 110s info: The user `syslog' is already a member of `adm'. 111s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 111s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 111s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 111s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 111s Setting up systemd (257.3-1ubuntu3) ... 111s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 111s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 112s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 112s Setting up libparted2t64:amd64 (3.6-5) ... 112s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 112s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 112s Setting up linux-headers-generic (6.14.0-10.10) ... 112s Setting up libjemalloc2:amd64 (5.3.0-3) ... 112s Setting up locales (2.41-1ubuntu1) ... 112s Installing new version of config file /etc/locale.alias ... 113s Generating locales (this might take a while)... 114s en_US.UTF-8... done 114s Generation complete. 114s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 114s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 114s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 115s Installing new version of config file /etc/apparmor.d/fusermount3 ... 115s Installing new version of config file /etc/apparmor.d/lsusb ... 115s Installing new version of config file /etc/apparmor.d/openvpn ... 115s Reloading AppArmor profiles 117s Setting up libftdi1-2:amd64 (1.5-8build1) ... 117s Setting up libglib2.0-data (2.84.0-1) ... 117s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 117s Setting up libncurses6:amd64 (6.5+20250216-2) ... 117s Setting up strace (6.13+ds-1ubuntu1) ... 117s Setting up xz-utils (5.6.4-1) ... 117s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 117s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 117s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 117s Setting up udev (257.3-1ubuntu3) ... 119s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 120s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 120s Setting up libpci3:amd64 (1:3.13.0-2) ... 120s Setting up whiptail (0.52.24-4ubuntu2) ... 120s Setting up python-apt-common (2.9.9build1) ... 120s Setting up pnp.ids (0.393-3) ... 120s Setting up libnl-3-200:amd64 (3.7.0-1) ... 120s Setting up python3.13-minimal (3.13.2-2) ... 121s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 121s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 121s Setting up libc-dev-bin (2.41-1ubuntu1) ... 121s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 121s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 121s Setting up rsync (3.4.1+ds1-3) ... 121s rsync.service is a disabled or a static unit not running, not starting it. 121s Setting up python3.13-gdbm (3.13.2-2) ... 121s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 121s Setting up systemd-resolved (257.3-1ubuntu3) ... 122s Setting up initramfs-tools-bin (0.146ubuntu1) ... 122s Setting up ncurses-term (6.5+20250216-2) ... 122s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 122s Setting up libpython3.13:amd64 (3.13.2-2) ... 122s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 122s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 122s Setting up systemd-sysv (257.3-1ubuntu3) ... 122s Setting up linux-headers-virtual (6.14.0-10.10) ... 122s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 122s Setting up python3.13 (3.13.2-2) ... 123s Setting up htop (3.4.0-2) ... 123s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 125s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 125s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 125s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 125s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 125s Setting up parted (3.6-5) ... 125s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 125s Setting up python3 (3.13.2-2) ... 125s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 126s Setting up python3-markupsafe (2.1.5-1build4) ... 126s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 128s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 128s Setting up hwdata (0.393-3) ... 128s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 128s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 128s No schema files found: doing nothing. 128s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 128s Setting up linux-perf (6.14.0-10.10) ... 128s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 128s Setting up pciutils (1:3.13.0-2) ... 128s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 128s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 128s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 128s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 129s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 129s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 129s Setting up curl (8.12.1-3ubuntu1) ... 129s Setting up linux-image-virtual (6.14.0-10.10) ... 129s Setting up initramfs-tools-core (0.146ubuntu1) ... 129s Setting up linux-tools-common (6.14.0-10.10) ... 129s Setting up python3-systemd (235-1build6) ... 129s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 129s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 129s Setting up linux-image-generic (6.14.0-10.10) ... 129s Setting up python3-dbus (1.3.2-5build5) ... 129s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 129s Setting up initramfs-tools (0.146ubuntu1) ... 129s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 129s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 129s update-initramfs: deferring update (trigger activated) 129s Setting up linux-generic (6.14.0-10.10) ... 129s Setting up ubuntu-minimal (1.549) ... 129s Setting up python3-apt (2.9.9build1) ... 129s Setting up python3-bcrypt (4.2.0-2.1build1) ... 129s Setting up python3-yaml (6.0.2-1build2) ... 129s Setting up libfwupd3:amd64 (2.0.6-4) ... 129s Setting up python3-lazr.uri (1.0.6-6) ... 129s Setting up binutils (2.44-3ubuntu1) ... 129s Setting up ubuntu-standard (1.549) ... 129s Setting up cloud-init-base (25.1-0ubuntu3) ... 131s Setting up linux-virtual (6.14.0-10.10) ... 131s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 131s Setting up python3-gi (3.50.0-4build1) ... 131s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 131s Setting up fwupd (2.0.6-4) ... 131s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 131s fwupd.service is a disabled or a static unit not running, not starting it. 132s Setting up cloud-init (25.1-0ubuntu3) ... 132s Processing triggers for man-db (2.13.0-1) ... 133s Processing triggers for dbus (1.16.2-1ubuntu1) ... 133s Processing triggers for shared-mime-info (2.4-5) ... 133s Warning: program compiled against libxml 212 using older 209 134s Processing triggers for libc-bin (2.41-1ubuntu1) ... 134s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 134s /etc/kernel/postinst.d/initramfs-tools: 134s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 134s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 143s /etc/kernel/postinst.d/zz-update-grub: 143s Sourcing file `/etc/default/grub' 143s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 143s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 143s Generating grub configuration file ... 143s Found linux image: /boot/vmlinuz-6.14.0-10-generic 143s Found initrd image: /boot/initrd.img-6.14.0-10-generic 144s Found linux image: /boot/vmlinuz-6.12.0-16-generic 144s Found initrd image: /boot/initrd.img-6.12.0-16-generic 144s Found linux image: /boot/vmlinuz-6.11.0-8-generic 144s Found initrd image: /boot/initrd.img-6.11.0-8-generic 144s Warning: os-prober will not be executed to detect other bootable partitions. 144s Systems on them will not be added to the GRUB boot configuration. 144s Check GRUB_DISABLE_OS_PROBER documentation entry. 144s Adding boot menu entry for UEFI Firmware Settings ... 144s done 144s Processing triggers for initramfs-tools (0.146ubuntu1) ... 144s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 144s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Solving dependencies... 154s The following packages will be REMOVED: 154s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 154s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 154s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 154s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 154s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 154s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 154s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 154s linux-tools-6.12.0-16-generic* 155s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 155s After this operation, 545 MB disk space will be freed. 155s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 148643 files and directories currently installed.) 155s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 155s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 155s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 155s Removing libpython3.12t64:amd64 (3.12.9-1) ... 155s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 155s Removing libnsl2:amd64 (1.3.0-3build3) ... 155s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 155s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 156s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 158s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 158s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 160s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 160s /etc/kernel/postrm.d/initramfs-tools: 160s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 161s /etc/kernel/postrm.d/zz-update-grub: 161s Sourcing file `/etc/default/grub' 161s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 161s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 161s Generating grub configuration file ... 161s Found linux image: /boot/vmlinuz-6.14.0-10-generic 161s Found initrd image: /boot/initrd.img-6.14.0-10-generic 161s Found linux image: /boot/vmlinuz-6.12.0-16-generic 161s Found initrd image: /boot/initrd.img-6.12.0-16-generic 161s Warning: os-prober will not be executed to detect other bootable partitions. 161s Systems on them will not be added to the GRUB boot configuration. 161s Check GRUB_DISABLE_OS_PROBER documentation entry. 161s Adding boot menu entry for UEFI Firmware Settings ... 161s done 161s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 161s W: Removing the running kernel 161s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 161s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 161s /etc/kernel/postrm.d/initramfs-tools: 161s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 161s /etc/kernel/postrm.d/zz-update-grub: 161s Sourcing file `/etc/default/grub' 161s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 161s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 161s Generating grub configuration file ... 162s Found linux image: /boot/vmlinuz-6.14.0-10-generic 162s Found initrd image: /boot/initrd.img-6.14.0-10-generic 162s Warning: os-prober will not be executed to detect other bootable partitions. 162s Systems on them will not be added to the GRUB boot configuration. 162s Check GRUB_DISABLE_OS_PROBER documentation entry. 162s Adding boot menu entry for UEFI Firmware Settings ... 162s done 162s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 162s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 164s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 164s Processing triggers for libc-bin (2.41-1ubuntu1) ... 164s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76972 files and directories currently installed.) 164s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 164s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 164s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 164s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 164s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 164s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 164s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 164s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 164s autopkgtest [22:22:13]: upgrading testbed (apt dist-upgrade and autopurge) 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 166s Entering ResolveByKeep 166s 167s Calculating upgrade... 167s The following packages will be upgraded: 167s libc-bin libc-dev-bin libc6 libc6-dev locales 167s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 10.5 MB of archives. 167s After this operation, 1024 B of additional disk space will be used. 167s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 168s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 168s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 168s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 168s Preconfiguring packages ... 168s Fetched 10.5 MB in 1s (9333 kB/s) 168s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 168s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc6:amd64 (2.41-1ubuntu2) ... 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 169s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 169s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc-bin (2.41-1ubuntu2) ... 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 169s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 169s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 170s Setting up locales (2.41-1ubuntu2) ... 170s Generating locales (this might take a while)... 172s en_US.UTF-8... done 172s Generation complete. 172s Setting up libc-dev-bin (2.41-1ubuntu2) ... 172s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 172s Processing triggers for man-db (2.13.0-1) ... 172s Processing triggers for systemd (257.3-1ubuntu3) ... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 174s Solving dependencies... 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [22:22:23]: rebooting testbed after setup commands that affected boot 188s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 194s autopkgtest [22:22:43]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 197s autopkgtest [22:22:46]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ordinal 199s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ordinal 2023.12-4.1-1 (dsc) [2258 B] 199s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ordinal 2023.12-4.1-1 (tar) [804 kB] 199s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ordinal 2023.12-4.1-1 (diff) [3132 B] 199s gpgv: Signature made Wed Oct 9 23:44:36 2024 UTC 199s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 199s gpgv: issuer "plessy@debian.org" 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./r-cran-ordinal_2023.12-4.1-1.dsc: no acceptable signature found 199s autopkgtest [22:22:48]: testing package r-cran-ordinal version 2023.12-4.1-1 200s autopkgtest [22:22:49]: build not needed 201s autopkgtest [22:22:50]: test run-unit-test: preparing testbed 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 202s The following NEW packages will be installed: 202s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 202s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 202s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 202s liblapack3 liblerc4 libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 202s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 202s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 202s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core 202s r-cran-boot r-cran-brio r-cran-callr r-cran-cli r-cran-crayon r-cran-desc 202s r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-fs r-cran-glue 202s r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 202s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-minqa r-cran-nlme 202s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-ordinal r-cran-pkgbuild 202s r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-processx r-cran-ps 202s r-cran-r6 r-cran-rbibutils r-cran-rcpp r-cran-rcppeigen r-cran-rdpack 202s r-cran-reformulas r-cran-rlang r-cran-rprojroot r-cran-statmod 202s r-cran-testthat r-cran-ucminf r-cran-waldo r-cran-withr r-cran-xtable unzip 202s x11-common xdg-utils zip 202s 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. 202s Need to get 73.9 MB of archives. 202s After this operation, 153 MB of additional disk space will be used. 202s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 203s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 203s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 203s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 203s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 203s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 203s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 203s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 203s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 203s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 203s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 203s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 203s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 203s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 203s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 203s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 203s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 203s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 203s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 203s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 203s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 203s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 203s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 203s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 203s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 203s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 203s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 203s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 203s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 203s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 203s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 203s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 203s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 203s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 203s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 203s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 203s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 203s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 203s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 203s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 203s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 203s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 204s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 204s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B] 204s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-boot all 1.3-31-1 [635 kB] 204s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB] 204s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB] 204s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 204s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB] 204s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-callr all 3.7.6-1 [458 kB] 204s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 204s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB] 204s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-desc all 1.4.3-1 [359 kB] 204s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-diffobj amd64 0.3.5-1 [1117 kB] 204s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB] 204s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 204s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB] 204s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 204s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 204s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 204s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 204s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 204s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 205s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 205s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 205s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 205s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 205s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 205s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB] 205s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nloptr amd64 2.1.1-1 [251 kB] 205s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 205s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 205s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reformulas all 0.4.0-1 [91.5 kB] 205s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 205s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 205s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lme4 amd64 1.1-36-1 [4135 kB] 205s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 205s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 205s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 205s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ucminf amd64 1.2.2-1 [35.9 kB] 205s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ordinal amd64 2023.12-4.1-1 [1268 kB] 205s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgbuild all 1.4.6-1 [213 kB] 205s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rprojroot all 2.0.4-2 [125 kB] 205s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 205s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgload all 1.4.0-1 [247 kB] 205s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 205s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-waldo all 0.6.1-2 [150 kB] 205s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB] 205s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] 205s Preconfiguring packages ... 205s Fetched 73.9 MB in 3s (25.3 MB/s) 206s Selecting previously unselected package fonts-dejavu-mono. 206s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 206s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 206s Unpacking fonts-dejavu-mono (2.37-8) ... 206s Selecting previously unselected package fonts-dejavu-core. 206s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 206s Unpacking fonts-dejavu-core (2.37-8) ... 206s Selecting previously unselected package fontconfig-config. 206s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 206s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 206s Selecting previously unselected package libfontconfig1:amd64. 206s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 206s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 206s Selecting previously unselected package fontconfig. 206s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 206s Unpacking fontconfig (2.15.0-2ubuntu1) ... 206s Selecting previously unselected package libblas3:amd64. 206s Preparing to unpack .../05-libblas3_3.12.1-2_amd64.deb ... 206s Unpacking libblas3:amd64 (3.12.1-2) ... 206s Selecting previously unselected package libpixman-1-0:amd64. 206s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ... 206s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 206s Selecting previously unselected package libxcb-render0:amd64. 206s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ... 206s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 206s Selecting previously unselected package libxcb-shm0:amd64. 206s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_amd64.deb ... 206s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 206s Selecting previously unselected package libxrender1:amd64. 206s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 206s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 206s Selecting previously unselected package libcairo2:amd64. 206s Preparing to unpack .../10-libcairo2_1.18.2-2_amd64.deb ... 206s Unpacking libcairo2:amd64 (1.18.2-2) ... 206s Selecting previously unselected package libdatrie1:amd64. 206s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_amd64.deb ... 206s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 206s Selecting previously unselected package libdeflate0:amd64. 206s Preparing to unpack .../12-libdeflate0_1.23-1_amd64.deb ... 206s Unpacking libdeflate0:amd64 (1.23-1) ... 206s Selecting previously unselected package libgfortran5:amd64. 206s Preparing to unpack .../13-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 206s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 206s Selecting previously unselected package libgomp1:amd64. 206s Preparing to unpack .../14-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 206s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 206s Selecting previously unselected package libgraphite2-3:amd64. 206s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 206s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 206s Selecting previously unselected package libharfbuzz0b:amd64. 206s Preparing to unpack .../16-libharfbuzz0b_10.2.0-1_amd64.deb ... 206s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 207s Selecting previously unselected package x11-common. 207s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 207s Unpacking x11-common (1:7.7+23ubuntu3) ... 207s Selecting previously unselected package libice6:amd64. 207s Preparing to unpack .../18-libice6_2%3a1.1.1-1_amd64.deb ... 207s Unpacking libice6:amd64 (2:1.1.1-1) ... 207s Selecting previously unselected package libjpeg-turbo8:amd64. 207s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 207s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 207s Selecting previously unselected package libjpeg8:amd64. 207s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 207s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 207s Selecting previously unselected package liblapack3:amd64. 207s Preparing to unpack .../21-liblapack3_3.12.1-2_amd64.deb ... 207s Unpacking liblapack3:amd64 (3.12.1-2) ... 207s Selecting previously unselected package liblerc4:amd64. 207s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 207s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 207s Selecting previously unselected package libthai-data. 207s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 207s Unpacking libthai-data (0.1.29-2build1) ... 207s Selecting previously unselected package libthai0:amd64. 207s Preparing to unpack .../24-libthai0_0.1.29-2build1_amd64.deb ... 207s Unpacking libthai0:amd64 (0.1.29-2build1) ... 207s Selecting previously unselected package libpango-1.0-0:amd64. 207s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_amd64.deb ... 207s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 207s Selecting previously unselected package libpangoft2-1.0-0:amd64. 207s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 207s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 207s Selecting previously unselected package libpangocairo-1.0-0:amd64. 207s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 207s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 207s Selecting previously unselected package libpaper2:amd64. 207s Preparing to unpack .../28-libpaper2_2.2.5-0.3_amd64.deb ... 207s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 207s Selecting previously unselected package libpaper-utils. 207s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_amd64.deb ... 207s Unpacking libpaper-utils (2.2.5-0.3) ... 207s Selecting previously unselected package libsharpyuv0:amd64. 207s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_amd64.deb ... 207s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 207s Selecting previously unselected package libsm6:amd64. 207s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_amd64.deb ... 207s Unpacking libsm6:amd64 (2:1.2.4-1) ... 207s Selecting previously unselected package libtcl8.6:amd64. 207s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 207s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 207s Selecting previously unselected package libjbig0:amd64. 207s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 207s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 207s Selecting previously unselected package libwebp7:amd64. 207s Preparing to unpack .../34-libwebp7_1.5.0-0.1_amd64.deb ... 207s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 207s Selecting previously unselected package libtiff6:amd64. 207s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 207s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 207s Selecting previously unselected package libxft2:amd64. 207s Preparing to unpack .../36-libxft2_2.3.6-1build1_amd64.deb ... 207s Unpacking libxft2:amd64 (2.3.6-1build1) ... 207s Selecting previously unselected package libxss1:amd64. 207s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_amd64.deb ... 207s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 207s Selecting previously unselected package libtk8.6:amd64. 207s Preparing to unpack .../38-libtk8.6_8.6.16-1_amd64.deb ... 207s Unpacking libtk8.6:amd64 (8.6.16-1) ... 207s Selecting previously unselected package libxt6t64:amd64. 207s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 207s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 207s Selecting previously unselected package zip. 207s Preparing to unpack .../40-zip_3.0-14ubuntu2_amd64.deb ... 207s Unpacking zip (3.0-14ubuntu2) ... 207s Selecting previously unselected package unzip. 207s Preparing to unpack .../41-unzip_6.0-28ubuntu6_amd64.deb ... 207s Unpacking unzip (6.0-28ubuntu6) ... 207s Selecting previously unselected package xdg-utils. 207s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 207s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 207s Selecting previously unselected package r-base-core. 207s Preparing to unpack .../43-r-base-core_4.4.3-1_amd64.deb ... 207s Unpacking r-base-core (4.4.3-1) ... 208s Selecting previously unselected package r-cran-littler. 208s Preparing to unpack .../44-r-cran-littler_0.3.20-2_amd64.deb ... 208s Unpacking r-cran-littler (0.3.20-2) ... 208s Selecting previously unselected package littler. 208s Preparing to unpack .../45-littler_0.3.20-2_all.deb ... 208s Unpacking littler (0.3.20-2) ... 208s Selecting previously unselected package 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R version 4.4.3 (2025-02-28) -- "Trophy Case" 216s Copyright (C) 2025 The R Foundation for Statistical Computing 216s Platform: x86_64-pc-linux-gnu 216s 216s R is free software and comes with ABSOLUTELY NO WARRANTY. 216s You are welcome to redistribute it under certain conditions. 216s Type 'license()' or 'licence()' for distribution details. 216s 216s R is a collaborative project with many contributors. 216s Type 'contributors()' for more information and 216s 'citation()' on how to cite R or R packages in publications. 216s 216s Type 'demo()' for some demos, 'help()' for on-line help, or 216s 'help.start()' for an HTML browser interface to help. 216s Type 'q()' to quit R. 216s 216s > library(ordinal) 217s > data(wine) 217s > 217s > fm1 <- clm(rating ~ temp, data=wine) 217s > fmm1 <- clmm(rating ~ temp + (1|judge), data=wine) 217s > 217s > ## These now give identical printed results: 217s > ## Previously the printed model names were messed up when anova.clmm 217s > ## were called. 217s > anova(fm1, fmm1) 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fm1 rating ~ temp logit flexible 217s fmm1 rating ~ temp + (1 | judge) logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fm1 5 194.03 -92.013 217s fmm1 6 189.48 -88.739 6.5492 1 0.01049 * 217s --- 217s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 217s > anova(fmm1, fm1) 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fm1 rating ~ temp logit flexible 217s fmm1 rating ~ temp + (1 | judge) logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fm1 5 194.03 -92.013 217s fmm1 6 189.48 -88.739 6.5492 1 0.01049 * 217s --- 217s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 217s > 217s > ## Testing if 'test' and 'type' arguments are ignored properly: 217s > fm1 <- clm(rating ~ temp + contact, data=wine) 217s > fm2 <- clm(rating ~ temp, data=wine) 217s > anova(fm1, fm2, test="Chi") 217s 'test' argument ignored in anova.clm 217s 217s 'test' argument ignored in anova.clm 217s 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fm2 rating ~ temp logit flexible 217s fm1 rating ~ temp + contact logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fm2 5 194.03 -92.013 217s fm1 6 184.98 -86.492 11.043 1 0.0008902 *** 217s --- 217s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 217s > anova(fm1, fm2, type="Chi") 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fm2 rating ~ temp logit flexible 217s fm1 rating ~ temp + contact logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fm2 5 194.03 -92.013 217s fm1 6 184.98 -86.492 11.043 1 0.0008902 *** 217s --- 217s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 217s > anova(fm1, fm2) 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fm2 rating ~ temp logit flexible 217s fm1 rating ~ temp + contact logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fm2 5 194.03 -92.013 217s fm1 6 184.98 -86.492 11.043 1 0.0008902 *** 217s --- 217s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 217s > ## calling anova.clmm 217s > anova(fmm1, fm1, test="Chi") 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fmm1 rating ~ temp + (1 | judge) logit flexible 217s fm1 rating ~ temp + contact logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fmm1 6 189.48 -88.739 217s fm1 6 184.98 -86.492 4.4938 0 217s > anova(fmm1, fm1, type="Chi") 217s Likelihood ratio tests of cumulative link models: 217s 217s formula: link: threshold: 217s fmm1 rating ~ temp + (1 | judge) logit flexible 217s fm1 rating ~ temp + contact logit flexible 217s 217s no.par AIC logLik LR.stat df Pr(>Chisq) 217s fmm1 6 189.48 -88.739 217s fm1 6 184.98 -86.492 4.4938 0 217s > 217s > 217s BEGIN TEST clm.fit.R 217s 217s R version 4.4.3 (2025-02-28) -- "Trophy Case" 217s Copyright (C) 2025 The R Foundation for Statistical Computing 217s Platform: x86_64-pc-linux-gnu 217s 217s R is free software and comes with ABSOLUTELY NO WARRANTY. 217s You are welcome to redistribute it under certain conditions. 217s Type 'license()' or 'licence()' for distribution details. 217s 217s R is a collaborative project with many contributors. 217s Type 'contributors()' for more information and 217s 'citation()' on how to cite R or R packages in publications. 217s 217s Type 'demo()' for some demos, 'help()' for on-line help, or 217s 'help.start()' for an HTML browser interface to help. 217s Type 'q()' to quit R. 217s 217s > library(ordinal) 218s > data(wine) 218s > 218s > ## clm.fit with nominal and scale effects: 218s > 218s > ## get simple model: 218s > fm1 <- clm(rating ~ temp, scale=~temp, nominal=~ contact, 218s + data=wine, method="design") 218s > str(fm1, give.attr=FALSE) 218s List of 23 218s $ y : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 2 3 3 4 4 4 5 5 1 2 ... 218s $ y.levels : chr [1:5] "1" "2" "3" "4" ... 218s $ X : num [1:72, 1:2] 1 1 1 1 1 1 1 1 1 1 ... 218s $ offset : num [1:72] 0 0 0 0 0 0 0 0 0 0 ... 218s $ terms :Classes 'terms', 'formula' language rating ~ temp 218s $ contrasts :List of 1 218s ..$ temp: chr "contr.treatment" 218s $ xlevels :List of 1 218s ..$ temp: chr [1:2] "cold" "warm" 218s $ weights : num [1:72] 1 1 1 1 1 1 1 1 1 1 ... 218s $ S : num [1:72, 1:2] 1 1 1 1 1 1 1 1 1 1 ... 218s $ S.terms :Classes 'terms', 'formula' language ~temp 218s $ S.off : num [1:72] 0 0 0 0 0 0 0 0 0 0 ... 218s $ S.contrasts :List of 1 218s ..$ temp: chr "contr.treatment" 218s $ S.xlevels :List of 1 218s ..$ temp: chr [1:2] "cold" "warm" 218s $ NOM : num [1:72, 1:2] 1 1 1 1 1 1 1 1 1 1 ... 218s $ nom.terms :Classes 'terms', 'formula' language ~contact 218s $ nom.contrasts:List of 1 218s ..$ contact: chr "contr.treatment" 218s $ nom.xlevels :List of 1 218s ..$ contact: chr [1:2] "no" "yes" 218s $ doFit : logi TRUE 218s $ control :List of 11 218s ..$ method : chr "design" 218s ..$ sign.location: chr "negative" 218s ..$ sign.nominal : chr "positive" 218s ..$ convergence : chr "warn" 218s ..$ trace : int 0 218s ..$ maxIter : int 100 218s ..$ gradTol : num 1e-06 218s ..$ relTol : num 1e-06 218s ..$ tol : num 1.49e-08 218s ..$ maxLineIter : int 15 218s ..$ maxModIter : int 5 218s $ link : chr "logit" 218s $ threshold : chr "flexible" 218s $ start : NULL 218s $ formulas :List of 4 218s ..$ formula :Class 'formula' language rating ~ temp 218s ..$ scale :Class 'formula' language ~temp 218s ..$ nominal :Class 'formula' language ~contact 218s ..$ fullForm:Class 'formula' language rating ~ temp + temp + contact 218s > fm1$control$method <- "Newton" 218s > res <- clm.fit(fm1) 218s > names(res) 218s [1] "aliased" "alpha" "alpha.mat" "beta" 218s [5] "coefficients" "cond.H" "convergence" "df.residual" 218s [9] "edf" "fitted.values" "gradient" "Hessian" 218s [13] "logLik" "maxGradient" "message" "n" 218s [17] "niter" "nobs" "Theta" "tJac" 218s [21] "vcov" "zeta" 218s > res$Theta 218s contact 1|2 2|3 3|4 4|5 218s 1 no -1.357136 1.2482871 3.839568 5.114111 218s 2 yes -2.969353 -0.2819631 1.959306 3.923477 218s > 218s > ## construct some weights and offsets: 218s > set.seed(1) 218s > off1 <- runif(length(fm1$y)) 218s > set.seed(1) 218s > off2 <- rnorm(length(fm1$y)) 218s > set.seed(1) 218s > wet <- runif(length(fm1$y)) 218s > 218s > ## Fit various models: 218s > fit <- clm.fit(fm1$y, fm1$X, fm1$S, fm1$NOM, weights=wet) 218s > Coef <- 218s + c(-0.905224120279548, 1.31043498891987, 3.34235590523008, 218s + 4.52389661722693, -3.03954652971192, -1.56922389038976, 218s + -1.75662549320839, -1.16845464236365, 2.52988580848393, 218s + -0.0261457032829033) 218s > stopifnot(all.equal(coef(fit), Coef, check.attributes=FALSE, tol=1e-6)) 218s > str(fit) 218s List of 20 218s $ aliased :List of 3 218s ..$ alpha: Named logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... 218s .. ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s ..$ beta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s ..$ zeta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s $ alpha : Named num [1:8] -0.905 1.31 3.342 4.524 -3.04 ... 218s ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ beta : Named num 2.53 218s ..- attr(*, "names")= chr "tempwarm" 218s $ coefficients : Named num [1:10] -0.905 1.31 3.342 4.524 -3.04 ... 218s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ cond.H : num 161 218s $ convergence :List of 3 218s ..$ code : int 0 218s ..$ messages : chr "successful convergence" 218s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 218s $ df.residual : num 27 218s $ edf : int 10 218s $ fitted.values: num [1:72] 0.5 0.178 0.394 0.136 0.188 ... 218s $ gradient : Named num [1:10] 7.85e-15 2.69e-13 2.68e-13 -5.17e-13 3.75e-16 ... 218s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ Hessian : num [1:10, 1:10] 2.488 -1.01 0 0 0.207 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ logLik : num -44.9 218s $ maxGradient : num 8.91e-13 218s $ message : chr "Absolute and relative convergence criteria were met" 218s $ n : int 72 218s $ niter : Named num [1:2] 9 0 218s ..- attr(*, "names")= chr [1:2] "outer" "inner" 218s $ nobs : num 37 218s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ vcov : num [1:10, 1:10] 0.5338 0.1835 0.0254 -0.0626 -0.511 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ zeta : Named num -0.0261 218s ..- attr(*, "names")= chr "tempwarm" 218s - attr(*, "class")= chr "clm.fit" 218s > 218s > fit <- clm.fit(fm1$y, fm1$X, fm1$S, fm1$NOM, offset=off1) 218s Warning message: 218s Cannot assess if all thresholds are increasing 218s > str(fit) 218s List of 20 218s Warning message: 218s Cannot assess if all thresholds are increasing 218s $ aliased :List of 3 218s ..$ alpha: Named logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... 218s .. ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s ..$ beta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s ..$ zeta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s $ alpha : Named num [1:8] -0.864 1.746 4.342 5.615 -1.567 ... 218s ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ beta : Named num 2.7 218s ..- attr(*, "names")= chr "tempwarm" 218s $ coefficients : Named num [1:10] -0.864 1.746 4.342 5.615 -1.567 ... 218s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ cond.H : num 196 218s $ convergence :List of 3 218s ..