0s autopkgtest [16:08:43]: starting date and time: 2025-03-15 16:08:43+0000 0s autopkgtest [16:08:43]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:08:43]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s528v02y/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-gee --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.239 lxd-armhf-10.145.243.239:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [16:09:03]: testbed dpkg architecture: armhf 21s autopkgtest [16:09:04]: testbed apt version: 2.9.33 25s autopkgtest [16:09:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [16:09:10]: testbed release detected to be: None 34s autopkgtest [16:09:17]: updating testbed package index (apt update) 36s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 37s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 37s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 37s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 38s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 38s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 38s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 38s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 38s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 38s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 38s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 39s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 41s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 66s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 68s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 68s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 68s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 88s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 90s Fetched 41.0 MB in 53s (767 kB/s) 91s Reading package lists... 96s autopkgtest [16:10:19]: upgrading testbed (apt dist-upgrade and autopurge) 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 100s Entering ResolveByKeep 100s 100s Calculating upgrade... 101s The following packages will be upgraded: 101s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 101s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 8683 kB of archives. 101s After this operation, 23.6 kB of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 117s Preconfiguring packages ... 117s Fetched 8683 kB in 16s (559 kB/s) 117s (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 ... 64655 files and directories currently installed.) 117s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 117s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 117s Setting up libc6:armhf (2.41-1ubuntu2) ... 118s (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 ... 64655 files and directories currently installed.) 118s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 118s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 118s Setting up libc-bin (2.41-1ubuntu2) ... 118s (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 ... 64655 files and directories currently installed.) 118s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 118s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 118s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 118s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 118s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 118s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 118s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 118s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 118s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 119s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 119s Setting up sos (4.9.0-5) ... 119s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 119s Setting up locales (2.41-1ubuntu2) ... 120s Generating locales (this might take a while)... 122s en_US.UTF-8... done 122s Generation complete. 122s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 122s Setting up strace (6.13+ds-1ubuntu1) ... 122s Processing triggers for man-db (2.13.0-1) ... 123s Processing triggers for systemd (257.3-1ubuntu3) ... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 126s Solving dependencies... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [16:10:52]: rebooting testbed after setup commands that affected boot 168s autopkgtest [16:11:31]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 191s autopkgtest [16:11:54]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-gee 201s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (dsc) [2061 B] 201s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (tar) [53.1 kB] 201s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (diff) [3696 B] 201s gpgv: Signature made Tue Jan 28 23:41:44 2025 UTC 201s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 201s gpgv: issuer "plessy@debian.org" 201s gpgv: Can't check signature: No public key 201s dpkg-source: warning: cannot verify inline signature for ./r-cran-gee_4.13-29-1.dsc: no acceptable signature found 202s autopkgtest [16:12:05]: testing package r-cran-gee version 4.13-29-1 204s autopkgtest [16:12:07]: build not needed 208s autopkgtest [16:12:11]: test run-unit-test: preparing testbed 209s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 211s The following NEW packages will be installed: 211s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 211s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 211s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 211s libjpeg8 liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 211s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 211s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 211s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-gee 211s r-cran-mass unzip x11-common xdg-utils zip 211s 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 38.8 MB of archives. 211s After this operation, 72.0 MB of additional disk space will be used. 211s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 212s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 213s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 213s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 213s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 214s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 214s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 214s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 214s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 214s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 214s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 215s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 215s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 215s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 215s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 215s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 215s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 216s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 216s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 216s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 216s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 216s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 219s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 219s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 219s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 219s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.2-1 [216 kB] 219s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.2-1 [43.6 kB] 219s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.2-1 [25.1 kB] 219s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 219s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 219s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 219s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 219s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 221s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 221s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 221s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 221s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 221s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 221s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 223s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 223s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 223s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 223s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 223s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 259s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-gee armhf 4.13-29-1 [71.1 kB] 259s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mass armhf 7.3-64-1 [1105 kB] 261s Preconfiguring packages ... 261s Fetched 38.8 MB in 49s (786 kB/s) 261s Selecting previously unselected package libfreetype6:armhf. 261s (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 ... 64655 files and directories currently installed.) 261s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 261s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 261s Selecting previously unselected package fonts-dejavu-mono. 261s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 261s Unpacking fonts-dejavu-mono (2.37-8) ... 261s Selecting previously unselected package fonts-dejavu-core. 261s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 261s Unpacking fonts-dejavu-core (2.37-8) ... 261s Selecting previously unselected package fontconfig-config. 261s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 261s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 261s Selecting previously unselected package libfontconfig1:armhf. 261s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 261s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 261s Selecting previously unselected package fontconfig. 261s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 261s Unpacking fontconfig (2.15.0-2ubuntu1) ... 261s Selecting previously unselected package libblas3:armhf. 261s Preparing to unpack .../06-libblas3_3.12.1-2_armhf.deb ... 261s Unpacking libblas3:armhf (3.12.1-2) ... 261s Selecting previously unselected package libpixman-1-0:armhf. 261s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_armhf.deb ... 261s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 261s Selecting previously unselected package libxcb-render0:armhf. 261s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 261s Unpacking libxcb-render0:armhf (1.17.0-2) ... 261s Selecting previously unselected package libxcb-shm0:armhf. 261s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 261s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 261s Selecting previously unselected package libxrender1:armhf. 261s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 261s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 261s Selecting previously unselected package libcairo2:armhf. 261s Preparing to unpack .../11-libcairo2_1.18.2-2_armhf.deb ... 261s Unpacking libcairo2:armhf (1.18.2-2) ... 261s Selecting previously unselected package libdatrie1:armhf. 261s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 261s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 261s Selecting previously unselected package libdeflate0:armhf. 