$ code : int 0 218s ..$ messages : chr "successful convergence" 218s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 218s $ df.residual : num 62 218s $ edf : int 10 218s $ fitted.values: num [1:72] 0.57 0.183 0.452 0.145 0.135 ... 218s $ gradient : Named num [1:10] 2.19e-09 6.14e-08 5.92e-08 -1.23e-07 4.69e-10 ... 218s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ Hessian : num [1:10, 1:10] 4.48 -1.89 0 0 1.02 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ logLik : num -86.1 218s $ maxGradient : num 2.17e-07 218s $ message : chr "Absolute and relative convergence criteria were met" 218s $ n : int 72 218s $ niter : Named num [1:2] 8 0 218s ..- attr(*, "names")= chr [1:2] "outer" "inner" 218s $ nobs : num 72 218s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ vcov : num [1:10, 1:10] 0.33117 0.09074 0.00108 -0.04015 -0.31468 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ zeta : Named num 0.114 218s ..- attr(*, "names")= chr "tempwarm" 218s - attr(*, "class")= chr "clm.fit" 218s > 218s > fit <- clm.fit(fm1$y, fm1$X, fm1$S, fm1$NOM, offset=off1, 218s + S.offset=off2) 218s > str(fit) 218s List of 20 218s $ aliased :List of 3 218s ..$ alpha: Named logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... 218s .. ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s ..$ beta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s ..$ zeta :Warning message: 218s Cannot assess if all thresholds are increasing 218s Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s $ alpha : Named num [1:8] -0.585 1.951 3.24 4.18 -6.481 ... 218s ..- attr(*, "names")= chr [1:8] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ beta : Named num 2.12 218s ..- attr(*, "names")= chr "tempwarm" 218s $ coefficients : Named num [1:10] -0.585 1.951 3.24 4.18 -6.481 ... 218s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ cond.H : num 634 218s $ convergence :List of 3 218s ..$ code : int 0 218s ..$ messages : chr "successful convergence" 218s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 218s $ df.residual : num 62 218s $ edf : int 10 218s $ fitted.values: num [1:72] 0.7899 0.1277 0.7 0.0888 0.1521 ... 218s $ gradient : Named num [1:10] 6.72e-12 8.06e-10 7.28e-10 -7.85e-10 1.15e-12 ... 218s ..- attr(*, "names")= chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ Hessian : num [1:10, 1:10] 4.126 -1.006 0 0 0.079 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ logLik : num -87.6 218s $ maxGradient : num 9.74e-10 218s $ message : chr "Absolute and relative convergence criteria were met" 218s $ n : int 72 218s $ niter : Named num [1:2] 13 0 218s ..- attr(*, "names")= chr [1:2] "outer" "inner" 218s $ nobs : num 72 218s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ vcov : num [1:10, 1:10] 0.2616 0.0523 0.0345 0.0236 -0.2449 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s .. ..$ : chr [1:10] "1|2.(Intercept)" "2|3.(Intercept)" "3|4.(Intercept)" "4|5.(Intercept)" ... 218s $ zeta : Named num -0.502 218s ..- attr(*, "names")= chr "tempwarm" 218s - attr(*, "class")= chr "clm.fit" 218s > 218s > fit <- clm.fit(fm1$y, fm1$X, fm1$S) 218s > str(fit) 218s List of 21 218s $ aliased :List of 3 218s ..$ alpha: Named logi [1:4] FALSE FALSE FALSE FALSE 218s .. ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s ..$ beta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s ..$ zeta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s $ alpha : Named num [1:4] -1.988 0.418 2.648 4.306 218s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ beta : Named num 2.51 218s ..- attr(*, "names")= chr "tempwarm" 218s $ coefficients : Named num [1:6] -1.988 0.418 2.648 4.306 2.512 ... 218s ..- attr(*, "names")= chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 218s $ cond.H : num 80.6 218s $ convergence :List of 3 218s ..$ code : int 0 218s ..$ messages : chr "successful convergence" 218s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 218s $ df.residual : num 66 218s $ edf : int 6 218s $ fitted.values: num [1:72] 0.4826 0.3308 0.3308 0.0528 0.2897 ... 218s $ gradient : Named num [1:6] 7.03e-09 6.91e-08 5.99e-07 -7.42e-07 2.76e-08 ... 218s ..- attr(*, "names")= chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 218s $ Hessian : num [1:6, 1:6] 4.8066 -2.4889 0 0 -0.0926 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 218s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 218s $ logLik : num -91.8 218s $ maxGradient : num 8.53e-07 218s $ message : chr "Absolute and relative convergence criteria were met" 218s $ n : int 72 218s $ niter : Named num [1:2] 8 0 218s ..- attr(*, "names")= chr [1:2] "outer" "inner" 218s $ nobs : num 72 218s $ Theta : num [1, 1:4] -1.988 0.418 2.648 4.306 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : NULL 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ vcov : num [1:6, 1:6] 0.2481 0.0622 0.0179 -0.0253 0.0197 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 218s .. ..$ : chr [1:6] "1|2" "2|3" "3|4" "4|5" ... 218s $ zeta : Named num 0.176 218s ..- attr(*, "names")= chr "tempwarm" 218s - attr(*, "class")= chr "clm.fit" 218s > 218s > fit <- clm.fit(fm1$y, fm1$X) 218s > str(fit) 218s List of 20 218s $ aliased :List of 2 218s ..$ alpha: Named logi [1:4] FALSE FALSE FALSE FALSE 218s .. ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s ..$ beta : Named logi FALSE 218s .. ..- attr(*, "names")= chr "tempwarm" 218s $ alpha : Named num [1:4] -1.936 0.435 2.432 3.827 218s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ beta : Named num 2.29 218s ..- attr(*, "names")= chr "tempwarm" 218s $ coefficients : Named num [1:5] -1.936 0.435 2.432 3.827 2.287 218s ..- attr(*, "names")= chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 218s $ cond.H : num 16.8 218s $ convergence :List of 3 218s ..$ code : int 0 218s ..$ messages : chr "successful convergence" 218s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 218s $ df.residual : num 67 218s $ edf : int 5 218s $ fitted.values: num [1:72] 0.481 0.3122 0.3122 0.0594 0.2871 ... 218s $ gradient : Named num [1:5] 4.07e-14 8.24e-14 -9.90e-14 6.66e-16 -2.22e-14 218s ..- attr(*, "names")= chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 218s $ Hessian : num [1:5, 1:5] 4.8983 -2.499 0 0 -0.0854 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 218s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 218s $ logLik : num -92 218s $ maxGradient : num 9.9e-14 218s $ message : chr "Absolute and relative convergence criteria were met" 218s $ n : int 72 218s $ niter : Named num [1:2] 6 0 218s ..- attr(*, "names")= chr [1:2] "outer" "inner" 218s $ nobs : num 72 218s $ Theta : num [1, 1:4] -1.936 0.435 2.432 3.827 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : NULL 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ vcov : num [1:5, 1:5] 0.2345 0.0577 0.0505 0.0512 0.0537 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 218s .. ..$ : chr [1:5] "1|2" "2|3" "3|4" "4|5" ... 218s - attr(*, "class")= chr "clm.fit" 218s > 218s > fit <- clm.fit(fm1$y) 218s > coef(fit) 218s 1|2 2|3 3|4 4|5 218s -2.5952547 -0.5108256 1.0258529 2.2284771 218s > str(fit) 218s List of 19 218s $ aliased :List of 2 218s ..$ alpha: Named logi [1:4] FALSE FALSE FALSE FALSE 218s .. ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s ..$ beta : Named logi(0) 218s .. ..- attr(*, "names")= chr(0) 218s $ alpha : Named num [1:4] -2.595 -0.511 1.026 2.228 218s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ coefficients : Named num [1:4] -2.595 -0.511 1.026 2.228 218s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ cond.H : num 8.38 218s $ convergence :List of 3 218s ..$ code : int 0 218s ..$ messages : chr "successful convergence" 218s ..$ alg.message: chr "Absolute and relative convergence criteria were met" 218s $ df.residual : num 68 218s $ edf : int 4 218s $ fitted.values: num [1:72] 0.306 0.361 0.361 0.167 0.167 ... 218s $ gradient : Named num [1:4] 7.23e-08 -5.51e-08 -1.72e-11 -4.86e-12 218s ..- attr(*, "names")= chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ Hessian : num [1:4, 1:4] 5.31 -3.57 0 0 -3.57 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ logLik : num -104 218s $ maxGradient : num 7.23e-08 218s $ message : chr "Absolute and relative convergence criteria were met" 218s $ n : int 72 218s $ niter : Named num [1:2] 5 0 218s ..- attr(*, "names")= chr [1:2] "outer" "inner" 218s $ nobs : num 72 218s $ Theta : num [1, 1:4] -2.595 -0.511 1.026 2.228 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : NULL 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ tJac : num [1:4, 1:4] 1 0 0 0 0 1 0 0 0 0 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s $ vcov : num [1:4, 1:4] 0.2149 0.0398 0.0203 0.0165 0.0398 ... 218s ..- attr(*, "dimnames")=List of 2 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s .. ..$ : chr [1:4] "1|2" "2|3" "3|4" "4|5" 218s - attr(*, "class")= chr "clm.fit" 218s > 218s > ## Remember: compare with corresponding .Rout file 218s > 218s BEGIN TEST clm.formula.R 218s 218s R version 4.4.3 (2025-02-28) -- "Trophy Case" 218s Copyright (C) 2025 The R Foundation for Statistical Computing 218s Platform: x86_64-pc-linux-gnu 218s 218s R is free software and comes with ABSOLUTELY NO WARRANTY. 218s You are welcome to redistribute it under certain conditions. 218s Type 'license()' or 'licence()' for distribution details. 218s 218s R is a collaborative project with many contributors. 218s Type 'contributors()' for more information and 218s 'citation()' on how to cite R or R packages in publications. 218s 218s Type 'demo()' for some demos, 'help()' for on-line help, or 218s 'help.start()' for an HTML browser interface to help. 218s Type 'q()' to quit R. 218s 218s > library(ordinal) 219s > ## library(devtools) 219s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 219s > ## clean_dll(pkg = r2path) 219s > ## load_all(r2path) 219s > 219s > ################################# 219s > ## Appropriate evaluation of formulas: 219s > 219s > ## These fail and give appropriate error messages: 219s > ## fm1 <- clm(rating ~ contact, scale=temp, data=wine) 219s > ## fm1 <- clm(rating ~ contact, scale=~Temp, data=wine) 219s > ## fm1 <- clm(rating ~ contact, scale="temp", data=wine) 219s > ## sca <- "temp" 219s > ## fm1 <- clm(rating ~ contact, scale=sca, data=wine) 219s > ## sca <- as.formula(sca) 219s > ## sca <- as.formula(temp) 219s > ## sca <- with(wine, as.formula(temp)) 219s > 219s > ## These all work as intended with no warnings or errors: 219s > fm1 <- clm(rating ~ contact, scale="~temp", data=wine) 219s > fm1 <- clm(rating ~ contact, scale=~temp, data=wine) 219s > sca <- "~temp" 219s > fm1 <- clm(rating ~ contact, scale=sca, data=wine) 219s > sca <- as.formula("~temp") 219s > fm1 <- clm(rating ~ contact, scale=sca, data=wine) 219s > fm1 <- clm(rating ~ contact, scale=as.formula(~temp), data=wine) 219s > fm1 <- clm(rating ~ contact, scale=as.formula("~temp"), data=wine) 219s > 219s > ################################# 219s > ## can evaluate if 'formula' is a character: 219s > f <- "rating ~ contact + temp" 219s > clm(f, data=wine) 219s formula: rating ~ contact + temp 219s data: wine 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 219s 219s Coefficients: 219s contactyes tempwarm 219s 1.528 2.503 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > clm(as.formula(f), data=wine) 219s formula: rating ~ contact + temp 219s data: wine 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 219s 219s Coefficients: 219s contactyes tempwarm 219s 1.528 2.503 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > 219s > ################################# 219s > 219s > ### finding variables in the environment of the formula: 219s > makeform <- function() { 219s + f1 <- as.formula(rating ~ temp + contact) 219s + rating <- wine$rating 219s + temp <- wine$temp 219s + contact <- wine$contact 219s + f1 219s + } 219s > ## 'makeform' makes are formula object in the environment of the 219s > ## function makeform: 219s > f1 <- makeform() 219s > f1 # print 219s rating ~ temp + contact 219s 219s > class(f1) 219s [1] "formula" 219s > ## If we give the data, we can evaluate the model: 219s > fm1 <- clm(f1, data=wine) 219s > ## We can also evaluate the model because the data are available in 219s > ## the environment associated with the formula: 219s > fm1 <- clm(f1) 219s > ## For instance, the 'rating' variable is not found in the Global 219s > ## environment; we have to evaluate the 'name' of 'rating' in the 219s > ## appropriate environment: 219s > (try(rating, silent=TRUE)) 219s [1] "Error : object 'rating' not found\n" 219s attr(,"class") 219s [1] "try-error" 219s attr(,"condition") 219s 219s > eval(as.name("rating"), envir=environment(f1)) 219s [1] 2 3 3 4 4 4 5 5 1 2 1 3 2 3 5 4 2 3 3 2 5 5 4 4 3 2 3 2 3 2 5 3 2 3 4 3 3 3 219s [39] 3 3 3 2 3 2 2 4 5 4 1 1 2 2 2 3 2 3 2 2 2 3 3 3 3 4 1 2 3 2 3 2 4 4 219s Levels: 1 < 2 < 3 < 4 < 5 219s > ## If instead we generate the formula in the Global environment where 219s > ## the variables are not found, we cannot evaluate the model: 219s > f2 <- as.formula(rating ~ temp + contact) 219s > (try(fm2 <- clm(f2), silent=TRUE)) 219s [1] "Error in eval(predvars, data, env) : object 'rating' not found\n" 219s attr(,"class") 219s [1] "try-error" 219s attr(,"condition") 219s 219s > environment(f2) <- environment(f1) 219s > fm2 <- clm(f2) 219s > 219s > 219s > ################################# 219s > ## Use of formula-objects in location, scale and nominal: 219s > ## Bug-report from Llus Marco Almagro 219s > ## 5 May 2010 17:58 219s > f <- formula(rating ~ temp) 219s > fs <- formula( ~ contact) 219s > m2 <- clm(f, scale = fs, data = wine) 219s > summary(m2) 219s formula: rating ~ temp 219s scale: ~contact 219s data: wine 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -91.92 195.83 8(0) 1.57e-09 5.6e+01 219s 219s Coefficients: 219s Estimate Std. Error z value Pr(>|z|) 219s tempwarm 2.1690 0.5527 3.924 8.69e-05 *** 219s --- 219s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 219s 219s log-scale coefficients: 219s Estimate Std. Error z value Pr(>|z|) 219s contactyes -0.1222 0.2775 -0.44 0.66 219s 219s Threshold coefficients: 219s Estimate Std. Error z value 219s 1|2 -1.8957 0.4756 -3.986 219s 2|3 0.3668 0.3442 1.066 219s 3|4 2.2483 0.5932 3.790 219s 4|5 3.5393 0.8336 4.246 219s > 219s > ################################# 219s > ## Other ways to construct formulas: 219s > set.seed(12345) 219s > y <- factor(sample(1:4,20,replace=TRUE)) 219s > x <- rnorm(20) 219s > data <- data.frame(y=y,x=x) 219s > rm(x, y) 219s > fit <- clm(data$y ~ data$x) 219s > fit 219s formula: data$y ~ data$x 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 20 -25.37 58.74 5(0) 2.68e-09 8.4e+00 219s 219s Coefficients: 219s data$x 219s 0.2527 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 219s -2.18234 0.06059 0.92746 219s > fit <- clm(data[,1] ~ data[,2]) 219s > fit 219s formula: data[, 1] ~ data[, 2] 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 20 -25.37 58.74 5(0) 2.68e-09 8.4e+00 219s 219s Coefficients: 219s data[, 2] 219s 0.2527 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 219s -2.18234 0.06059 0.92746 219s > ## This previously failed, but now works: 219s > fit <- clm(data$y ~ data$x, ~data$x) 219s > fit 219s formula: data$y ~ data$x 219s scale: ~data$x 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 20 -25.32 60.64 7(0) 1.86e-09 9.7e+00 219s 219s Coefficients: 219s data$x 219s 0.2477 219s 219s log-scale coefficients: 219s data$x 219s -0.1136 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 219s -2.16950 0.07039 0.91381 219s > 219s > ################################# 219s > ## Evaluation within other functions: 219s > ## date: January 18th 2012. 219s > ## 219s > ## The problem was raised by Stefan Herzog (stefan.herzog@unibas.ch) 219s > ## January 12th 2012 in trying to make clm work with glmulti. 219s > 219s > fun.clm <- function(formula, data) 219s + ### This only works because clm via eclm.model.frame is careful to 219s + ### evaluate the 'formula' in the parent environment such it is not the 219s + ### character "formula" that is attempted evaluated. 219s + clm(formula, data = data) 219s > 219s > fun2.clm <- function(formula, data, weights, subset) { 219s + ### This should be the safe way to ensure evaluation of clm in the 219s + ### right environment. 219s + mc <- match.call() 219s + mc[[1]] <- as.name("clm") 219s + eval.parent(mc) 219s + } 219s > 219s > fun.clm(rating ~ temp + contact, data=wine) ## works 219s formula: rating ~ temp + contact 219s data: data 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.02e-12 2.7e+01 219s 219s Coefficients: 219s tempwarm contactyes 219s 2.503 1.528 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > fun2.clm(rating ~ temp + contact, data=wine) ## works 219s formula: rating ~ temp + contact 219s data: wine 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.02e-12 2.7e+01 219s 219s Coefficients: 219s tempwarm contactyes 219s 2.503 1.528 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > 219s > form1 <- "rating ~ temp + contact" 219s > fun.clm(form1, data=wine) ## works 219s formula: rating ~ temp + contact 219s data: data 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.02e-12 2.7e+01 219s 219s Coefficients: 219s tempwarm contactyes 219s 2.503 1.528 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > fun2.clm(form1, data=wine) ## works 219s formula: rating ~ temp + contact 219s data: wine 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.02e-12 2.7e+01 219s 219s Coefficients: 219s tempwarm contactyes 219s 2.503 1.528 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > 219s > form2 <- formula(rating ~ temp + contact) 219s > fun.clm(form2, data=wine) ## works 219s formula: rating ~ temp + contact 219s data: data 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.02e-12 2.7e+01 219s 219s Coefficients: 219s tempwarm contactyes 219s 2.503 1.528 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > fun2.clm(form2, data=wine) ## works 219s formula: rating ~ temp + contact 219s data: wine 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 72 -86.49 184.98 6(0) 4.02e-12 2.7e+01 219s 219s Coefficients: 219s tempwarm contactyes 219s 2.503 1.528 219s 219s Threshold coefficients: 219s 1|2 2|3 3|4 4|5 219s -1.344 1.251 3.467 5.006 219s > ## Notice that clm is not able to get the name of the data (wine) 219s > ## correct when using fun.clm. 219s > 219s > ################################# 219s > ## Evaluation of long formulas: no line breaking in getFullForm: 219s > data(soup, package="ordinal") 219s > 219s > rhs <- paste(names(soup)[c(3, 5:12)], collapse=" + ") 219s > Location <- as.formula(paste("SURENESS ~ ", rhs, sep=" ")) 219s > Scale <- as.formula("~ PROD") 219s > 219s > fm5 <- clm(Location, scale=Scale, data=soup) 219s > summary(fm5) 219s formula: 219s SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ + COLD + EASY + GENDER + AGEGROUP + LOCATION 219s scale: ~PROD 219s data: soup 219s 219s link threshold nobs logLik AIC niter max.grad cond.H 219s logit flexible 1847 -2651.65 5367.30 8(1) 4.65e-07 1.1e+04 219s 219s Coefficients: 219s Estimate Std. Error z value Pr(>|z|) 219s PRODID2 1.09324 0.14790 7.392 1.45e-13 *** 219s PRODID3 1.54233 0.21252 7.257 3.95e-13 *** 219s PRODID4 0.95602 0.18180 5.258 1.45e-07 *** 219s PRODID5 1.52404 0.20311 7.504 6.21e-14 *** 219s PRODID6 1.83964 0.21750 8.458 < 2e-16 *** 219s DAY2 -0.26999 0.10280 -2.626 0.00863 ** 219s SOUPTYPECanned -0.31340 0.11745 -2.668 0.00762 ** 219s SOUPTYPEDry-mix 0.22429 0.14295 1.569 0.11665 219s SOUPFREQ1-4/month -0.06459 0.10551 -0.612 0.54046 219s SOUPFREQ<1/month 0.03664 0.21310 0.172 0.86350 219s COLDYes 0.31373 0.14894 2.106 0.03517 * 219s EASY2 0.16689 0.55063 0.303 0.76182 219s EASY3 0.34765 0.50432 0.689 0.49061 219s EASY4 0.30008 0.48283 0.621 0.53428 219s EASY5 0.23492 0.47686 0.493 0.62226 219s EASY6 -0.03205 0.46993 -0.068 0.94562 219s EASY7 0.02823 0.46963 0.060 0.95208 219s EASY8 -0.04600 0.47066 -0.098 0.92215 219s EASY9 -0.04084 0.49595 -0.082 0.93437 219s EASY10 1.03641 0.60080 1.725 0.08452 . 219s GENDERFemale -0.05092 0.10738 -0.474 0.63534 219s AGEGROUP31-40 0.02098 0.14822 0.142 0.88745 219s AGEGROUP41-50 0.23712 0.15824 1.498 0.13401 219s AGEGROUP51-65 -0.13791 0.14393 -0.958 0.33798 219s LOCATIONRegion 2 -0.09641 0.13225 -0.729 0.46599 219s LOCATIONRegion 3 0.06062 0.11981 0.506 0.61290 219s --- 219s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 219s 219s log-scale coefficients: 219s Estimate Std. Error z value Pr(>|z|) 219s PRODTest 0.14545 0.06621 2.197 0.028 * 219s --- 219s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 219s 219s Threshold coefficients: 219s Estimate Std. Error z value 219s 1|2 -1.64700 0.49982 -3.295 219s 2|3 -0.58840 0.49681 -1.184 219s 3|4 -0.23496 0.49669 -0.473 219s 4|5 0.04394 0.49679 0.088 219s 5|6 0.78551 0.49869 1.575 219s > 219s > ################################# 219s > ## Check that "."-notation works in formula: 219s > ## December 25th 2014, RHBC 219s > data(wine) 219s > wine2 <- wine[c("rating", "contact", "temp")] 219s > str(wine2) 219s 'data.frame': 72 obs. of 3 variables: 219s $ rating : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 2 3 3 4 4 4 5 5 1 2 ... 219s $ contact: Factor w/ 2 levels "no","yes": 1 1 2 2 1 1 2 2 1 1 ... 219s $ temp : Factor w/ 2 levels "cold","warm": 1 1 1 1 2 2 2 2 1 1 ... 219s > fm0 <- clm(rating ~ ., data=wine2) 219s > fm1 <- clm(rating ~ contact + temp, data=wine2) 219s > keep <- c("coefficients", "logLik", "info") 219s > fun <- function(x, y) stopifnot(isTRUE(all.equal(x, y))) 219s > mapply(fun, fm0[keep], fm1[keep]) 219s $coefficients 219s NULL 219s 219s $logLik 219s NULL 219s 219s $info 219s NULL 219s 219s > ################################# 219s > 219s BEGIN TEST clmm.R 219s 219s R version 4.4.3 (2025-02-28) -- "Trophy Case" 219s Copyright (C) 2025 The R Foundation for Statistical Computing 219s Platform: x86_64-pc-linux-gnu 219s 219s R is free software and comes with ABSOLUTELY NO WARRANTY. 219s You are welcome to redistribute it under certain conditions. 219s Type 'license()' or 'licence()' for distribution details. 219s 219s R is a collaborative project with many contributors. 219s Type 'contributors()' for more information and 219s 'citation()' on how to cite R or R packages in publications. 219s 219s Type 'demo()' for some demos, 'help()' for on-line help, or 219s 'help.start()' for an HTML browser interface to help. 219s Type 'q()' to quit R. 219s 219s > library(ordinal) 220s > data(wine) 220s > 220s > ################################# 220s > ## Estimation with a single simple RE term: 220s > ## Laplace: 220s > fmm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine) 220s > summary(fmm1) 220s Cumulative Link Mixed Model fitted with the Laplace approximation 220s 220s formula: rating ~ contact + temp + (1 | judge) 220s data: wine 220s 220s link threshold nobs logLik AIC niter max.grad cond.H 220s logit flexible 72 -81.57 177.13 332(999) 1.04e-05 2.8e+01 220s 220s Random effects: 220s Groups Name Variance Std.Dev. 220s judge (Intercept) 1.279 1.131 220s Number of groups: judge 9 220s 220s Coefficients: 220s Estimate Std. Error z value Pr(>|z|) 220s contactyes 1.8349 0.5125 3.580 0.000344 *** 220s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 220s --- 220s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 220s 220s Threshold coefficients: 220s Estimate Std. Error z value 220s 1|2 -1.6237 0.6824 -2.379 220s 2|3 1.5134 0.6038 2.507 220s 3|4 4.2285 0.8090 5.227 220s 4|5 6.0888 0.9725 6.261 220s > ## GHQ: 220s > fmm.ghq <- clmm(rating ~ contact + temp + (1|judge), data=wine, 220s + nAGQ=-10) 220s > summary(fmm.ghq) 220s Cumulative Link Mixed Model fitted with the Gauss-Hermite 220s quadrature approximation with 10 quadrature points 220s 220s formula: rating ~ contact + temp + (1 | judge) 220s data: wine 220s 220s link threshold nobs logLik AIC niter max.grad cond.H 220s logit flexible 72 -81.53 177.06 304(3) 1.67e-05 2.8e+01 220s 220s Random effects: 220s Groups Name Variance Std.Dev. 220s judge (Intercept) 1.288 1.135 220s Number of groups: judge 9 220s 220s Coefficients: 220s Estimate Std. Error z value Pr(>|z|) 220s contactyes 1.8335 0.5122 3.580 0.000344 *** 220s tempwarm 3.0620 0.5951 5.145 2.67e-07 *** 220s --- 220s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 220s 220s Threshold coefficients: 220s Estimate Std. Error z value 220s 1|2 -1.6231 0.6829 -2.377 220s 2|3 1.5133 0.6045 2.503 220s 3|4 4.2277 0.8094 5.223 220s 4|5 6.0869 0.9726 6.258 220s > ## AGQ: 220s > fmm.agq <- clmm(rating ~ contact + temp + (1|judge), data=wine, 220s + nAGQ=10) 220s > summary(fmm.agq) 220s Cumulative Link Mixed Model fitted with the adaptive Gauss-Hermite 220s quadrature approximation with 10 quadrature points 220s 220s formula: rating ~ contact + temp + (1 | judge) 220s data: wine 220s 220s link threshold nobs logLik AIC niter max.grad cond.H 220s logit flexible 72 -81.53 177.06 304(915) 2.26e-05 2.8e+01 220s 220s Random effects: 220s Groups Name Variance Std.Dev. 220s judge (Intercept) 1.288 1.135 220s Number of groups: judge 9 220s 220s Coefficients: 220s Estimate Std. Error z value Pr(>|z|) 220s contactyes 1.8334 0.5122 3.580 0.000344 *** 220s tempwarm 3.0619 0.5951 5.145 2.67e-07 *** 220s --- 220s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 220s 220s Threshold coefficients: 220s Estimate Std. Error z value 220s 1|2 -1.6235 0.6834 -2.376 220s 2|3 1.5128 0.6044 2.503 220s 3|4 4.2271 0.8090 5.225 220s 4|5 6.0862 0.9719 6.262 220s > ## tests: 220s > ## Notice warning about Laplace with multiple REs when nAGQ != 1: 220s > fmm1 <- try(clmm(rating ~ contact + temp + (1|judge) + (1|bottle), 220s + data=wine, nAGQ=10)) 220s > stopifnot(inherits(fmm1, "try-error")) 220s > 220s > ################################# 220s > ## Estimation with several RE terms: 220s > data(soup, package="ordinal") 220s Error : Quadrature methods are not available with more than one random effects term 220s > fmm <- clmm(SURENESS ~ PROD + (1|RESP) + (1|PROD:RESP), data=soup, 220s + threshold="equidistant") 222s > summary(fmm) 222s Cumulative Link Mixed Model fitted with the Laplace approximation 222s 222s formula: SURENESS ~ PROD + (1 | RESP) + (1 | PROD:RESP) 222s data: soup 222s 222s link threshold nobs logLik AIC niter max.grad cond.H 222s logit equidistant 1847 -2766.32 5542.63 261(837) 1.55e-03 1.3e+02 222s 222s Random effects: 222s Groups Name Variance Std.Dev. 222s PROD:RESP (Intercept) 0.4069 0.6379 222s RESP (Intercept) 0.1308 0.3616 222s Number of groups: PROD:RESP 370, RESP 185 222s 222s Coefficients: 222s Estimate Std. Error z value Pr(>|z|) 222s PRODTest 1.2865 0.1156 11.12 <2e-16 *** 222s --- 222s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 222s 222s Threshold coefficients: 222s Estimate Std. Error z value 222s threshold.1 -1.35103 0.09526 -14.18 222s spacing 0.56472 0.01905 29.65 222s > 222s > ################################# 222s > 222s > ## Estimation with implicit intercept: 222s > fm1 <- clmm(rating ~ 1 + (1|judge), data = wine) 222s > fm2 <- clmm(rating ~ (1|judge), data = wine) 222s > fm3 <- clmm(rating ~ 0 + (1|judge), data = wine) 222s > stopifnot(isTRUE(all.equal(coef(fm1), coef(fm2), tolerance=1e-5)), 222s + isTRUE(all.equal(coef(fm1), coef(fm3), tolerance=1e-5))) 222s > 222s Warning message: 222s In getX(fullmf, fixedmf, contrasts) : an intercept is needed and assumed 222s BEGIN TEST clmm.control.R 222s 222s R version 4.4.3 (2025-02-28) -- "Trophy Case" 222s Copyright (C) 2025 The R Foundation for Statistical Computing 222s Platform: x86_64-pc-linux-gnu 222s 222s R is free software and comes with ABSOLUTELY NO WARRANTY. 222s You are welcome to redistribute it under certain conditions. 222s Type 'license()' or 'licence()' for distribution details. 222s 222s R is a collaborative project with many contributors. 222s Type 'contributors()' for more information and 222s 'citation()' on how to cite R or R packages in publications. 222s 222s Type 'demo()' for some demos, 'help()' for on-line help, or 222s 'help.start()' for an HTML browser interface to help. 222s Type 'q()' to quit R. 222s 222s > library(ordinal) 223s > data(wine) 223s > 223s > 223s > ### 3 options for specifying control arguments: 223s > ## 1) control is a simple list, e.g. list(trace=-1) 223s > ## 2) control is a call to clmm.control 223s > ## 3) control is an empty list; list() 223s > ## all in combination with extra control arguments. 223s > 223s > ordinal:::getCtrlArgs(clmm.control(), list(maxIter=200)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 200 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(list(), list(maxIter=200)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 200 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(list(), list(trace=-1)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 1 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(list(), list(trace=1)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(list(), list()) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(list(maxIter=2), list()) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 2 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > 223s > ordinal:::getCtrlArgs(clmm.control(), list()) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(maxIter=100), list(maxIter=200)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 200 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(maxIter=100), list(maxIter=200)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 200 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(), list(trace=1)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(), list(trace=-1)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 1 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(trace=1), list()) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(trace=-1), list()) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 1 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(trace=0), list()) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 0 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 0 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ## Don't specify trace twice - surprising behavior might occur: 223s > ordinal:::getCtrlArgs(clmm.control(trace=1), list(trace=-1)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 1 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > ordinal:::getCtrlArgs(clmm.control(trace=-1), list(trace=1)) 223s $method 223s [1] "nlminb" 223s 223s $useMatrix 223s [1] FALSE 223s 223s $ctrl 223s $ctrl$trace 223s [1] 1 223s 223s $ctrl$maxIter 223s [1] 50 223s 223s $ctrl$gradTol 223s [1] 1e-04 223s 223s $ctrl$maxLineIter 223s [1] 50 223s 223s $ctrl$innerCtrl 223s [1] "warnOnly" 223s 223s 223s $optCtrl 223s $optCtrl$trace 223s [1] 1 223s 223s 223s $checkRanef 223s [1] "warn" 223s 223s > 223s BEGIN TEST clmm.formula.R 223s 223s R version 4.4.3 (2025-02-28) -- "Trophy Case" 223s Copyright (C) 2025 The R Foundation for Statistical Computing 223s Platform: x86_64-pc-linux-gnu 223s 223s R is free software and comes with ABSOLUTELY NO WARRANTY. 223s You are welcome to redistribute it under certain conditions. 223s Type 'license()' or 'licence()' for distribution details. 223s 223s R is a collaborative project with many contributors. 223s Type 'contributors()' for more information and 223s 'citation()' on how to cite R or R packages in publications. 223s 223s Type 'demo()' for some demos, 'help()' for on-line help, or 223s 'help.start()' for an HTML browser interface to help. 223s Type 'q()' to quit R. 223s 223s > library(ordinal) 224s > data(wine) 224s > 224s > ################################# 224s > ## Appropriate evaluation of formulas: 224s > 224s > ## These all work as intended with no warnings or errors: 224s > fm1 <- clmm(rating ~ contact + (1|judge), data=wine) 224s > fm1 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 0.4428 0.6654 224s Number of groups: judge 9 224s 224s Coefficients: 224s contactyes 224s 1.3 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -2.28331 0.04325 1.86062 3.20298 224s > fm1 <- clmm("rating ~ contact + (1|judge)", data=wine) 224s > fm1 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 0.4428 0.6654 224s Number of groups: judge 9 224s 224s Coefficients: 224s contactyes 224s 1.3 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -2.28331 0.04325 1.86062 3.20298 224s > fm1 <- clmm(as.formula("rating ~ contact + (1|judge)"), data=wine) 224s > fm1 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 0.4428 0.6654 224s Number of groups: judge 9 224s 224s Coefficients: 224s contactyes 224s 1.3 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -2.28331 0.04325 1.86062 3.20298 224s > fm1 <- clmm(as.formula(rating ~ contact + (1|judge)), data=wine) 224s > fm1 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -98.80 209.59 228(686) 3.67e-06 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 0.4428 0.6654 224s Number of groups: judge 9 224s 224s Coefficients: 224s contactyes 224s 1.3 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -2.28331 0.04325 1.86062 3.20298 224s > 224s > ################################# 224s > 224s > ### finding variables in the environment of the formula: 224s > makeform <- function() { 224s + f1 <- as.formula(rating ~ temp + contact + (1|judge)) 224s + rating <- wine$rating 224s + temp <- wine$temp 224s + contact <- wine$contact 224s + judge <- wine$judge 224s + f1 224s + } 224s > ## 'makeform' makes are formula object in the environment of the 224s > ## function makeform: 224s > f1 <- makeform() 224s > f1 # print 224s rating ~ temp + contact + (1 | judge) 224s 224s > class(f1) 224s [1] "formula" 224s > ## If we give the data, we can evaluate the model: 224s > fm1 <- clmm(f1, data=wine) 224s > ## We can also evaluate the model because the data are available in 224s > ## the environment associated with the formula: 224s > fm1 <- clmm(f1) 224s > ## For instance, the 'rating' variable is not found in the Global 224s > ## environment; we have to evaluate the 'name' of 'rating' in the 224s > ## appropriate environment: 224s > (try(rating, silent=TRUE)) 224s [1] "Error : object 'rating' not found\n" 224s attr(,"class") 224s [1] "try-error" 224s attr(,"condition") 224s 224s > eval(as.name("rating"), envir=environment(f1)) 224s [1] 2 3 3 4 4 4 5 5 1 2 1 3 2 3 5 4 2 3 3 2 5 5 4 4 3 2 3 2 3 2 5 3 2 3 4 3 3 3 224s [39] 3 3 3 2 3 2 2 4 5 4 1 1 2 2 2 3 2 3 2 2 2 3 3 3 3 4 1 2 3 2 3 2 4 4 224s Levels: 1 < 2 < 3 < 4 < 5 224s > ## If instead we generate the formula in the Global environment where 224s > ## the variables are not found, we cannot evaluate the model: 224s > f2 <- as.formula(rating ~ temp + contact + (1|judge)) 224s > (try(fm2 <- clmm(f2), silent=TRUE)) 224s [1] "Error in eval(predvars, data, env) : object 'rating' not found\n" 224s attr(,"class") 224s [1] "try-error" 224s attr(,"condition") 224s 224s > environment(f2) <- environment(f1) 224s > fm2 <- clmm(f2) 224s > 224s > ################################# 224s > ## Use of formula-objects 224s > f <- formula(rating ~ temp + contact + (1|judge)) 224s > m2 <- clmm(f, data = wine) 224s > summary(m2) 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad cond.H 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 2.8e+01 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s Estimate Std. Error z value Pr(>|z|) 224s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 224s contactyes 1.8349 0.5125 3.580 0.000344 *** 224s --- 224s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 224s 224s Threshold coefficients: 224s Estimate Std. Error z value 224s 1|2 -1.6237 0.6824 -2.379 224s 2|3 1.5134 0.6038 2.507 224s 3|4 4.2285 0.8090 5.227 224s 4|5 6.0888 0.9725 6.261 224s > 224s > ################################# 224s > ## Other ways to construct formulas: 224s > set.seed(12345) 224s > y <- factor(sample(1:4,20,replace=TRUE)) 224s > x <- rnorm(20) 224s > b <- gl(5, 4, labels=letters[1:5]) 224s > data <- data.frame(y=y, x=x, b=b) 224s > rm(x, y, b) 224s > clmm(y ~ x + (1|b), data=data) 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: y ~ x + (1 | b) 224s data: data 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 20 -25.37 60.74 338(288) 7.12e-08 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s b (Intercept) 9.736e-09 9.867e-05 224s Number of groups: b 5 224s 224s Coefficients: 224s x 224s 0.2527 224s 224s Thresholds: 224s 1|2 2|3 3|4 224s -2.18234 0.06059 0.92746 224s > fit <- clmm(data$y ~ data$x + (1|data$b)) 224s > fit 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: data$y ~ data$x + (1 | data$b) 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 20 -25.37 60.74 338(288) 7.12e-08 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s data$b (Intercept) 9.736e-09 9.867e-05 224s Number of groups: data$b 5 224s 224s Coefficients: 224s data$x 224s 0.2527 224s 224s Thresholds: 224s 1|2 2|3 3|4 224s -2.18234 0.06059 0.92746 224s > fit <- clmm(data[, 1] ~ data[, 2] + (1|data[, 3])) 224s > fit 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: data[, 1] ~ data[, 2] + (1 | data[, 3]) 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 20 -25.37 60.74 338(288) 7.12e-08 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s data[, 3] (Intercept) 9.736e-09 9.867e-05 224s Number of groups: data[, 3] 5 224s 224s Coefficients: 224s data[, 2] 224s 0.2527 224s 224s Thresholds: 224s 1|2 2|3 3|4 224s -2.18234 0.06059 0.92746 224s > 224s > ################################# 224s > ## Evaluation within other functions: 224s > ## date: January 18th 2012. 224s > ## 224s > ## The problem was raised by Stefan Herzog (stefan.herzog@unibas.ch) 224s > ## January 12th 2012 in trying to make clmm work with glmulti. 224s > 224s > fun.clmm <- function(formula, data) 224s + ### This only works because clmm via eclmm.model.frame is careful to 224s + ### evaluate the 'formula' in the parent environment such it is not the 224s + ### character "formula" that is attempted evaluated. 224s + clmm(formula, data = data) 224s > 224s > fun2.clmm <- function(formula, data, weights, subset) { 224s + ### This should be the safe way to ensure evaluation of clmm in the 224s + ### right environment. 224s + mc <- match.call() 224s + mc[[1]] <- as.name("clmm") 224s + eval.parent(mc) 224s + } 224s > 224s > fun.clmm(rating ~ temp + contact + (1|judge), data=wine) ## works 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: data 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s tempwarm contactyes 224s 3.063 1.835 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -1.624 1.513 4.229 6.089 224s > fun2.clmm(rating ~ temp + contact + (1|judge), data=wine) ## works 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s tempwarm contactyes 224s 3.063 1.835 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -1.624 1.513 4.229 6.089 224s > 224s > form1 <- "rating ~ temp + contact + (1|judge)" 224s > fun.clmm(form1, data=wine) ## works 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: data 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s tempwarm contactyes 224s 3.063 1.835 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -1.624 1.513 4.229 6.089 224s > fun2.clmm(form1, data=wine) ## works 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s tempwarm contactyes 224s 3.063 1.835 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -1.624 1.513 4.229 6.089 224s > 224s > form2 <- formula(rating ~ temp + contact + (1|judge)) 224s > fun.clmm(form2, data=wine) ## works 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: data 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s tempwarm contactyes 224s 3.063 1.835 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -1.624 1.513 4.229 6.089 224s > fun2.clmm(form2, data=wine) ## works 224s Cumulative Link Mixed Model fitted with the Laplace approximation 224s 224s formula: rating ~ temp + contact + (1 | judge) 224s data: wine 224s 224s link threshold nobs logLik AIC niter max.grad 224s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 224s 224s Random effects: 224s Groups Name Variance Std.Dev. 224s judge (Intercept) 1.279 1.131 224s Number of groups: judge 9 224s 224s Coefficients: 224s tempwarm contactyes 224s 3.063 1.835 224s 224s Thresholds: 224s 1|2 2|3 3|4 4|5 224s -1.624 1.513 4.229 6.089 224s > ## Notice that clmm is not able to get the name of the data (wine) 224s > ## correct when using fun.clmm. 224s > 224s > ################################# 224s > 224s > ## ## Example 2: using clmm function 224s > ## # 224s > ## ## Now I want to consider judge as a random effect to account for 224s > ## ## grouping structure of data 224s > ## mod2 <- clmm(rating ~ temp + contact + (1|judge), data=wine) 224s > ## 224s > ## ##Again, I started by using my own code to run all potential models: 224s > ## ## put names of all your variables in this vector: 224s > ## vl2 <- c("temp", "contact") 224s > ## ## generate list of possible combinations of variables: 224s > ## combos2 <- NULL 224s > ## for(i in 1:length(vl2)) { 224s > ## combos2 <- c(combos2, combn(vl2, i, simplify = F)) 224s > ## } 224s > ## ## create formulae and run models one by one, saving them as model1, 224s > ## ## model2 etc... 224s > ## for (i in 1:length(combos2)) { 224s > ## vs2 <- paste(combos2[[i]], collapse=" + ") 224s > ## f2 <- formula(paste("rating ~ ", vs2, "+(1|judge)", sep="")) 224s > ## print(f2) 224s > ## assign(paste("model", i, sep=""), clmm(f2, data=wine)) 224s > ## } 224s > ## summary(model1) # etc 224s > ## summary(model2) # etc 224s > ## summary(model3) # etc 224s > ## 224s > ## models <- vector("list", length(combos2)) 224s > ## for(i in 1:length(combos2)) { 224s > ## vs2 <- paste(combos2[[i]], collapse=" + ") 224s > ## f2 <- formula(paste("rating ~ ", vs2, "+(1|judge)", sep="")) 224s > ## print(f2) 224s > ## models[[i]] <- clmm(f2, data=wine) 224s > ## ## assign(paste("model", i, sep=""), clmm(f2, data=wine)) 224s > ## } 224s > ## 224s > ## ## Coefficients, AIC and BIC: 224s > ## lapply(models, function(m) coef(summary(m))) 224s > ## lapply(models, AIC) 224s > ## lapply(models, BIC) 224s > ## 224s > ## ## library(MuMIn) 224s > ## ## dd2 <- dredge(mod2) ## does not work 224s > ## ## ?dredge 224s > ## ## traceback() 224s > ## ## mod2$formula 224s > ## ## terms(as.formula(formula(mod2))) 224s > ## ## 224s > ## ## library(lme4) 224s > ## ## fmm1 <- lmer(response ~ temp + contact + (1|judge), data=wine) 224s > ## ## fmm1 224s > ## ## terms(as.formula(lme4:::formula(fmm1))) 224s > ## ## terms(as.formula(formula(fmm1))) 224s > 224s BEGIN TEST clmm.methods.R 224s 224s R version 4.4.3 (2025-02-28) -- "Trophy Case" 224s Copyright (C) 2025 The R Foundation for Statistical Computing 224s Platform: x86_64-pc-linux-gnu 224s 224s R is free software and comes with ABSOLUTELY NO WARRANTY. 224s You are welcome to redistribute it under certain conditions. 224s Type 'license()' or 'licence()' for distribution details. 224s 224s R is a collaborative project with many contributors. 224s Type 'contributors()' for more information and 224s 'citation()' on how to cite R or R packages in publications. 224s 224s Type 'demo()' for some demos, 'help()' for on-line help, or 224s 'help.start()' for an HTML browser interface to help. 224s Type 'q()' to quit R. 224s 225s > library(ordinal) 225s > data(wine) 225s > 225s > ################################# 225s > ## model.matrix method for clmm-objects: 225s > fmm1 <- clmm(rating ~ contact + temp + (1|judge), data=wine) 225s > mm <- model.matrix(fmm1) 225s > stopifnot(inherits(mm, "matrix"), 225s + dim(mm) == c(72, 3)) 225s > 225s > ################################# 225s > ## anova.clmm works even if formula does not have an environment: 225s > fmm1 <- clmm(rating ~ temp * contact + (1|judge), data = wine) 225s > fmm2 <- clmm(rating ~ temp + contact + (1|judge), data = wine) 225s > environment(fmm1$formula) <- NULL 225s > environment(fmm2$formula) <- NULL 225s > anova(fmm1, fmm2) 225s Likelihood ratio tests of cumulative link models: 225s 225s formula: link: threshold: 225s fmm2 rating ~ temp + contact + (1 | judge) logit flexible 225s fmm1 rating ~ temp * contact + (1 | judge) logit flexible 225s 225s no.par AIC logLik LR.stat df Pr(>Chisq) 225s fmm2 7 177.13 -81.565 225s fmm1 8 179.07 -81.536 0.0589 1 0.8082 225s > 225s > 225s > ################################# 225s > ## Test that ranef, condVar and VarCorr work as they are supposed to whether or 225s > ## not nlme and lme4 are loaded: 225s > 225s > fm <- clmm(rating ~ temp + contact + (1|judge), data = wine) 225s > fm 226s Cumulative Link Mixed Model fitted with the Laplace approximation 226s 226s formula: rating ~ temp + contact + (1 | judge) 226s data: wine 226s 226s link threshold nobs logLik AIC niter max.grad 226s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 226s 226s Random effects: 226s Groups Name Variance Std.Dev. 226s judge (Intercept) 1.279 1.131 226s Number of groups: judge 9 226s 226s Coefficients: 226s tempwarm contactyes 226s 3.063 1.835 226s 226s Thresholds: 226s 1|2 2|3 3|4 4|5 226s -1.624 1.513 4.229 6.089 226s > ranef(fm) 226s $judge 226s (Intercept) 226s 1 1.69617818 226s 2 -0.56578308 226s 3 0.96880828 226s 4 -0.05954989 226s 5 0.23051011 226s 6 0.47703864 226s 7 -1.91097339 226s 8 -0.27294385 226s 9 -0.55467576 226s 226s > VarCorr(fm) 226s $judge 226s (Intercept) 226s (Intercept) 1.279461 226s attr(,"stddev") 226s (Intercept) 226s 1.131133 226s 226s > condVar(fm) 226s $judge 226s (Intercept) 226s 1 0.3067453 226s 2 0.3779358 226s 3 0.3545529 226s 4 0.3651870 226s 5 0.3566066 226s 6 0.3485475 226s 7 0.3435693 226s 8 0.3050453 226s 9 0.3183194 226s 226s > summary(fm) 226s Cumulative Link Mixed Model fitted with the Laplace approximation 226s 226s formula: rating ~ temp + contact + (1 | judge) 226s data: wine 226s 226s link threshold nobs logLik AIC niter max.grad cond.H 226s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 2.8e+01 226s 226s Random effects: 226s Groups Name Variance Std.Dev. 226s judge (Intercept) 1.279 1.131 226s Number of groups: judge 9 226s 226s Coefficients: 226s Estimate Std. Error z value Pr(>|z|) 226s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 226s contactyes 1.8349 0.5125 3.580 0.000344 *** 226s --- 226s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 226s 226s Threshold coefficients: 226s Estimate Std. Error z value 226s 1|2 -1.6237 0.6824 -2.379 226s 2|3 1.5134 0.6038 2.507 226s 3|4 4.2285 0.8090 5.227 226s 4|5 6.0888 0.9725 6.261 226s > 226s > library(nlme) 226s > ranef(fm) 226s $judge 226s (Intercept) 226s 1 1.69617818 226s 2 -0.56578308 226s 3 0.96880828 226s 4 -0.05954989 226s 5 0.23051011 226s 6 0.47703864 226s 7 -1.91097339 226s 8 -0.27294385 226s 9 -0.55467576 226s 226s > VarCorr(fm) 226s $judge 226s (Intercept) 226s (Intercept) 1.279461 226s attr(,"stddev") 226s (Intercept) 226s 1.131133 226s 226s > condVar(fm) 226s $judge 226s (Intercept) 226s 1 0.3067453 226s 2 0.3779358 226s 3 0.3545529 226s 4 0.3651870 226s 5 0.3566066 226s 6 0.3485475 226s 7 0.3435693 226s 8 0.3050453 226s 9 0.3183194 226s 226s > library(lme4) 226s Loading required package: Matrix 226s > ranef(fm) 226s $judge 226s 226s Attaching package: ‘lme4’ 226s 226s The following object is masked from ‘package:nlme’: 226s 226s lmList 226s 226s (Intercept) 226s 1 1.69617818 226s 2 -0.56578308 226s 3 0.96880828 226s 4 -0.05954989 226s 5 0.23051011 226s 6 0.47703864 226s 7 -1.91097339 226s 8 -0.27294385 226s 9 -0.55467576 226s 226s > VarCorr(fm) 226s $judge 226s (Intercept) 226s (Intercept) 1.279461 226s attr(,"stddev") 226s (Intercept) 226s 1.131133 226s 226s > condVar(fm) 226s $judge 226s (Intercept) 226s 1 0.3067453 226s 2 0.3779358 226s 3 0.3545529 226s 4 0.3651870 226s 5 0.3566066 226s 6 0.3485475 226s 7 0.3435693 226s 8 0.3050453 226s 9 0.3183194 226s 226s > fm1 <- lmer(Reaction ~ Days + (Days | Subject), data=sleepstudy) 226s > ranef(fm1) 226s $Subject 226s (Intercept) Days 226s 308 2.2585509 9.1989758 226s 309 -40.3987381 -8.6196806 226s 310 -38.9604090 -5.4488565 226s 330 23.6906196 -4.8143503 226s 331 22.2603126 -3.0699116 226s 332 9.0395679 -0.2721770 226s 333 16.8405086 -0.2236361 226s 334 -7.2326151 1.0745816 226s 335 -0.3336684 -10.7521652 226s 337 34.8904868 8.6282652 226s 349 -25.2102286 1.1734322 226s 350 -13.0700342 6.6142178 226s 351 4.5778642 -3.0152621 226s 352 20.8636782 3.5360011 226s 369 3.2754656 0.8722149 226s 370 -25.6129993 4.8224850 226s 371 0.8070461 -0.9881562 226s 372 12.3145921 1.2840221 226s 226s with conditional variances for “Subject” 226s > VarCorr(fm1) 226s Groups Name Std.Dev. Corr 226s Subject (Intercept) 24.7407 226s Days 5.9221 0.066 226s Residual 25.5918 226s > 226s > ranef(fm) 226s $judge 226s (Intercept) 226s 1 1.69617818 226s 2 -0.56578308 226s 3 0.96880828 226s 4 -0.05954989 226s 5 0.23051011 226s 6 0.47703864 226s 7 -1.91097339 226s 8 -0.27294385 226s 9 -0.55467576 226s 226s > VarCorr(fm) 226s $judge 226s (Intercept) 226s (Intercept) 1.279461 226s attr(,"stddev") 226s (Intercept) 226s 1.131133 226s 226s > condVar(fm) 226s $judge 226s (Intercept) 226s 1 0.3067453 226s 2 0.3779358 226s 3 0.3545529 226s 4 0.3651870 226s 5 0.3566066 226s 6 0.3485475 226s 7 0.3435693 226s 8 0.3050453 226s 9 0.3183194 226s 226s > summary(fm) 226s Cumulative Link Mixed Model fitted with the Laplace approximation 226s 226s formula: rating ~ temp + contact + (1 | judge) 226s data: wine 226s 226s link threshold nobs logLik AIC niter max.grad cond.H 226s logit flexible 72 -81.57 177.13 332(999) 1.03e-05 2.8e+01 226s 226s Random effects: 226s Groups Name Variance Std.Dev. 226s judge (Intercept) 1.279 1.131 226s Number of groups: judge 9 226s 226s Coefficients: 226s Estimate Std. Error z value Pr(>|z|) 226s tempwarm 3.0630 0.5954 5.145 2.68e-07 *** 226s contactyes 1.8349 0.5125 3.580 0.000344 *** 226s --- 226s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 226s 226s Threshold coefficients: 226s Estimate Std. Error z value 226s 1|2 -1.6237 0.6824 -2.379 226s 2|3 1.5134 0.6038 2.507 226s 3|4 4.2285 0.8090 5.227 226s 4|5 6.0888 0.9725 6.261 226s > 226s BEGIN TEST confint.R 226s 226s R version 4.4.3 (2025-02-28) -- "Trophy Case" 226s Copyright (C) 2025 The R Foundation for Statistical Computing 226s Platform: x86_64-pc-linux-gnu 226s 226s R is free software and comes with ABSOLUTELY NO WARRANTY. 226s You are welcome to redistribute it under certain conditions. 226s Type 'license()' or 'licence()' for distribution details. 226s 226s R is a collaborative project with many contributors. 226s Type 'contributors()' for more information and 226s 'citation()' on how to cite R or R packages in publications. 226s 226s Type 'demo()' for some demos, 'help()' for on-line help, or 226s 'help.start()' for an HTML browser interface to help. 226s Type 'q()' to quit R. 226s 226s > ################################# 226s > ## test profile and confint methods: 226s > library(ordinal) 227s > data(wine) 227s > fm1 <- clm(rating ~ contact + temp, data = wine) 227s > summary(fm1) 227s formula: rating ~ contact + temp 227s data: wine 227s 227s link threshold nobs logLik AIC niter max.grad cond.H 227s logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 227s 227s Coefficients: 227s Estimate Std. Error z value Pr(>|z|) 227s contactyes 1.5278 0.4766 3.205 0.00135 ** 227s tempwarm 2.5031 0.5287 4.735 2.19e-06 *** 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s Threshold coefficients: 227s Estimate Std. Error z value 227s 1|2 -1.3444 0.5171 -2.600 227s 2|3 1.2508 0.4379 2.857 227s 3|4 3.4669 0.5978 5.800 227s 4|5 5.0064 0.7309 6.850 227s > 227s > ## profile.clm and confint.clm: 227s > pr1 <- profile(fm1) 227s > confint(pr1) 227s 2.5 % 97.5 % 227s contactyes 0.6158045 2.492424 227s tempwarm 1.5097839 3.595251 227s > pr1 <- profile(fm1, which.beta = 1:2) 227s > confint(pr1) 227s 2.5 % 97.5 % 227s contactyes 0.6158045 2.492424 227s tempwarm 1.5097839 3.595251 227s > pr1 <- profile(fm1, which.beta = 2:1) 227s > confint(pr1) 227s 2.5 % 97.5 % 227s tempwarm 1.5097839 3.595251 227s contactyes 0.6158045 2.492424 227s > pr1 <- profile(fm1, which.beta = 1) 227s > confint(pr1) 227s 2.5 % 97.5 % 227s contactyes 0.6158045 2.492424 227s > pr1 <- profile(fm1, which.beta = 2) 227s > confint(pr1) 227s 2.5 % 97.5 % 227s tempwarm 1.509784 3.595251 227s > pr1 <- try(profile(fm1, which.beta = 0), silent = TRUE) ## error 227s > pr1 <- try(profile(fm1, which.beta = "no.par"), silent = TRUE) ## error 227s > pr1 <- try(profile(fm1, which.beta = -1), silent = TRUE) ## error 227s > pr1 <- profile(fm1, which.beta = "tempwarm") 227s > confint(pr1) 227s 2.5 % 97.5 % 227s tempwarm 1.509784 3.595251 227s > pr1 <- profile(fm1, alpha = 0.1) 227s > confint(pr1) ## should give NA in this case? 227s 2.5 % 97.5 % 227s contactyes NA NA 227s tempwarm NA NA 227s > pr1 <- profile(fm1, max.steps = 9) 227s > pr1 <- profile(fm1, step.warn = 7) 227s > pr1 <- profile(fm1, nsteps = 6) 227s > pr1 <- profile(fm1, trace = 1) 227s 227s Parameter: contactyes down 227s 227s Parameter: contactyes up 227s 227s Parameter: tempwarm down 227s 227s Parameter: tempwarm up 227s > pr1 <- profile(fm1, control = list(gradTol = .1)) 227s > confint(pr1) ## not at all unreliable... 227s 2.5 % 97.5 % 227s contactyes 0.6158045 2.492424 227s tempwarm 1.5097839 3.595251 227s > 227s > ## single regression coef setting: 227s > fm2 <- clm(rating ~ contact, data = wine) 227s > summary(fm2) 227s formula: rating ~ contact 227s data: wine 227s 227s link threshold nobs logLik AIC niter max.grad cond.H 227s logit flexible 72 -99.96 209.91 5(0) 1.67e-07 1.7e+01 227s 227s Coefficients: 227s Estimate Std. Error z value Pr(>|z|) 227s contactyes 1.2070 0.4499 2.683 0.0073 ** 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s Threshold coefficients: 227s Estimate Std. Error z value 227s 1|2 -2.13933 0.48981 -4.368 227s 2|3 0.04257 0.32063 0.133 227s 3|4 1.71449 0.38637 4.437 227s 4|5 2.97875 0.50207 5.933 227s > pr2 <- profile(fm2) 227s > confint(pr2) 227s 2.5 % 97.5 % 227s contactyes 0.3403978 2.110952 227s > 227s > ## confint.clm: 227s > confint(fm1) 227s argument 'parm' ignored 227s 2.5 % 97.5 % 227s contactyes 0.6157925 2.492404 227s tempwarm 1.5097627 3.595225 227s > confint(fm1, 2) 227s 2.5 % 97.5 % 227s contactyes 0.6157925 2.492404 227s tempwarm 1.5097627 3.595225 227s > confint(fm1, 1) 227s argument 'parm' ignored 227s 2.5 % 97.5 % 227s contactyes 0.6157925 2.492404 227s tempwarm 1.5097627 3.595225 227s > confint(fm1, "tempwarm") 227s argument 'parm' ignored 227s 2.5 % 97.5 % 227s contactyes 0.6157925 2.492404 227s tempwarm 1.5097627 3.595225 227s > confint(fm1, type = "profile") 227s 2.5 % 97.5 % 227s contactyes 0.6157925 2.492404 227s tempwarm 1.5097627 3.595225 227s > confint(fm1, type = "Wald") 227s 2.5 % 97.5 % 227s 1|2 -2.3578848 -0.330882 227s 2|3 0.3925794 2.109038 227s 3|4 2.2952980 4.638476 227s 4|5 3.5738541 6.438954 227s contactyes 0.5936345 2.461961 227s tempwarm 1.4669081 3.539296 227s > confint(fm1, 2, type = "Wald") 227s argument 'parm' ignored 227s 2.5 % 97.5 % 227s 1|2 -2.3578848 -0.330882 227s 2|3 0.3925794 2.109038 227s 3|4 2.2952980 4.638476 227s 4|5 3.5738541 6.438954 227s contactyes 0.5936345 2.461961 227s tempwarm 1.4669081 3.539296 227s > confint(fm1, level = 0.5) 227s 25 % 75 % 227s contactyes 1.209254 1.852544 227s tempwarm 2.152051 2.865757 227s > confint(fm1, level = 1 - 1e-6) 227s 0 % 100 % 227s contactyes -0.7003630 4.091731 227s tempwarm 0.1351282 5.520007 227s > confint(fm1, level = 1 - 1e-10) ## extreme, but it works 227s 0 % 100 % 227s contactyes -1.4045009 5.059182 227s tempwarm -0.5753928 6.774556 227s > confint(fm1, trace = 1) 227s Wait for profiling to be done... 227s 227s Parameter: contactyes down 227s 227s Parameter: contactyes up 227s 227s Parameter: tempwarm down 227s 227s Parameter: tempwarm up 227s 2.5 % 97.5 % 227s contactyes 0.6157925 2.492404 227s tempwarm 1.5097627 3.595225 227s > 227s > ## plot.profile: 227s > pr1 <- profile(fm1, which.beta=1:2, alpha = 1e-3) 227s > par(mfrow = c(1,2)) 227s > plot(pr1) 227s > plot(pr1, 1) 227s > plot(pr1, "contactyes") 227s > plot(pr1, level = .97) 227s > plot(pr1, Log = TRUE) 227s > plot(pr1, relative = FALSE) 227s > plot(pr1, root = TRUE) 227s > plot(pr1, approx = TRUE) 227s > plot(pr1, n=10) 227s > plot(pr1, ylim = c(0,2)) 227s > plot(pr1, las = 1) 227s > plot(pr2) 228s > 228s > 228s BEGIN TEST nominal.test.R 228s 228s R version 4.4.3 (2025-02-28) -- "Trophy Case" 228s Copyright (C) 2025 The R Foundation for Statistical Computing 228s Platform: x86_64-pc-linux-gnu 228s 228s R is free software and comes with ABSOLUTELY NO WARRANTY. 228s You are welcome to redistribute it under certain conditions. 228s Type 'license()' or 'licence()' for distribution details. 228s 228s R is a collaborative project with many contributors. 228s Type 'contributors()' for more information and 228s 'citation()' on how to cite R or R packages in publications. 228s 228s Type 'demo()' for some demos, 'help()' for on-line help, or 228s 'help.start()' for an HTML browser interface to help. 228s Type 'q()' to quit R. 228s 228s > library(ordinal) 229s > 229s > if(require(MASS)) { 229s + fm1 <- clm(Sat ~ Infl + Type + Cont, data=housing, weights=Freq) 229s + scale_test(fm1) 229s + nominal_test(fm1) 229s + 229s + fm2 <- update(fm1, scale=~Cont) 229s + scale_test(fm2) 229s + nominal_test(fm2) 229s + fm3 <- update(fm1, nominal=~ Cont) 229s + fm3$Theta 229s + anova(fm2, fm3) 229s + fm3$alpha.mat 229s + summary(fm3) 229s + } 229s Loading required package: MASS 229s formula: Sat ~ Infl + Type + Cont 229s nominal: ~Cont 229s data: housing 229s 229s link threshold nobs logLik AIC niter max.grad cond.H 229s logit flexible 1681 -1738.35 3494.70 4(0) 1.31e-07 6.3e+01 229s 229s Coefficients: (1 not defined because of singularities) 229s Estimate Std. Error z value Pr(>|z|) 229s InflMedium 0.5695 0.1048 5.436 5.45e-08 *** 229s InflHigh 1.2884 0.1271 10.137 < 2e-16 *** 229s TypeApartment -0.5706 0.1192 -4.788 1.68e-06 *** 229s TypeAtrium -0.3643 0.1552 -2.348 0.0189 * 229s TypeTerrace -1.0980 0.1516 -7.242 4.43e-13 *** 229s ContHigh NA NA NA NA 229s --- 229s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 229s 229s Threshold coefficients: 229s Estimate Std. Error z value 229s Low|Medium.(Intercept) -0.4494 0.1279 -3.515 229s Medium|High.(Intercept) 0.6480 0.1279 5.066 229s Low|Medium.ContHigh -0.4440 0.1095 -4.056 229s Medium|High.ContHigh -0.2861 0.1063 -2.691 229s > 229s > ################################# 229s > ### Testing nominal_test and scale_test: 229s > fm1 <- clm(rating ~ temp * contact, data=wine) 229s > ## names(fm1) 229s > fm2 <- clm(rating ~ temp * contact, data=wine, nominal=~contact) 229s > (an <- anova(fm1, fm2)) 229s Likelihood ratio tests of cumulative link models: 229s 229s formula: nominal: link: threshold: 229s fm1 rating ~ temp * contact ~1 logit flexible 229s fm2 rating ~ temp * contact ~contact logit flexible 229s 229s no.par AIC logLik LR.stat df Pr(>Chisq) 229s fm1 7 186.83 -86.416 229s fm2 10 192.17 -86.083 0.6669 3 0.881 229s > (nm <- nominal_test(fm1)) 229s Tests of nominal effects 229s 229s formula: rating ~ temp * contact 229s Df logLik AIC LRT Pr(>Chi) 229s -86.416 186.83 229s temp 3 -84.874 189.75 3.08352 0.3789 229s contact 3 -86.083 192.16 0.66691 0.8810 229s temp:contact 229s > stopifnot(isTRUE(all.equal(an[2, 6], nm["contact", 5]))) 229s > 229s > fm2 <- clm(rating ~ temp * contact, data=wine, scale=~contact) 229s > (an <- anova(fm1, fm2)) 229s Likelihood ratio tests of cumulative link models: 229s 229s formula: scale: link: threshold: 229s fm1 rating ~ temp * contact ~1 logit flexible 229s fm2 rating ~ temp * contact ~contact logit flexible 229s 229s no.par AIC logLik LR.stat df Pr(>Chisq) 229s fm1 7 186.83 -86.416 229s fm2 8 188.60 -86.300 0.2325 1 0.6297 229s > (sc <- scale_test(fm1)) 229s Tests of scale effects 229s 229s formula: rating ~ temp * contact 229s Df logLik AIC LRT Pr(>Chi) 229s -86.416 186.83 229s temp 1 -86.326 188.65 0.18061 0.6709 229s contact 1 -86.300 188.60 0.23252 0.6297 229s temp:contact 3 -86.259 192.52 0.31391 0.9574 229s > stopifnot(isTRUE(all.equal(an[2, 6], sc["contact", "Pr(>Chi)"]))) 229s > 229s > fm1 <- clm(rating ~ temp + contact, 229s + nominal=~temp + contact, data=wine) 229s > fm1 229s formula: rating ~ temp + contact 229s nominal: ~temp + contact 229s data: wine 229s 229s link threshold nobs logLik AIC niter max.grad cond.H 229s logit flexible 72 -84.61 193.22 20(0) 4.36e-09 5.0e+10 229s 229s Coefficients: (2 not defined because of singularities) 229s tempwarm contactyes 229s NA NA 229s 229s Threshold coefficients: 229s 1|2 2|3 3|4 4|5 229s (Intercept) -1.226 1.033 3.946 24.553 229s tempwarm -21.118 -2.111 -2.940 -22.432 229s contactyes -1.659 -1.343 -1.693 -1.162 229s > try(nominal_test(fm1), silent=TRUE)[1] ## gives error OK 229s Df 229s 229s > scale_test(fm1) 229s Warning message: 229s (1) Hessian is numerically singular: parameters are not uniquely determined 229s In addition: Absolute convergence criterion was met, but relative criterion was not met 229s 229s no additional terms to add to nominal 229s 229s Tests of scale effects 229s 229s formula: rating ~ temp + contact 229s nominal: ~temp + contact 229s Df logLik AIC LRT Pr(>Chi) 229s -84.611 193.22 229s temp 1 -84.604 195.21 0.0129568 0.9094 229s contact 1 -84.610 195.22 0.0012219 0.9721 229s Warning messages: 229s 1: (1) Hessian is numerically singular: parameters are not uniquely determined 229s In addition: Absolute convergence criterion was met, but relative criterion was not met 229s 2: (1) Hessian is numerically singular: parameters are not uniquely determined 229s In addition: Absolute convergence criterion was met, but relative criterion was not met 229s > fm1 <- clm(rating ~ temp + contact, 229s + scale=~temp + contact, data=wine) 229s > fm1 229s formula: rating ~ temp + contact 229s scale: ~temp + contact 229s data: wine 229s 229s link threshold nobs logLik 229s no relevant terms to add to scale 229s 229s AIC niter max.grad cond.H 229s logit flexible 72 -86.34 188.68 8(0) 7.40e-09 2.0e+02 229s 229s Coefficients: 229s tempwarm contactyes 229s 2.446 1.482 229s 229s log-scale coefficients: 229s tempwarm contactyes 229s 0.05008 -0.11418 229s 229s Threshold coefficients: 229s 1|2 2|3 3|4 4|5 229s -1.303 1.219 3.377 4.872 229s > try(scale_test(fm1), silent=TRUE)[1] ## gives error OK 229s Df 229s 229s > nominal_test(fm1) 229s Tests of nominal effects 229s 229s formula: rating ~ temp + contact 229s scale: ~temp + contact 229s Df logLik AIC LRT Pr(>Chi) 229s -86.342 188.69 229s temp 3 -84.851 191.70 2.98202 0.3944 229s contact 3 -86.008 194.02 0.66808 0.8807 229s > 229s > 229s > ## Using weights: 229s > set.seed(123454321) 229s > wt <- runif(nrow(wine)) 229s > fm1 <- clm(rating ~ temp * contact, data=wine, weigths=wt) 229s > nominal_test(fm1) 229s Tests of nominal effects 229s 229s formula: rating ~ temp * contact 229s Df logLik AIC LRT Pr(>Chi) 229s -86.416 186.83 229s temp 3 -84.874 189.75 3.08352 0.3789 229s contact 3 -86.083 192.16 0.66691 0.8810 229s temp:contact 229s > scale_test(fm1) 229s Tests of scale effects 229s 229s formula: rating ~ temp * contact 229s Df logLik AIC LRT Pr(>Chi) 229s -86.416 186.83 229s temp 1 -86.326 188.65 0.18061 0.6709 229s contact 1 -86.300 188.60 0.23252 0.6297 229s temp:contact 3 -86.259 192.52 0.31391 0.9574 229s > 229s > ## No nominal test for judge since that model is not identifiable: 229s > fm1 <- clm(rating ~ judge + temp + contact, data=wine) 229s > nominal_test(fm1) 229s Tests of nominal effects 229s 229s formula: rating ~ judge + temp + contact 229s Df logLik AIC LRT Pr(>Chi) 229s -70.921 169.84 229s judge 229s temp 3 -69.900 173.80 2.04253 0.5636 229s contact 3 -70.708 175.42 0.42612 0.9348 229s > scale_test(fm1) 229s Tests of scale effects 229s 229s formula: rating ~ judge + temp + contact 229s Df logLik AIC LRT Pr(>Chi) 229s -70.921 169.84 229s judge 8 -64.731 173.46 12.3790 0.1351 229s temp 1 -70.897 171.79 0.0474 0.8276 229s contact 1 -70.870 171.74 0.1018 0.7497 229s > fm1 <- clm(rating ~ judge + temp, nominal=~contact, data=wine) 229s > nominal_test(fm1) 229s Tests of nominal effects 229s 229s formula: rating ~ judge + temp 229s nominal: ~contact 229s Df logLik AIC LRT Pr(>Chi) 229s -70.708 175.42 229s judge 229s temp 3 -69.707 179.41 2.0015 0.5721 229s > summary(fm1) 229s formula: rating ~ judge + temp 229s nominal: ~contact 229s data: wine 229s 229s link threshold nobs logLik AIC niter max.grad cond.H 229s logit flexible 72 -70.71 175.42 6(0) 8.07e-08 9.9e+01 229s 229s Coefficients: 229s Estimate Std. Error z value Pr(>|z|) 229s judge2 -3.2395 1.0683 -3.032 0.00243 ** 229s judge3 -0.9556 0.9699 -0.985 0.32452 229s judge4 -2.4613 1.0321 -2.385 0.01709 * 229s judge5 -2.0248 1.0093 -2.006 0.04484 * 229s judge6 -1.6379 0.9770 -1.677 0.09364 . 229s judge7 -5.2222 1.1381 -4.589 4.46e-06 *** 229s judge8 -2.7648 0.9776 -2.828 0.00468 ** 229s judge9 -3.1751 1.0028 -3.166 0.00154 ** 229s tempwarm 3.3309 0.6174 5.395 6.87e-08 *** 229s --- 229s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 229s 229s Threshold coefficients: 229s Estimate Std. Error z value 229s 1|2.(Intercept) -4.1549 0.9897 -4.198 229s 2|3.(Intercept) -0.7354 0.7920 -0.928 229s 3|4.(Intercept) 2.3388 0.8909 2.625 229s 4|5.(Intercept) 3.8873 1.0352 3.755 229s 1|2.contactyes -2.0216 1.3072 -1.547 229s 2|3.contactyes -1.9865 0.6904 -2.877 229s 3|4.contactyes -2.1825 0.7774 -2.807 229s 4|5.contactyes -1.5077 1.0044 -1.501 229s > 229s > ## A continuous variable: 229s > set.seed(123454321) 229s > x <- rnorm(nrow(wine), sd=1) 229s > fm <- clm(rating ~ temp, nominal=~contact * x, data=wine) 229s > nominal_test(fm) 229s Warning message: 229s (1) Hessian is numerically singular: parameters are not uniquely determined 229s In addition: Absolute convergence criterion was met, but relative criterion was not met 229s Tests of nominal effects 229s 229s formula: rating ~ temp 229s nominal: ~contact * x 229s Df logLik AIC LRT Pr(>Chi) 229s -77.858 189.72 229s temp 3 -76.738 193.48 2.24 0.5241 229s > scale_test(fm) 229s Tests of scale effects 229s 229s formula: rating ~ temp 229s nominal: ~contact * x 229s Df logLik AIC LRT Pr(>Chi) 229s -77.858 189.72 229s temp 1 -77.684 191.37 0.34804 0.5552 229s > fm <- clm(rating ~ temp + x, nominal=~contact, data=wine) 229s > nominal_test(fm) 229s Warning message: 229s (1) Hessian is numerically singular: parameters are not uniquely determined 229s In addition: Absolute convergence criterion was met, but relative criterion was not met 229s Tests of nominal effects 229s 229s formula: rating ~ temp + x 229s nominal: ~contact 229s Df logLik AIC LRT Pr(>Chi) 229s -84.949 189.90 229s temp 3 -83.421 192.84 3.0560 0.3831 229s x 3 -84.333 194.67 1.2322 0.7453 229s > scale_test(fm) 229s Tests of scale effects 229s 229s formula: rating ~ temp + x 229s nominal: ~contact 229s Df logLik AIC LRT Pr(>Chi) 229s -84.949 189.90 229s temp 1 -84.737 191.47 0.42504 0.5144 229s x 1 -84.896 191.79 0.10781 0.7426 229s > ## poly: 229s > fm <- clm(rating ~ temp + poly(x, 2), nominal=~contact, data=wine) 229s > nominal_test(fm) 229s Tests of nominal effects 229s 229s formula: rating ~ temp + poly(x, 2) 229s nominal: ~contact 229s Df logLik AIC LRT Pr(>Chi) 229s -84.079 190.16 229s temp 3 -82.694 193.39 2.7693 0.4286 229s poly(x, 2) 6 -80.941 195.88 6.2762 0.3930 229s > scale_test(fm) 229s Tests of scale effects 229s 229s formula: rating ~ temp + poly(x, 2) 229s nominal: ~contact 229s Df logLik AIC LRT Pr(>Chi) 229s -84.079 190.16 229s temp 1 -84.020 192.04 0.11784 0.7314 229s poly(x, 2) 2 -83.314 192.63 1.53017 0.4653 229s > ## another combination: 229s > fm1 <- clm(SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ, 229s + scale=~PROD, 229s + nominal=~ DAY*GENDER, data=soup) 229s > fm1 229s formula: SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ 229s scale: ~PROD 229s nominal: ~DAY * GENDER 229s data: soup 229s 229s link threshold nobs logLik AIC niter max.grad cond.H 229s logit flexible 1847 -2657.84 5375.68 8(2) 3.50e-07 4.0e+03 229s 229s Coefficients: (1 not defined because of singularities) 229s PRODID2 PRODID3 PRODID4 PRODID5 229s 1.0780 1.5090 0.9482 1.4910 229s PRODID6 DAY2 SOUPTYPECanned SOUPTYPEDry-mix 229s 1.8174 NA -0.2337 0.1832 229s SOUPFREQ1-4/month SOUPFREQ<1/month 229s -0.0954 -0.1137 229s 229s log-scale coefficients: 229s PRODTest 229s 0.1427 229s 229s Threshold coefficients: 229s 1|2 2|3 3|4 4|5 5|6 229s (Intercept) -1.65979 -0.75912 -0.36903 0.02374 0.66929 229s DAY2 -0.22291 0.13711 0.16406 0.10279 0.23721 229s GENDERFemale 0.06531 0.06089 -0.01938 -0.13670 -0.01594 229s DAY2:GENDERFemale 0.36194 0.25429 0.25482 0.23375 0.05243 229s > nominal_test(fm1) 230s Tests of nominal effects 230s 230s formula: SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ 230s scale: ~PROD 230s nominal: ~DAY * GENDER 230s Df logLik AIC LRT Pr(>Chi) 230s -2657.8 5375.7 230s PRODID 20 -2644.7 5389.4 26.2387 0.1580707 230s SOUPTYPE 8 -2654.0 5384.1 7.5969 0.4738067 230s SOUPFREQ 8 -2644.6 5365.1 26.5587 0.0008423 *** 230s PROD 4 -2654.7 5377.5 6.2011 0.1846258 230s --- 230s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 230s > scale_test(fm1) 230s Tests of scale effects 230s 230s formula: SURENESS ~ PRODID + DAY + SOUPTYPE + SOUPFREQ 230s scale: ~PROD 230s nominal: ~DAY * GENDER 230s Df logLik AIC LRT Pr(>Chi) 230s -2657.8 5375.7 230s PRODID 4 -2657.3 5382.5 1.1526 0.885842 230s DAY 1 -2655.9 5373.8 3.8544 0.049616 * 230s SOUPTYPE 2 -2657.6 5379.1 0.5416 0.762771 230s SOUPFREQ 2 -2652.7 5369.3 10.3447 0.005671 ** 230s --- 230s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 230s > 230s > ################################# 230s > 230s > 230s BEGIN TEST ranef.loading.R 230s 230s R version 4.4.3 (2025-02-28) -- "Trophy Case" 230s Copyright (C) 2025 The R Foundation for Statistical Computing 230s Platform: x86_64-pc-linux-gnu 230s 230s R is free software and comes with ABSOLUTELY NO WARRANTY. 230s You are welcome to redistribute it under certain conditions. 230s Type 'license()' or 'licence()' for distribution details. 230s 230s R is a collaborative project with many contributors. 230s Type 'contributors()' for more information and 230s 'citation()' on how to cite R or R packages in publications. 230s 230s Type 'demo()' for some demos, 'help()' for on-line help, or 230s 'help.start()' for an HTML browser interface to help. 230s Type 'q()' to quit R. 230s 230s > # check that ranef and VarCorr work even after loading ordinal: 230s > library(lme4) 230s Loading required package: Matrix 231s > fm1 <- lmer(Reaction ~ Days + (Days | Subject), data=sleepstudy) 231s > ranef(fm1) 231s $Subject 231s (Intercept) Days 231s 308 2.2585509 9.1989758 231s 309 -40.3987381 -8.6196806 231s 310 -38.9604090 -5.4488565 231s 330 23.6906196 -4.8143503 231s 331 22.2603126 -3.0699116 231s 332 9.0395679 -0.2721770 231s 333 16.8405086 -0.2236361 231s 334 -7.2326151 1.0745816 231s 335 -0.3336684 -10.7521652 231s 337 34.8904868 8.6282652 231s 349 -25.2102286 1.1734322 231s 350 -13.0700342 6.6142178 231s 351 4.5778642 -3.0152621 231s 352 20.8636782 3.5360011 231s 369 3.2754656 0.8722149 231s 370 -25.6129993 4.8224850 231s 371 0.8070461 -0.9881562 231s 372 12.3145921 1.2840221 231s 231s with conditional variances for “Subject” 231s > VarCorr(fm1) 231s Groups Name Std.Dev. Corr 231s Subject (Intercept) 24.7407 231s Days 5.9221 0.066 231s Residual 25.5918 231s > library(ordinal) 231s > ranef(fm1) 232s $Subject 232s (Intercept) Days 232s 308 2.2585509 9.1989758 232s 309 -40.3987381 -8.6196806 232s 310 -38.9604090 -5.4488565 232s 330 23.6906196 -4.8143503 232s 331 22.2603126 -3.0699116 232s 332 9.0395679 -0.2721770 232s 333 16.8405086 -0.2236361 232s 334 -7.2326151 1.0745816 232s 335 -0.3336684 -10.7521652 232s 337 34.8904868 8.6282652 232s 349 -25.2102286 1.1734322 232s 350 -13.0700342 6.6142178 232s 351 4.5778642 -3.0152621 232s 352 20.8636782 3.5360011 232s 369 3.2754656 0.8722149 232s 370 -25.6129993 4.8224850 232s 371 0.8070461 -0.9881562 232s 372 12.3145921 1.2840221 232s 232s with conditional variances for “Subject” 232s > VarCorr(fm1) 232s Groups Name Std.Dev. Corr 232s Subject (Intercept) 24.7407 232s Days 5.9221 0.066 232s Residual 25.5918 232s > 232s BEGIN TEST test-all.R 232s 232s R version 4.4.3 (2025-02-28) -- "Trophy Case" 232s Copyright (C) 2025 The R Foundation for Statistical Computing 232s Platform: x86_64-pc-linux-gnu 232s 232s R is free software and comes with ABSOLUTELY NO WARRANTY. 232s You are welcome to redistribute it under certain conditions. 232s Type 'license()' or 'licence()' for distribution details. 232s 232s R is a collaborative project with many contributors. 232s Type 'contributors()' for more information and 232s 'citation()' on how to cite R or R packages in publications. 232s 232s Type 'demo()' for some demos, 'help()' for on-line help, or 232s 'help.start()' for an HTML browser interface to help. 232s Type 'q()' to quit R. 232s 232s > 232s > if(require(testthat) && require(ordinal)) { 232s + test_check("ordinal") 232s + } 232s Loading required package: testthat 232s Loading required package: ordinal 237s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 81 ] 237s > 237s BEGIN TEST test.clm.Theta.R 237s 237s R version 4.4.3 (2025-02-28) -- "Trophy Case" 237s Copyright (C) 2025 The R Foundation for Statistical Computing 237s Platform: x86_64-pc-linux-gnu 237s 237s R is free software and comes with ABSOLUTELY NO WARRANTY. 237s You are welcome to redistribute it under certain conditions. 237s Type 'license()' or 'licence()' for distribution details. 237s 237s R is a collaborative project with many contributors. 237s Type 'contributors()' for more information and 237s 'citation()' on how to cite R or R packages in publications. 237s 237s Type 'demo()' for some demos, 'help()' for on-line help, or 237s 'help.start()' for an HTML browser interface to help. 237s Type 'q()' to quit R. 237s 237s > library(ordinal) 238s > 238s > ################################# 238s > ## 1 categorical variable in nominal: 238s > fm <- clm(rating ~ temp, nominal=~contact, data=wine) 238s Warning message: 238s (1) Hessian is numerically singular: parameters are not uniquely determined 238s In addition: Absolute convergence criterion was met, but relative criterion was not met 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.323043 1.2464435 3.550044 4.660247 238s 2 yes -2.938103 -0.2651238 1.875288 3.609624 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.323043 1.246444 3.550044 4.660247 238s contactyes -1.615059 -1.511567 -1.674756 -1.050623 238s > ## Threshold effects: 238s > fm <- clm(rating ~ temp, nominal=~contact, data=wine, 238s + threshold="symmetric") 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.054279 1.083892 3.383980 5.522152 238s 2 yes -2.360683 -0.356889 1.753317 3.757111 238s > fm$alpha.mat 238s central.1 central.2 spacing.1 238s (Intercept) 1.083892 3.383980 2.1381713 238s contactyes -1.440781 -1.630663 -0.1343777 238s > fm <- clm(rating ~ temp, nominal=~contact, data=wine, 238s + threshold="equidistant") 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.089140 1.1176064 3.324353 5.531099 238s 2 yes -2.386361 -0.3365063 1.713348 3.763202 238s > fm$alpha.mat 238s threshold.1 spacing 238s (Intercept) -1.08914 2.2067465 238s contactyes -1.29722 -0.1568922 238s > ## Singular fit is still ok (with a warning, though) 238s > fm <- clm(rating ~ contact, nominal=~temp, data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.265638 1.104045 3.765661 24.89643 238s tempwarm -21.095417 -2.153024 -2.873317 -22.55000 238s > fm$Theta 238s temp 1|2 2|3 3|4 4|5 238s 1 cold -1.265638 1.104045 3.7656606 24.896432 238s 2 warm -22.361055 -1.048979 0.8923431 2.346436 238s > 238s > ################################# 238s > ## 1 continuous variable: 238s > set.seed(123) 238s > x <- rnorm(nrow(wine), sd=1) 238s > fm <- clm(rating ~ temp, nominal=~ x, data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.93392115 0.4251062 2.4798775 3.9190335 238s x 0.09463825 0.3805713 0.4261607 0.3809099 238s > fm$Theta 238s 1|2 2|3 3|4 4|5 238s 1 -1.933921 0.4251062 2.479878 3.919034 238s > fm <- clm(rating ~ temp, nominal=~ poly(x, 2), data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.9310988 0.4469436 2.517523 4.094448 238s poly(x, 2)1 0.8763914 3.2908002 3.471603 4.422045 238s poly(x, 2)2 -0.3826811 0.2518184 -2.064209 5.810095 238s > fm$Theta 238s 1|2 2|3 3|4 4|5 238s 1 -1.931099 0.4469436 2.517523 4.094448 238s > 238s > ################################# 238s > ## 1 categorical + 1 continuous variable: 238s > set.seed(123) 238s > x <- rnorm(nrow(wine), sd=1) 238s > fm <- clm(rating ~ temp, nominal=~contact + x, data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.279484 1.2782515 3.612766 4.7496630 238s contactyes -1.770377 -1.6715296 -1.647335 -0.9575417 238s x 0.300792 0.5330593 0.351517 0.3320371 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.279484 1.2782515 3.612766 4.749663 238s 2 yes -3.049860 -0.3932781 1.965431 3.792121 238s > fm <- clm(rating ~ temp, nominal=~contact + x, data=wine, 238s + threshold="symmetric") 238s > fm$alpha.mat 238s central.1 central.2 spacing.1 238s (Intercept) 1.1195535 3.4384752 2.134429723 238s contactyes -1.5864032 -1.5904314 -0.007568099 238s x 0.5069573 0.3485632 0.137951085 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.014876 1.1195535 3.438475 5.572905 238s 2 yes -2.593711 -0.4668497 1.848044 3.974905 238s > ################################# 238s > ### NOTE: To get the by-threshold nominal effects of continuous terms 238s > ## use: 238s > with(fm, t(apply(alpha.mat, 1, function(th) tJac %*% th))) 238s [,1] [,2] [,3] [,4] 238s (Intercept) -1.0148763 1.1195535 3.4384752 5.5729049 238s contactyes -1.5788351 -1.5864032 -1.5904314 -1.5979995 238s x 0.3690062 0.5069573 0.3485632 0.4865143 238s > ################################# 238s > ## Interactions: 238s > fm <- clm(rating ~ temp, nominal=~contact:x, data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.9577944 0.5997213 2.6863244 4.1510613 238s contactno:x 0.1127629 0.7818026 0.4423216 0.9364319 238s contactyes:x 0.2129232 -0.2720801 0.3848893 0.1730418 238s > fm$Theta 238s 1|2 2|3 3|4 4|5 238s 1 -1.957794 0.5997213 2.686324 4.151061 238s > fm <- clm(rating ~ temp, nominal=~contact+x+contact:x, data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.3000385 1.4056290 3.8340494 5.195521 238s contactyes -2.2801110 -1.5685386 -1.7308097 -1.318630 238s x 0.1790630 0.8754972 0.5140440 1.061857 238s contactyes:x 0.7541913 -0.8829449 -0.2203363 -1.055090 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.300039 1.4056290 3.834049 5.195521 238s 2 yes -3.580150 -0.1629096 2.103240 3.876891 238s > fm <- clm(rating ~ temp, nominal=~contact*x, data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.3000385 1.4056290 3.8340494 5.195521 238s contactyes -2.2801110 -1.5685386 -1.7308097 -1.318630 238s x 0.1790630 0.8754972 0.5140440 1.061857 238s contactyes:x 0.7541913 -0.8829449 -0.2203363 -1.055090 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.300039 1.4056290 3.834049 5.195521 238s 2 yes -3.580150 -0.1629096 2.103240 3.876891 238s > ## polynomial terms: 238s > fm <- clm(rating ~ temp, nominal=~contact + poly(x, 2), data=wine) 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.2704762 1.3058436 3.635351 4.984803 238s contactyes -1.7725959 -1.6863567 -1.668402 -1.045016 238s poly(x, 2)1 2.4660191 4.4257770 3.395876 4.572499 238s poly(x, 2)2 -0.5079931 -0.4326472 -2.815490 5.853814 238s > fm$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.270476 1.3058436 3.635351 4.984803 238s 2 yes -3.043072 -0.3805131 1.966949 3.939787 238s > ## logical variables: (treated like numeric variables) 238s > wine$Con <- as.character(wine$contact) == "yes" 238s > fm <- clm(rating ~ temp, nominal=~Con, data=wine) 238s > fm$Theta 238s 1|2 2|3 3|4 4|5 238s 1 -1.323043 1.246444 3.550044 4.660247 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.323043 1.246444 3.550044 4.660247 238s ConTRUE -1.615059 -1.511567 -1.674756 -1.050623 238s > wine$Con.num <- 1 * wine$Con 238s > fm <- clm(rating ~ temp, nominal=~Con.num, data=wine) 238s > fm$Theta 238s 1|2 2|3 3|4 4|5 238s 1 -1.323043 1.246444 3.550044 4.660247 238s > fm$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.323043 1.246444 3.550044 4.660247 238s Con.num -1.615059 -1.511567 -1.674756 -1.050623 238s > ################################# 238s > ## Two continuous variables: 238s > set.seed(321) 238s > y <- rnorm(nrow(wine), sd=1) 238s > fm1 <- clm(rating ~ temp, nominal=~y + x, data=wine) 238s > fm1$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -2.0361734 0.4221202 2.4970718 3.92796873 238s y 0.4687950 0.1396038 0.3125431 0.08012751 238s x 0.1283933 0.3903469 0.4322374 0.37584062 238s > fm1$Theta 238s 1|2 2|3 3|4 4|5 238s 1 -2.036173 0.4221202 2.497072 3.927969 238s > ## summary(fm1) 238s > 238s > ################################# 238s > ## 1 categorical + 2 continuous variables: 238s > fm1 <- clm(rating ~ temp, nominal=~y + contact + x, data=wine) 238s > fm1$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.3789903 1.2645381 3.5778844 4.76356985 238s y 0.4385042 0.1049073 0.2439721 -0.01655843 238s contactyes -1.7688345 -1.6608152 -1.5801690 -0.98076349 238s x 0.3414184 0.5436276 0.3683201 0.33263316 238s > fm1$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.378990 1.2645381 3.577884 4.763570 238s 2 yes -3.147825 -0.3962771 1.997715 3.782806 238s > 238s > fm1 <- clm(rating ~ temp, nominal=~contact + x + contact:x + y, 238s + data=wine) 238s > summary(fm1) 238s formula: rating ~ temp 238s nominal: ~contact + x + contact:x + y 238s data: wine 238s 238s link threshold nobs logLik AIC niter max.grad cond.H 238s logit flexible 72 -81.86 205.72 7(0) 6.30e-12 9.3e+01 238s 238s Coefficients: 238s Estimate Std. Error z value Pr(>|z|) 238s tempwarm 2.8541 0.6159 4.634 3.58e-06 *** 238s --- 238s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 238s 238s Threshold coefficients: 238s Estimate Std. Error z value 238s 1|2.