261s Preparing to unpack .../13-libdeflate0_1.23-1_armhf.deb ... 261s Unpacking libdeflate0:armhf (1.23-1) ... 261s Selecting previously unselected package libgfortran5:armhf. 261s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 261s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 261s Selecting previously unselected package libgomp1:armhf. 261s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 261s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 262s Selecting previously unselected package libgraphite2-3:armhf. 262s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 262s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 262s Selecting previously unselected package libharfbuzz0b:armhf. 262s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_armhf.deb ... 262s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 262s Selecting previously unselected package x11-common. 262s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 262s Unpacking x11-common (1:7.7+23ubuntu3) ... 262s Selecting previously unselected package libice6:armhf. 262s Preparing to unpack .../19-libice6_2%3a1.1.1-1_armhf.deb ... 262s Unpacking libice6:armhf (2:1.1.1-1) ... 262s Selecting previously unselected package libjpeg-turbo8:armhf. 262s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 262s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 262s Selecting previously unselected package libjpeg8:armhf. 262s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_armhf.deb ... 262s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 262s Selecting previously unselected package liblapack3:armhf. 262s Preparing to unpack .../22-liblapack3_3.12.1-2_armhf.deb ... 262s Unpacking liblapack3:armhf (3.12.1-2) ... 262s Selecting previously unselected package liblerc4:armhf. 262s Preparing to unpack .../23-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 262s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 262s Selecting previously unselected package libthai-data. 262s Preparing to unpack .../24-libthai-data_0.1.29-2build1_all.deb ... 262s Unpacking libthai-data (0.1.29-2build1) ... 262s Selecting previously unselected package libthai0:armhf. 262s Preparing to unpack .../25-libthai0_0.1.29-2build1_armhf.deb ... 262s Unpacking libthai0:armhf (0.1.29-2build1) ... 262s Selecting previously unselected package libpango-1.0-0:armhf. 262s Preparing to unpack .../26-libpango-1.0-0_1.56.2-1_armhf.deb ... 262s Unpacking libpango-1.0-0:armhf (1.56.2-1) ... 262s Selecting previously unselected package libpangoft2-1.0-0:armhf. 262s Preparing to unpack .../27-libpangoft2-1.0-0_1.56.2-1_armhf.deb ... 262s Unpacking libpangoft2-1.0-0:armhf (1.56.2-1) ... 262s Selecting previously unselected package libpangocairo-1.0-0:armhf. 262s Preparing to unpack .../28-libpangocairo-1.0-0_1.56.2-1_armhf.deb ... 262s Unpacking libpangocairo-1.0-0:armhf (1.56.2-1) ... 262s Selecting previously unselected package libpaper2:armhf. 262s Preparing to unpack .../29-libpaper2_2.2.5-0.3_armhf.deb ... 262s Unpacking libpaper2:armhf (2.2.5-0.3) ... 262s Selecting previously unselected package libpaper-utils. 262s Preparing to unpack .../30-libpaper-utils_2.2.5-0.3_armhf.deb ... 262s Unpacking libpaper-utils (2.2.5-0.3) ... 262s Selecting previously unselected package libsharpyuv0:armhf. 262s Preparing to unpack .../31-libsharpyuv0_1.5.0-0.1_armhf.deb ... 262s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 262s Selecting previously unselected package libsm6:armhf. 262s Preparing to unpack .../32-libsm6_2%3a1.2.4-1_armhf.deb ... 262s Unpacking libsm6:armhf (2:1.2.4-1) ... 262s Selecting previously unselected package libtcl8.6:armhf. 262s Preparing to unpack .../33-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 262s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 262s Selecting previously unselected package libjbig0:armhf. 262s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 262s 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/usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 264s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 264s Setting up libpaper-utils (2.2.5-0.3) ... 264s Setting up libthai0:armhf (0.1.29-2build1) ... 264s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 264s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 264s Setting up libsm6:armhf (2:1.2.4-1) ... 264s Setting up fontconfig (2.15.0-2ubuntu1) ... 266s Regenerating fonts cache... done. 266s Setting up libxft2:armhf (2.3.6-1build1) ... 266s Setting up libtk8.6:armhf (8.6.16-1) ... 266s Setting up libpango-1.0-0:armhf (1.56.2-1) ... 266s Setting up libcairo2:armhf (1.18.2-2) ... 266s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 266s Setting up libpangoft2-1.0-0:armhf (1.56.2-1) ... 266s Setting up libpangocairo-1.0-0:armhf (1.56.2-1) ... 266s Setting up r-base-core (4.4.3-1) ... 266s Creating config file /etc/R/Renviron with new version 266s Setting up r-cran-gee (4.13-29-1) ... 266s Setting up r-cran-mass (7.3-64-1) ... 266s Processing triggers for install-info (7.1.1-1) ... 266s Processing triggers for libc-bin (2.41-1ubuntu2) ... 266s Processing triggers for man-db (2.13.0-1) ... 279s autopkgtest [16:13:22]: test run-unit-test: [----------------------- 283s BEGIN TEST divergence.R 283s 283s R version 4.4.3 (2025-02-28) -- "Trophy Case" 283s Copyright (C) 2025 The R Foundation for Statistical Computing 283s Platform: arm-unknown-linux-gnueabihf (32-bit) 283s 283s R is free software and comes with ABSOLUTELY NO WARRANTY. 283s You are welcome to redistribute it under certain conditions. 