(Intercept) -1.40166 0.63306 -2.214 238s 2|3.(Intercept) 1.38723 0.49672 2.793 238s 3|4.(Intercept) 3.78725 0.71352 5.308 238s 4|5.(Intercept) 5.19478 1.07162 4.848 238s 1|2.contactyes -2.25974 1.68593 -1.340 238s 2|3.contactyes -1.54343 0.62658 -2.463 238s 3|4.contactyes -1.65472 0.68161 -2.428 238s 4|5.contactyes -1.34417 1.10192 -1.220 238s 1|2.x 0.21217 0.60781 0.349 238s 2|3.x 0.88433 0.41592 2.126 238s 3|4.x 0.47072 0.57857 0.814 238s 4|5.x 0.98582 0.94345 1.045 238s 1|2.y 0.41959 0.59889 0.701 238s 2|3.y 0.08377 0.27912 0.300 238s 3|4.y 0.27724 0.33118 0.837 238s 4|5.y -0.03370 0.59652 -0.056 238s 1|2.contactyes:x 0.71850 1.19479 0.601 238s 2|3.contactyes:x -0.89167 0.68974 -1.293 238s 3|4.contactyes:x -0.10843 0.74237 -0.146 238s 4|5.contactyes:x -0.98243 1.06343 -0.924 238s > fm1$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.401661 1.3872281 3.787248 5.194782 238s 2 yes -3.661402 -0.1562067 2.132530 3.850615 238s > fm1$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.4016606 1.38722808 3.7872478 5.19478152 238s contactyes -2.2597419 -1.54343480 -1.6547177 -1.34416691 238s x 0.2121750 0.88432858 0.4707237 0.98581604 238s y 0.4195947 0.08377343 0.2772447 -0.03369796 238s contactyes:x 0.7184952 -0.89166532 -0.1084271 -0.98242663 238s > fm1 <- clm(rating ~ temp, nominal=~contact*x + y, data=wine) 238s > fm1$Theta 238s contact 1|2 2|3 3|4 4|5 238s 1 no -1.401661 1.3872281 3.787248 5.194782 238s 2 yes -3.661402 -0.1562067 2.132530 3.850615 238s > fm1$alpha.mat 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.4016606 1.38722808 3.7872478 5.19478152 238s contactyes -2.2597419 -1.54343480 -1.6547177 -1.34416691 238s x 0.2121750 0.88432858 0.4707237 0.98581604 238s y 0.4195947 0.08377343 0.2772447 -0.03369796 238s contactyes:x 0.7184952 -0.89166532 -0.1084271 -0.98242663 238s > t(fm1$alpha.mat) 238s (Intercept) contactyes x y contactyes:x 238s 1|2 -1.401661 -2.259742 0.2121750 0.41959467 0.7184952 238s 2|3 1.387228 -1.543435 0.8843286 0.08377343 -0.8916653 238s 3|4 3.787248 -1.654718 0.4707237 0.27724473 -0.1084271 238s 4|5 5.194782 -1.344167 0.9858160 -0.03369796 -0.9824266 238s > fm1 238s formula: rating ~ temp 238s nominal: ~contact * x + y 238s data: wine 238s 238s link threshold nobs logLik AIC niter max.grad cond.H 238s logit flexible 72 -81.86 205.72 7(0) 6.30e-12 9.3e+01 238s 238s Coefficients: 238s tempwarm 238s 2.854 238s 238s Threshold coefficients: 238s 1|2 2|3 3|4 4|5 238s (Intercept) -1.40166 1.38723 3.78725 5.19478 238s contactyes -2.25974 -1.54343 -1.65472 -1.34417 238s x 0.21217 0.88433 0.47072 0.98582 238s y 0.41959 0.08377 0.27724 -0.03370 238s contactyes:x 0.71850 -0.89167 -0.10843 -0.98243 238s > 238s > ################################# 238s > ## ordered factors (behaves like numerical variables): 238s > data(soup, package="ordinal") 238s > fm2 <- clm(SURENESS ~ 1, nominal=~PRODID + DAY, data=soup) 238s > fm2$Theta 238s PRODID DAY 1|2 2|3 3|4 4|5 5|6 238s 1 1 1 -1.541481 -0.5738506 -0.21399538 0.04222703 0.75684062 238s 2 2 1 -2.260759 -1.5442697 -1.21890789 -0.91689299 -0.24659733 238s 3 3 1 -2.662588 -1.8500284 -1.67612929 -1.15745279 -0.65265582 238s 4 4 1 -2.230317 -1.3875834 -1.10527201 -0.70760465 -0.16454916 238s 5 5 1 -2.291960 -1.8870049 -1.51852627 -1.32708454 -0.64222204 238s 6 6 1 -2.765844 -2.1222058 -1.93080891 -1.76177831 -0.87239437 238s 7 1 2 -1.497366 -0.2765643 0.08617449 0.27652240 0.97863135 238s 8 2 2 -2.216645 -1.2469835 -0.91873802 -0.68259762 -0.02480661 238s 9 3 2 -2.618473 -1.5527421 -1.37595942 -0.92315742 -0.43086509 238s 10 4 2 -2.186203 -1.0902972 -0.80510215 -0.47330927 0.05724157 238s 11 5 2 -2.247845 -1.5897187 -1.21835640 -1.09278917 -0.42043131 238s 12 6 2 -2.721729 -1.8249196 -1.63063905 -1.52748294 -0.65060365 238s > fm2$alpha.mat 238s 1|2 2|3 3|4 4|5 5|6 238s (Intercept) -1.54148084 -0.5738506 -0.2139954 0.04222703 0.7568406 238s PRODID2 -0.71927809 -0.9704192 -1.0049125 -0.95912001 -1.0034380 238s PRODID3 -1.12110698 -1.2761778 -1.4621339 -1.19967981 -1.4094964 238s PRODID4 -0.68883656 -0.8137329 -0.8912766 -0.74983167 -0.9213898 238s PRODID5 -0.75047874 -1.3131544 -1.3045309 -1.36931157 -1.3990627 238s PRODID6 -1.22436292 -1.5483553 -1.7168135 -1.80400534 -1.6292350 238s DAY2 0.04411439 0.2972862 0.3001699 0.23429537 0.2217907 238s > prodid <- factor(soup$PRODID, ordered=TRUE) 238s > fm2 <- clm(SURENESS ~ 1, nominal=~prodid + DAY, data=soup) 238s > fm2$alpha.mat 238s 1|2 2|3 3|4 4|5 5|6 238s (Intercept) -2.29215806 -1.5608238 -1.2772733 -0.9714310 -0.3035963 238s prodid.L -0.69121817 -0.9929406 -1.0651956 -1.1714141 -1.0571728 238s prodid.Q 0.28234300 0.3165731 0.3424949 0.1207237 0.3905959 239s prodid.C -0.56889235 -0.5360906 -0.6536897 -0.5924148 -0.5462885 239s prodid^4 -0.08220340 0.2121409 0.0953785 0.2423256 0.1732012 239s prodid^5 0.20500444 0.3017272 0.3458281 0.2989342 0.3294562 239s DAY2 0.04411439 0.2972862 0.3001699 0.2342954 0.2217907 239s > fm2$Theta 239s DAY 1|2 2|3 3|4 4|5 5|6 239s 1 1 -2.292158 -1.560824 -1.2772733 -0.9714310 -0.30359635 239s 2 2 -2.248044 -1.263538 -0.9771034 -0.7371357 -0.08180562 239s > fm2 <- clm(SURENESS ~ 1, nominal=~prodid, data=soup) 239s > fm2$alpha.mat 239s 1|2 2|3 3|4 4|5 5|6 239s (Intercept) -2.2615449 -1.4231189 -1.13844940 -0.8610163 -0.20025662 239s prodid.L -0.6802192 -1.0171675 -1.08713192 -1.1713363 -1.05578526 239s prodid.Q 0.2551357 0.3521163 0.37511177 0.1651463 0.43182970 239s prodid.C -0.6064464 -0.5635065 -0.68182671 -0.6050149 -0.55490977 239s prodid^4 -0.1115795 0.1036958 -0.01443457 0.1577696 0.09355651 239s prodid^5 0.2349647 0.4222560 0.46856405 0.3867234 0.41280490 239s > fm2$Theta 239s 1|2 2|3 3|4 4|5 5|6 239s 1 -2.261545 -1.423119 -1.138449 -0.8610163 -0.2002566 239s > ################################# 239s > ## Aliased Coefficients: 239s > ## 239s > ## Example where the interaction in the nominal effects is aliased (by 239s > ## design). Here the two Theta matrices coincide. The alpha.mat 239s > ## matrices are similar except one has an extra row with NAs: 239s > soup2 <- soup 239s > levels(soup2$DAY) 239s [1] "1" "2" 239s > levels(soup2$GENDER) 239s [1] "Male" "Female" 239s > xx <- with(soup2, DAY == "2" & GENDER == "Female") 239s > ## Model with additive nominal effects: 239s > fm8 <- clm(SURENESS ~ PRODID, nominal= ~ DAY + GENDER, data=soup2, subset=!xx) 239s > fm8$alpha.mat 239s 1|2 2|3 3|4 4|5 5|6 239s (Intercept) -1.5296912 -0.68765358 -0.3255117394 0.03773041 0.629325973 239s DAY2 -0.2553049 0.08584421 0.1101987830 0.05149732 0.168514829 239s GENDERFemale 0.0790841 0.07464904 -0.0001589362 -0.11045608 -0.005418789 239s > fm8$Theta 239s DAY GENDER 1|2 2|3 3|4 4|5 5|6 239s 1 1 Male -1.529691 -0.6876536 -0.3255117 0.03773041 0.6293260 239s 2 2 Male -1.784996 -0.6018094 -0.2153130 0.08922773 0.7978408 239s 3 1 Female -1.450607 -0.6130045 -0.3256707 -0.07272568 0.6239072 239s 4 2 Female -1.705912 -0.5271603 -0.2154719 -0.02122835 0.7924220 239s > ## Model with non-additive, but aliased nominal effects: 239s > fm9 <- clm(SURENESS ~ PRODID, nominal= ~ DAY * GENDER, data=soup2, subset=!xx) 239s > fm9$alpha.mat 239s 1|2 2|3 3|4 4|5 5|6 239s (Intercept) -1.5296912 -0.68765358 -0.3255117394 0.03773041 0.629325973 239s DAY2 -0.2553049 0.08584421 0.1101987830 0.05149732 0.168514829 239s GENDERFemale 0.0790841 0.07464904 -0.0001589362 -0.11045608 -0.005418789 239s DAY2:GENDERFemale NA NA NA NA NA 239s > fm9$Theta 239s DAY GENDER 1|2 2|3 3|4 4|5 5|6 239s 1 1 Male -1.529691 -0.6876536 -0.3255117 0.03773041 0.6293260 239s 2 2 Male -1.784996 -0.6018094 -0.2153130 0.08922773 0.7978408 239s 3 1 Female -1.450607 -0.6130045 -0.3256707 -0.07272568 0.6239072 239s 4 2 Female -1.705912 -0.5271603 -0.2154719 -0.02122835 0.7924220 239s > 239s > stopEqual <- function(x, y, ca=FALSE) 239s + stopifnot(isTRUE(all.equal(x, y, check.attributes=ca))) 239s > 239s > stopEqual(fm8$alpha.mat, fm9$alpha.mat[1:3, ]) 239s > stopEqual(fm8$Theta, fm9$Theta) 239s > stopEqual(logLik(fm8), logLik(fm9)) 239s > 239s > ################################# 239s > ## Weights: 239s > set.seed(12345) 239s > wts <- runif(nrow(soup)) 239s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE + DAY, data=soup, weights=wts) 239s > fm2$Theta 239s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 239s 1 Self-made 1 -1.957136 -1.2051740 -0.8829317 -0.6651699 -0.03270025 239s 2 Canned 1 -1.665918 -0.9408556 -0.6818962 -0.4277315 0.14356406 239s 3 Dry-mix 1 -2.180024 -1.2221288 -1.1502087 -0.8113657 -0.24840514 239s 4 Self-made 2 -1.988269 -0.9456030 -0.5614139 -0.3852570 0.23978932 239s 5 Canned 2 -1.697051 -0.6812846 -0.3603783 -0.1478186 0.41605363 239s 6 Dry-mix 2 -2.211157 -0.9625577 -0.8286909 -0.5314528 0.02408443 239s > 239s > ## Offset (correctly gives and error) 239s > fm2 <- try(clm(SURENESS ~ 1, nominal=~SOUPTYPE + DAY + offset(wts), 239s + data=soup), silent=TRUE) 239s > stopifnot(inherits(fm2, "try-error")) 239s > 239s > ################################# 239s > ### Other (misc) examples: 239s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE + DAY, data=soup) 239s > fm2$Theta 239s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 239s 1 Self-made 1 -2.040111 -1.2615146 -0.9302684 -0.6740629 -0.05003069 239s 2 Canned 1 -1.816274 -1.0347697 -0.7305192 -0.4563265 0.15972072 239s 3 Dry-mix 1 -2.313198 -1.3029029 -1.1328903 -0.8076982 -0.23529457 239s 4 Self-made 2 -1.956698 -0.9371883 -0.5968669 -0.4131354 0.21403949 239s 5 Canned 2 -1.732861 -0.7104435 -0.3971177 -0.1953990 0.42379090 239s 6 Dry-mix 2 -2.229785 -0.9785767 -0.7994888 -0.5467707 0.02877561 239s > fm2 239s formula: SURENESS ~ 1 239s nominal: ~SOUPTYPE + DAY 239s data: soup 239s 239s link threshold nobs logLik AIC niter max.grad cond.H 239s logit flexible 1847 -2758.02 5556.03 6(2) 1.77e-11 8.7e+02 239s 239s Threshold coefficients: 239s 1|2 2|3 3|4 4|5 5|6 239s (Intercept) -2.04011 -1.26151 -0.93027 -0.67406 -0.05003 239s SOUPTYPECanned 0.22384 0.22674 0.19975 0.21774 0.20975 239s SOUPTYPEDry-mix -0.27309 -0.04139 -0.20262 -0.13364 -0.18526 239s DAY2 0.08341 0.32433 0.33340 0.26093 0.26407 239s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE * DAY, data=soup) 239s > fm2$Theta 239s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 239s 1 Self-made 1 -2.062794 -1.3083328 -0.9935434 -0.7187896 -0.05107493 239s 2 Canned 1 -1.757074 -0.9398212 -0.6286087 -0.3721287 0.15415068 239s 3 Dry-mix 1 -2.369525 -1.3618033 -1.1700713 -0.8661663 -0.23795864 239s 4 Self-made 2 -1.945910 -0.9005649 -0.5459555 -0.3731219 0.21392690 239s 5 Canned 2 -1.775759 -0.7985077 -0.4924765 -0.2776317 0.43428555 239s 6 Dry-mix 2 -2.182299 -0.9257695 -0.7649729 -0.4964369 0.02702867 239s > fm2 239s formula: SURENESS ~ 1 239s nominal: ~SOUPTYPE * DAY 239s data: soup 239s 239s link threshold nobs logLik AIC niter max.grad cond.H 239s logit flexible 1847 -2755.60 5571.21 6(2) 1.76e-11 4.9e+03 239s 239s Threshold coefficients: 239s 1|2 2|3 3|4 4|5 5|6 239s (Intercept) -2.063e+00 -1.308e+00 -9.935e-01 -7.188e-01 -5.107e-02 239s SOUPTYPECanned 3.057e-01 3.685e-01 3.649e-01 3.467e-01 2.052e-01 239s SOUPTYPEDry-mix -3.067e-01 -5.347e-02 -1.765e-01 -1.474e-01 -1.869e-01 239s DAY2 1.169e-01 4.078e-01 4.476e-01 3.457e-01 2.650e-01 239s SOUPTYPECanned:DAY2 -1.356e-01 -2.665e-01 -3.115e-01 -2.512e-01 1.513e-02 239s SOUPTYPEDry-mix:DAY2 7.034e-02 2.827e-02 -4.249e-02 2.406e-02 -1.452e-05 239s > fm2$alpha.mat 239s 1|2 2|3 3|4 4|5 239s (Intercept) -2.06279431 -1.30833282 -0.99354336 -0.71878961 239s SOUPTYPECanned 0.30572040 0.36851159 0.36493470 0.34666092 239s SOUPTYPEDry-mix -0.30673027 -0.05347052 -0.17652789 -0.14737673 239s DAY2 0.11688416 0.40776793 0.44758789 0.34566775 239s SOUPTYPECanned:DAY2 -0.13556938 -0.26645440 -0.31145572 -0.25117080 239s SOUPTYPEDry-mix:DAY2 0.07034149 0.02826594 -0.04248955 0.02406171 239s 5|6 239s (Intercept) -5.107493e-02 239s SOUPTYPECanned 2.052256e-01 239s SOUPTYPEDry-mix -1.868837e-01 239s DAY2 2.650018e-01 239s SOUPTYPECanned:DAY2 1.513304e-02 239s SOUPTYPEDry-mix:DAY2 -1.451666e-05 239s > fm2 <- clm(SURENESS ~ 1, nominal=~SOUPTYPE * DAY, data=soup, 239s + threshold="symmetric") 239s > fm2$Theta 239s SOUPTYPE DAY 1|2 2|3 3|4 4|5 5|6 239s 1 Self-made 1 -2.023473 -1.3261580 -1.0328445 -0.7395310 -0.04221610 239s 2 Canned 1 -1.650803 -1.0121961 -0.7301243 -0.4480525 0.19055466 239s 3 Dry-mix 1 -2.214507 -1.4643357 -1.2132431 -0.9621504 -0.21197912 239s 4 Self-made 2 -1.757994 -1.0009894 -0.7422397 -0.4834900 0.27351461 239s 5 Canned 2 -1.673970 -0.8581393 -0.5997040 -0.3412687 0.47456211 239s 6 Dry-mix 2 -1.899340 -1.1167968 -0.9013722 -0.6859476 0.09659551 239s > fm2$alpha.mat 239s central spacing.1 spacing.2 239s (Intercept) -1.03284450 0.293313471 0.99062841 239s SOUPTYPECanned 0.30272022 -0.011241697 -0.06994946 239s SOUPTYPEDry-mix -0.18039855 -0.042220836 0.01063552 239s DAY2 0.29060480 -0.034563797 0.02512591 239s SOUPTYPECanned:DAY2 -0.16018453 0.010927306 0.12846128 239s SOUPTYPEDry-mix:DAY2 0.02126607 -0.001104241 -0.02842214 239s > 239s > ################################# 239s > ### Check correctness of Theta matrix when intercept is removed in 239s > ### nominal formula: 239s > ### December 25th 2014, RHBC 239s > fm1 <- clm(rating ~ temp, nominal=~contact-1, data=wine) 239s > fm2 <- clm(rating ~ temp, nominal=~contact, data=wine) 239s Warning message: 239s an intercept is needed and assumed in 'nominal' 239s > stopifnot(isTRUE(all.equal(fm1$Theta, fm2$Theta))) 239s > stopifnot(isTRUE(all.equal(fm1$logLik, fm2$logLik))) 239s > wine2 <- wine 239s > wine2$contact <- relevel(wine2$contact, "yes") 239s > fm3 <- clm(rating ~ temp, nominal=~contact, data=wine2) 239s > stopifnot(isTRUE(all.equal(coef(fm1, na.rm=TRUE), coef(fm3)))) 239s > ################################# 239s > 239s > 239s BEGIN TEST test.clm.convergence.R 239s 239s R version 4.4.3 (2025-02-28) -- "Trophy Case" 239s Copyright (C) 2025 The R Foundation for Statistical Computing 239s Platform: x86_64-pc-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > library(ordinal) 240s > 240s > 240s > ## Testing that errors in chol() are caught soon enough: 240s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 240s > wine2 <- subset(wine, subset=(!1:nrow(wine) %in% cy)) 240s > wine2[c(9, 15, 46), "rating"] <- NA 240s > fm1 <- clm(rating ~ temp, scale=~contact, nominal=~contact, 240s + data=wine2) 240s Warning message: 240s (1) Hessian is numerically singular: parameters are not uniquely determined 240s In addition: Absolute convergence criterion was met, but relative criterion was not met 240s > fm1 <- try(clm(rating ~ temp, scale=~contact, nominal=~contact, 240s + data=wine2, control=list(gradTol=1e-12)), silent=TRUE) 240s Warning message: 240s (1) Hessian is numerically singular: parameters are not uniquely determined 240s In addition: Absolute convergence criterion was met, but relative criterion was not met 240s > fm2 <- try(clm(rating ~ temp, scale=~contact, nominal=~contact, 240s + data=wine2, control=list(gradTol=1e-15)), silent=TRUE) 240s > ## These gave errors in version 2014.11-12. 240s > stopifnot(!inherits(fm1, "try-error")) 240s > stopifnot(!inherits(fm2, "try-error")) 240s > summary(fm1) 240s Warning message: 240s (-1) Model failed to converge with max|grad| = 1.11481e-07 (tol = 1e-15) 240s In addition: iteration limit reached 240s formula: rating ~ temp 240s scale: ~contact 240s nominal: ~contact 240s data: wine2 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 51 -60.44 140.87 63(39) 1.51e-13 -2.1e+16 240s 240s Coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s tempwarm 2.306 NA NA NA 240s 240s log-scale coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s contactyes -0.07119 NA NA NA 240s 240s Threshold coefficients: 240s Estimate Std. Error z value 240s 1|2.(Intercept) -1.354 NA NA 240s 2|3.(Intercept) 1.092 NA NA 240s 3|4.(Intercept) 3.469 NA NA 240s 4|5.(Intercept) 5.066 NA NA 240s 1|2.contactyes -30.684 NA NA 240s 2|3.contactyes -1.425 NA NA 240s 3|4.contactyes -1.808 NA NA 240s 4|5.contactyes -1.870 NA NA 240s (3 observations deleted due to missingness) 240s > summary(fm2) 240s formula: rating ~ temp 240s scale: ~contact 240s nominal: ~contact 240s data: wine2 240s 240s link threshold nobs logLik AIC niter max.grad cond.H 240s logit flexible 51 -60.44 140.87 111(86) 1.11e-07 1.8e+17 240s 240s Coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s tempwarm 2.3060 0.7713 2.99 0.00279 ** 240s --- 240s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 240s 240s log-scale coefficients: 240s Estimate Std. Error z value Pr(>|z|) 240s contactyes -0.07126 2995.02357 0 1 240s 240s Threshold coefficients: 240s Estimate Std. Error z value 240s 1|2.(Intercept) -1.354e+00 5.707e-01 -2.373 240s 2|3.(Intercept) 1.092e+00 5.251e-01 2.080 240s 3|4.(Intercept) 3.469e+00 7.982e-01 4.346 240s 4|5.(Intercept) 5.066e+00 1.193e+00 4.246 240s 1|2.contactyes -3.822e+01 1.282e+09 0.000 240s 2|3.contactyes -1.425e+00 7.902e+03 0.000 240s 3|4.contactyes -1.808e+00 1.933e+03 -0.001 240s 4|5.contactyes -1.870e+00 2.665e+03 -0.001 240s (3 observations deleted due to missingness) 240s > 240s > ## Error in convergence.clm() due to bad evaluation of model 240s > ## environment with update(object, doFit=FALSE): 240s > wine3 <- wine 240s > set.seed(1234) 240s > wts <- runif(nrow(wine3), 0, 2) 240s > fm3 <- clm(rating ~ temp + contact, data=wine3, 240s + weights=wts) 240s > c0 <- convergence(fm3) 240s > set.seed(1234) 240s > fm3 <- clm(rating ~ temp + contact, data=wine3, 240s + weights=runif(nrow(wine3), 0, 2)) 240s > c1 <- convergence(fm3) 240s > c0$info$logLik.Error 240s [1] "<1e-10" 240s > c1$info$logLik.Error 240s [1] "<1e-10" 240s > all.equal(c0$info$logLik.Error, c1$info$logLik.Error) 240s [1] TRUE 240s > ## In version 2014.11-14: 240s > ## > wine3 <- wine 240s > ## > set.seed(1234) 240s > ## > wts <- runif(nrow(wine3), 0, 2) 240s > ## > fm3 <- clm(rating ~ temp + contact, data=wine3, 240s > ## + weights=wts) 240s > ## > c0 <- convergence(fm3) 240s > ## > set.seed(1234) 240s > ## > fm3 <- clm(rating ~ temp + contact, data=wine3, 240s > ## + weights=runif(nrow(wine3), 0, 2)) 240s > ## > c1 <- convergence(fm3) 240s > ## > c0$info$logLik.Error 240s > ## [1] "<1e-10" 240s > ## > c1$info$logLik.Error 240s > ## [1] "4.80e+00" 240s > ## > all.equal(c0$info$logLik.Error, c1$info$logLik.Error) 240s > ## [1] "1 string mismatch" 240s > stopifnot(c0$info$logLik.Error == 240s + c1$info$logLik.Error) 240s > 240s BEGIN TEST test.clm.flex.link.R 240s 240s R version 4.4.3 (2025-02-28) -- "Trophy Case" 240s Copyright (C) 2025 The R Foundation for Statistical Computing 240s Platform: x86_64-pc-linux-gnu 240s 240s R is free software and comes with ABSOLUTELY NO WARRANTY. 240s You are welcome to redistribute it under certain conditions. 240s Type 'license()' or 'licence()' for distribution details. 240s 240s R is a collaborative project with many contributors. 240s Type 'contributors()' for more information and 240s 'citation()' on how to cite R or R packages in publications. 240s 240s Type 'demo()' for some demos, 'help()' for on-line help, or 240s 'help.start()' for an HTML browser interface to help. 240s Type 'q()' to quit R. 240s 240s > # test.clm.flex.link.R 240s > 240s > library(ordinal) 241s > 241s > fm <- clm(rating ~ contact + temp, data=wine, link="log-gamma") 241s Changing to 'nlminb' optimizer for flexible link function 241s > fm 241s formula: rating ~ contact + temp 241s data: wine 241s 241s Warning message: 241s (-1) Model failed to converge with max|grad| = 9.92567e-05 (tol = 1e-06) 241s link threshold nobs logLik AIC niter max.grad cond.H 241s log-gamma flexible 72 -85.72 185.44 27(179) 9.93e-05 5.9e+01 241s 241s Coefficients: 241s contactyes tempwarm 241s 0.8614 1.5072 241s 241s Link coefficient: 241s lambda 241s 0.1615 241s 241s Threshold coefficients: 241s 1|2 2|3 3|4 4|5 241s -0.8798 0.6678 1.9807 2.8593 241s > summary(fm) 241s formula: rating ~ contact + temp 241s data: wine 241s 241s link threshold nobs logLik AIC niter max.grad cond.H 241s log-gamma flexible 72 -85.72 185.44 27(179) 9.93e-05 5.9e+01 241s 241s Coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s contactyes 0.8614 0.2675 3.220 0.00128 ** 241s tempwarm 1.5072 0.2947 5.114 3.16e-07 *** 241s --- 241s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 241s 241s Link coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s lambda 0.1615 0.5752 0.281 0.779 241s 241s Threshold coefficients: 241s Estimate Std. Error z value 241s 1|2 -0.8798 0.5003 -1.759 241s 2|3 0.6678 0.3450 1.936 241s 3|4 1.9807 0.3826 5.177 241s 4|5 2.8593 0.4656 6.141 241s > vcov(fm) 241s 1|2 2|3 3|4 4|5 contactyes 241s 1|2 0.25029666 0.12858124 0.11888119 0.14341730 0.03339111 241s 2|3 0.12858124 0.11899384 0.10688715 0.12363922 0.04117758 241s 3|4 0.11888119 0.10688715 0.14635447 0.15493865 0.05320442 241s 4|5 0.14341730 0.12363922 0.15493865 0.21676904 0.06051103 241s contactyes 0.03339111 0.04117758 0.05320442 0.06051103 0.07156735 241s tempwarm 0.00707258 0.03006561 0.05390802 0.06549176 0.01159715 241s lambda -0.23173314 -0.13979170 -0.12509774 -0.15581154 -0.01157950 241s tempwarm lambda 241s 1|2 0.00707258 -0.23173314 241s 2|3 0.03006561 -0.13979170 241s 3|4 0.05390802 -0.12509774 241s 4|5 0.06549176 -0.15581154 241s contactyes 0.01159715 -0.01157950 241s tempwarm 0.08687099 0.01970691 241s lambda 0.01970691 0.33082448 241s > logLik(fm) 241s 'log Lik.' -85.72141 (df=7) 241s > extractAIC(fm) 241s [1] 7.0000 185.4428 241s > fm2 <- update(fm, link="probit") 241s > anova(fm, fm2) 241s Likelihood ratio tests of cumulative link models: 241s 241s formula: link: threshold: 241s fm2 rating ~ contact + temp probit flexible 241s fm rating ~ contact + temp log-gamma flexible 241s 241s no.par AIC logLik LR.stat df Pr(>Chisq) 241s fm2 6 183.52 -85.761 241s fm 7 185.44 -85.721 0.0795 1 0.778 241s > head(model.matrix(fm)$X) 241s (Intercept) contactyes tempwarm 241s 1 1 0 0 241s 2 1 0 0 241s 3 1 1 0 241s 4 1 1 0 241s 5 1 0 1 241s 6 1 0 1 241s > head(model.frame(fm)) 241s rating contact temp 241s 1 2 no cold 241s 2 3 no cold 241s 3 3 yes cold 241s 4 4 yes cold 241s 5 4 no warm 241s 6 4 no warm 241s > coef(fm) 241s 1|2 2|3 3|4 4|5 contactyes tempwarm lambda 241s -0.8797774 0.6678307 1.9806826 2.8593125 0.8614400 1.5071959 0.1614741 241s > coef(summary(fm)) 241s Estimate Std. Error z value Pr(>|z|) 241s 1|2 -0.8797774 0.5002966 -1.7585117 7.866049e-02 241s 2|3 0.6678307 0.3449548 1.9359945 5.286837e-02 241s 3|4 1.9806826 0.3825630 5.1774020 2.249970e-07 241s 4|5 2.8593125 0.4655846 6.1413379 8.182929e-10 241s contactyes 0.8614400 0.2675208 3.2200868 1.281518e-03 241s tempwarm 1.5071959 0.2947388 5.1136658 3.159661e-07 241s lambda 0.1614741 0.5751734 0.2807398 7.789100e-01 241s > nobs(fm) 241s [1] 72 241s > terms(fm) 241s Profile intervals not available for models with flexible link function: 241s reporting Wald intervals instead 241s rating ~ contact + temp 241s attr(,"variables") 241s list(rating, contact, temp) 241s attr(,"factors") 241s contact temp 241s rating 0 0 241s contact 1 0 241s temp 0 1 241s attr(,"term.labels") 241s [1] "contact" "temp" 241s attr(,"order") 241s [1] 1 1 241s attr(,"intercept") 241s [1] 1 241s attr(,"response") 241s [1] 1 241s attr(,".Environment") 241s 241s attr(,"predvars") 241s list(rating, contact, temp) 241s attr(,"dataClasses") 241s rating contact temp 241s "ordered" "factor" "factor" 241s > # profile(fm) # not implemented 241s > confint(fm) 241s 2.5 % 97.5 % 241s 1|2 -1.860340621 0.1007859 241s 2|3 -0.008268388 1.3439298 241s 3|4 1.230872848 2.7304924 241s 4|5 1.946783408 3.7718416 241s contactyes 0.337108998 1.3857711 241s tempwarm 0.929518434 2.0848735 241s lambda -0.965845153 1.2887933 241s > 241s > predict(fm, se=TRUE, interval = TRUE) 241s $fit 241s [1] 0.55792544 0.21565445 0.44140779 0.09846706 0.22428321 0.22428321 241s [7] 0.29090567 0.29090567 0.21042288 0.55792544 0.05388914 0.44140779 241s [13] 0.20737471 0.48129483 0.29090567 0.33832254 0.55792544 0.21565445 241s [19] 0.44140779 0.39099052 0.07269587 0.07269587 0.33832254 0.33832254 241s [25] 0.21565445 0.55792544 0.44140779 0.39099052 0.48129483 0.20737471 241s [31] 0.29090567 0.31272339 0.55792544 0.21565445 0.09846706 0.44140779 241s [37] 0.48129483 0.48129483 0.31272339 0.31272339 0.21565445 0.55792544 241s [43] 0.44140779 0.39099052 0.20737471 0.22428321 0.29090567 0.33832254 241s [49] 0.21042288 0.21042288 0.39099052 0.39099052 0.20737471 0.48129483 241s [55] 0.05636253 0.31272339 0.55792544 0.55792544 0.39099052 0.44140779 241s [61] 0.48129483 0.48129483 0.31272339 0.33832254 0.21042288 0.55792544 241s [67] 0.44140779 0.39099052 0.48129483 0.20737471 0.33832254 0.33832254 241s 241s $se.fit 241s [1] 0.09164058 0.09494135 0.08777656 0.05464347 0.08112461 0.08112461 241s [7] 0.13494788 0.13494788 0.13693811 0.09164058 0.04809909 0.08777656 241s [13] 0.09512593 0.07373113 0.13494788 0.08236628 0.09164058 0.09494135 241s [19] 0.08777656 0.09756681 0.06362571 0.06362571 0.08236628 0.08236628 241s [25] 0.09494135 0.09164058 0.08777656 0.09756681 0.07373113 0.09512593 241s [31] 0.13494788 0.09451059 0.09164058 0.09494135 0.05464347 0.08777656 241s [37] 0.07373113 0.07373113 0.09451059 0.09451059 0.09494135 0.09164058 241s [43] 0.08777656 0.09756681 0.09512593 0.08112461 0.13494788 0.08236628 241s [49] 0.13693811 0.13693811 0.09756681 0.09756681 0.09512593 0.07373113 241s [55] 0.03866211 0.09451059 0.09164058 0.09164058 0.09756681 0.08777656 241s [61] 0.07373113 0.07373113 0.09451059 0.08236628 0.13693811 0.09164058 241s [67] 0.08777656 0.09756681 0.07373113 0.09512593 0.08236628 0.08236628 241s 241s $lwr 241s [1] 0.378604419 0.083839590 0.282278456 0.031650566 0.103885179 0.103885179 241s [7] 0.102183450 0.102183450 0.050316478 0.378604419 0.008885132 0.282278456 241s [13] 0.077621509 0.342154617 0.102183450 0.199101469 0.378604419 0.083839590 241s [19] 0.282278456 0.223352982 0.012177667 0.012177667 0.199101469 0.199101469 241s [25] 0.083839590 0.378604419 0.282278456 0.223352982 0.342154617 0.077621509 241s [31] 0.102183450 0.161206607 0.378604419 0.083839590 0.031650566 0.282278456 241s [37] 0.342154617 0.342154617 0.161206607 0.161206607 0.083839590 0.378604419 241s [43] 0.282278456 0.223352982 0.077621509 0.103885179 0.102183450 0.199101469 241s [49] 0.050316478 0.050316478 0.223352982 0.223352982 0.077621509 0.342154617 241s [55] 0.014165414 0.161206607 0.378604419 0.378604419 0.223352982 0.282278456 241s [61] 0.342154617 0.342154617 0.161206607 0.199101469 0.050316478 0.378604419 241s [67] 0.282278456 0.223352982 0.342154617 0.077621509 0.199101469 0.199101469 241s 241s $upr 241s [1] 0.7233159 0.4523801 0.6135565 0.2673887 0.4189772 0.4189772 0.5965756 241s [8] 0.5965756 0.5727401 0.7233159 0.2657272 0.6135565 0.4485489 0.6233979 241s [15] 0.5965756 0.5125880 0.7233159 0.4523801 0.6135565 0.5890239 0.3326786 241s [22] 0.3326786 0.5125880 0.5125880 0.4523801 0.7233159 0.6135565 0.5890239 241s [29] 0.6233979 0.4485489 0.5965756 0.5186019 0.7233159 0.4523801 0.2673887 241s [36] 0.6135565 0.6233979 0.6233979 0.5186019 0.5186019 0.4523801 0.7233159 241s [43] 0.6135565 0.5890239 0.4485489 0.4189772 0.5965756 0.5125880 0.5727401 241s [50] 0.5727401 0.5890239 0.5890239 0.4485489 0.6233979 0.1988990 0.5186019 241s [57] 0.7233159 0.7233159 0.5890239 0.6135565 0.6233979 0.6233979 0.5186019 241s [64] 0.5125880 0.5727401 0.7233159 0.6135565 0.5890239 0.6233979 0.4485489 241s [71] 0.5125880 0.5125880 241s 241s > predict(fm, type="class") 241s $fit 241s [1] 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 241s [39] 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 241s Levels: 1 2 3 4 5 241s 241s > newData <- expand.grid(temp = c("cold", "warm"), 241s + contact = c("no", "yes")) 241s > 241s > ## Predicted probabilities in all five response categories for each of 241s > ## the four cases in newData: 241s > predict(fm, newdata=newData, type="prob") 241s $fit 241s 1 2 3 4 5 241s 1 0.210422885 0.55792544 0.2156545 0.01517801 0.0008192112 241s 2 0.014351371 0.20737471 0.4812948 0.22428321 0.0726958749 241s 3 0.053889141 0.39099052 0.4414078 0.09846706 0.0152454936 241s 4 0.001685878 0.05636253 0.3127234 0.33832254 0.2909056663 241s 241s > predict(fm, newdata=newData, type="class") 241s $fit 241s [1] 2 3 3 4 241s Levels: 1 2 3 4 5 241s 241s > 241s > predict(fm, newdata=newData, type="prob", se.fit = TRUE, interval = TRUE) 241s $fit 241s 1 2 3 4 5 241s 1 0.210422885 0.55792544 0.2156545 0.01517801 0.0008192112 241s 2 0.014351371 0.20737471 0.4812948 0.22428321 0.0726958749 241s 3 0.053889141 0.39099052 0.4414078 0.09846706 0.0152454936 241s 4 0.001685878 0.05636253 0.3127234 0.33832254 0.2909056663 241s 241s $se.fit 241s 1 2 3 4 5 241s 1 0.136938109 0.09164058 0.09494135 0.01696529 0.002047363 241s 2 0.016247015 0.09512593 0.07373113 0.08112461 0.063625711 241s 3 0.048099092 0.09756681 0.08777656 0.05464347 0.019268560 241s 4 0.002046575 0.03866211 0.09451059 0.08236628 0.134947885 241s 241s $lwr 241s 1 2 3 4 5 241s 1 0.0503164778 0.37860442 0.08383959 0.001663553 6.091054e-06 241s 2 0.0015305241 0.07762151 0.34215462 0.103885179 1.217767e-02 241s 3 0.0088851324 0.22335298 0.28227846 0.031650566 1.249665e-03 241s 4 0.0001557499 0.01416541 0.16120661 0.199101469 1.021834e-01 241s 241s $upr 241s 1 2 3 4 5 241s 1 0.57274013 0.7233159 0.4523801 0.1247616 0.09939053 241s 2 0.12150065 0.4485489 0.6233979 0.4189772 0.33267865 241s 3 0.26572719 0.5890239 0.6135565 0.2673887 0.16075952 241s 4 0.01797808 0.1988990 0.5186019 0.5125880 0.59657563 241s 241s > 241s > 241s > ## Aranda-Ordaz link: 241s > fm <- clm(rating ~ contact + temp, data=wine, link="Aranda-Ordaz") 241s Changing to 'nlminb' optimizer for flexible link function 241s > fm 241s Warning message: 241s (-1) Model failed to converge with max|grad| = 1.21391e-05 (tol = 1e-06) 241s formula: rating ~ contact + temp 241s data: wine 241s 241s link threshold nobs logLik AIC niter max.grad cond.H 241s Aranda-Ordaz flexible 72 -86.34 186.68 32(214) 1.21e-05 3.9e+02 241s 241s Coefficients: 241s contactyes tempwarm 241s 1.193 2.076 241s 241s Link coefficient: 241s lambda 241s 0.4994 241s 241s Threshold coefficients: 241s 1|2 2|3 3|4 4|5 241s -1.5284 0.7669 2.6021 3.7962 241s > summary(fm) 241s formula: rating ~ contact + temp 241s data: wine 241s 241s link threshold nobs logLik AIC niter max.grad cond.H 241s Aranda-Ordaz flexible 72 -86.34 186.68 32(214) 1.21e-05 3.9e+02 241s 241s Coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s contactyes 1.1927 0.6526 1.828 0.0676 . 241s tempwarm 2.0758 0.8196 2.533 0.0113 * 241s --- 241s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 241s 241s Link coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s lambda 0.4994 0.7840 0.637 0.524 241s 241s Threshold coefficients: 241s Estimate Std. Error z value 241s 1|2 -1.5284 0.5775 -2.647 241s 2|3 0.7669 0.8234 0.931 241s 3|4 2.6021 1.4335 1.815 241s 4|5 3.7962 1.9674 1.930 241s > vcov(fm) 241s 1|2 2|3 3|4 4|5 contactyes tempwarm 241s 1|2 0.3335060 0.2983831 0.4851478 0.6557867 0.2132245 0.2586680 241s 2|3 0.2983831 0.6780281 1.1261332 1.5330566 0.4699073 0.5953101 241s 3|4 0.4851478 1.1261332 2.0550131 2.7755711 0.8214407 1.0831426 241s 4|5 0.6557867 1.5330566 2.7755711 3.8705149 1.1194947 1.4831338 241s contactyes 0.2132245 0.4699073 0.8214407 1.1194947 0.4259337 0.3965114 241s tempwarm 0.2586680 0.5953101 1.0831426 1.4831338 0.3965114 0.6717718 241s lambda 0.2424390 0.5895695 1.0675177 1.4810300 0.4153800 0.5471764 241s lambda 241s 1|2 0.2424390 241s 2|3 0.5895695 241s 3|4 1.0675177 241s 4|5 1.4810300 241s contactyes 0.4153800 241s tempwarm 0.5471764 241s lambda 0.6146953 241s > logLik(fm) 241s 'log Lik.' -86.34171 (df=7) 241s > extractAIC(fm) 241s [1] 7.0000 186.6834 241s > fm2 <- update(fm, link="logit") 241s > anova(fm, fm2) 241s Likelihood ratio tests of cumulative link models: 241s 241s formula: link: threshold: 241s fm2 rating ~ contact + temp logit flexible 241s fm rating ~ contact + temp Aranda-Ordaz flexible 241s 241s no.par AIC logLik LR.stat df Pr(>Chisq) 241s fm2 6 184.98 -86.492 241s fm 7 186.68 -86.342 0.3004 1 0.5836 241s > head(model.matrix(fm)$X) 241s (Intercept) contactyes tempwarm 241s 1 1 0 0 241s 2 1 0 0 241s 3 1 1 0 241s 4 1 1 0 241s 5 1 0 1 241s 6 1 0 1 241s > head(model.frame(fm)) 241s rating contact temp 241s 1 2 no cold 241s 2 3 no cold 241s 3 3 yes cold 241s 4 4 yes cold 241s 5 4 no warm 241s 6 4 no warm 241s > coef(fm) 241s 1|2 2|3 3|4 4|5 contactyes tempwarm lambda 241s -1.5283880 0.7668896 2.6021283 3.7962201 1.1927250 2.0757935 0.4994416 241s > coef(summary(fm)) 241s Estimate Std. Error z value Pr(>|z|) 241s 1|2 -1.5283880 0.5774998 -2.6465602 0.008131504 241s 2|3 0.7668896 0.8234246 0.9313416 0.351676870 241s 3|4 2.6021283 1.4335317 1.8151871 0.069495154 241s 4|5 3.7962201 1.9673624 1.9295988 0.053656573 241s contactyes 1.1927250 0.6526360 1.8275501 0.067617093 241s tempwarm 2.0757935 0.8196168 2.5326389 0.011320750 241s lambda 0.4994416 0.7840251 0.6370225 0.524110192 241s > nobs(fm) 241s [1] 72 241s > terms(fm) 241s rating ~ contact + temp 241s attr(,"variables") 241s list(rating, contact, temp) 241s attr(,"factors") 241s contact temp 241s rating 0 0 241s contact 1 0 241s temp 0 1 241s attr(,"term.labels") 241s [1] "contact" "temp" 241s attr(,"order") 241s [1] 1 1 241s attr(,"intercept") 241s [1] 1 241s attr(,"response") 241s [1] 1 241s attr(,".Environment") 241s 241s attr(,"predvars") 241s list(rating, contact, temp) 241s attr(,"dataClasses") 241s rating contact temp 241s "ordered" "factor" "factor" 241s > # profile(fm) # not implemented 241s > confint(fm) 241s 2.5 % 97.5 % 241s 1|2 -2.66026679 -0.3965092 241s 2|3 -0.84699296 2.3807722 241s 3|4 -0.20754218 5.4117988 241s 4|5 -0.05973941 7.6521796 241s contactyes -0.08641803 2.4718680 241s tempwarm 0.46937402 3.6822130 241s lambda -1.03721931 2.0361025 241s > 241s > predict(fm, se=TRUE, interval = TRUE) 241s Profile intervals not available for models with flexible link function: 241s reporting Wald intervals instead 241s $fit 241s [1] 0.58209325 0.21518048 0.46054752 0.09103830 0.22383773 0.22383773 241s [7] 0.29286879 0.29286879 0.18610442 0.58209325 0.06269201 0.46054752 241s [13] 0.19716621 0.48293293 0.29286879 0.34021076 0.58209325 0.21518048 241s [19] 0.46054752 0.36913989 0.06939859 0.06939859 0.34021076 0.34021076 241s [25] 0.21518048 0.58209325 0.46054752 0.36913989 0.48293293 0.19716621 241s [31] 0.29286879 0.28974268 0.58209325 0.21518048 0.09103830 0.46054752 241s [37] 0.48293293 0.48293293 0.28974268 0.28974268 0.21518048 0.58209325 241s [43] 0.46054752 0.36913989 0.19716621 0.22383773 0.29286879 0.34021076 241s [49] 0.18610442 0.18610442 0.36913989 0.36913989 0.19716621 0.48293293 241s [55] 0.06897334 0.28974268 0.58209325 0.58209325 0.36913989 0.46054752 241s [61] 0.48293293 0.48293293 0.28974268 0.34021076 0.18610442 0.58209325 241s [67] 0.46054752 0.36913989 0.48293293 0.19716621 0.34021076 0.34021076 241s 241s $se.fit 241s [1] 0.14151187 0.09458707 0.10284385 0.06173008 0.06089158 0.06089158 241s [7] 0.17401315 0.17401315 0.08458285 0.14151187 0.03342713 0.10284385 241s [13] 0.06151483 0.16022476 0.17401315 0.14317218 0.14151187 0.09458707 241s [19] 0.10284385 0.09671233 0.16165491 0.16165491 0.14317218 0.14317218 241s [25] 0.09458707 0.14151187 0.10284385 0.09671233 0.16022476 0.06151483 241s [31] 0.17401315 0.08680258 0.14151187 0.09458707 0.06173008 0.10284385 241s [37] 0.16022476 0.16022476 0.08680258 0.08680258 0.09458707 0.14151187 241s [43] 0.10284385 0.09671233 0.06151483 0.06089158 0.17401315 0.14317218 241s [49] 0.08458285 0.08458285 0.09671233 0.09671233 0.06151483 0.16022476 241s [55] 0.03861752 0.08680258 0.14151187 0.14151187 0.09671233 0.10284385 241s [61] 0.16022476 0.16022476 0.08680258 0.14317218 0.08458285 0.14151187 241s [67] 0.10284385 0.09671233 0.16022476 0.06151483 0.14317218 0.14317218 241s 241s $lwr 241s [1] 0.308147105 0.083805034 0.274985966 0.022684752 0.126708383 0.126708383 241s [7] 0.073894276 0.073894276 0.071094501 0.308147105 0.021463145 0.274985966 241s [13] 0.102866209 0.209838512 0.073894276 0.128702471 0.308147105 0.083805034 241s [19] 0.274985966 0.205891005 0.000551725 0.000551725 0.128702471 0.128702471 241s [25] 0.083805034 0.308147105 0.274985966 0.205891005 0.209838512 0.102866209 241s [31] 0.073894276 0.151441083 0.308147105 0.083805034 0.022684752 0.274985966 241s [37] 0.209838512 0.209838512 0.151441083 0.151441083 0.083805034 0.308147105 241s [43] 0.274985966 0.205891005 0.102866209 0.126708383 0.073894276 0.128702471 241s [49] 0.071094501 0.071094501 0.205891005 0.205891005 0.102866209 0.209838512 241s [55] 0.022286640 0.151441083 0.308147105 0.308147105 0.205891005 0.274985966 241s [61] 0.209838512 0.209838512 0.151441083 0.128702471 0.071094501 0.308147105 241s [67] 0.274985966 0.205891005 0.209838512 0.102866209 0.128702471 0.128702471 241s 241s $upr 241s [1] 0.8132915 0.4511025 0.6577298 0.3017604 0.3643579 0.3643579 0.6825185 241s [8] 0.6825185 0.4058734 0.8132915 0.1694071 0.6577298 0.3446985 0.7666175 241s [15] 0.6825185 0.6428533 0.8132915 0.4511025 0.6577298 0.5690698 0.9097002 241s [22] 0.9097002 0.6428533 0.6428533 0.4511025 0.8132915 0.6577298 0.5690698 241s [29] 0.7666175 0.3446985 0.6825185 0.4825258 0.8132915 0.4511025 0.3017604 241s [36] 0.6577298 0.7666175 0.7666175 0.4825258 0.4825258 0.4511025 0.8132915 241s [43] 0.6577298 0.5690698 0.3446985 0.3643579 0.6825185 0.6428533 0.4058734 241s [50] 0.4058734 0.5690698 0.5690698 0.3446985 0.7666175 0.1940499 0.4825258 241s [57] 0.8132915 0.8132915 0.5690698 0.6577298 0.7666175 0.7666175 0.4825258 241s [64] 0.6428533 0.4058734 0.8132915 0.6577298 0.5690698 0.7666175 0.3446985 241s [71] 0.6428533 0.6428533 241s 241s > predict(fm, type="class") 241s $fit 241s [1] 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 241s [39] 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 2 2 3 3 3 3 4 4 241s Levels: 1 2 3 4 5 241s 241s > newData <- expand.grid(temp = c("cold", "warm"), 241s + contact = c("no", "yes")) 241s > 241s > ## Predicted probabilities in all five response categories for each of 241s > ## the four cases in newData: 241s > predict(fm, newdata=newData, type="prob") 241s $fit 241s 1 2 3 4 5 241s 1 0.186104423 0.58209325 0.2151805 0.01478353 0.001838317 241s 2 0.026664532 0.19716621 0.4829329 0.22383773 0.069398592 241s 3 0.062692007 0.36913989 0.4605475 0.09103830 0.016582284 241s 4 0.008204432 0.06897334 0.2897427 0.34021076 0.292868788 241s 241s > predict(fm, newdata=newData, type="class") 241s $fit 241s [1] 2 3 3 4 241s Levels: 1 2 3 4 5 241s 241s > 241s > predict(fm, newdata=newData, type="prob", se.fit = TRUE, interval = TRUE) 241s $fit 241s 1 2 3 4 5 241s 1 0.186104423 0.58209325 0.2151805 0.01478353 0.001838317 241s 2 0.026664532 0.19716621 0.4829329 0.22383773 0.069398592 241s 3 0.062692007 0.36913989 0.4605475 0.09103830 0.016582284 241s 4 0.008204432 0.06897334 0.2897427 0.34021076 0.292868788 241s 241s $se.fit 241s 1 2 3 4 5 241s 1 0.084582846 0.14151187 0.09458707 0.05105461 0.04225889 241s 2 0.018013151 0.06151483 0.16022476 0.06089158 0.16165491 241s 3 0.033427135 0.09671233 0.10284385 0.06173008 0.09203687 241s 4 0.009189042 0.03861752 0.08680258 0.14317218 0.17401315 241s 241s $lwr 241s 1 2 3 4 5 241s 1 0.071094501 0.30814710 0.08380503 1.557844e-05 4.591076e-23 241s 2 0.006979909 0.10286621 0.20983851 1.267084e-01 5.517250e-04 241s 3 0.021463145 0.20589100 0.27498597 2.268475e-02 2.647331e-07 241s 4 0.000903636 0.02228664 0.15144108 1.287025e-01 7.389428e-02 241s 241s $upr 241s 1 2 3 4 5 241s 1 0.40587337 0.8132915 0.4511025 0.9352883 1.0000000 241s 2 0.09647029 0.3446985 0.7666175 0.3643579 0.9097002 241s 3 0.16940715 0.5690698 0.6577298 0.3017604 0.9990698 241s 4 0.07033825 0.1940499 0.4825258 0.6428533 0.6825185 241s 241s > 241s > ######################################################################## 241s > ### Models with scale + flex link (or cauchit link) 241s > ######################################################################## 241s > 241s > fm <- clm(SURENESS ~ PRODID, scale=~PROD, data = soup, link="Aranda-Ordaz") 241s Changing to 'nlminb' optimizer for flexible link function 241s > summary(fm) 241s formula: SURENESS ~ PRODID 241s Warning message: 241s (-1) Model failed to converge with max|grad| = 0.000374031 (tol = 1e-06) 241s scale: ~PROD 241s data: soup 241s 241s link threshold nobs logLik AIC niter max.grad cond.H 241s Aranda-Ordaz flexible 1847 -2674.65 5373.30 57(719) 3.74e-04 9.0e+03 241s 241s Coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s PRODID2 1.3604 0.4137 3.289 0.001007 ** 241s PRODID3 2.2066 0.6659 3.314 0.000921 *** 241s PRODID4 1.2553 0.4086 3.072 0.002124 ** 241s PRODID5 1.9820 0.5886 3.367 0.000759 *** 241s PRODID6 2.4715 0.7713 3.204 0.001355 ** 241s --- 241s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 241s 241s log-scale coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s PRODTest 0.2807 0.1553 1.808 0.0706 . 241s --- 241s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 241s 241s Link coefficients: 241s Estimate Std. Error z value Pr(>|z|) 241s lambda 2.063 1.136 1.816 0.0693 . 241s --- 241s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 241s 241s Threshold coefficients: 241s Estimate Std. Error z value 241s 1|2 -1.3927 0.1491 -9.344 241s 2|3 -0.1449 0.3533 -0.410 241s 3|4 0.3051 0.4699 0.649 241s 4|5 0.6733 0.5802 1.160 241s 5|6 1.7210 0.9594 1.794 241s > 241s > fm <- clm(SURENESS ~ PRODID, scale=~PROD, data = soup, link="log-gamma") 242s Changing to 'nlminb' optimizer for flexible link function 244s > summary(fm) 244s formula: SURENESS ~ PRODID 244s scale: ~PROD 244s data: soup 244s 244s link threshold nobs logLik AIC niter max.grad cond.H 244s log-gamma flexible 1847 -2676.84 5377.68 87(1058) 1.38e-03 8.9e+03 244s 244s Coefficients: 244s Warning message: 244s (-1) Model failed to converge with max|grad| = 0.00138434 (tol = 1e-06) 244s Changing to 'nlminb' optimizer for flexible link function 244s Warning message: 244s (-1) Model failed to converge with max|grad| = 9.92567e-05 (tol = 1e-06) 244s Changing to 'nlminb' optimizer for flexible link function 244s Warning message: 244s (-1) Model failed to converge with max|grad| = 9.92567e-05 (tol = 1e-06) 244s Changing to 'nlminb' optimizer for flexible link function 244s Warning message: 244s (-1) Model failed to converge with max|grad| = 1.21391e-05 (tol = 1e-06) 244s Changing to 'nlminb' optimizer for flexible link function 244s Warning message: 244s (-1) Model failed to converge with max|grad| = 1.21391e-05 (tol = 1e-06) 244s Estimate Std. Error z value Pr(>|z|) 244s PRODID2 0.62876 0.09223 6.817 9.27e-12 *** 244s PRODID3 1.02757 0.13449 7.640 2.16e-14 *** 244s PRODID4 0.59157 0.11435 5.173 2.30e-07 *** 244s PRODID5 0.91936 0.12977 7.085 1.39e-12 *** 244s PRODID6 1.13201 0.13927 8.128 4.35e-16 *** 244s --- 244s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 244s 244s log-scale coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s PRODTest 0.09066 0.18406 0.493 0.622 244s 244s Link coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s lambda 0.4749 0.7031 0.675 0.499 244s 244s Threshold coefficients: 244s Estimate Std. Error z value 244s 1|2 -1.15649 0.45774 -2.527 244s 2|3 -0.47329 0.29575 -1.600 244s 3|4 -0.24744 0.26544 -0.932 244s 4|5 -0.07223 0.24988 -0.289 244s 5|6 0.37913 0.24136 1.571 244s > 244s > fm <- clm(SURENESS ~ PRODID, scale=~PROD, data = soup, link="cauchit") 244s > summary(fm) 244s formula: SURENESS ~ PRODID 244s scale: ~PROD 244s data: soup 244s 244s link threshold nobs logLik AIC niter max.grad cond.H 244s cauchit flexible 1847 -2679.34 5380.67 11(1) 3.10e-07 3.0e+02 244s 244s Coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s PRODID2 0.70550 0.09611 7.341 2.12e-13 *** 244s PRODID3 1.06186 0.13882 7.649 2.02e-14 *** 244s PRODID4 0.66876 0.11911 5.614 1.97e-08 *** 244s PRODID5 1.01135 0.13277 7.617 2.59e-14 *** 244s PRODID6 1.12784 0.14159 7.966 1.64e-15 *** 244s --- 244s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 244s 244s log-scale coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s PRODTest -0.20801 0.09524 -2.184 0.029 * 244s --- 244s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 244s 244s Threshold coefficients: 244s Estimate Std. Error z value 244s 1|2 -1.70920 0.14977 -11.412 244s 2|3 -0.36737 0.06302 -5.830 244s 3|4 -0.06736 0.05734 -1.175 244s 4|5 0.14657 0.05708 2.568 244s 5|6 0.67063 0.07072 9.483 244s > 244s > ######################################################################## 244s > ### clm.fit 244s > ######################################################################## 244s > 244s > ## Example with log-gamma: 244s > fm1 <- clm(rating ~ contact + temp, data=wine, link="log-gamma") 244s > summary(fm1) 244s formula: rating ~ contact + temp 244s data: wine 244s 244s link threshold nobs logLik AIC niter max.grad cond.H 244s log-gamma flexible 72 -85.72 185.44 27(179) 9.93e-05 5.9e+01 244s 244s Coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s contactyes 0.8614 0.2675 3.220 0.00128 ** 244s tempwarm 1.5072 0.2947 5.114 3.16e-07 *** 244s --- 244s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 244s 244s Link coefficients: 244s Estimate Std. Error z value Pr(>|z|) 244s lambda 0.1615 0.5752 0.281 0.779 244s 244s Threshold coefficients: 244s Estimate Std. Error z value 244s 1|2 -0.8798 0.5003 -1.759 244s 2|3 0.6678 0.3450 1.936 244s 3|4 1.9807 0.3826 5.177 244s 4|5 2.8593 0.4656 6.141 244s > ## get the model frame containing y and X: 244s > mf1 <- update(fm1, method="design") 244s > names(mf1) 244s [1] "y" "y.levels" "X" "offset" "terms" "contrasts" 244s [7] "xlevels" "weights" "doFit" "control" "link" "threshold" 244s [13] "start" "formulas" 244s > res <- clm.fit(mf1$y, mf1$X, link="log-gamma") ## invoking the factor method 244s > coef(res) 244s 1|2 2|3 3|4 4|5 contactyes tempwarm lambda 244s -0.8797774 0.6678307 1.9806826 2.8593125 0.8614400 1.5071959 0.1614741 244s > stopifnot(all.equal(coef(res), coef(fm1))) 244s > 244s > ## Example with Aranda-Ordaz: 244s > fm1 <- clm(rating ~ contact + temp, data=wine, link="Aranda-Ordaz") 244s > mf1 <- update(fm1, method="design") 244s > res <- clm.fit(mf1$y, mf1$X, link="Aranda") ## invoking the factor method 244s > stopifnot(all.equal(coef(res), coef(fm1))) 244s > 244s > 244s BEGIN TEST test.clm.model.matrix.R 244s 244s R version 4.4.3 (2025-02-28) -- "Trophy Case" 244s Copyright (C) 2025 The R Foundation for Statistical Computing 244s Platform: x86_64-pc-linux-gnu 244s 244s R is free software and comes with ABSOLUTELY NO WARRANTY. 244s You are welcome to redistribute it under certain conditions. 244s Type 'license()' or 'licence()' for distribution details. 244s 244s R is a collaborative project with many contributors. 244s Type 'contributors()' for more information and 244s 'citation()' on how to cite R or R packages in publications. 244s 244s Type 'demo()' for some demos, 'help()' for on-line help, or 244s 'help.start()' for an HTML browser interface to help. 244s Type 'q()' to quit R. 244s 244s > library(ordinal) 244s > ## source("test.clm.model.matrix.R") 244s > 244s > ## library(devtools) 244s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 244s > ## clean_dll(pkg = r2path) 244s > ## load_all(r2path) 244s > 244s > ## Check that get_clmDesign works in standard setting: 244s > fm1 <- clm(rating ~ temp, scale=~contact, nominal=~contact, data=wine) 244s > contr <- c(fm1$contrasts, fm1$S.contrasts, fm1$nom.contrasts) 244s > XX <- ordinal:::get_clmDesign(fm1$model, terms(fm1, "all"), contrasts=contr) 244s > XX2 <- update(fm1, method="design") 244s > (keep <- intersect(names(XX), names(XX2))) 244s [1] "y" "y.levels" "X" "offset" 244s [5] "terms" "contrasts" "xlevels" "weights" 244s [9] "S" "S.terms" "S.off" "S.contrasts" 244s [13] "S.xlevels" "NOM" "nom.terms" "nom.contrasts" 244s [17] "nom.xlevels" 244s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 244s + XX[keep], XX2[keep])) 244s y y.levels X offset terms 244s TRUE TRUE TRUE TRUE TRUE 244s contrasts xlevels weights S S.terms 244s TRUE TRUE TRUE TRUE TRUE 244s S.off S.contrasts S.xlevels NOM nom.terms 244s TRUE TRUE TRUE TRUE TRUE 244s nom.contrasts nom.xlevels 244s TRUE TRUE 244s > stopifnot(all(test)) 244s > 244s > ## Check that get_clmDesign works with singular fit and NAs: 244s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 244s > wine2 <- subset(wine, subset=(!1:nrow(wine) %in% cy)) 244s > wine2[c(9, 15, 46), "rating"] <- NA 244s > fm1 <- clm(rating ~ temp, scale=~contact, nominal=~contact, 244s + data=wine2) 244s > contr <- c(fm1$contrasts, fm1$S.contrasts, fm1$nom.contrasts) 244s > XX <- ordinal:::get_clmDesign(fm1$model, terms(fm1, "all"), contrasts=contr) 244s > XX2 <- update(fm1, method="design") 244s Warning message: 244s (1) Hessian is numerically singular: parameters are not uniquely determined 244s In addition: Absolute convergence criterion was met, but relative criterion was not met 244s > (keep <- intersect(names(XX), names(XX2))) 244s [1] "y" "y.levels" "X" "offset" 244s [5] "terms" "contrasts" "xlevels" "na.action" 244s [9] "weights" "S" "S.terms" "S.off" 244s [13] "S.contrasts" "S.xlevels" "NOM" "nom.terms" 244s [17] "nom.contrasts" "nom.xlevels" 244s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 244s + XX[keep], XX2[keep])) 244s y y.levels X offset terms 244s TRUE TRUE TRUE TRUE TRUE 244s contrasts xlevels na.action weights S 244s TRUE TRUE TRUE TRUE TRUE 244s S.terms S.off S.contrasts S.xlevels NOM 244s TRUE TRUE TRUE TRUE TRUE 244s nom.terms nom.contrasts nom.xlevels 244s TRUE TRUE TRUE 244s > stopifnot(all(test)) 244s > 244s > ## In this situation update and get_clmRho give the same results: 244s > wine2 <- wine 244s > fm1 <- clm(rating ~ temp + contact, data=wine2) ## OK 244s > rho1 <- ordinal:::get_clmRho.clm(fm1) 244s > l1 <- as.list(rho1) 244s > l2 <- as.list(update(fm1, doFit=FALSE)) 244s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 244s + l1, l2[names(l1)])) 244s nlambda link gfun dfun pfun par clm.hess clm.grad 244s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 244s clm.nll wts fitted has.scale sigma k Soff S 244s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 244s n.psi o2 o1 B2 B1 244s TRUE TRUE TRUE TRUE TRUE 244s > stopifnot(all(test)) 244s > ## If we modify the data (or other subset, weights, formulae, etc.) 244s > ## used in the model call, the results from update no longer correspond 244s > ## to the elements of the fitted model object. get_clmRho gets it 244s > ## right on the other hand: 244s > wine2[10:13, "rating"] <- NA 244s > l3 <- as.list(ordinal:::get_clmRho.clm(fm1)) 244s > l4 <- as.list(update(fm1, doFit=FALSE)) 244s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 244s + l1, l3)) 244s nlambda link gfun dfun pfun par clm.hess clm.grad 244s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 244s clm.nll wts fitted has.scale sigma k Soff S 244s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 244s n.psi o2 o1 B2 B1 244s TRUE TRUE TRUE TRUE TRUE 244s > stopifnot(all(test)) ## same 244s > (test <- mapply(function(x, y) isTRUE(all.equal(x, y)), 244s + l3, l4[names(l3)])) 244s nlambda link gfun dfun pfun par clm.hess clm.grad 244s TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE 244s clm.nll wts fitted has.scale sigma k Soff S 244s TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE 244s n.psi o2 o1 B2 B1 244s TRUE FALSE FALSE FALSE FALSE 244s > stopifnot(sum(!test) == 8) ## not all the same anymore! 244s > ## In conclusion l1, l2, and l3 are identical. l4 is different. 244s > 244s > ################################# 244s > ## Test that checkContrasts give appropriate warnings: 244s > contr <- c(temp="contr.sum", contact="contr.sum") 244s > fm1 <- clm(rating ~ temp + contact, scale=~contact, data=wine) ## OK 244s > fm1 <- clm(rating ~ temp + contact, scale=~contact, data=wine, 244s + contrasts=contr) ## OK 244s > fm1 <- clm(rating ~ temp, scale=~contact, data=wine, 244s + contrasts=contr) ## OK 244s > ## These should give warnings: 244s > fm1 <- clm(rating ~ temp, contrasts=c(contact="contr.sum"), data=wine) 244s > fm1 <- clm(rating ~ temp, contrasts=contr, data=wine) 244s Warning messages: 244s 1: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s Warning messages: 244s 1: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s Warning messages: 244s 1: variable 'contact' is absent: its contrasts will be ignored 244s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s Warning messages: 244s 1: variable 'contact' is absent: its contrasts will be ignored 244s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s > fm1 <- clm(rating ~ 1, scale=~contact, contrasts=c(temp="contr.sum"), 244s + data=wine) 244s Warning messages: 244s 1: variable 'temp' is absent: its contrasts will be ignored 244s 2: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s non-list contrasts argument ignored 244s 3: In model.matrix.default(terms, data = fullmf, contrasts.arg = getContrasts(terms, : 244s > fm1 <- clm(rating ~ 1, scale=~contact, contrasts=list(temp="contr.sum"), 244s + data=wine) 244s > 244s > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 244s non-list contrasts argument ignored 244s Warning message: 244s variable 'temp' is absent: its contrasts will be ignored 244s Warning message: 244s variable 'temp' is absent: its contrasts will be ignored 244s > ordinal:::checkContrasts(fm0$S.terms, fm0$contrasts) 244s > ordinal:::checkContrasts(fm0$S.terms, fm0$S.contrasts) 244s > ordinal:::checkContrasts(fm0$terms, fm0$contrasts) 244s > ordinal:::checkContrasts(fm0$terms, fm0$S.contrasts) 244s > 244s > ################################# 244s > ## Check that clm and model.matrix respects contrast settings: 244s > options("contrasts" = c("contr.treatment", "contr.poly")) 244s > fm0 <- clm(rating ~ temp + contact, data=wine) 244s > options("contrasts" = c("contr.sum", "contr.poly")) 244s > fm1 <- clm(rating ~ temp + contact, data=wine) 244s > stopifnot(all(model.matrix(fm0)$X[, 2] %in% c(0, 1))) 244s > stopifnot(all(model.matrix(fm1)$X[, 2] %in% c(1, -1))) 244s > 244s > ################################# 244s > ## Check that model.matrix results do not depend on global contrast 244s > ## setting: 244s > options("contrasts" = c("contr.sum", "contr.poly")) 244s > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 244s > MM <- model.matrix(fm0) 244s > options("contrasts" = c("contr.treatment", "contr.poly")) 244s > MM2 <- model.matrix(fm0) 244s > for(x in MM) print(head(x)) 244s (Intercept) temp1 contact1 244s 1 1 1 1 244s 2 1 1 1 244s 3 1 1 -1 244s 4 1 1 -1 244s 5 1 -1 1 244s 6 1 -1 1 244s (Intercept) contact1 244s 1 1 1 244s 2 1 1 244s 3 1 -1 244s 4 1 -1 244s 5 1 1 244s 6 1 1 244s > for(x in MM2) print(head(x)) 244s (Intercept) temp1 contact1 244s 1 1 1 1 244s 2 1 1 1 244s 3 1 1 -1 244s 4 1 1 -1 244s 5 1 -1 1 244s 6 1 -1 1 244s (Intercept) contact1 244s 1 1 1 244s 2 1 1 244s 3 1 -1 244s 4 1 -1 244s 5 1 1 244s 6 1 1 244s > stopifnot(all(mapply(all.equal, MM, MM2))) 244s > 244s > ################################# 244s > ## This gave a warning before getContrasts was implemented: 244s > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 244s > MM <- model.matrix(fm0) 244s > ## > fm0 <- clm(rating ~ temp + contact, scale=~contact, data=wine) 244s > ## > MM <- model.matrix(fm0) 244s > ## Warning message: 244s > ## In model.matrix.default(res$S.terms, data = fullmf, contrasts.arg = getContrasts(res$S.terms, : 244s > ## variable 'temp' is absent, its contrast will be ignored 244s > for(x in MM) print(head(x)) 244s (Intercept) tempwarm contactyes 244s 1 1 0 0 244s 2 1 0 0 244s 3 1 0 1 244s 4 1 0 1 244s 5 1 1 0 244s 6 1 1 0 244s (Intercept) contactyes 244s 1 1 0 244s 2 1 0 244s 3 1 1 244s 4 1 1 244s 5 1 0 244s 6 1 0 244s > 244s > 245s BEGIN TEST test.clm.predict.R 245s 245s R version 4.4.3 (2025-02-28) -- "Trophy Case" 245s Copyright (C) 2025 The R Foundation for Statistical Computing 245s Platform: x86_64-pc-linux-gnu 245s 245s R is free software and comes with ABSOLUTELY NO WARRANTY. 245s You are welcome to redistribute it under certain conditions. 245s Type 'license()' or 'licence()' for distribution details. 245s 245s R is a collaborative project with many contributors. 245s Type 'contributors()' for more information and 245s 'citation()' on how to cite R or R packages in publications. 245s 245s Type 'demo()' for some demos, 'help()' for on-line help, or 245s 'help.start()' for an HTML browser interface to help. 245s Type 'q()' to quit R. 245s 245s > library(ordinal) 245s > ## source("test.clm.predict.R") 245s > 245s > ## library(devtools) 245s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 245s > ## clean_dll(pkg = r2path) 245s > ## load_all(r2path) 245s > 245s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 245s > options("contrasts" = c("contr.treatment", "contr.poly")) 245s > getOption("contrasts") 245s [1] "contr.treatment" "contr.poly" 245s > 245s > ## Example model 245s > 245s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine) 245s > summary(wine1.clm) 245s formula: rating ~ temp * contact 245s data: wine 245s subset: -cy 245s 245s link threshold nobs logLik AIC niter max.grad cond.H 245s logit flexible 54 -65.47 142.93 6(0) 2.80e-12 2.9e+01 245s 245s Coefficients: (1 not defined because of singularities) 245s Estimate Std. Error z value Pr(>|z|) 245s tempwarm 2.2892 0.7192 3.183 0.00146 ** 245s contactyes 1.6505 0.6698 2.464 0.01374 * 245s tempwarm:contactyes NA NA NA NA 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s Threshold coefficients: 245s Estimate Std. Error z value 245s 1|2 -1.3971 0.5728 -2.439 245s 2|3 1.1349 0.5262 2.157 245s 3|4 3.3351 0.6987 4.774 245s 4|5 4.7924 0.7996 5.994 245s > names(wine1.clm) 245s [1] "aliased" "alpha" "beta" "call" 245s [5] "coefficients" "cond.H" "contrasts" "control" 245s [9] "convergence" "df.residual" "edf" "fitted.values" 245s [13] "formula" "formulas" "gradient" "Hessian" 245s [17] "info" "link" "logLik" "maxGradient" 245s [21] "message" "model" "n" "niter" 245s [25] "nobs" "start" "terms" "Theta" 245s [29] "threshold" "tJac" "vcov" "xlevels" 245s [33] "y" "y.levels" 245s > 245s > wine.clm <- clm(rating~temp*contact, data=wine) 245s > summary(wine.clm) 245s formula: rating ~ temp * contact 245s data: wine 245s 245s link threshold nobs logLik AIC niter max.grad cond.H 245s logit flexible 72 -86.42 186.83 6(0) 5.22e-12 5.1e+01 245s 245s Coefficients: 245s Estimate Std. Error z value Pr(>|z|) 245s tempwarm 2.3212 0.7009 3.311 0.000928 *** 245s contactyes 1.3475 0.6604 2.041 0.041300 * 245s tempwarm:contactyes 0.3595 0.9238 0.389 0.697129 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s Threshold coefficients: 245s Estimate Std. Error z value 245s 1|2 -1.4113 0.5454 -2.588 245s 2|3 1.1436 0.5097 2.244 245s 3|4 3.3771 0.6382 5.292 245s 4|5 4.9420 0.7509 6.581 245s > names(wine.clm) 245s [1] "aliased" "alpha" "beta" "call" 245s [5] "coefficients" "cond.H" "contrasts" "control" 245s [9] "convergence" "df.residual" "edf" "fitted.values" 245s [13] "formula" "formulas" "gradient" "Hessian" 245s [17] "info" "link" "logLik" "maxGradient" 245s [21] "message" "model" "n" "niter" 245s [25] "nobs" "start" "terms" "Theta" 245s [29] "threshold" "tJac" "vcov" "xlevels" 245s [33] "y" "y.levels" 245s > ## Make sure the same elements are present with a rank deficient model 245s > ## fit: 245s > stopifnot(all(names(wine1.clm) == names(wine.clm))) 245s > 245s > ## With treatment contrasts: 245s > options("contrasts" = c("contr.treatment", "contr.poly")) 245s > wine.clm <- clm(rating~temp*contact, data=wine) 245s > coef(summary(wine.clm)) 245s Estimate Std. Error z value Pr(>|z|) 245s 1|2 -1.4112620 0.5453532 -2.5877943 9.659266e-03 245s 2|3 1.1435537 0.5096555 2.2437776 2.484671e-02 245s 3|4 3.3770825 0.6381617 5.2918913 1.210578e-07 245s 4|5 4.9419823 0.7509113 6.5813133 4.663108e-11 245s tempwarm 2.3211843 0.7009479 3.3114931 9.279953e-04 245s contactyes 1.3474604 0.6603557 2.0405072 4.129984e-02 245s tempwarm:contactyes 0.3595489 0.9238188 0.3891985 6.971293e-01 245s > head(model.matrix(wine.clm)$X) 245s (Intercept) tempwarm contactyes tempwarm:contactyes 245s 1 1 0 0 0 245s 2 1 0 0 0 245s 3 1 0 1 0 245s 4 1 0 1 0 245s 5 1 1 0 0 245s 6 1 1 0 0 245s > wine.clm$contrasts 245s $temp 245s [1] "contr.treatment" 245s 245s $contact 245s [1] "contr.treatment" 245s 245s > head(pred1 <- predict(wine.clm)$fit) 245s [1] 0.56229641 0.20864908 0.43467309 0.08938852 0.19028226 0.19028226 245s > 245s > ## With sum contrasts: 245s > options("contrasts" = c("contr.sum", "contr.poly")) 245s > wine.clm <- clm(rating~temp*contact, data=wine) 245s > coef(summary(wine.clm)) 245s Estimate Std. Error z value Pr(>|z|) 245s 1|2 -3.33547153 0.5253364 -6.3492103 2.164231e-10 245s 2|3 -0.78065590 0.2945538 -2.6503003 8.042025e-03 245s 3|4 1.45287292 0.3367529 4.3143590 1.600667e-05 245s 4|5 3.01777269 0.4813097 6.2699186 3.612370e-10 245s temp1 -1.25047935 0.2641023 -4.7348292 2.192396e-06 245s contact1 -0.76361743 0.2380971 -3.2071683 1.340485e-03 245s temp1:contact1 0.08988722 0.2309547 0.3891985 6.971293e-01 245s > head(model.matrix(wine.clm)$X) 245s (Intercept) temp1 contact1 temp1:contact1 245s 1 1 1 1 1 245s 2 1 1 1 1 245s 3 1 1 -1 -1 245s 4 1 1 -1 -1 245s 5 1 -1 1 -1 245s 6 1 -1 1 -1 245s > wine.clm$contrasts 245s $temp 245s [1] "contr.sum" 245s 245s $contact 245s [1] "contr.sum" 245s 245s > head(pred2 <- predict(wine.clm)$fit) 245s [1] 0.56229641 0.20864908 0.43467309 0.08938852 0.19028226 0.19028226 245s > 245s > ## Mixture of sum and treatment contrasts: 245s > options("contrasts" = c("contr.treatment", "contr.poly")) 245s > wine.clm <- clm(rating~temp*contact, data=wine, 245s + contrasts=list(temp="contr.sum")) 245s > coef(summary(wine.clm)) 245s Estimate Std. Error z value Pr(>|z|) 245s 1|2 -2.57185410 0.5227165 -4.92016984 8.646915e-07 245s 2|3 -0.01703847 0.3611634 -0.04717662 9.623725e-01 245s 3|4 2.21649036 0.4529312 4.89365773 9.897892e-07 245s 4|5 3.78139013 0.5957919 6.34683010 2.197966e-10 245s temp1 -1.16059213 0.3504740 -3.31149309 9.279953e-04 245s contactyes 1.52723487 0.4761942 3.20716830 1.340485e-03 245s temp1:contactyes -0.17977444 0.4619094 -0.38919847 6.971293e-01 245s > head(model.matrix(wine.clm)$X) 245s (Intercept) temp1 contactyes temp1:contactyes 245s 1 1 1 0 0 245s 2 1 1 0 0 245s 3 1 1 1 1 245s 4 1 1 1 1 245s 5 1 -1 0 0 245s 6 1 -1 0 0 245s > wine.clm$contrasts 245s $temp 245s [1] "contr.sum" 245s 245s $contact 245s [1] "contr.treatment" 245s 245s > head(pred3 <- predict(wine.clm)$fit) 245s [1] 0.56229641 0.20864908 0.43467309 0.08938852 0.19028226 0.19028226 245s > 245s > stopifnot(isTRUE(all.equal(pred1, pred2))) 245s > stopifnot(isTRUE(all.equal(pred1, pred3))) 245s > 245s > ################################# 245s > ### Now for a rank deficient fit: 245s > ################################# 245s > 245s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 245s > options("contrasts" = c("contr.treatment", "contr.poly")) 245s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine) 245s > coef(summary(wine1.clm)) 245s Estimate Std. Error z value Pr(>|z|) 245s 1|2 -1.397134 0.5727918 -2.439164 1.472127e-02 245s 2|3 1.134907 0.5261653 2.156940 3.101038e-02 245s 3|4 3.335090 0.6986647 4.773521 1.810331e-06 245s 4|5 4.792428 0.7995580 5.993846 2.049352e-09 245s tempwarm 2.289221 0.7191705 3.183140 1.456870e-03 245s contactyes 1.650538 0.6698484 2.464047 1.373782e-02 245s tempwarm:contactyes NA NA NA NA 245s > attributes(model.matrix(wine1.clm)$X)$contrasts 245s $temp 245s [1] "contr.treatment" 245s 245s $contact 245s [1] "contr.treatment" 245s 245s > wine1.clm$contrasts 245s $temp 245s [1] "contr.treatment" 245s 245s $contact 245s [1] "contr.treatment" 245s 245s > head(pred4 <- predict(wine1.clm)$fit) 245s [1] 0.5584719 0.2088699 0.1843854 0.1843854 0.2988733 0.2988733 245s > 245s > options("contrasts" = c("contr.sum", "contr.poly")) 245s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine) 245s > attributes(model.matrix(wine1.clm)$X)$contrasts 245s $temp 245s [1] "contr.sum" 245s 245s $contact 245s [1] "contr.sum" 245s 245s > options("contrasts" = c("contr.treatment", "contr.poly")) 245s > attributes(model.matrix(wine1.clm)$X)$contrasts 245s $temp 245s [1] "contr.sum" 245s 245s $contact 245s [1] "contr.sum" 245s 245s > ## Notice that the contrasts change in the attributes of the fit!!! 245s > coef(summary(wine1.clm)) 245s Estimate Std. Error z value Pr(>|z|) 245s 1|2 -3.3670128 0.6149672 -5.475110 4.372411e-08 245s 2|3 -0.8349725 0.4231096 -1.973419 4.844787e-02 245s 3|4 1.3652108 0.4310181 3.167409 1.538037e-03 245s 4|5 2.8225483 0.5190089 5.438343 5.377826e-08 245s temp1 -1.1446104 0.3595853 -3.183140 1.456870e-03 245s contact1 -0.8252689 0.3349242 -2.464047 1.373782e-02 245s temp1:contact1 NA NA NA NA 245s > wine1.clm$contrasts 245s $temp 245s [1] "contr.sum" 245s 245s $contact 245s [1] "contr.sum" 245s 245s > head(pred5 <- predict(wine1.clm)$fit) 245s [1] 0.5584719 0.2088699 0.1843854 0.1843854 0.2988733 0.2988733 245s > 245s > head(cbind(pred4, pred5)) 245s pred4 pred5 245s [1,] 0.5584719 0.5584719 245s [2,] 0.2088699 0.2088699 245s [3,] 0.1843854 0.1843854 245s [4,] 0.1843854 0.1843854 245s [5,] 0.2988733 0.2988733 245s [6,] 0.2988733 0.2988733 245s > stopifnot(isTRUE(all.equal(pred4, pred5))) 245s > 245s > options("contrasts" = c("contr.treatment", "contr.poly")) 245s > wine1.clm <- clm(rating ~ temp*contact, subset = -cy, data = wine, 245s + contrasts=list(temp="contr.sum")) 245s > coef(summary(wine1.clm)) 245s Estimate Std. Error z value Pr(>|z|) 245s 1|2 -2.54174387 0.5792622 -4.38789851 1.144512e-05 245s 2|3 -0.00970353 0.3737929 -0.02595964 9.792895e-01 246s 3|4 2.19047975 0.4965589 4.41131906 1.027428e-05 246s 4|5 3.64781729 0.6257007 5.82997171 5.543677e-09 246s temp1 -1.14461036 0.3595853 -3.18314035 1.456870e-03 246s contactyes 1.65053789 0.6698484 2.46404685 1.373782e-02 246s temp1:contactyes NA NA NA NA 246s > head(model.matrix(wine1.clm)$X) 246s (Intercept) temp1 contactyes temp1:contactyes 246s 1 1 1 0 0 246s 2 1 1 0 0 246s 5 1 -1 0 0 246s 6 1 -1 0 0 246s 7 1 -1 1 -1 246s 8 1 -1 1 -1 246s > attributes(model.matrix(wine1.clm)$X)$contrasts 246s $temp 246s [1] "contr.sum" 246s 246s $contact 246s [1] "contr.treatment" 246s 246s > wine1.clm$contrasts 246s $temp 246s [1] "contr.sum" 246s 246s $contact 246s [1] "contr.treatment" 246s 246s > head(pred6 <- predict(wine1.clm)$fit) 246s [1] 0.5584719 0.2088699 0.1843854 0.1843854 0.2988733 0.2988733 246s > 246s > head(cbind(pred4, pred5, pred6)) 246s pred4 pred5 pred6 246s [1,] 0.5584719 0.5584719 0.5584719 246s [2,] 0.2088699 0.2088699 0.2088699 246s [3,] 0.1843854 0.1843854 0.1843854 246s [4,] 0.1843854 0.1843854 0.1843854 246s [5,] 0.2988733 0.2988733 0.2988733 246s [6,] 0.2988733 0.2988733 0.2988733 246s > stopifnot(isTRUE(all.equal(pred4, pred6))) 246s > ################################################################## 246s > 246s > ## Compare equality of fitted values for models with different contrasts: 246s > options("contrasts" = c("contr.treatment", "contr.poly")) 246s > fm1 <- clm(rating ~ temp + contact, data=wine) 246s > fitted(fm1) 246s [1] 0.57064970 0.19229094 0.44305990 0.09582084 0.20049402 0.20049402 246s [7] 0.27378469 0.27378469 0.20679013 0.57064970 0.05354601 0.44305990 246s [13] 0.20141572 0.50157554 0.27378469 0.36359581 0.57064970 0.19229094 246s [19] 0.44305990 0.37764614 0.07562701 0.07562701 0.36359581 0.36359581 246s [25] 0.19229094 0.57064970 0.44305990 0.37764614 0.50157554 0.20141572 246s [31] 0.27378469 0.30420994 0.57064970 0.19229094 0.09582084 0.44305990 246s [37] 0.50157554 0.50157554 0.30420994 0.30420994 0.19229094 0.57064970 246s [43] 0.44305990 0.37764614 0.20141572 0.20049402 0.27378469 0.36359581 246s [49] 0.20679013 0.20679013 0.37764614 0.37764614 0.20141572 0.50157554 246s [55] 0.05380128 0.30420994 0.57064970 0.57064970 0.37764614 0.44305990 246s [61] 0.50157554 0.50157554 0.30420994 0.36359581 0.20679013 0.57064970 246s [67] 0.44305990 0.37764614 0.50157554 0.20141572 0.36359581 0.36359581 246s > options("contrasts" = c("contr.sum", "contr.poly")) 246s > fm2 <- clm(rating ~ temp + contact, data=wine) 246s > fitted(fm2) 246s [1] 0.57064970 0.19229094 0.44305990 0.09582084 0.20049402 0.20049402 246s [7] 0.27378469 0.27378469 0.20679013 0.57064970 0.05354601 0.44305990 246s [13] 0.20141572 0.50157554 0.27378469 0.36359581 0.57064970 0.19229094 246s [19] 0.44305990 0.37764614 0.07562701 0.07562701 0.36359581 0.36359581 246s [25] 0.19229094 0.57064970 0.44305990 0.37764614 0.50157554 0.20141572 246s [31] 0.27378469 0.30420994 0.57064970 0.19229094 0.09582084 0.44305990 246s [37] 0.50157554 0.50157554 0.30420994 0.30420994 0.19229094 0.57064970 246s [43] 0.44305990 0.37764614 0.20141572 0.20049402 0.27378469 0.36359581 246s [49] 0.20679013 0.20679013 0.37764614 0.37764614 0.20141572 0.50157554 246s [55] 0.05380128 0.30420994 0.57064970 0.57064970 0.37764614 0.44305990 246s [61] 0.50157554 0.50157554 0.30420994 0.36359581 0.20679013 0.57064970 246s [67] 0.44305990 0.37764614 0.50157554 0.20141572 0.36359581 0.36359581 246s > options("contrasts" = c("contr.treatment", "contr.poly")) 246s > fm3 <- clm(rating ~ temp + contact, data=wine, 246s + contrasts=list(contact="contr.sum")) 246s > fitted(fm3) 246s [1] 0.57064970 0.19229094 0.44305990 0.09582084 0.20049402 0.20049402 246s [7] 0.27378469 0.27378469 0.20679013 0.57064970 0.05354601 0.44305990 246s [13] 0.20141572 0.50157554 0.27378469 0.36359581 0.57064970 0.19229094 246s [19] 0.44305990 0.37764614 0.07562701 0.07562701 0.36359581 0.36359581 246s [25] 0.19229094 0.57064970 0.44305990 0.37764614 0.50157554 0.20141572 246s [31] 0.27378469 0.30420994 0.57064970 0.19229094 0.09582084 0.44305990 246s [37] 0.50157554 0.50157554 0.30420994 0.30420994 0.19229094 0.57064970 246s [43] 0.44305990 0.37764614 0.20141572 0.20049402 0.27378469 0.36359581 246s [49] 0.20679013 0.20679013 0.37764614 0.37764614 0.20141572 0.50157554 246s [55] 0.05380128 0.30420994 0.57064970 0.57064970 0.37764614 0.44305990 246s [61] 0.50157554 0.50157554 0.30420994 0.36359581 0.20679013 0.57064970 246s [67] 0.44305990 0.37764614 0.50157554 0.20141572 0.36359581 0.36359581 246s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm2)))) 246s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm3)))) 246s > 246s > ################################################################## 246s > ## Compare equality of fitted values for models with different 246s > ## contrasts in face of aliased coefficients: 246s > options("contrasts" = c("contr.treatment", "contr.poly")) 246s > cy <- with(wine, which(temp == "cold" & contact == "yes")) 246s > Wine <- subset(wine, subset=!(temp == "cold" & contact == "yes")) 246s > fm1 <- clm(rating ~ temp + contact, data=Wine) 246s > options("contrasts" = c("contr.sum", "contr.poly")) 246s > fm2 <- clm(rating ~ temp + contact, data=Wine) 246s > options("contrasts" = c("contr.treatment", "contr.poly")) 246s > fm3 <- clm(rating ~ temp + contact, data=Wine, 246s + contrasts=list(contact="contr.sum")) 246s > 246s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm2)))) 246s > stopifnot(isTRUE(all.equal(fitted(fm1), fitted(fm3)))) 246s > stopifnot(isTRUE(all.equal(predict(fm1)$fit, predict(fm2)$fit))) 246s > stopifnot(isTRUE(all.equal(predict(fm1)$fit, predict(fm3)$fit))) 246s > 246s > ################################# 246s > ## Does this also happen if the wine data has changed? 246s > options("contrasts" = c("contr.treatment", "contr.poly")) 246s > Wine <- subset(wine, subset=!(temp == "cold" & contact == "yes")) 246s > fm1 <- clm(rating ~ temp + contact, data=Wine) 246s > fit1 <- fitted(fm1) 246s > pred1 <- predict(fm1)$fit 246s > Wine <- wine 246s > pred2 <- predict(fm1)$fit 246s > stopifnot(isTRUE(all.equal(fit1, pred1))) 246s > stopifnot(isTRUE(all.equal(fit1, pred2))) 246s > 246s > ## What if weights, say, is an expression? 246s > ## Notice that updating the model object changes it: 246s > set.seed(123) 246s > fm1 <- clm(rating ~ temp + contact, data=wine, 246s + weights=runif(nrow(wine), .5, 1.5)) 246s > fm2 <- update(fm1) 246s > stopifnot(isTRUE(all.equal(fitted(fm1), predict(fm1)$fit))) 246s > stopifnot(!isTRUE(all.equal(fitted(fm1), fitted(fm2)))) 246s > 246s > ################################# 246s > ## Test equality of fits and predictions of models with: 246s > ## 'x + I(x^2)' and 'poly(x, 2)': 246s > ## December 25th 2014, RHBC. 246s > data(wine) 246s > set.seed(1) 246s > x <- rnorm(nrow(wine), sd=2) + as.numeric(wine$rating) 246s > range(x) 246s [1] -1.429400 7.803236 246s > 246s > ## Comparison of 'x + I(x^2)' and 'poly(x, 2)': 246s > fm3 <- clm(rating ~ temp + x + I(x^2), data=wine) 246s > fm4 <- clm(rating ~ temp + poly(x, 2), data=wine) 246s > ## Same model fits, but different parameterizations: 246s > stopifnot( 246s + !isTRUE(all.equal(coef(fm3), coef(fm4), check.names=FALSE)) 246s + ) 246s > stopifnot(isTRUE(all.equal(logLik(fm3), logLik(fm4)))) 246s > newData <- expand.grid(temp = levels(wine$temp), 246s + x=seq(-1, 7, 3)) 246s > predict(fm3, newdata=newData)$fit 246s 1 2 3 4 5 246s 1 0.206057293 0.56152859 0.2029812 0.0245885 0.004844463 246s 2 0.036289668 0.28766182 0.5031703 0.1404155 0.032462707 246s 3 0.147105364 0.53988789 0.2693657 0.0363691 0.007271946 246s 4 0.024413857 0.21711772 0.5192073 0.1912002 0.048060899 246s 5 0.035397238 0.28292433 0.5050762 0.1433185 0.033283705 246s 6 0.005296054 0.05815716 0.3400568 0.4047024 0.191787585 246s > predict(fm4, newdata=newData)$fit 246s 1 2 3 4 5 246s 1 0.206057293 0.56152859 0.2029812 0.0245885 0.004844463 246s 2 0.036289668 0.28766182 0.5031703 0.1404155 0.032462707 246s 3 0.147105364 0.53988789 0.2693657 0.0363691 0.007271946 246s 4 0.024413857 0.21711772 0.5192073 0.1912002 0.048060899 246s 5 0.035397238 0.28292433 0.5050762 0.1433185 0.033283705 246s 6 0.005296054 0.05815716 0.3400568 0.4047024 0.191787585 246s > stopifnot(isTRUE(all.equal(fitted(fm3), fitted(fm4)))) 246s > stopifnot(isTRUE( 246s + all.equal(predict(fm3, newdata=newData)$fit, 246s + predict(fm4, newdata=newData)$fit))) 246s > ################################# 246s > 246s BEGIN TEST test.clm.profile.R 246s 246s R version 4.4.3 (2025-02-28) -- "Trophy Case" 246s Copyright (C) 2025 The R Foundation for Statistical Computing 246s Platform: x86_64-pc-linux-gnu 246s 246s R is free software and comes with ABSOLUTELY NO WARRANTY. 246s You are welcome to redistribute it under certain conditions. 246s Type 'license()' or 'licence()' for distribution details. 246s 246s R is a collaborative project with many contributors. 246s Type 'contributors()' for more information and 246s 'citation()' on how to cite R or R packages in publications. 246s 246s Type 'demo()' for some demos, 'help()' for on-line help, or 246s 'help.start()' for an HTML browser interface to help. 246s Type 'q()' to quit R. 246s 246s > library(ordinal) 246s > 246s > ## Testing that the profile remains the same - that the model object 246s > ## is not 'distorted' by update(object/fitted, doFit=FALSE) 246s > set.seed(1234) 246s > wts <- runif(nrow(wine), 0, 2) 246s > fm3 <- clm(rating ~ temp + contact, data=wine, 246s + weights=wts) 246s > pr <- profile(fm3) 247s > 247s > set.seed(1234) 247s > fm3 <- clm(rating ~ temp + contact, data=wine, 247s + weights=runif(nrow(wine), 0, 2)) 247s > pr3 <- profile(fm3) 247s > ## > set.seed(1234) 247s > ## > fm3 <- clm(rating ~ temp + contact, data=wine, 247s > ## + weights=runif(nrow(wine), 0, 2)) 247s > ## > pr3 <- profile(fm3) 247s > ## Warning messages: 247s > ## 1: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 247s > ## profile may be unreliable for tempwarm because only 1 247s > ## steps were taken down 247s > ## 2: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 247s > ## profile may be unreliable for tempwarm because only 1 247s > ## steps were taken up 247s > ## 3: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 247s > ## profile may be unreliable for contactyes because only 1 247s > ## steps were taken down 247s > ## 4: In profile.clm.beta(fitted, which.beta, alpha, max.steps, nsteps, : 247s > ## profile may be unreliable for contactyes because only 1 247s > ## steps were taken up 247s > ## 247s > stopifnot(isTRUE(all.equal(pr, pr3, check.attributes=FALSE))) 247s > stopifnot( 247s + isTRUE(all.equal(pr$tempwarm[, "lroot"], pr3$tempwarm[, "lroot"])), 247s + isTRUE(all.equal(pr$contactyes[, "lroot"], pr3$contactyes[, "lroot"]))) 247s > 247s BEGIN TEST test.clm.single.anova.R 247s 247s R version 4.4.3 (2025-02-28) -- "Trophy Case" 247s Copyright (C) 2025 The R Foundation for Statistical Computing 247s Platform: x86_64-pc-linux-gnu 247s 247s R is free software and comes with ABSOLUTELY NO WARRANTY. 247s You are welcome to redistribute it under certain conditions. 247s Type 'license()' or 'licence()' for distribution details. 247s 247s R is a collaborative project with many contributors. 247s Type 'contributors()' for more information and 247s 'citation()' on how to cite R or R packages in publications. 247s 247s Type 'demo()' for some demos, 'help()' for on-line help, or 247s 'help.start()' for an HTML browser interface to help. 247s Type 'q()' to quit R. 247s 247s > # test.clm.single.anova.R 247s > 247s > library(ordinal) 247s > 247s > # WRE says "using if(requireNamespace("pkgname")) is preferred, if possible." 247s > # even in tests: 247s > assertError <- function(expr, ...) 247s + if(requireNamespace("tools")) tools::assertError(expr, ...) else invisible() 247s > assertWarning <- function(expr, ...) 247s + if(requireNamespace("tools")) tools::assertWarning(expr, ...) else invisible() 247s > 247s > fm <- clm(rating ~ temp * contact, scale=~contact, data=wine) 247s > 247s > anova(fm, type="I") 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 17.1046 3.538e-05 *** 248s contact 1 9.1574 0.002477 ** 248s temp:contact 1 0.1097 0.740512 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type="II") 248s Type II Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 17.1046 3.538e-05 *** 248s contact 1 9.1574 0.002477 ** 248s temp:contact 1 0.1097 0.740512 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type="III") 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 9.5681 0.00198 ** 248s contact 1 4.1830 0.04083 * 248s temp:contact 1 0.1097 0.74051 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type=1) 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 17.1046 3.538e-05 *** 248s contact 1 9.1574 0.002477 ** 248s temp:contact 1 0.1097 0.740512 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type=2) 248s Type II Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 17.1046 3.538e-05 *** 248s contact 1 9.1574 0.002477 ** 248s temp:contact 1 0.1097 0.740512 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type=3) 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 9.5681 0.00198 ** 248s contact 1 4.1830 0.04083 * 248s temp:contact 1 0.1097 0.74051 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type="1") 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 17.1046 3.538e-05 *** 248s contact 1 9.1574 0.002477 ** 248s temp:contact 1 0.1097 0.740512 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type="2") 248s Type II Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 17.1046 3.538e-05 *** 248s contact 1 9.1574 0.002477 ** 248s temp:contact 1 0.1097 0.740512 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type="3") 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 9.5681 0.00198 ** 248s contact 1 4.1830 0.04083 * 248s temp:contact 1 0.1097 0.74051 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type="marginal") 248s Marginal Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 9.5681 0.00198 ** 248s contact 1 4.1830 0.04083 * 248s temp:contact 1 0.1097 0.74051 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > 248s > # Nominal effects: 248s > fm <- clm(rating ~ temp, nominal=~contact, data=wine) 248s > anova(fm) 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 22.166 2.501e-06 *** 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > 248s > # Flexible links: 248s > fm1 <- clm(rating ~ temp + contact, link="log-gamma", data=wine) 248s Changing to 'nlminb' optimizer for flexible link function 248s Warning message: 248s (-1) Model failed to converge with max|grad| = 9.92642e-05 (tol = 1e-06) 248s > anova(fm1, type=1) 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 26.150 3.16e-07 *** 248s contact 1 10.369 0.001282 ** 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm1, type=2) 248s Type II Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 26.150 3.16e-07 *** 248s contact 1 10.369 0.001282 ** 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm1, type=3) 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 26.150 3.16e-07 *** 248s contact 1 10.369 0.001282 ** 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > 248s > # Equivalence of tests irrespective of contrasts: 248s > fm1 <- clm(SURENESS ~ PRODID * SOUPFREQ, data=soup) 248s > # summary(fm1) 248s > (an1 <- anova(fm1, type=3)) 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s PRODID 5 72.5901 2.959e-14 *** 248s SOUPFREQ 2 1.8132 0.4039 248s PRODID:SOUPFREQ 10 8.5837 0.5720 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > fm2 <- clm(SURENESS ~ PRODID * SOUPFREQ, data=soup, 248s + contrasts = list(SOUPFREQ = "contr.sum", PRODID = "contr.SAS")) 248s > # summary(fm2) 248s > anova(fm1, fm2) 248s Likelihood ratio tests of cumulative link models: 248s 248s formula: link: threshold: 248s fm1 SURENESS ~ PRODID * SOUPFREQ logit flexible 248s fm2 SURENESS ~ PRODID * SOUPFREQ logit flexible 248s 248s no.par AIC logLik LR.stat df Pr(>Chisq) 248s fm1 22 5388 -2672 248s fm2 22 5388 -2672 0 0 248s > (an2 <- anova(fm2, type=3)) 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s PRODID 5 72.5901 2.959e-14 *** 248s SOUPFREQ 2 1.8132 0.4039 248s PRODID:SOUPFREQ 10 8.5837 0.5720 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > stopifnot( 248s + isTRUE(all.equal(an1, an2, check.attributes=FALSE)) 248s + ) 248s > 248s > 248s > # Aliased coefficients: 248s > fm1 <- clm(SURENESS ~ PRODID * DAY, data=soup) 248s > anova(fm1, type=1) 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s PRODID 5 185.2017 < 2e-16 *** 248s DAY 1 4.1131 0.04255 * 248s PRODID:DAY 4 5.1186 0.27534 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm1, type=2) 248s Type II Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s PRODID 5 181.5967 < 2e-16 *** 248s DAY 1 4.1131 0.04255 * 248s PRODID:DAY 4 5.1186 0.27534 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm1, type=3) 248s Missing cells for: PRODID3:DAY2. 248s Interpret type III hypotheses with care. 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s PRODID 5 76.3722 4.81e-15 *** 248s DAY 1 10.1485 0.001444 ** 248s PRODID:DAY 4 5.1186 0.275344 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > 248s > # Aliased term (due to nominal effects): 248s > fm <- clm(rating ~ temp * contact, nominal=~contact, data=wine) 248s > anova(fm, type=1) 248s Type I Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 22.066 2.634e-06 *** 248s contact 248s temp:contact 1 0.250 0.6171 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type=2) 248s Type II Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 22.066 2.634e-06 *** 248s contact 248s temp:contact 1 0.250 0.6171 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > anova(fm, type=3) 248s Type III Analysis of Deviance Table with Wald chi-square tests 248s 248s Df Chisq Pr(>Chisq) 248s temp 1 9.6335 0.001911 ** 248s contact 248s temp:contact 1 0.2500 0.617071 248s --- 248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 248s > 248s > # model with all NA in vcov(object): 248s > fm <- clm(rating ~ temp * contact, nominal=~contact, scale=~contact, data=wine) 248s > assertError(anova(fm, type=1)) # error 248s Warning message: 248s (1) Hessian is numerically singular: parameters are not uniquely determined 248s In addition: Absolute and relative convergence criteria were met 248s Loading required namespace: tools 248s > assertError(anova(fm, type=2)) # error 248s > assertError(anova(fm, type=3)) # error 248s > all(is.na(vcov(fm))) 248s [1] TRUE 248s > 248s BEGIN TEST test.general.R 248s 248s R version 4.4.3 (2025-02-28) -- "Trophy Case" 248s Copyright (C) 2025 The R Foundation for Statistical Computing 248s Platform: x86_64-pc-linux-gnu 248s 248s R is free software and comes with ABSOLUTELY NO WARRANTY. 248s You are welcome to redistribute it under certain conditions. 248s Type 'license()' or 'licence()' for distribution details. 248s 248s R is a collaborative project with many contributors. 248s Type 'contributors()' for more information and 248s 'citation()' on how to cite R or R packages in publications. 248s 248s Type 'demo()' for some demos, 'help()' for on-line help, or 248s 'help.start()' for an HTML browser interface to help. 248s Type 'q()' to quit R. 248s 248s > 248s > txt <- citation("ordinal") 248s > stopifnot(as.logical(grep("year", txt))) 248s > 248s BEGIN TEST test.makeThresholds.R 248s 248s R version 4.4.3 (2025-02-28) -- "Trophy Case" 248s Copyright (C) 2025 The R Foundation for Statistical Computing 248s Platform: x86_64-pc-linux-gnu 248s 248s R is free software and comes with ABSOLUTELY NO WARRANTY. 248s You are welcome to redistribute it under certain conditions. 248s Type 'license()' or 'licence()' for distribution details. 248s 248s R is a collaborative project with many contributors. 248s Type 'contributors()' for more information and 248s 'citation()' on how to cite R or R packages in publications. 248s 248s Type 'demo()' for some demos, 'help()' for on-line help, or 248s 'help.start()' for an HTML browser interface to help. 248s Type 'q()' to quit R. 248s 248s > # test.makeThresholds.R 248s > 248s > library(ordinal) 249s > 249s > # Prvious bug which is now fixed: 249s > res <- ordinal:::makeThresholds(letters[1:3], "symmetric") 249s > stopifnot(length(res$alpha.names) == res$nalpha) 249s > # length(res$alpha.names) used to be 4 249s > 249s > # Real data example: 249s > wine <- within(wine, { 249s + rating_comb3b <- rating 249s + levels(rating_comb3b) <- c("1-2", "1-2", "3", "4-5", "4-5") 249s + }) 249s > wine$rating_comb3b[1] <- "4-5" # Need to remove the zero here to avoid inf MLE 249s > ftable(rating_comb3b ~ temp + contact, data=wine) 249s rating_comb3b 1-2 3 4-5 249s temp contact 249s cold no 12 5 1 249s yes 8 8 2 249s warm no 5 8 5 249s yes 1 5 12 249s > 249s > fm.comb3_c <- clm(rating_comb3b ~ contact, #scale=~contact, 249s + threshold = "symmetric", data=wine) # no error 249s > 249s BEGIN TEST test.sign.R 249s 249s R version 4.4.3 (2025-02-28) -- "Trophy Case" 249s Copyright (C) 2025 The R Foundation for Statistical Computing 249s Platform: x86_64-pc-linux-gnu 249s 249s R is free software and comes with ABSOLUTELY NO WARRANTY. 249s You are welcome to redistribute it under certain conditions. 249s Type 'license()' or 'licence()' for distribution details. 249s 249s R is a collaborative project with many contributors. 249s Type 'contributors()' for more information and 249s 'citation()' on how to cite R or R packages in publications. 249s 249s Type 'demo()' for some demos, 'help()' for on-line help, or 249s 'help.start()' for an HTML browser interface to help. 249s Type 'q()' to quit R. 249s 249s > # test.sign.R 249s > 249s > # Test the use of sign.location and sign.nominal in clm.control(): 249s > 249s > library(ordinal) 250s > 250s > fm1 <- clm(rating ~ temp + contact, data=wine) 250s > fm2 <- clm(rating ~ temp + contact, data=wine, 250s + sign.location="positive") 250s > # dput(names(fm1)) 250s > keep <- c("aliased", "alpha", "cond.H", 250s + "contrasts", "convergence", "df.residual", "edf", 250s + "fitted.values", "formula", "formulas", "gradient", 250s + "info", "link", "logLik", "maxGradient", "message", "model", 250s + "n", "niter", "nobs", "start", "terms", "Theta", "threshold", 250s + "tJac", "xlevels", "y", "y.levels") 250s > check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1[keep], fm2[keep]) 250s > stopifnot(all(check)) 250s > stopifnot(isTRUE(all.equal( 250s + fm1$beta, - fm2$beta 250s + ))) 250s > 250s > fm1 <- clm(rating ~ temp, nominal=~ contact, data=wine) 250s > fm2 <- clm(rating ~ temp, nominal=~ contact, data=wine, 250s + sign.nominal="negative") 250s > keep <- c("aliased", "beta", "cond.H", 250s + "contrasts", "convergence", "df.residual", "edf", 250s + "fitted.values", "formula", "formulas", "gradient", 250s + "info", "link", "logLik", "maxGradient", "message", "model", 250s + "n", "niter", "nobs", "start", "terms", "Theta", "threshold", 250s + "tJac", "xlevels", "y", "y.levels") 250s > # check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1, fm2) 250s > check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1[keep], fm2[keep]) 250s > stopifnot(all(check)) 250s > stopifnot(isTRUE(all.equal( 250s + fm1$alpha[5:8], -fm2$alpha[5:8] 250s + ))) 250s > 250s > 250s > fm1 <- clm(rating ~ temp, nominal=~ contact, data=wine) 250s > fm2 <- clm(rating ~ temp, nominal=~ contact, data=wine, 250s + sign.nominal="negative", sign.location="positive") 250s > keep <- c("aliased", "cond.H", 250s + "contrasts", "convergence", "df.residual", "edf", 250s + "fitted.values", "formula", "formulas", "gradient", 250s + "info", "link", "logLik", "maxGradient", "message", "model", 250s + "n", "niter", "nobs", "start", "terms", "Theta", "threshold", 250s + "tJac", "xlevels", "y", "y.levels") 250s > # check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1, fm2) 250s > check <- mapply(function(x, y) isTRUE(all.equal(x, y)), fm1[keep], fm2[keep]) 250s > stopifnot(all(check)) 250s > stopifnot( 250s + isTRUE(all.equal(fm1$alpha[5:8], -fm2$alpha[5:8])), 250s + isTRUE(all.equal(fm1$beta, -fm2$beta)) 250s + ) 250s > 250s > # Check predict method: 250s > newData <- with(wine, expand.grid(temp=levels(temp), contact=levels(contact))) 250s > (p1 <- predict(fm1, newdata=newData)) 250s $fit 250s 1 2 3 4 5 250s 1 0.210312404 0.56637121 0.1953950 0.0185460 0.009375394 250s 2 0.020998377 0.19781391 0.5182972 0.1577343 0.105156202 250s 3 0.050301839 0.38380275 0.4329644 0.1065821 0.026348960 250s 4 0.004247588 0.05393811 0.2862121 0.4040930 0.251509196 250s 250s > (p2 <- predict(fm2, newdata=newData)) 250s $fit 250s 1 2 3 4 5 250s 1 0.210312404 0.56637121 0.1953950 0.0185460 0.009375394 250s 2 0.020998377 0.19781391 0.5182972 0.1577343 0.105156202 250s 3 0.050301839 0.38380275 0.4329644 0.1065821 0.026348960 250s 4 0.004247588 0.05393811 0.2862121 0.4040930 0.251509196 250s 250s > stopifnot(isTRUE(all.equal(p1, p2))) 250s > 250s > stopifnot(isTRUE( 250s + all.equal(predict(fm1, newdata=wine, se=TRUE, interval=TRUE), 250s + predict(fm2, newdata=wine, se=TRUE, interval=TRUE)) 250s + )) 250s > 250s > # Check profile and confint methods: 250s > confint.default(fm1) 250s 2.5 % 97.5 % 250s 1|2.(Intercept) -2.4250844 -0.2210024 250s 2|3.(Intercept) 0.3158056 2.1770814 250s 3|4.(Intercept) 2.2642614 4.8358258 250s 4|5.(Intercept) 2.9738888 6.3466053 250s 1|2.contactyes -3.8921464 0.6620280 250s 2|3.contactyes -2.6692032 -0.3539315 250s 3|4.contactyes -2.9464535 -0.4030579 250s 4|5.contactyes -2.8077520 0.7065061 250s tempwarm 1.4703720 3.5677176 250s > confint.default(fm2) 250s 2.5 % 97.5 % 250s 1|2.(Intercept) -2.4250844 -0.2210024 250s 2|3.(Intercept) 0.3158056 2.1770814 250s 3|4.(Intercept) 2.2642614 4.8358258 250s 4|5.(Intercept) 2.9738888 6.3466053 250s 1|2.contactyes -0.6620280 3.8921464 250s 2|3.contactyes 0.3539315 2.6692032 250s 3|4.contactyes 0.4030579 2.9464535 250s 4|5.contactyes -0.7065061 2.8077520 250s tempwarm -3.5677176 -1.4703720 250s > 250s > stopifnot( 250s + isTRUE(all.equal(confint(fm1), -confint(fm2)[, 2:1, drop=FALSE], 250s + check.attributes=FALSE)) 250s + ) 250s > 250s > fm1 <- clm(rating ~ temp + contact, data=wine) 250s > fm2 <- clm(rating ~ temp + contact, data=wine, 250s + sign.location="positive") 250s > pr1 <- profile(fm1) 250s > pr2 <- profile(fm2) 250s > stopifnot( 250s + isTRUE(all.equal(confint(fm1), - confint(fm2)[, 2:1], check.attributes=FALSE)) 250s + ) 250s > 250s > 250s BEGIN TEST test0weights.R 250s 250s R version 4.4.3 (2025-02-28) -- "Trophy Case" 250s Copyright (C) 2025 The R Foundation for Statistical Computing 250s Platform: x86_64-pc-linux-gnu 250s 250s R is free software and comes with ABSOLUTELY NO WARRANTY. 250s You are welcome to redistribute it under certain conditions. 250s Type 'license()' or 'licence()' for distribution details. 250s 250s R is a collaborative project with many contributors. 250s Type 'contributors()' for more information and 250s 'citation()' on how to cite R or R packages in publications. 250s 250s Type 'demo()' for some demos, 'help()' for on-line help, or 250s 'help.start()' for an HTML browser interface to help. 250s Type 'q()' to quit R. 250s 250s > library(ordinal) 251s > options(contrasts = c("contr.treatment", "contr.poly")) 251s > ## library(devtools) 251s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 251s > ## clean_dll(pkg = r2path) 251s > ## load_all(r2path) 251s > 251s > ## one zero weight: 251s > data(wine, package="ordinal") 251s > wts <- rep(1, nrow(wine)) 251s > wine$rating 251s [1] 2 3 3 4 4 4 5 5 1 2 1 3 2 3 5 4 2 3 3 2 5 5 4 4 3 2 3 2 3 2 5 3 2 3 4 3 3 3 251s [39] 3 3 3 2 3 2 2 4 5 4 1 1 2 2 2 3 2 3 2 2 2 3 3 3 3 4 1 2 3 2 3 2 4 4 251s Levels: 1 < 2 < 3 < 4 < 5 251s > wts[1] <- 0 251s > fm1 <- clm(rating ~ contact + temp, data=wine, weights=wts) 251s > fm1 251s formula: rating ~ contact + temp 251s data: wine 251s 251s link threshold nobs logLik AIC niter max.grad cond.H 251s logit flexible 71 -85.92 183.84 6(0) 3.43e-12 2.7e+01 251s 251s Coefficients: 251s contactyes tempwarm 251s 1.511 2.482 251s 251s Threshold coefficients: 251s 1|2 2|3 3|4 4|5 251s -1.295 1.220 3.437 4.975 251s > fm1$n ## 72 251s [1] 72 251s > fm1$nobs ## 71 251s [1] 71 251s > confint(fm1) 252s 2.5 % 97.5 % 252s contactyes 0.5951066 2.478924 252s tempwarm 1.4856829 3.577621 252s > plot(profile(fm1)) 252s > plot(slice(fm1), 5) 252s > convergence(fm1) 252s nobs logLik niter max.grad cond.H logLik.Error 252s 71 -85.92 6(0) 3.43e-12 2.7e+01 <1e-10 252s 252s Estimate Std.Err Gradient Error Cor.Dec Sig.Dig 252s 1|2 -1.295 0.5220 7.57e-13 7.84e-14 12 13 252s 2|3 1.220 0.4436 2.65e-12 -1.27e-13 12 13 252s 3|4 3.437 0.6014 -3.43e-12 -7.17e-13 11 12 252s 4|5 4.975 0.7341 -6.06e-14 -7.01e-13 11 12 252s contactyes 1.511 0.4785 1.53e-13 -1.95e-13 12 13 252s tempwarm 2.482 0.5303 -4.07e-13 -4.95e-13 12 13 252s 252s Eigen values of Hessian: 252s 21.7419 18.5476 10.4115 5.2426 4.0755 0.8013 252s 252s Convergence message from clm: 252s (0) successful convergence 252s In addition: Absolute and relative convergence criteria were met 252s 252s > drop1(fm1, test="Chi") 252s Single term deletions 252s 252s Model: 252s rating ~ contact + temp 252s Df AIC LRT Pr(>Chi) 252s 183.84 252s contact 1 192.54 10.698 0.001072 ** 252s temp 1 208.07 26.234 3.024e-07 *** 252s --- 252s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 252s > add1(fm1, scope=~.^2, test="Chi") 252s Single term additions 252s 252s Model: 252s rating ~ contact + temp 252s Df AIC LRT Pr(>Chi) 252s 183.84 252s contact:temp 1 185.66 0.18256 0.6692 252s > ## clm_anova(fm1) 252s > pred <- predict(fm1, newdata=wine) ## OK 252s > step.fm1 <- step(fm1, trace=0) 252s > fitted(fm1) 252s [1] 0.19683278 0.44514183 0.09677403 0.20147980 0.20147980 0.27261558 252s [7] 0.27261558 0.21497073 0.55705124 0.05699435 0.44514183 0.19814731 252s [13] 0.50160837 0.27261558 0.36288756 0.55705124 0.19683278 0.44514183 252s [19] 0.37073110 0.07640020 0.07640020 0.36288756 0.36288756 0.19683278 252s [25] 0.55705124 0.44514183 0.37073110 0.50160837 0.19814731 0.27261558 252s [31] 0.30572865 0.55705124 0.19683278 0.09677403 0.44514183 0.50160837 252s [37] 0.50160837 0.30572865 0.30572865 0.19683278 0.55705124 0.44514183 252s [43] 0.37073110 0.19814731 0.20147980 0.27261558 0.36288756 0.21497073 252s [49] 0.21497073 0.37073110 0.37073110 0.19814731 0.50160837 0.05374460 252s [55] 0.30572865 0.55705124 0.55705124 0.37073110 0.44514183 0.50160837 252s [61] 0.50160837 0.30572865 0.36288756 0.21497073 0.55705124 0.44514183 252s [67] 0.37073110 0.50160837 0.19814731 0.36288756 0.36288756 252s > dim(model.matrix(fm1)$X) 252s [1] 72 3 252s > dim(model.matrix(fm1, "B")$B1) 252s [1] 71 6 252s > mf <- update(fm1, method="model.frame") 252s > str(mf) 252s 'data.frame': 72 obs. of 4 variables: 252s $ rating : Ord.factor w/ 5 levels "1"<"2"<"3"<"4"<..: 2 3 3 4 4 4 5 5 1 2 ... 252s $ contact : Factor w/ 2 levels "no","yes": 1 1 2 2 1 1 2 2 1 1 ... 252s $ temp : Factor w/ 2 levels "cold","warm": 1 1 1 1 2 2 2 2 1 1 ... 252s $ (weights): num 0 1 1 1 1 1 1 1 1 1 ... 252s - attr(*, "terms")=Classes 'terms', 'formula' language rating ~ contact + temp 252s .. ..- attr(*, "variables")= language list(rating, contact, temp) 252s .. ..- attr(*, "factors")= int [1:3, 1:2] 0 1 0 0 0 1 252s .. .. ..- attr(*, "dimnames")=List of 2 252s .. .. .. ..$ : chr [1:3] "rating" "contact" "temp" 252s .. .. .. ..$ : chr [1:2] "contact" "temp" 252s .. ..- attr(*, "term.labels")= chr [1:2] "contact" "temp" 252s .. ..- attr(*, "order")= int [1:2] 1 1 252s .. ..- attr(*, "intercept")= int 1 252s .. ..- attr(*, "response")= int 1 252s .. ..- attr(*, ".Environment")= 252s .. ..- attr(*, "predvars")= language list(rating, contact, temp) 252s .. ..- attr(*, "dataClasses")= Named chr [1:4] "ordered" "factor" "factor" "numeric" 252s .. .. ..- attr(*, "names")= chr [1:4] "rating" "contact" "temp" "(weights)" 252s > wts <- mf$wts 252s > dim(model.matrix(fm1)$X[wts > 0, , drop=FALSE]) 252s [1] 0 3 252s > 252s > fm1b <- clm(rating ~ temp, scale=~contact, data=wine, weights=wts) 252s > summary(fm1b) 252s formula: rating ~ temp 252s scale: ~contact 252s data: wine 252s 252s link threshold nobs logLik AIC niter max.grad cond.H 252s logit flexible 72 -91.92 195.83 8(0) 1.57e-09 5.6e+01 252s 252s Coefficients: 252s Estimate Std. Error z value Pr(>|z|) 252s tempwarm 2.1690 0.5527 3.924 8.69e-05 *** 252s --- 252s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 252s 252s log-scale coefficients: 252s Estimate Std. Error z value Pr(>|z|) 252s contactyes -0.1222 0.2775 -0.44 0.66 252s 252s Threshold coefficients: 252s Estimate Std. Error z value 252s 1|2 -1.8957 0.4756 -3.986 252s 2|3 0.3668 0.3442 1.066 252s 3|4 2.2483 0.5932 3.790 252s 4|5 3.5393 0.8336 4.246 252s > pr <- profile(fm1b) 252s > confint(pr) 252s 2.5 % 97.5 % 252s tempwarm 1.2122036 3.4033767 252s sca.contactyes -0.6721766 0.4156449 252s > plot(pr, 1) 252s > fm1c <- clm(rating ~ temp, nominal=~contact, data=wine, weights=wts) 252s > summary(fm1c) 252s formula: rating ~ temp 252s nominal: ~contact 252s data: wine 252s 252s link threshold nobs logLik AIC niter max.grad cond.H 252s logit flexible 72 -86.21 190.42 6(0) 1.64e-10 4.8e+01 252s 252s Coefficients: 252s Estimate Std. Error z value Pr(>|z|) 252s tempwarm 2.519 0.535 4.708 2.5e-06 *** 252s --- 252s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 252s 252s Threshold coefficients: 252s Estimate Std. Error z value 252s 1|2.(Intercept) -1.3230 0.5623 -2.353 252s 2|3.(Intercept) 1.2464 0.4748 2.625 252s 3|4.(Intercept) 3.5500 0.6560 5.411 252s 4|5.(Intercept) 4.6602 0.8604 5.416 252s 1|2.contactyes -1.6151 1.1618 -1.390 252s 2|3.contactyes -1.5116 0.5906 -2.559 252s 3|4.contactyes -1.6748 0.6488 -2.581 252s 4|5.contactyes -1.0506 0.8965 -1.172 252s > pr <- profile(fm1c) 252s > confint(pr) 252s 2.5 % 97.5 % 252s tempwarm 1.516862 3.629098 252s > plot(pr, 1) 252s > 252s > ## nominal.test(fm1) 252s > ## scale.test(fm1) 252s > 252s > ## zero out an entire response category: 252s > wts2 <- 1 * with(wine, rating != "2") 252s > fm2 <- clm(rating ~ contact + temp, data=wine, weights=wts2) 252s > fm2 252s formula: rating ~ contact + temp 252s data: wine 252s 252s link threshold nobs logLik AIC niter max.grad cond.H 252s logit flexible 50 -46.76 103.52 7(0) 3.56e-13 4.2e+01 252s 252s Coefficients: 252s contactyes tempwarm 252s 1.593 3.062 252s 252s Threshold coefficients: 252s 1|3 3|4 4|5 252s -0.5173 3.6238 5.3657 252s > fm2$n ## 72 252s [1] 72 252s > fm2$nobs ## 50 252s [1] 50 252s > ## Dimension of X and B1, B2 differ: 252s > dim(model.matrix(fm2)$X) 252s [1] 72 3 252s > dim(model.matrix(fm2, "B")$B1) 252s [1] 50 5 252s > ## Cannot directly evaluate predictions on the original data: 252s > try(predict(fm2, newdata=wine), silent=TRUE)[1] 252s [1] "Error in predict.clm(fm2, newdata = wine) : \n response factor 'rating' has new levels\n" 252s > confint(fm2) 252s 2.5 % 97.5 % 252s contactyes 0.4216272 2.876550 252s tempwarm 1.5970977 5.026527 252s > profile(fm2) 252s $contactyes 252s lroot par.vals.1|3 par.vals.3|4 par.vals.4|5 par.vals.contactyes 252s 1 3.4747852 -1.448538968 2.255543944 3.804439509 -0.447374822 252s 2 3.0276372 -1.308493024 2.407453551 3.967827135 -0.192380808 252s 3 2.5822211 -1.174976592 2.565043880 4.140537415 0.062613207 252s 4 2.1395315 -1.048101582 2.728199207 4.322490592 0.317607222 252s 5 1.7005507 -0.927983229 2.896810974 4.513576014 0.572601236 252s 6 1.2662317 -0.814738724 3.070776301 4.713647671 0.827595251 252s 7 0.8374817 -0.708483160 3.249996208 4.922519451 1.082589265 252s 8 0.4151468 -0.609322477 3.434373593 5.139960291 1.337583280 252s 9 0.0000000 -0.517343412 3.623810880 5.365689290 1.592577294 252s 10 -0.4072702 -0.432600941 3.818207180 5.599370818 1.847571309 252s 11 -0.8060673 -0.355104205 4.017454848 5.840609731 2.102565323 252s 12 -1.1958918 -0.284802472 4.221435388 6.088946911 2.357559338 252s 13 -1.5763436 -0.221573075 4.430015019 6.343855637 2.612553352 252s 14 -1.9471215 -0.165213368 4.643040370 6.604739566 2.867547367 252s 15 -2.3080198 -0.115438462 4.860335061 6.870933284 3.122541381 252s 16 -2.6589228 -0.071885700 5.081697900 7.141706504 3.377535396 252s 17 -2.9997972 -0.034125762 5.306903276 7.416272839 3.632529410 252s 18 -3.3306833 -0.001679093 5.535703885 7.693803770 3.887523425 252s par.vals.tempwarm 252s 1 2.840981986 252s 2 2.848907417 252s 3 2.863086150 252s 4 2.883227511 252s 5 2.909025226 252s 6 2.940155181 252s 7 2.976272850 252s 8 3.017010511 252s 9 3.061974244 252s 10 3.110740675 252s 11 3.162853507 252s 12 3.217819929 252s 13 3.275107380 252s 14 3.334141312 252s 15 3.394304942 252s 16 3.454942107 252s 17 3.515364293 252s 18 3.574862708 252s 252s $tempwarm 252s lroot par.vals.1|3 par.vals.3|4 par.vals.4|5 par.vals.contactyes 252s 1 3.4300164 -1.3083735 1.7272573 3.1899360 1.3296606 252s 2 2.8813858 -1.1550431 1.9737448 3.4740817 1.3627908 252s 3 2.3491188 -1.0148529 2.2280703 3.7683888 1.3992293 252s 4 1.8354355 -0.8881411 2.4904988 4.0722937 1.4379639 252s 5 1.3422735 -0.7751174 2.7612331 4.3850175 1.4778669 252s 6 0.8712358 -0.6758159 3.0403898 4.7055883 1.5177348 252s 7 0.4235444 -0.5900448 3.3279674 5.0328829 1.5563515 252s 8 0.0000000 -0.5173434 3.6238109 5.3656893 1.5925773 252s 9 -0.3990485 -0.4569595 3.9275814 5.7027863 1.6254526 252s 10 -0.7737184 -0.4078590 4.2387443 6.0430310 1.6542958 252s 11 -1.1245809 -0.3687765 4.5565843 6.3854348 1.6787668 252s 12 -1.4526173 -0.3383014 4.8802522 6.7292117 1.6988730 252s 13 -1.7591420 -0.3149843 5.2088333 7.0737893 1.7149136 252s 14 -2.0457031 -0.2974396 5.5414220 7.4187857 1.7273842 252s 15 -2.3139760 -0.2844232 5.8771833 7.7639689 1.7368704 252s 16 -2.5656664 -0.2748765 6.2153929 8.1092106 1.7439599 252s 17 -2.8024328 -0.2679376 6.5554528 8.4544482 1.7491850 252s 18 -3.0258332 -0.2629290 6.8968876 8.7996559 1.7529951 252s 19 -3.2372944 -0.2593326 7.2393314 9.1448275 1.7557514 252s 20 -3.4380992 -0.2567600 7.5825083 9.4899654 1.7577335 252s par.vals.tempwarm 252s 1 0.6468007 252s 2 0.9918255 252s 3 1.3368503 252s 4 1.6818751 252s 5 2.0268999 252s 6 2.3719247 252s 7 2.7169495 252s 8 3.0619742 252s 9 3.4069990 252s 10 3.7520238 252s 11 4.0970486 252s 12 4.4420734 252s 13 4.7870982 252s 14 5.1321230 252s 15 5.4771478 252s 16 5.8221726 252s 17 6.1671974 252s 18 6.5122222 252s 19 6.8572470 252s 20 7.2022718 252s 252s attr(,"original.fit") 252s formula: rating ~ contact + temp 252s data: wine 252s 252s link threshold nobs logLik AIC niter max.grad cond.H 252s logit flexible 50 -46.76 103.52 7(0) 3.56e-13 4.2e+01 252s 252s Coefficients: 252s contactyes tempwarm 252s 1.593 3.062 252s 252s Threshold coefficients: 252s 1|3 3|4 4|5 252s -0.5173 3.6238 5.3657 252s attr(,"class") 252s [1] "profile.clm" 252s > plot(slice(fm2), 5) 252s > step.fm2 <- step(fm2, trace=0) 252s > fitted(fm2) 252s [1] 0.60053892 0.77590129 0.09349820 0.27230685 0.27230685 0.32934749 252s [7] 0.32934749 0.37347364 0.10813631 0.77590129 0.60973967 0.32934749 252s [13] 0.40771198 0.60053892 0.77590129 0.09081575 0.09081575 0.40771198 252s [19] 0.40771198 0.60053892 0.77590129 0.60973967 0.32934749 0.25729874 252s [25] 0.60053892 0.09349820 0.77590129 0.60973967 0.60973967 0.25729874 252s [31] 0.25729874 0.60053892 0.77590129 0.27230685 0.32934749 0.40771198 252s [37] 0.37347364 0.37347364 0.60973967 0.25729874 0.77590129 0.60973967 252s [43] 0.60973967 0.25729874 0.40771198 0.37347364 0.77590129 0.60973967 252s [49] 0.40771198 0.40771198 252s > ## Scale and nominal effects: 252s > fm2b <- clm(rating ~ temp, scale=~contact, data=wine, weights=wts2) 252s > summary(fm2b) 252s formula: rating ~ temp 252s scale: ~contact 252s data: wine 252s 252s link threshold nobs logLik AIC niter max.grad cond.H 252s logit flexible 50 -50.35 110.71 9(0) 2.51e-08 1.2e+02 252s 252s Coefficients: 252s Estimate Std. Error z value Pr(>|z|) 252s tempwarm 2.667 1.059 2.519 0.0118 * 252s --- 252s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 252s 252s log-scale coefficients: 252s Estimate Std. Error z value Pr(>|z|) 252s contactyes -0.09812 0.38836 -0.253 0.801 252s 252s Threshold coefficients: 252s Estimate Std. Error z value 252s 1|3 -1.2009 0.5033 -2.386 252s 3|4 2.3219 1.0427 2.227 252s 4|5 3.7986 1.3876 2.738 252s > pr <- profile(fm2b) 252s > confint(pr) 252s 2.5 % 97.5 % 252s tempwarm 1.1319929 6.0851931 252s sca.contactyes -0.8403892 0.7190847 252s > plot(pr, 1) 252s > fm2c <- clm(rating ~ temp, nominal=~contact, data=wine, weights=wts2) 252s > summary(fm2c) 252s formula: rating ~ temp 252s nominal: ~contact 252s data: wine 252s 252s link threshold nobs logLik AIC niter max.grad cond.H 252s logit flexible 50 -46.36 106.72 7(0) 1.22e-12 4.8e+01 252s 252s Coefficients: 252s Estimate Std. Error z value Pr(>|z|) 252s tempwarm 3.1100 0.8529 3.646 0.000266 *** 252s --- 252s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 252s 252s Threshold coefficients: 252s Estimate Std. Error z value 252s 1|3.(Intercept) -0.4250 0.6381 -0.666 252s 3|4.(Intercept) 3.6911 0.9505 3.883 252s 4|5.(Intercept) 4.8968 1.1001 4.451 252s 1|3.contactyes -1.8993 1.2128 -1.566 252s 3|4.contactyes -1.7003 0.7432 -2.288 252s 4|5.contactyes -0.9153 0.9243 -0.990 252s > pr <- profile(fm2c) 252s > confint(pr) 252s 2.5 % 97.5 % 252s tempwarm 1.623761 5.102185 252s > plot(pr, 1) 252s > pred <- predict(fm2c, newdata=wine[!names(wine) %in% "rating"]) 252s > pred <- predict(fm2b, newdata=wine[!names(wine) %in% "rating"]) 252s > 252s > ## nominal.test(fm2) 252s > ## scale.test(fm2) 252s > 252s > ## Different data sets (error): 252s > try(anova(fm1, fm2), silent=TRUE)[1] ## OK 252s [1] "Error in anova.clm(fm1, fm2) : \n models were not all fitted to the same dataset\n" 252s > 252s > ## Test clm.fit: 252s > wts2 <- 1 * with(wine, rating != "2") 252s > mf2 <- update(fm2, method="design") 252s > fm3 <- with(mf2, clm.fit(y, X, weights=wts)) 252s > 252s > ################################# 252s > 252s BEGIN TEST testAnova.clm2.R 252s 252s R version 4.4.3 (2025-02-28) -- "Trophy Case" 252s Copyright (C) 2025 The R Foundation for Statistical Computing 252s Platform: x86_64-pc-linux-gnu 252s 252s R is free software and comes with ABSOLUTELY NO WARRANTY. 252s You are welcome to redistribute it under certain conditions. 252s Type 'license()' or 'licence()' for distribution details. 252s 252s R is a collaborative project with many contributors. 252s Type 'contributors()' for more information and 252s 'citation()' on how to cite R or R packages in publications. 252s 252s Type 'demo()' for some demos, 'help()' for on-line help, or 252s 'help.start()' for an HTML browser interface to help. 252s Type 'q()' to quit R. 252s 252s > library(ordinal) 253s > options(contrasts = c("contr.treatment", "contr.poly")) 253s > 253s > ## More manageable data set: 253s > (tab26 <- with(soup, table("Product" = PROD, "Response" = SURENESS))) 253s Response 253s Product 1 2 3 4 5 6 253s Ref 132 161 65 41 121 219 253s Test 96 99 50 57 156 650 253s > dimnames(tab26)[[2]] <- c("Sure", "Not Sure", "Guess", "Guess", "Not Sure", "Sure") 253s > dat26 <- expand.grid(sureness = as.factor(1:6), prod = c("Ref", "Test")) 253s > dat26$wghts <- c(t(tab26)) 253s > m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26, 253s + weights = wghts, link = "logit") 253s > 253s > ## anova 253s > m2 <- update(m1, scale = ~1) 253s > anova(m1, m2) 253s Likelihood ratio tests of cumulative link models: 253s 253s formula: scale: link: threshold: 253s m2 sureness ~ prod ~1 logit flexible 253s m1 sureness ~ prod ~prod logit flexible 253s 253s no.par AIC logLik LR.stat df Pr(>Chisq) 253s m2 6 5392.7 -2690.3 253s m1 7 5389.5 -2687.7 5.1749 1 0.02292 * 253s --- 253s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 253s > mN1 <- clm(sureness ~ 1, nominal = ~prod, data = dat26, 253s + link = "logit") 253s > anova(m1, mN1) 253s Likelihood ratio tests of cumulative link models: 253s 253s formula: nominal: scale: link: threshold: 253s m1 sureness ~ prod ~1 ~prod logit flexible 253s mN1 sureness ~ 1 ~prod ~1 logit flexible 253s 253s no.par AIC logLik LR.stat df Pr(>Chisq) 253s m1 7 5389.489 -2687.745 253s mN1 10 63.002 -21.501 5332.5 3 < 2.2e-16 *** 253s --- 253s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 253s > anova(m1, m2, mN1) 253s Likelihood ratio tests of cumulative link models: 253s 253s formula: nominal: scale: link: threshold: 253s m2 sureness ~ prod ~1 ~1 logit flexible 253s m1 sureness ~ prod ~1 ~prod logit flexible 253s mN1 sureness ~ 1 ~prod ~1 logit flexible 253s 253s no.par AIC logLik LR.stat df Pr(>Chisq) 253s m2 6 5392.664 -2690.332 253s m1 7 5389.489 -2687.745 5.1749 1 0.02292 * 253s mN1 10 63.002 -21.501 5332.4869 3 < 2e-16 *** 253s --- 253s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 253s > 253s > ## dropterm 253s > if(require(MASS)) { 253s + dropterm(m1, test = "Chi") 253s + mB1 <- clm(SURENESS ~ PROD + GENDER + SOUPTYPE, 253s + scale = ~ COLD, data = soup, link = "probit") 253s + dropterm(mB1, test = "Chi") # or 253s + 253s + ## addterm 253s + addterm(mB1, scope = ~.^2, test = "Chi") 253s + ## addterm(mB1, scope = ~ . + AGEGROUP + SOUPFREQ, 253s + ## test = "Chi", which = "location") 253s + ## addterm(mB1, scope = ~ . + GENDER + SOUPTYPE, 253s + ## test = "Chi", which = "scale") 253s + 253s + ## Fit model from polr example: 253s + ## data(housing, package = "MASS") 253s + 253s + fm1 <- clm(Sat ~ Infl + Type + Cont, weights = Freq, data = housing) 253s + ## addterm(fm1, ~ Infl + Type + Cont, test= "Chisq", which = "scale") 253s + dropterm(fm1, test = "Chisq") 253s + fm2 <- update(fm1, scale =~ Cont) 253s + fm3 <- update(fm1, formula =~.-Cont, nominal =~ Cont) 253s + anova(fm1, fm2, fm3) 253s + } 253s Loading required package: MASS 253s Likelihood ratio tests of cumulative link models: 253s 253s formula: nominal: scale: link: threshold: 253s fm1 Sat ~ Infl + Type + Cont ~1 ~1 logit flexible 253s fm2 Sat ~ Infl + Type + Cont ~1 ~Cont logit flexible 253s fm3 Sat ~ Infl + Type ~Cont ~1 logit flexible 253s 253s no.par AIC logLik LR.stat df Pr(>Chisq) 253s fm1 8 3495.1 -1739.6 253s fm2 9 3491.5 -1736.7 5.6559 1 0.0174 * 253s fm3 9 3494.7 -1738.4 -3.2113 0 253s --- 253s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 253s > 253s > 253s BEGIN TEST testCLM.R 253s 253s R version 4.4.3 (2025-02-28) -- "Trophy Case" 253s Copyright (C) 2025 The R Foundation for Statistical Computing 253s Platform: x86_64-pc-linux-gnu 253s 253s R is free software and comes with ABSOLUTELY NO WARRANTY. 253s You are welcome to redistribute it under certain conditions. 253s Type 'license()' or 'licence()' for distribution details. 253s 253s R is a collaborative project with many contributors. 253s Type 'contributors()' for more information and 253s 'citation()' on how to cite R or R packages in publications. 253s 253s Type 'demo()' for some demos, 'help()' for on-line help, or 253s 'help.start()' for an HTML browser interface to help. 253s Type 'q()' to quit R. 253s 253s > library(ordinal) 254s > options(contrasts = c("contr.treatment", "contr.poly")) 254s > ## library(devtools) 254s > ## r2path <- "/Users/rhbc/Documents/Rpackages/ordinal/pkg/ordinal" 254s > ## clean_dll(pkg = r2path) 254s > ## load_all(r2path) 254s > 254s > ## More manageable data set: 254s > data(soup, package="ordinal") 254s > (tab26 <- with(soup, table("Product" = PROD, "Response" = SURENESS))) 254s Response 254s Product 1 2 3 4 5 6 254s Ref 132 161 65 41 121 219 254s Test 96 99 50 57 156 650 254s > dimnames(tab26)[[2]] <- c("Sure", "Not Sure", "Guess", "Guess", "Not Sure", "Sure") 254s > dat26 <- expand.grid(sureness = as.factor(1:6), prod = c("Ref", "Test")) 254s > dat26$wghts <- c(t(tab26)) 254s > m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26, 254s + weights = wghts, link = "logit") 254s > ## print, summary, vcov, logLik, AIC: 254s > m1 254s formula: sureness ~ prod 254s scale: ~prod 254s data: dat26 254s 254s link threshold nobs logLik AIC niter max.grad cond.H 254s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 254s 254s Coefficients: 254s prodTest 254s 1.296 254s 254s log-scale coefficients: 254s prodTest 254s 0.148 254s 254s Threshold coefficients: 254s 1|2 2|3 3|4 4|5 5|6 254s -1.4913 -0.4522 -0.1072 0.1634 0.8829 254s > summary(m1) 254s formula: sureness ~ prod 254s scale: ~prod 254s data: dat26 254s 254s link threshold nobs logLik AIC niter max.grad cond.H 254s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 254s 254s Coefficients: 254s Estimate Std. Error z value Pr(>|z|) 254s prodTest 1.296 0.119 10.89 <2e-16 *** 254s --- 254s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 254s 254s log-scale coefficients: 254s Estimate Std. Error z value Pr(>|z|) 254s prodTest 0.1480 0.0651 2.273 0.023 * 254s --- 254s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 254s 254s Threshold coefficients: 254s Estimate Std. Error z value 254s 1|2 -1.49126 0.09215 -16.183 254s 2|3 -0.45218 0.07182 -6.296 254s 3|4 -0.10721 0.06995 -1.533 254s 4|5 0.16337 0.07025 2.325 254s 5|6 0.88291 0.07957 11.096 254s > vcov(m1) 254s 1|2 2|3 3|4 4|5 5|6 254s 1|2 0.0084917417 0.0046258673 0.0038492096 0.003316006 0.002036170 254s 2|3 0.0046258673 0.0051586967 0.0044974099 0.004099300 0.003352323 254s 3|4 0.0038492096 0.0044974099 0.0048935739 0.004528181 0.003948048 254s 4|5 0.0033160059 0.0040993002 0.0045281811 0.004935721 0.004489054 254s 5|6 0.0020361699 0.0033523229 0.0039480481 0.004489054 0.006331523 254s prodTest 0.0009111749 0.0031074167 0.0039832831 0.004738959 0.007064828 254s prodTest -0.0024312129 -0.0007825923 -0.0001820514 0.000338977 0.001989991 254s prodTest prodTest 254s 1|2 0.0009111749 -0.0024312129 254s 2|3 0.0031074167 -0.0007825923 254s 3|4 0.0039832831 -0.0001820514 254s 4|5 0.0047389591 0.0003389770 254s 5|6 0.0070648284 0.0019899912 254s prodTest 0.0141687135 0.0045752922 254s prodTest 0.0045752922 0.0042385585 254s > 254s > logLik(m1) 254s 'log Lik.' -2687.745 (df=7) 254s > ll.m1 <- structure(-2687.74456343981, df = 7L, nobs = 1847, 254s + class = "logLik") 254s > stopifnot(all.equal(logLik(m1), ll.m1)) 254s > 254s > AIC(m1) 254s [1] 5389.489 254s > 254s > coef(m1) 254s 1|2 2|3 3|4 4|5 5|6 prodTest prodTest 254s -1.4912570 -0.4521846 -0.1072083 0.1633653 0.8829135 1.2958776 0.1479862 254s > cm1 <- c(-1.49125702755587, -0.45218462707814, -0.107208315524318, 0.163365282774162, 254s + 0.88291347877514, 1.29587762626394, 0.147986162902775) 254s > stopifnot(all.equal(as.vector(coef(m1)), cm1)) 254s > 254s > coef(summary(m1)) 254s Estimate Std. Error z value Pr(>|z|) 254s 1|2 -1.4912570 0.09215065 -16.182817 6.667319e-59 254s 2|3 -0.4521846 0.07182407 -6.295726 3.059652e-10 254s 3|4 -0.1072083 0.06995408 -1.532553 1.253861e-01 255s 4|5 0.1633653 0.07025469 2.325329 2.005437e-02 255s 5|6 0.8829135 0.07957087 11.095938 1.312749e-28 255s prodTest 1.2958776 0.11903241 10.886763 1.332938e-27 255s prodTest 0.1479862 0.06510421 2.273066 2.302222e-02 255s > csm1 <- structure(c(-1.49125702755587, -0.45218462707814, -0.107208315524318, 255s + 0.163365282774162, 0.88291347877514, 1.29587762626394, 0.147986162902775, 255s + 0.0921506468161812, 0.0718240681909781, 0.069954084652323, 0.0702546879687391, 255s + 0.0795708692869622, 0.119032405993894, 0.065104213008022, -16.1828167145758, 255s + -6.2957256316336, -1.53255261729392, 2.32532927691394, 11.0959385851501, 255s + 10.8867632762999, 2.27306584421104, 6.66732036748908e-59, 3.05965144996025e-10, 255s + 0.125386123756898, 0.0200543599621069, 1.31274723412040e-28, 255s + 1.33293711602276e-27, 0.0230222123418036), .Dim = c(7L, 4L), .Dimnames = list( 255s + c("1|2", "2|3", "3|4", "4|5", "5|6", "prodTest", "prodTest" 255s + ), c("Estimate", "Std. Error", "z value", "Pr(>|z|)"))) 255s > stopifnot(all.equal(coef(summary(m1)), csm1)) 255s > 255s > ## link functions: 255s > m2 <- update(m1, link = "probit") 255s > m3 <- update(m1, link = "cloglog") 255s > 255s > m4 <- update(m1, link = "loglog") 255s > m5 <- update(m1, link = "cauchit", start = coef(m1)) 255s > ## m6 <- update(m1, link = "Aranda-Ordaz", lambda = 1) 255s > ## m7 <- update(m1, link = "Aranda-Ordaz") 255s > ## m8 <- update(m1, link = "log-gamma", lambda = 1) 255s > ## m9 <- update(m1, link = "log-gamma") 255s > ## nominal effects: 255s > mN1 <- clm(sureness ~ 1, nominal = ~ prod, data = dat26, 255s + weights = wghts) 255s > anova(m1, mN1) 255s Likelihood ratio tests of cumulative link models: 255s 255s formula: nominal: scale: link: threshold: 255s m1 sureness ~ prod ~1 ~prod logit flexible 255s mN1 sureness ~ 1 ~prod ~1 logit flexible 255s 255s no.par AIC logLik LR.stat df Pr(>Chisq) 255s m1 7 5389.5 -2687.7 255s mN1 10 5390.1 -2685.1 5.3755 3 0.1463 255s > ## optimizer / method: 255s > update(m1, scale = ~ 1, method = "Newton") 255s formula: sureness ~ prod 255s scale: ~1 255s data: dat26 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1847 -2690.33 5392.66 6(1) 3.44e-12 1.1e+02 255s 255s Coefficients: 255s prodTest 255s 1.144 255s 255s Threshold coefficients: 255s 1|2 2|3 3|4 4|5 5|6 255s -1.4050 -0.4247 -0.1013 0.1508 0.8126 255s > update(m1, scale = ~ 1, method = "ucminf") 255s formula: sureness ~ prod 255s scale: ~1 255s data: dat26 255s Warning message: 255s (-1) Model failed to converge with max|grad| = 3.36378e-06 (tol = 1e-06) 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1847 -2690.33 5392.66 18(0) 3.36e-06 1.1e+02 255s 255s Coefficients: 255s prodTest 255s 1.144 255s 255s Threshold coefficients: 255s 1|2 2|3 3|4 4|5 5|6 255s -1.4050 -0.4247 -0.1013 0.1508 0.8126 255s > update(m1, scale = ~ 1, method = "nlminb") 255s formula: sureness ~ prod 255s scale: ~1 255s data: dat26 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1847 -2690.33 5392.66 56(43) 4.13e-03 1.1e+02 255s 255s Coefficients: 255s prodTest 255s 1.144 255s 255s Threshold coefficients: 255s 1|2 2|3 3|4 4|5 5|6 255s -1.4050 -0.4247 -0.1013 0.1508 0.8126 255s > update(m1, scale = ~ 1, method = "optim") 255s Warning message: 255s (-1) Model failed to converge with max|grad| = 0.00413248 (tol = 1e-06) 255s formula: sureness ~ prod 255s scale: ~1 255s data: dat26 255s 255s link thresholdWarning message: 255s (-1) Model failed to converge with max|grad| = 0.00472568 (tol = 1e-06) 255s nobs logLik AIC niter max.grad cond.H 255s logit flexible 1847 -2690.33 5392.66 44(12) 4.73e-03 1.1e+02 255s 255s Coefficients: 255s prodTest 255s 1.144 255s 255s Threshold coefficients: 255s 1|2 2|3 3|4 4|5 5|6 255s -1.4050 -0.4247 -0.1013 0.1508 0.8126 255s > update(m1, scale = ~ 1, method = "model.frame") 255s sureness prod (weights) 255s 1 1 Ref 132 255s 2 2 Ref 161 255s 3 3 Ref 65 255s 4 4 Ref 41 255s 5 5 Ref 121 255s 6 6 Ref 219 255s 7 1 Test 96 255s 8 2 Test 99 255s 9 3 Test 50 255s 10 4 Test 57 255s 11 5 Test 156 255s 12 6 Test 650 255s > update(m1, ~.-prod, scale = ~ 1, 255s + nominal = ~ prod, method = "model.frame") 255s sureness prod (weights) 255s 1 1 Ref 132 255s 2 2 Ref 161 255s 3 3 Ref 65 255s 4 4 Ref 41 255s 5 5 Ref 121 255s 6 6 Ref 219 255s 7 1 Test 96 255s 8 2 Test 99 255s 9 3 Test 50 255s 10 4 Test 57 255s 11 5 Test 156 255s 12 6 Test 650 255s > ## threshold functions 255s > mT1 <- update(m1, threshold = "symmetric") 255s > mT2 <- update(m1, threshold = "equidistant") 255s > anova(m1, mT1, mT2) 255s Likelihood ratio tests of cumulative link models: 255s 255s formula: scale: link: threshold: 255s mT2 sureness ~ prod ~prod logit equidistant 255s mT1 sureness ~ prod ~prod logit symmetric 255s m1 sureness ~ prod ~prod logit flexible 255s 255s no.par AIC logLik LR.stat df Pr(>Chisq) 255s mT2 4 5585.6 -2788.8 255s mT1 5 5407.8 -2698.9 179.806Loading required package: MASS 255s 1 < 2.2e-16 *** 255s m1 7 5389.5 -2687.7 22.271 2 1.459e-05 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s > 255s > ## Extend example from polr in package MASS: 255s > ## Fit model from polr example: 255s > if(require(MASS)) { 255s + fm1 <- clm(Sat ~ Infl + Type + Cont, weights = Freq, data = housing) 255s + fm1 255s + summary(fm1) 255s + ## With probit link: 255s + summary(update(fm1, link = "probit")) 255s + ## Allow scale to depend on Cont-variable 255s + summary(fm2 <- update(fm1, scale =~ Cont)) 255s + summary(fm3 <- update(fm1, location =~.-Cont, nominal =~ Cont)) 255s + summary(fm4 <- update(fm2, location =~.-Cont, nominal =~ Cont)) 255s + anova(fm1, fm2, fm3, fm4) 255s + ## which seems to improve the fit 255s + } 255s Likelihood ratio tests of cumulative link models: 255s 255s formula: nominal: scale: link: threshold: 255s fm1 Sat ~ Infl + Type + Cont ~1 ~1 logit flexible 255s fm2 Sat ~ Infl + Type + Cont ~1 ~Cont logit flexible 255s fm3 Sat ~ Infl + Type + Cont ~Cont ~1 logit flexible 255s fm4 Sat ~ Infl + Type + Cont ~Cont ~Cont logit flexible 255s 255s no.par AIC logLik LR.stat df Pr(>Chisq) 255s fm1 8 3495.1 -1739.6 255s fm2 9 3491.5 -1736.7 5.6559 1 0.01740 * 255s fm3 9 3494.7 -1738.4 -3.2113 0 255s fm4 10 3492.5 -1736.2 4.2190 1 0.03997 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s > 255s > ################################# 255s > ## Better handling of ill-defined variance-covariance matrix of the 255s > ## parameters in summary methods for clm and clmm objects: 255s > dat26.2 <- data.frame(sureness = as.factor(1:12), 255s + prod = rep(c("One", "Two", "Three"),each=4)) 255s > fm1 <- clm(sureness ~ prod, ~prod, data = dat26.2) 255s > fm1 255s formula: sureness ~ prod 255s Warning message: 255s (1) Hessian is numerically singular: parameters are not uniquely determined 255s In addition: Absolute convergence criterion was met, but relative criterion was not met 255s scale: ~prod 255s data: dat26.2 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 12 -16.64 63.27 33(14) 6.18e-07 2.0e+12 255s 255s Coefficients: 255s prodThree prodTwo 255s 90.72 46.65 255s 255s log-scale coefficients: 255s prodThree prodTwo 255s -0.11719 -0.09167 255s 255s Threshold coefficients: 255s 1|2 2|3 3|4 4|5 5|6 6|7 7|8 255s -1.099e+00 2.045e-16 1.099e+00 2.441e+01 4.564e+01 4.665e+01 4.765e+01 255s 8|9 9|10 10|11 11|12 255s 6.888e+01 8.975e+01 9.072e+01 9.170e+01 255s > summary(fm1) 255s formula: sureness ~ prod 255s scale: ~prod 255s data: dat26.2 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 12 -16.64 63.27 33(14) 6.18e-07 2.0e+12 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s prodThree 90.72 NA NA NA 255s prodTwo 46.65 NA NA NA 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s prodThree -0.11719 NA NA NA 255s prodTwo -0.09167 NA NA NA 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.099e+00 NA NA 255s 2|3 2.045e-16 NA NA 255s 3|4 1.099e+00 NA NA 255s 4|5 2.441e+01 NA NA 255s 5|6 4.564e+01 NA NA 255s 6|7 4.665e+01 NA NA 255s 7|8 4.765e+01 NA NA 255s 8|9 6.888e+01 NA NA 255s 9|10 8.975e+01 NA NA 255s 10|11 9.072e+01 NA NA 255s 11|12 9.170e+01 NA NA 255s > summary(fm1, corr = 1) 255s formula: sureness ~ prod 255s scale: ~prod 255s data: dat26.2 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 12 -16.64 63.27 33(14) 6.18e-07 2.0e+12 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s prodThree 90.72 NA NA NA 255s prodTwo 46.65 NA NA NA 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s prodThree -0.11719 NA NA NA 255s prodTwo -0.09167 NA NA NA 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.099e+00 NA NA 255s 2|3 2.045e-16 NA NA 255s 3|4 1.099e+00 NA NA 255s 4|5 2.441e+01 NA NA 255s 5|6 4.564e+01 NA NA 255s 6|7 4.665e+01 NA NA 255s 7|8 4.765e+01 NA NA 255s 8|9 6.888e+01 NA NA 255s 9|10 8.975e+01 NA NA 255s 10|11 9.072e+01 NA NA 255s 11|12 9.170e+01 NA NA 255s > ## fm1$Hessian 255s > ## sl1 <- slice(fm1, 13) 255s Warning message: 255s In summary.clm(fm1, corr = 1) : Correlation matrix is unavailable 255s > ## fitted(fm1) 255s > ## convergence(fm1) 255s > ## eigen(fm1$Hessian)$values 255s > ## sqrt(diag(solve(fm1$Hessian))) 255s > ## sqrt(diag(ginv(fm1$Hessian))) 255s > 255s > ################################# 255s > ## Missing values: 255s > ## Bug-report from Jonathan Williams 255s > ## , 18 March 2010 12:42 255s > data(soup, package = "ordinal") 255s > soup$SURENESS[10] <- NA 255s > c1a <- clm(ordered(SURENESS)~PROD, data=soup); summary(c1a) 255s formula: ordered(SURENESS) ~ PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1846 -2688.71 5389.43 6(1) 2.49e-12 1.1e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.14251 0.08931 12.79 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.40460 0.08174 -17.184 255s 2|3 -0.42733 0.06965 -6.135 255s 3|4 -0.10357 0.06884 -1.505 255s 4|5 0.14862 0.06898 2.155 255s 5|6 0.81063 0.07185 11.282 255s (1 observation deleted due to missingness) 255s > c2a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup) 255s > summary(c2a) 255s formula: ordered(SURENESS) ~ PROD 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1846 -2686.16 5386.32 8(1) 4.81e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.293 0.119 10.87 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.14711 0.06514 2.258 0.0239 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.49041 0.09219 -16.166 255s 2|3 -0.45478 0.07189 -6.326 255s 3|4 -0.10961 0.07000 -1.566 255s 4|5 0.16104 0.07029 2.291 255s 5|6 0.88052 0.07959 11.064 255s (1 observation deleted due to missingness) 255s > c3a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup) 255s > summary(c3a) 255s formula: ordered(SURENESS) ~ 1 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1846 -2769.95 5551.91 10(1) 3.37e-13 6.9e+01 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest -0.15478 0.06683 -2.316 0.0206 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.85565 0.08111 -22.878 255s 2|3 -0.98626 0.05260 -18.752 255s 3|4 -0.70743 0.04676 -15.129 255s 4|5 -0.49243 0.04393 -11.208 255s 5|6 0.06504 0.04653 1.398 255s (1 observation deleted due to missingness) 255s > data(soup, package = "ordinal") 255s > soup$PROD[1] <- NA 255s > c1a <- clm(ordered(SURENESS)~PROD, data=soup) 255s > summary(c1a) 255s formula: ordered(SURENESS) ~ PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1846 -2689.15 5390.30 6(1) 3.37e-12 1.1e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.14774 0.08932 12.85 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.40278 0.08171 -17.167 255s 2|3 -0.42216 0.06962 -6.064 255s 3|4 -0.09849 0.06882 -1.431 255s 4|5 0.15373 0.06898 2.229 255s 5|6 0.81613 0.07188 11.353 255s (1 observation deleted due to missingness) 255s > c2a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup) 255s > summary(c2a) 255s formula: ordered(SURENESS) ~ PROD 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1846 -2686.51 5387.03 8(1) 5.41e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.3009 0.1192 10.91 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.1494 0.0651 2.295 0.0217 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.48982 0.09217 -16.163 255s 2|3 -0.44981 0.07186 -6.260 255s 3|4 -0.10441 0.07000 -1.492 255s 4|5 0.16655 0.07031 2.369 255s 5|6 0.88740 0.07969 11.136 255s (1 observation deleted due to missingness) 255s > c3a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup) 255s > summary(c3a) 255s formula: ordered(SURENESS) ~ 1 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1846 -2771.22 5554.43 10(1) 7.51e-13 6.9e+01 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest -0.15330 0.06689 -2.292 0.0219 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.85700 0.08108 -22.903 255s 2|3 -0.98437 0.05252 -18.742 255s 3|4 -0.70562 0.04673 -15.100 255s 4|5 -0.49061 0.04395 -11.163 255s 5|6 0.06723 0.04667 1.441 255s (1 observation deleted due to missingness) 255s > soup$SURENESS[10] <- NA 255s > c1a <- clm(ordered(SURENESS)~PROD, data=soup) 255s > summary(c1a) 255s formula: ordered(SURENESS) ~ PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1845 -2687.53 5387.07 6(1) 2.94e-12 1.1e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.14581 0.08934 12.82 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.40237 0.08175 -17.155 255s 2|3 -0.42475 0.06968 -6.096 255s 3|4 -0.10080 0.06887 -1.464 255s 4|5 0.15158 0.06902 2.196 255s 5|6 0.81421 0.07191 11.322 255s (2 observations deleted due to missingness) 255s > c2a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup) 255s > summary(c2a) 255s formula: ordered(SURENESS) ~ PROD 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1845 -2684.93 5383.86 8(1) 5.12e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.2979 0.1192 10.89 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.14853 0.06514 2.28 0.0226 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.48896 0.09222 -16.147 255s 2|3 -0.45241 0.07192 -6.290 255s 3|4 -0.10681 0.07004 -1.525 255s 4|5 0.16422 0.07034 2.335 255s 5|6 0.88500 0.07970 11.104 255s (2 observations deleted due to missingness) 255s > c3a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup) 255s > summary(c3a) 255s formula: ordered(SURENESS) ~ 1 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1845 -2769.23 5550.46 10(1) 9.65e-13 6.9e+01 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest -0.15410 0.06688 -2.304 0.0212 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.85563 0.08111 -22.877 255s 2|3 -0.98586 0.05259 -18.745 255s 3|4 -0.70689 0.04676 -15.116 255s 4|5 -0.49176 0.04395 -11.188 255s 5|6 0.06616 0.04661 1.419 255s (2 observations deleted due to missingness) 255s > 255s > ## na.actions: 255s > c4a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 255s + na.action=na.omit) 255s > summary(c4a) 255s formula: ordered(SURENESS) ~ PROD 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1845 -2684.93 5383.86 8(1) 5.12e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.2979 0.1192 10.89 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.14853 0.06514 2.28 0.0226 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.48896 0.09222 -16.147 255s 2|3 -0.45241 0.07192 -6.290 255s 3|4 -0.10681 0.07004 -1.525 255s 4|5 0.16422 0.07034 2.335 255s 5|6 0.88500 0.07970 11.104 255s (2 observations deleted due to missingness) 255s > 255s > tC1 <- try(clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 255s + na.action=na.fail), silent = TRUE) 255s > stopifnot(inherits(tC1, "try-error")) 255s > 255s > c4a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 255s + na.action=na.exclude) 255s > summary(c4a) 255s formula: ordered(SURENESS) ~ PROD 255s scale: ~PROD 255s data: soup 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1845 -2684.93 5383.86 8(1) 5.12e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.2979 0.1192 10.89 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.14853 0.06514 2.28 0.0226 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.48896 0.09222 -16.147 255s 2|3 -0.45241 0.07192 -6.290 255s 3|4 -0.10681 0.07004 -1.525 255s 4|5 0.16422 0.07034 2.335 255s 5|6 0.88500 0.07970 11.104 255s (2 observations deleted due to missingness) 255s > 255s > tC2 <- try(clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 255s + na.action=na.pass), silent = TRUE) 255s > stopifnot(inherits(tC2, "try-error")) 255s > 255s > ## Subset: 255s > data(soup, package="ordinal") 255s > c4a <- clm(ordered(SURENESS)~PROD, scale = ~PROD, data=soup, 255s + subset = 1:100) 255s > c4a <- clm(ordered(SURENESS)~1, scale = ~PROD, data=soup, 255s + subset = 1:100) 255s > c4a <- clm(ordered(SURENESS)~PROD, data=soup, 255s + subset = 1:100) 255s > c4a <- clm(ordered(SURENESS)~1, data=soup, 255s + subset = 1:100) 255s > 255s > ## Offset: 255s > data(soup, package = "ordinal") 255s > set.seed(290980) 255s > offs <- runif(nrow(soup)) 255s > c4a <- clm(ordered(SURENESS)~PROD + offset(offs), 255s + scale = ~PROD, data=soup, subset = 1:100) 255s > summary(c4a) 255s formula: ordered(SURENESS) ~ PROD + offset(offs) 255s scale: ~PROD 255s data: soup 255s subset: 1:100 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 100 -139.58 293.17 9(2) 1.41e-07 2.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 2.4410 0.7091 3.443 0.000576 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.5105 0.2671 1.911 0.056 . 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.0470 0.4019 -2.605 255s 2|3 0.4213 0.3106 1.356 255s 3|4 0.5488 0.3106 1.767 255s 4|5 0.9217 0.3162 2.915 255s 5|6 2.0775 0.4062 5.114 255s > 255s > c4a <- clm(ordered(SURENESS)~PROD + offset(offs), 255s + scale = ~PROD + offset(offs), data=soup, subset = 1:100) 255s > summary(c4a) 255s formula: ordered(SURENESS) ~ PROD + offset(offs) 255s scale: ~PROD + offset(offs) 255s data: soup 255s subset: 1:100 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 100 -143.12 300.24 9(2) 5.32e-09 1.9e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 3.344 1.020 3.277 0.00105 ** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.4412 0.2753 1.603 0.109 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -2.09797 0.62565 -3.353 255s 2|3 0.06671 0.46874 0.142 255s 3|4 0.25559 0.46525 0.549 255s 4|5 0.80178 0.46743 1.715 255s 5|6 2.46041 0.59193 4.157 255s > 255s > off2 <- offs 255s > c4a <- clm(ordered(SURENESS)~PROD + offset(offs), 255s + scale = ~PROD + offset(off2), data=soup, subset = 1:100) 255s > summary(c4a) 255s formula: ordered(SURENESS) ~ PROD + offset(offs) 255s scale: ~PROD + offset(off2) 255s data: soup 255s subset: 1:100 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 100 -143.12 300.24 9(2) 5.32e-09 1.9e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 3.344 1.020 3.277 0.00105 ** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.4412 0.2753 1.603 0.109 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -2.09797 0.62565 -3.353 255s 2|3 0.06671 0.46874 0.142 255s 3|4 0.25559 0.46525 0.549 255s 4|5 0.80178 0.46743 1.715 255s 5|6 2.46041 0.59193 4.157 255s > 255s > c4a <- clm(ordered(SURENESS)~PROD, 255s + scale = ~PROD + offset(offs), data=soup, subset = 1:100) 255s > summary(c4a) 255s formula: ordered(SURENESS) ~ PROD 255s scale: ~PROD + offset(offs) 255s data: soup 255s subset: 1:100 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 100 -142.15 298.31 10(2) 7.69e-10 1.8e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 3.283 1.016 3.231 0.00123 ** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.4263 0.2801 1.522 0.128 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -2.4698 0.6308 -3.915 255s 2|3 -0.2916 0.4668 -0.625 255s 3|4 -0.1005 0.4628 -0.217 255s 4|5 0.4484 0.4638 0.967 255s 5|6 2.1036 0.5864 3.587 255s > 255s > ## data as matrix: 255s > dat26M <- as.matrix(dat26) 255s > m1 <- clm(sureness ~ prod, scale = ~prod, data = dat26, 255s + weights = wghts, link = "logit") 255s > summary(m1) 255s formula: sureness ~ prod 255s scale: ~prod 255s data: dat26 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s prodTest 1.296 0.119 10.89 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s prodTest 0.1480 0.0651 2.273 0.023 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.49126 0.09215 -16.183 255s 2|3 -0.45218 0.07182 -6.296 255s 3|4 -0.10721 0.06995 -1.533 255s 4|5 0.16337 0.07025 2.325 255s 5|6 0.88291 0.07957 11.096 255s > 255s > ## data in enclosing environment: 255s > attach(soup) 255s > m1 <- clm(SURENESS ~ PROD, scale = ~PROD) 255s > summary(m1) 255s formula: SURENESS ~ PROD 255s scale: ~PROD 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 1847 -2687.74 5389.49 8(1) 5.09e-07 1.0e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 1.296 0.119 10.89 <2e-16 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s PRODTest 0.1480 0.0651 2.273 0.023 * 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -1.49126 0.09215 -16.183 255s 2|3 -0.45218 0.07182 -6.296 255s 3|4 -0.10721 0.06995 -1.533 255s 4|5 0.16337 0.07025 2.325 255s 5|6 0.88291 0.07957 11.096 255s > detach(soup) 255s > 255s > ################################################################## 255s > ### Parameter estimates were not correct with large scale effects due 255s > ### to end cut-points being \pm 100. This is not enough for 255s > ### location-scale model, but seems to be for location only models. 255s > ### Bug report from Ioannis Kosmidis : 255s > 255s > ### A 2x3 contigency table that will give a large estimated value of 255s > ### zeta 255s > x <- rep(0:1, each = 3) 255s > response <- factor(rep(c(1, 2, 3), times = 2)) 255s > freq <- c(1, 11, 1, 13, 1, 14) 255s > totals <- rep(tapply(freq, x, sum), each = 3) 255s > Dat <- data.frame(response, x, freq) 255s > 255s > ### Fitting a cumulative link model with dispersion effects 255s > modClm <- clm(response ~ x, scale = ~ x, weights = freq, data = Dat, 255s + control = clm.control(grtol = 1e-10, convTol = 1e-10)) 255s > summary(modClm) 255s formula: response ~ x 255s scale: ~x 255s data: Dat 255s 255s link threshold nobs logLik AIC niter max.grad cond.H 255s logit flexible 41 -29.98 67.96 10(3) 9.23e-10 2.4e+02 255s 255s Coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s x 2.485 13.168 0.189 0.85 255s 255s log-scale coefficients: 255s Estimate Std. Error z value Pr(>|z|) 255s x 3.548 1.023 3.468 0.000524 *** 255s --- 255s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 255s 255s Threshold coefficients: 255s Estimate Std. Error z value 255s 1|2 -2.485 1.041 -2.387 255s 2|3 2.485 1.041 2.387 255s > ### The maximized log-likelihood for this saturated model should be 255s > sum(freq*log(freq/totals)) 255s [1] -29.97808 255s > # > sum(freq*log(freq/totals)) 255s > # [1] -29.97808 255s > ### but apparently clm fails to maximixe the log-likelihood 255s > modClm$logLik 255s [1] -29.97808 255s > # > modClm$logLik 255s > # [1] -30.44452 255s > stopifnot(isTRUE(all.equal(sum(freq*log(freq/totals)), modClm$logLik))) 255s > 255s > ### The estimates reported by clm are 255s > coef(modClm) 255s 1|2 2|3 x x 255s -2.484907 2.484907 2.484907 3.547588 255s > coef.res <- structure(c(-2.48490664104217, 2.48490665578163, 255s + 2.48490659188594, 255s + 3.54758796387530), .Names = c("1|2", "2|3", 255s + "x", "x")) 255s > stopifnot(isTRUE(all.equal(coef.res, coef(modClm)))) 255s > # > modClm$coefficients 255s > # 1|2 2|3 x x 255s > # -2.297718 2.297038 1.239023 2.834285 255s > ### while they should be (from my own software) 255s > # 1|2 2|3 x disp.x 255s > #-2.484907 2.484907 2.484907 3.547588 255s > convergence(modClm) 255s nobs logLik niter max.grad cond.H logLik.Error 255s 41 -29.98 10(3) 9.23e-10 2.4e+02 <1e-10 255s 255s Estimate Std.Err Gradient Error Cor.Dec Sig.Dig 255s 1|2 -2.485 1.041 3.50e-10 5.32e-10 8 9 255s 2|3 2.485 1.041 -1.60e-10 -5.32e-10 8 9 255s x 2.485 13.168 -1.90e-10 -3.54e-08 7 8 255s x 3.548 1.023 -9.23e-10 -1.55e-09 8 9 255s 255s Eigen values of Hessian: 255s 1.374792 0.855786 0.785151 0.005766 255s 255s Convergence message from clm: 255s (0) successful convergence 255s In addition: Absolute and relative convergence criteria were met 255s 255s > 255s > ################################################################## 255s > 255s autopkgtest [22:23:44]: test run-unit-test: -----------------------] 256s run-unit-test PASS 256s autopkgtest [22:23:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 256s autopkgtest [22:23:45]: test pkg-r-autopkgtest: preparing testbed 330s autopkgtest [22:24:59]: testbed dpkg architecture: amd64 330s autopkgtest [22:24:59]: testbed apt version: 2.9.31ubuntu1 331s autopkgtest [22:25:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 331s autopkgtest [22:25:00]: testbed release detected to be: plucky 332s autopkgtest [22:25:01]: updating testbed package index (apt update) 332s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 332s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 332s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 332s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 333s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 333s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 333s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 333s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 333s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 333s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 333s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 333s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 333s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 333s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 333s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 333s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 333s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 333s Fetched 1265 kB in 1s (1486 kB/s) 334s Reading package lists... 335s Reading package lists... 335s Building dependency tree... 335s Reading state information... 336s Calculating upgrade... 336s Calculating upgrade... 336s The following package was automatically installed and is no longer required: 336s libnl-genl-3-200 336s Use 'sudo apt autoremove' to remove it. 337s The following NEW packages will be installed: 337s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 337s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 337s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 337s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 337s The following packages will be upgraded: 337s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 337s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 337s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 337s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 337s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 337s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 337s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 337s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 337s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 337s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 337s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 337s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 337s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 337s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 337s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 337s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 337s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 337s parted pci.ids pciutils pinentry-curses python-apt-common python3 337s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 337s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 337s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 337s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 337s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 337s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 337s xz-utils 337s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 337s Need to get 829 MB of archives. 337s After this operation, 325 MB of additional disk space will be used. 337s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 337s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 337s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 337s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 337s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 337s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 338s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 338s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 338s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 338s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 338s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 338s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 338s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 338s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 338s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 338s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 338s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 338s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 338s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 338s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 338s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 338s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 338s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 338s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 338s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 338s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 338s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 338s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 338s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 338s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 338s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 338s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 338s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 338s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 338s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 338s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 338s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 338s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 338s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 338s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 338s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 338s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 338s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 338s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 338s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 338s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 338s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 338s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 338s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 339s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 339s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 339s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 339s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 339s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 339s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 339s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 339s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 339s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 339s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 339s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 339s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 339s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 339s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 339s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 339s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 339s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 339s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 339s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 339s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 339s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 339s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 339s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 339s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 339s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 339s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 339s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 339s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 339s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 339s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 339s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 339s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 339s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 339s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 339s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 339s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 339s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 339s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 339s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 339s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 339s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 339s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 339s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 339s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 339s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 339s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 339s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 339s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 339s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 339s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 339s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 339s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 339s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 340s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 340s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 340s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 340s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 340s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 340s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 340s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 360s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 360s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 360s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 360s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 360s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 360s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 360s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 360s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 361s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 361s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 366s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 366s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 366s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 366s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 366s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 366s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 366s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 366s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 366s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 367s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 367s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 367s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 367s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 367s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 367s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 367s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 367s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 367s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 367s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 367s Preconfiguring packages ... 367s Fetched 829 MB in 30s (27.6 MB/s) 368s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109140 files and directories currently installed.) 368s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 368s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 368s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 368s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 368s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 368s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 368s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 369s Checking for services that may need to be restarted... 369s Checking init scripts... 369s Checking for services that may need to be restarted... 369s Checking init scripts... 369s Stopping some services possibly affected by the upgrade (will be restarted later): 369s cron: stopping...done. 369s 369s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 369s Setting up libc6:amd64 (2.41-1ubuntu1) ... 369s Checking for services that may need to be restarted... 369s Checking init scripts... 369s Restarting services possibly affected by the upgrade: 369s cron: restarting...done. 369s 369s Services restarted successfully. 369s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 370s Preparing to unpack .../libgcc-s1_15-20250222-0ubuntu1_amd64.deb ... 370s Unpacking libgcc-s1:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ... 370s Setting up libgcc-s1:amd64 (15-20250222-0ubuntu1) ... 370s (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 ... 109146 files and directories currently installed.) 370s Preparing to unpack .../libstdc++6_15-20250222-0ubuntu1_amd64.deb ... 370s Unpacking libstdc++6:amd64 (15-20250222-0ubuntu1) over (15-20250213-1ubuntu1) ... 370s Setting up libstdc++6:amd64 (15-20250222-0ubuntu1) ... 370s (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 ... 109146 files and directories currently installed.) 370s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 370s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 370s Setting up ncurses-base (6.5+20250216-2) ... 371s (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 ... 109146 files and directories currently installed.) 371s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 371s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 371s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 371s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 371s Setting up liblz4-1:amd64 (1.10.0-4) ... 371s (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 ... 109146 files and directories currently installed.) 371s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 371s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 371s Setting up liblzma5:amd64 (5.6.4-1) ... 372s (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 ... 109146 files and directories currently installed.) 372s Preparing to unpack .../libsystemd0_257.3-1ubuntu3_amd64.deb ... 372s Unpacking libsystemd0:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Setting up libsystemd0:amd64 (257.3-1ubuntu3) ... 372s (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 ... 109146 files and directories currently installed.) 372s Preparing to unpack .../libnss-systemd_257.3-1ubuntu3_amd64.deb ... 372s Unpacking libnss-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../systemd-sysv_257.3-1ubuntu3_amd64.deb ... 372s Unpacking systemd-sysv (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../systemd-resolved_257.3-1ubuntu3_amd64.deb ... 372s Unpacking systemd-resolved (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../libpam-systemd_257.3-1ubuntu3_amd64.deb ... 372s Unpacking libpam-systemd:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../libsystemd-shared_257.3-1ubuntu3_amd64.deb ... 372s Unpacking libsystemd-shared:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Setting up libsystemd-shared:amd64 (257.3-1ubuntu3) ... 372s (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 ... 109146 files and directories currently installed.) 372s Preparing to unpack .../systemd_257.3-1ubuntu3_amd64.deb ... 372s Unpacking systemd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../systemd-timesyncd_257.3-1ubuntu3_amd64.deb ... 372s Unpacking systemd-timesyncd (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../systemd-cryptsetup_257.3-1ubuntu3_amd64.deb ... 372s Unpacking systemd-cryptsetup (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 372s Preparing to unpack .../udev_257.3-1ubuntu3_amd64.deb ... 373s Unpacking udev (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 373s Preparing to unpack .../libudev1_257.3-1ubuntu3_amd64.deb ... 373s Unpacking libudev1:amd64 (257.3-1ubuntu3) over (257.2-3ubuntu1) ... 373s Setting up libudev1:amd64 (257.3-1ubuntu3) ... 373s (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 109146 files and directories currently installed.) 373s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ... 373s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ... 373s Setting up libcap-ng0:amd64 (0.8.5-4build1) ... 373s (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 ... 109146 files and directories currently installed.) 373s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 373s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 373s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 373s (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 ... 109146 files and directories currently installed.) 373s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu6_amd64.deb ... 373s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu6) over (2.5.5-1ubuntu5) ... 373s Setting up libseccomp2:amd64 (2.5.5-1ubuntu6) ... 373s (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 ... 109146 files and directories currently installed.) 373s Preparing to unpack .../libselinux1_3.7-3ubuntu3_amd64.deb ... 373s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ... 373s Setting up libselinux1:amd64 (3.7-3ubuntu3) ... 373s (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 ... 109146 files and directories currently installed.) 373s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu8_amd64.deb ... 373s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ... 373s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 373s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 374s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 374s (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 ... 109146 files and directories currently installed.) 374s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 374s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 374s Setting up apt (2.9.33) ... 375s (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 ... 109146 files and directories currently installed.) 375s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 375s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 375s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 375s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 375s Setting up python3-minimal (3.13.2-2) ... 375s (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 ... 109146 files and directories currently installed.) 375s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 375s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 375s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 375s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 375s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 375s Unpacking media-types (13.0.0) over (12.0.0) ... 375s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 375s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 375s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 375s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 375s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 375s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 375s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 375s (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 ... 109146 files and directories currently installed.) 375s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 375s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 375s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 376s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 376s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 376s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 376s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 376s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 376s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 376s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 376s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 376s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 376s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 376s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 376s Selecting previously unselected package libdebuginfod-common. 376s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 376s Unpacking libdebuginfod-common (0.192-4) ... 376s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 376s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 376s Setting up libsemanage-common (3.7-2.1build1) ... 376s (Reading database ... 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.../23-parted_3.6-5_amd64.deb ... 380s Unpacking parted (3.6-5) over (3.6-4build1) ... 380s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 380s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 380s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 380s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 380s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 380s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 380s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 380s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 380s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 380s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 380s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 380s Unpacking strace 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(1.0.6-6) over (1.0.6-5) ... 393s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 393s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 393s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 393s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 393s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 393s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 393s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 393s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 393s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 393s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 393s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 393s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 393s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 393s Setting up media-types (13.0.0) ... 393s Installing new version of config file /etc/mime.types ... 393s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 393s Setting up ubuntu-kernel-accessories (1.549) ... 393s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 393s Setting up pci.ids (0.0~2025.03.09-1) ... 393s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 393s Setting up apt-utils (2.9.33) ... 393s Setting up libdebuginfod-common (0.192-4) ... 394s Setting up exfatprogs (1.2.8-1) ... 394s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 394s Setting up bpftool (7.6.0+6.14.0-10.10) ... 394s Setting up libestr0:amd64 (0.1.11-2) ... 394s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 394s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 394s Setting up dosfstools (4.2-1.2) ... 394s Setting up rsyslog (8.2412.0-2ubuntu2) ... 394s info: The user `syslog' is already a member of `adm'. 395s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 395s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 395s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 395s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 395s Setting up systemd (257.3-1ubuntu3) ... 395s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 395s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 395s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 396s Setting up libparted2t64:amd64 (3.6-5) ... 396s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 396s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 396s Setting up linux-headers-generic (6.14.0-10.10) ... 396s Setting up libjemalloc2:amd64 (5.3.0-3) ... 396s Setting up locales (2.41-1ubuntu1) ... 396s Installing new version of config file /etc/locale.alias ... 397s Generating locales (this might take a while)... 398s en_US.UTF-8... done 398s Generation complete. 398s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 398s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 398s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 398s Installing new version of config file /etc/apparmor.d/fusermount3 ... 398s Installing new version of config file /etc/apparmor.d/lsusb ... 398s Installing new version of config file /etc/apparmor.d/openvpn ... 400s Reloading AppArmor profiles 401s Setting up libftdi1-2:amd64 (1.5-8build1) ... 401s Setting up libglib2.0-data (2.84.0-1) ... 401s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 401s Setting up libncurses6:amd64 (6.5+20250216-2) ... 401s Setting up strace (6.13+ds-1ubuntu1) ... 401s Setting up xz-utils (5.6.4-1) ... 401s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 402s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 402s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 402s Setting up udev (257.3-1ubuntu3) ... 403s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 405s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 405s Setting up libpci3:amd64 (1:3.13.0-2) ... 405s Setting up whiptail (0.52.24-4ubuntu2) ... 405s Setting up python-apt-common (2.9.9build1) ... 405s Setting up pnp.ids (0.393-3) ... 405s Setting up libnl-3-200:amd64 (3.7.0-1) ... 405s Setting up python3.13-minimal (3.13.2-2) ... 406s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 406s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 406s Setting up libc-dev-bin (2.41-1ubuntu1) ... 406s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 406s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 406s Setting up rsync (3.4.1+ds1-3) ... 407s rsync.service is a disabled or a static unit not running, not starting it. 407s Setting up python3.13-gdbm (3.13.2-2) ... 407s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 407s Setting up systemd-resolved (257.3-1ubuntu3) ... 407s Setting up initramfs-tools-bin (0.146ubuntu1) ... 407s Setting up ncurses-term (6.5+20250216-2) ... 407s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 407s Setting up libpython3.13:amd64 (3.13.2-2) ... 407s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 407s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 407s Setting up systemd-sysv (257.3-1ubuntu3) ... 407s Setting up linux-headers-virtual (6.14.0-10.10) ... 407s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 407s Setting up python3.13 (3.13.2-2) ... 408s Setting up htop (3.4.0-2) ... 408s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 411s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 411s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 411s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 411s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 411s Setting up parted (3.6-5) ... 411s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 411s Setting up python3 (3.13.2-2) ... 411s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 411s Setting up python3-markupsafe (2.1.5-1build4) ... 411s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 414s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 414s Setting up hwdata (0.393-3) ... 414s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 414s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 414s No schema files found: doing nothing. 414s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 414s Setting up linux-perf (6.14.0-10.10) ... 414s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 414s Setting up pciutils (1:3.13.0-2) ... 414s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 414s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 414s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 414s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 415s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 415s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 415s Setting up curl (8.12.1-3ubuntu1) ... 415s Setting up linux-image-virtual (6.14.0-10.10) ... 415s Setting up initramfs-tools-core (0.146ubuntu1) ... 415s Setting up linux-tools-common (6.14.0-10.10) ... 415s Setting up python3-systemd (235-1build6) ... 415s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 415s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 415s Setting up linux-image-generic (6.14.0-10.10) ... 415s Setting up python3-dbus (1.3.2-5build5) ... 415s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 415s Setting up initramfs-tools (0.146ubuntu1) ... 415s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 415s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 415s update-initramfs: deferring update (trigger activated) 415s Setting up linux-generic (6.14.0-10.10) ... 415s Setting up ubuntu-minimal (1.549) ... 415s Setting up python3-apt (2.9.9build1) ... 415s Setting up python3-bcrypt (4.2.0-2.1build1) ... 415s Setting up python3-yaml (6.0.2-1build2) ... 415s Setting up libfwupd3:amd64 (2.0.6-4) ... 415s Setting up python3-lazr.uri (1.0.6-6) ... 415s Setting up binutils (2.44-3ubuntu1) ... 415s Setting up ubuntu-standard (1.549) ... 415s Setting up cloud-init-base (25.1-0ubuntu3) ... 417s Setting up linux-virtual (6.14.0-10.10) ... 417s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 417s Setting up python3-gi (3.50.0-4build1) ... 417s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 417s Setting up fwupd (2.0.6-4) ... 418s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 418s fwupd.service is a disabled or a static unit not running, not starting it. 418s Setting up cloud-init (25.1-0ubuntu3) ... 418s Processing triggers for man-db (2.13.0-1) ... 420s Processing triggers for dbus (1.16.2-1ubuntu1) ... 420s Processing triggers for shared-mime-info (2.4-5) ... 420s Warning: program compiled against libxml 212 using older 209 420s Processing triggers for libc-bin (2.41-1ubuntu1) ... 420s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 420s /etc/kernel/postinst.d/initramfs-tools: 420s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 420s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 432s /etc/kernel/postinst.d/zz-update-grub: 432s Sourcing file `/etc/default/grub' 432s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 432s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 432s Generating grub configuration file ... 433s Found linux image: /boot/vmlinuz-6.14.0-10-generic 433s Found initrd image: /boot/initrd.img-6.14.0-10-generic 433s Found linux image: /boot/vmlinuz-6.12.0-16-generic 433s Found initrd image: /boot/initrd.img-6.12.0-16-generic 433s Found linux image: /boot/vmlinuz-6.11.0-8-generic 433s Found initrd image: /boot/initrd.img-6.11.0-8-generic 433s Warning: os-prober will not be executed to detect other bootable partitions. 433s Systems on them will not be added to the GRUB boot configuration. 433s Check GRUB_DISABLE_OS_PROBER documentation entry. 433s Adding boot menu entry for UEFI Firmware Settings ... 433s done 433s Processing triggers for initramfs-tools (0.146ubuntu1) ... 433s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 433s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 446s Reading package lists... 447s Building dependency tree... 447s Reading state information... 447s Solving dependencies... 447s The following packages will be REMOVED: 447s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 447s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 447s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 447s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 447s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 447s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 447s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 447s linux-tools-6.12.0-16-generic* 447s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 447s After this operation, 545 MB disk space will be freed. 448s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 148643 files and directories currently installed.) 448s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 448s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 448s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 448s Removing libpython3.12t64:amd64 (3.12.9-1) ... 448s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 448s Removing libnsl2:amd64 (1.3.0-3build3) ... 448s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 448s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 449s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 451s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 452s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 454s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 455s /etc/kernel/postrm.d/initramfs-tools: 455s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 455s /etc/kernel/postrm.d/zz-update-grub: 455s Sourcing file `/etc/default/grub' 455s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 455s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 455s Generating grub configuration file ... 455s Found linux image: /boot/vmlinuz-6.14.0-10-generic 455s Found initrd image: /boot/initrd.img-6.14.0-10-generic 455s Found linux image: /boot/vmlinuz-6.12.0-16-generic 455s Found initrd image: /boot/initrd.img-6.12.0-16-generic 455s Warning: os-prober will not be executed to detect other bootable partitions. 455s Systems on them will not be added to the GRUB boot configuration. 455s Check GRUB_DISABLE_OS_PROBER documentation entry. 455s Adding boot menu entry for UEFI Firmware Settings ... 455s done 455s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 456s W: Removing the running kernel 456s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 456s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 456s /etc/kernel/postrm.d/initramfs-tools: 456s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 456s /etc/kernel/postrm.d/zz-update-grub: 456s Sourcing file `/etc/default/grub' 456s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 456s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 456s Generating grub configuration file ... 456s Found linux image: /boot/vmlinuz-6.14.0-10-generic 456s Found initrd image: /boot/initrd.img-6.14.0-10-generic 456s Warning: os-prober will not be executed to detect other bootable partitions. 456s Systems on them will not be added to the GRUB boot configuration. 456s Check GRUB_DISABLE_OS_PROBER documentation entry. 456s Adding boot menu entry for UEFI Firmware Settings ... 456s done 457s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 457s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 459s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 459s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 459s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 459s Processing triggers for libc-bin (2.41-1ubuntu1) ... 459s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76972 files and directories currently installed.) 459s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 459s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 459s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 459s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 459s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 459s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 459s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 459s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 460s autopkgtest [22:27:09]: upgrading testbed (apt dist-upgrade and autopurge) 460s Reading package lists... 460s Building dependency tree... 460s Reading state information... 461s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 461s Starting 2 pkgProblemResolver with broken count: 0 461s Done 462s Entering ResolveByKeep 462s 462s Calculating upgrade... 463s The following packages will be upgraded: 463s libc-bin libc-dev-bin libc6 libc6-dev locales 463s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 463s Need to get 10.5 MB of archives. 463s After this operation, 1024 B of additional disk space will be used. 463s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 463s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 463s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 463s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 463s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 464s Preconfiguring packages ... 464s Fetched 10.5 MB in 1s (9508 kB/s) 464s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 464s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 464s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 464s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 464s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 464s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 465s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 465s Setting up libc6:amd64 (2.41-1ubuntu2) ... 465s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 465s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 465s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 465s Setting up libc-bin (2.41-1ubuntu2) ... 465s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 465s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 465s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 466s Setting up locales (2.41-1ubuntu2) ... 466s Generating locales (this might take a while)... 468s en_US.UTF-8... done 468s Generation complete. 468s Setting up libc-dev-bin (2.41-1ubuntu2) ... 468s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 468s Processing triggers for man-db (2.13.0-1) ... 469s Processing triggers for systemd (257.3-1ubuntu3) ... 470s Reading package lists... 470s Building dependency tree... 470s Reading state information... 471s Starting pkgProblemResolver with broken count: 0 471s Starting 2 pkgProblemResolver with broken count: 0 471s Done 471s Solving dependencies... 471s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 472s autopkgtest [22:27:21]: rebooting testbed after setup commands that affected boot 498s Reading package lists... 498s Building dependency tree... 498s Reading state information... 499s Starting pkgProblemResolver with broken count: 0 499s Starting 2 pkgProblemResolver with broken count: 0 499s Done 499s The following NEW packages will be installed: 499s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 499s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 499s g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 499s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 499s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 499s libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1 libdeflate-dev 499s libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev libgfortran5 499s libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 499s libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 499s libjpeg8-dev liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 499s libncurses-dev libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 499s libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 499s libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev 500s libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 500s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 500s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 500s littler pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 500s r-cran-boot r-cran-brio r-cran-callr r-cran-cli r-cran-crayon r-cran-desc 500s r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-fs r-cran-glue 500s r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-lme4 500s r-cran-magrittr r-cran-mass r-cran-matrix r-cran-minqa r-cran-nlme 500s r-cran-nloptr r-cran-nnet r-cran-numderiv r-cran-ordinal r-cran-pkgbuild 500s r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-processx r-cran-ps 500s r-cran-r6 r-cran-rbibutils r-cran-rcpp r-cran-rcppeigen r-cran-rdpack 500s r-cran-reformulas r-cran-rlang r-cran-rprojroot r-cran-statmod 500s r-cran-testthat r-cran-ucminf r-cran-waldo r-cran-withr r-cran-xtable unzip 500s x11-common xdg-utils zip zlib1g-dev 500s 0 upgraded, 146 newly installed, 0 to remove and 0 not upgraded. 500s Need to get 177 MB of archives. 500s After this operation, 516 MB of additional disk space will be used. 500s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 500s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 500s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 501s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 501s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 501s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 501s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 501s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 501s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 501s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 501s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 501s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 501s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 501s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 501s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 501s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 501s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 502s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 502s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 502s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 502s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 502s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 502s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 502s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 502s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 502s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 502s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 502s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 502s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 502s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 502s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 502s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 502s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 502s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 502s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 502s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 502s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 502s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 502s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 502s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 502s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 502s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 502s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 503s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 503s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 503s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 503s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 503s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 503s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 503s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 503s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 503s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 503s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 503s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 503s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 503s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 503s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 503s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 503s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 503s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 503s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 503s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 503s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 503s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 503s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 503s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 503s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 503s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 503s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 503s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 503s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 503s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 503s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 503s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 503s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 503s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 503s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 503s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 503s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 503s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 503s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 503s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 503s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 503s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 503s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 503s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 503s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 503s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 503s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 503s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 503s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 504s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 504s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 504s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 504s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B] 504s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB] 504s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 504s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 504s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 504s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 504s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 504s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-boot all 1.3-31-1 [635 kB] 505s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB] 505s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB] 505s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 505s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB] 505s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-callr all 3.7.6-1 [458 kB] 505s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 505s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB] 505s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-desc all 1.4.3-1 [359 kB] 505s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-diffobj amd64 0.3.5-1 [1117 kB] 505s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB] 505s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 505s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB] 505s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 505s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 505s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 505s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 505s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 505s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 505s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 505s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 505s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 505s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 505s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-minqa amd64 1.2.8-1 [119 kB] 505s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-6ubuntu3 [251 kB] 505s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nloptr amd64 2.1.1-1 [251 kB] 505s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rbibutils amd64 2.3-1 [1023 kB] 505s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rdpack all 2.6.2-1syncable1 [756 kB] 505s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-reformulas all 0.4.0-1 [91.5 kB] 505s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB] 506s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] 506s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lme4 amd64 1.1-36-1 [4135 kB] 506s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 506s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nnet amd64 7.3-20-1 [116 kB] 506s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB] 506s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ucminf amd64 1.2.2-1 [35.9 kB] 506s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ordinal amd64 2023.12-4.1-1 [1268 kB] 506s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgbuild all 1.4.6-1 [213 kB] 506s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rprojroot all 2.0.4-2 [125 kB] 506s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 506s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgload all 1.4.0-1 [247 kB] 506s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-praise all 1.0.0-4build1 [20.3 kB] 506s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-waldo all 0.6.1-2 [150 kB] 506s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB] 506s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] 506s Preconfiguring packages ... 507s Fetched 177 MB in 6s (27.9 MB/s) 507s Selecting previously unselected package libisl23:amd64. 507s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 507s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ... 507s Unpacking libisl23:amd64 (0.27-1) ... 507s Selecting previously unselected package libmpc3:amd64. 507s Preparing to unpack .../001-libmpc3_1.3.1-1build2_amd64.deb ... 507s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 507s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 507s Preparing to unpack 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previously unselected package libgfortran-14-dev:amd64. 510s Preparing to unpack .../033-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ... 510s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 510s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 510s Preparing to unpack .../034-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 510s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 510s Selecting previously unselected package gfortran-14. 510s Preparing to unpack .../035-gfortran-14_14.2.0-17ubuntu3_amd64.deb ... 510s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 510s Selecting previously unselected package gfortran-x86-64-linux-gnu. 510s Preparing to unpack .../036-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 510s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 510s Selecting previously unselected package gfortran. 510s Preparing to unpack .../037-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 510s Unpacking 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unselected package libpkgconf3:amd64. 512s Preparing to unpack .../075-libpkgconf3_1.8.1-4_amd64.deb ... 512s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 512s Selecting previously unselected package zlib1g-dev:amd64. 512s Preparing to unpack .../076-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 512s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 513s Selecting previously unselected package libpng-dev:amd64. 513s Preparing to unpack .../077-libpng-dev_1.6.47-1_amd64.deb ... 513s Unpacking libpng-dev:amd64 (1.6.47-1) ... 513s Selecting previously unselected package libreadline-dev:amd64. 513s Preparing to unpack .../078-libreadline-dev_8.2-6_amd64.deb ... 513s Unpacking libreadline-dev:amd64 (8.2-6) ... 513s Selecting previously unselected package libsharpyuv0:amd64. 513s Preparing to unpack .../079-libsharpyuv0_1.5.0-0.1_amd64.deb ... 513s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 513s Selecting previously unselected package libsm6:amd64. 513s Preparing to unpack .../080-libsm6_2%3a1.2.4-1_amd64.deb ... 513s Unpacking libsm6:amd64 (2:1.2.4-1) ... 513s Selecting previously unselected package libtcl8.6:amd64. 513s Preparing to unpack .../081-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 513s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 513s Selecting previously unselected package libjbig0:amd64. 513s Preparing to unpack .../082-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 513s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 513s Selecting previously unselected package libwebp7:amd64. 513s Preparing to unpack .../083-libwebp7_1.5.0-0.1_amd64.deb ... 513s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 513s Selecting previously unselected package libtiff6:amd64. 513s Preparing to unpack .../084-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 513s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 513s Selecting previously unselected package libxft2:amd64. 513s Preparing to unpack .../085-libxft2_2.3.6-1build1_amd64.deb ... 513s Unpacking libxft2:amd64 (2.3.6-1build1) ... 513s Selecting previously unselected package libxss1:amd64. 513s Preparing to unpack .../086-libxss1_1%3a1.2.3-1build3_amd64.deb ... 513s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 513s Selecting previously unselected package libtk8.6:amd64. 513s Preparing to unpack .../087-libtk8.6_8.6.16-1_amd64.deb ... 513s Unpacking libtk8.6:amd64 (8.6.16-1) ... 513s Selecting previously unselected package libxt6t64:amd64. 513s Preparing to unpack .../088-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 513s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 513s Selecting previously unselected package zip. 513s Preparing to unpack .../089-zip_3.0-14ubuntu2_amd64.deb ... 513s Unpacking zip (3.0-14ubuntu2) ... 513s Selecting previously unselected package unzip. 513s Preparing to unpack .../090-unzip_6.0-28ubuntu6_amd64.deb ... 513s Unpacking unzip (6.0-28ubuntu6) ... 513s Selecting previously unselected package xdg-utils. 513s Preparing to unpack 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Preparing to unpack .../097-pkgconf_1.8.1-4_amd64.deb ... 514s Unpacking pkgconf:amd64 (1.8.1-4) ... 514s Selecting previously unselected package libtirpc-dev:amd64. 514s Preparing to unpack .../098-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... 514s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 514s Selecting previously unselected package r-base-dev. 514s Preparing to unpack .../099-r-base-dev_4.4.3-1_all.deb ... 514s Unpacking r-base-dev (4.4.3-1) ... 514s Selecting previously unselected package pkg-r-autopkgtest. 514s Preparing to unpack .../100-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 514s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 514s Selecting previously unselected package r-cran-boot. 514s Preparing to unpack .../101-r-cran-boot_1.3-31-1_all.deb ... 514s Unpacking r-cran-boot (1.3-31-1) ... 514s Selecting previously unselected package r-cran-brio. 514s Preparing to unpack .../102-r-cran-brio_1.1.5-1_amd64.deb ... 514s Unpacking r-cran-brio (1.1.5-1) ... 514s Selecting previously unselected package r-cran-ps. 514s Preparing to unpack .../103-r-cran-ps_1.9.0-1_amd64.deb ... 514s Unpacking r-cran-ps (1.9.0-1) ... 514s Selecting previously unselected package r-cran-r6. 514s Preparing to unpack .../104-r-cran-r6_2.6.1-1_all.deb ... 514s Unpacking r-cran-r6 (2.6.1-1) ... 514s Selecting previously unselected package r-cran-processx. 514s Preparing to unpack .../105-r-cran-processx_3.8.6-1_amd64.deb ... 514s Unpacking r-cran-processx (3.8.6-1) ... 514s Selecting previously unselected package r-cran-callr. 514s Preparing to unpack .../106-r-cran-callr_3.7.6-1_all.deb ... 514s Unpacking r-cran-callr (3.7.6-1) ... 514s Selecting previously unselected package r-cran-cli. 514s Preparing to unpack .../107-r-cran-cli_3.6.4-1_amd64.deb ... 514s Unpacking r-cran-cli (3.6.4-1) ... 514s Selecting previously unselected package r-cran-crayon. 514s Preparing to unpack .../108-r-cran-crayon_1.5.3-1_all.deb ... 514s Unpacking r-cran-crayon (1.5.3-1) ... 514s Selecting previously unselected package r-cran-desc. 514s Preparing to unpack .../109-r-cran-desc_1.4.3-1_all.deb ... 514s Unpacking r-cran-desc (1.4.3-1) ... 514s Selecting previously unselected package r-cran-diffobj. 514s Preparing to unpack .../110-r-cran-diffobj_0.3.5-1_amd64.deb ... 514s Unpacking r-cran-diffobj (0.3.5-1) ... 514s Selecting previously unselected package r-cran-digest. 514s Preparing to unpack .../111-r-cran-digest_0.6.37-1_amd64.deb ... 514s Unpacking r-cran-digest (0.6.37-1) ... 515s Selecting previously unselected package r-cran-evaluate. 515s Preparing to unpack .../112-r-cran-evaluate_1.0.3-1_all.deb ... 515s Unpacking r-cran-evaluate (1.0.3-1) ... 515s Selecting previously unselected package r-cran-fs. 515s Preparing to unpack .../113-r-cran-fs_1.6.5+dfsg-1_amd64.deb ... 515s Unpacking r-cran-fs (1.6.5+dfsg-1) ... 515s Selecting previously unselected package r-cran-glue. 515s Preparing to unpack .../114-r-cran-glue_1.8.0-1_amd64.deb ... 515s Unpacking r-cran-glue 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(0.6.1-2) ... 520s Setting up r-cran-matrix (1.7-3-1) ... 520s Setting up g++ (4:14.2.0-1ubuntu1) ... 520s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 520s Setting up build-essential (12.10ubuntu1) ... 520s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 520s Setting up r-cran-minqa (1.2.8-1) ... 520s Setting up r-cran-callr (3.7.6-1) ... 520s Setting up r-cran-ordinal (2023.12-4.1-1) ... 520s Setting up r-cran-desc (1.4.3-1) ... 520s Setting up r-cran-rdpack (2.6.2-1syncable1) ... 520s Setting up gfortran (4:14.2.0-1ubuntu1) ... 520s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 520s 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 520s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 520s 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 520s Setting up r-cran-pkgbuild (1.4.6-1) ... 520s Setting up r-cran-reformulas (0.4.0-1) ... 520s Setting up r-cran-pkgload (1.4.0-1) ... 520s Setting up r-base-dev (4.4.3-1) ... 520s Setting up r-cran-lme4 (1.1-36-1) ... 520s Setting up r-cran-testthat (3.2.3-1) ... 520s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 520s Processing triggers for libc-bin (2.41-1ubuntu2) ... 520s Processing triggers for man-db (2.13.0-1) ... 522s Processing triggers for install-info (7.1.1-1) ... 525s autopkgtest [22:28:14]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 525s autopkgtest [22:28:14]: test pkg-r-autopkgtest: [----------------------- 525s Test: Try to load the R library ordinal 525s 525s R version 4.4.3 (2025-02-28) -- "Trophy Case" 525s Copyright (C) 2025 The R Foundation for Statistical Computing 525s Platform: x86_64-pc-linux-gnu 525s 525s R is free software and comes with ABSOLUTELY NO WARRANTY. 525s You are welcome to redistribute it under certain conditions. 525s Type 'license()' or 'licence()' for distribution details. 525s 525s R is a collaborative project with many contributors. 525s Type 'contributors()' for more information and 525s 'citation()' on how to cite R or R packages in publications. 525s 525s Type 'demo()' for some demos, 'help()' for on-line help, or 525s 'help.start()' for an HTML browser interface to help. 525s Type 'q()' to quit R. 525s 525s > library('ordinal') 527s > 527s > 527s Other tests are currently unsupported! 527s They will be progressively added. 527s autopkgtest [22:28:16]: test pkg-r-autopkgtest: -----------------------] 527s autopkgtest [22:28:16]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 527s pkg-r-autopkgtest PASS 528s autopkgtest [22:28:17]: @@@@@@@@@@@@@@@@@@@@ summary 528s run-unit-test PASS 528s pkg-r-autopkgtest PASS 545s nova [W] Skipping flock for amd64 545s Creating nova instance adt-plucky-amd64-r-cran-ordinal-20250315-221929-juju-7f2275-prod-proposed-migration-environment-20-6e349ed0-2ecf-4c61-bd04-fd6c043b3ff9 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 545s nova [W] Timed out waiting for a6ac6824-7c98-479b-bade-de7cb9d8eaf6 to get deleted. 545s nova [W] Skipping flock for amd64 545s Creating nova instance adt-plucky-amd64-r-cran-ordinal-20250315-221929-juju-7f2275-prod-proposed-migration-environment-20-6e349ed0-2ecf-4c61-bd04-fd6c043b3ff9 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 545s nova [W] Timed out waiting for 1d95ca94-fba8-411e-bd93-a852caefc883 to get deleted.