283s Type 'license()' or 'licence()' for distribution details. 283s 283s R is a collaborative project with many contributors. 283s Type 'contributors()' for more information and 283s 'citation()' on how to cite R or R packages in publications. 283s 283s Type 'demo()' for some demos, 'help()' for on-line help, or 283s 'help.start()' for an HTML browser interface to help. 283s Type 'q()' to quit R. 283s 283s > options(digits=5) 283s > library(gee) 283s > load("data_for_gee_binomial.RData") 283s > try(gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed")) 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s (Intercept) x 283s -0.1291219 0.0019241 283s > ## infinite looped in gee 4.3-14 283s > 283s > 283s > 283s Error in gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed") : 283s Cgee: error: logistic model for probability has fitted value very close to 1. 283s estimates diverging; iteration terminated. 283s BEGIN TEST tests.R 283s 283s R version 4.4.3 (2025-02-28) -- "Trophy Case" 283s Copyright (C) 2025 The R Foundation for Statistical Computing 283s Platform: arm-unknown-linux-gnueabihf (32-bit) 283s 283s R is free software and comes with ABSOLUTELY NO WARRANTY. 283s You are welcome to redistribute it under certain conditions. 283s Type 'license()' or 'licence()' for distribution details. 283s 283s R is a collaborative project with many contributors. 283s Type 'contributors()' for more information and 283s 'citation()' on how to cite R or R packages in publications. 283s 283s Type 'demo()' for some demos, 'help()' for on-line help, or 283s 'help.start()' for an HTML browser interface to help. 283s Type 'q()' to quit R. 283s 283s > 283s > # gee support @(#) tests.q 1.2 96/09/27 283s > 283s > library(gee) 283s > 283s > source("testgee.dump") 283s > 283s > myr <- gee(gsind~x2+x3+x4,id=id,data=testgee) 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s (Intercept) x2 x3 x4 283s 0.8107414 2.2933133 -1.1806841 1.4415174 283s > myr 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Identity 283s Variance to Mean Relation: Gaussian 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 283s 283s Number of observations : 500 283s 283s Maximum cluster size : 20 283s 283s 283s Coefficients: 283s (Intercept) x2 x3 x4 283s 0.8107414 2.2933133 -1.1806841 1.4415174 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s 283s Estimated Scale Parameter: 2.899625 283s Number of Iterations: 1 283s 283s Working Correlation[1:4,1:4] 283s [,1] [,2] [,3] [,4] 283s [1,] 1 0 0 0 283s [2,] 0 1 0 0 283s [3,] 0 0 1 0 283s [4,] 0 0 0 1 283s 283s 283s Returned Error Value: 283s [1] 0 283s > summary(myr) 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Identity 283s Variance to Mean Relation: Gaussian 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -5.12638044 -1.17212201 0.07530777 1.13873892 5.69264860 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 0.8107414 0.75420946 1.074955 0.76905602 1.054203 283s x2 2.2933133 0.04546161 50.445055 0.04589797 49.965459 283s x3 -1.1806841 0.05974921 -19.760664 0.06847056 -17.243677 283s x4 1.4415174 0.03154513 45.696983 0.03153448 45.712418 283s 283s Estimated Scale Parameter: 2.899625 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > summary(gee(gs~x2+x4,id=id,data=testgee,corstr="exchangeable")) 283s (Intercept) x2 x4 283s -21.504384 4.643727 3.065537 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Identity 283s Variance to Mean Relation: Gaussian 283s Correlation Structure: Exchangeable 283s 283s Call: 283s gee(formula = gs ~ x2 + x4, id = id, data = testgee, corstr = "exchangeable") 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -32.6076365 -9.8240277 0.4309459 10.2768319 44.8278747 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) -21.675077 3.7046983 -5.85070 3.5007586 -6.191537 283s x2 4.676098 0.3786822 12.34835 0.3336659 14.014313 283s x4 3.057583 0.2632230 11.61594 0.2251384 13.580903 283s 283s Estimated Scale Parameter: 202.3612 283s Number of Iterations: 2 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] 283s [1,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [2,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [3,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 283s [4,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 283s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 283s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 283s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [,7] [,8] [,9] [,10] [,11] [,12] 283s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [5,]Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [7,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [8,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [9,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 283s [10,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 283s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 283s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 283s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [,13] [,14] [,15] [,16] [,17] [,18] 283s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [13,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [14,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [15,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 283s [16,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 283s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 283s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 283s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 283s [,19] [,20] 283s [1,] -0.01037861 -0.01037861 283s [2,] -0.01037861 -0.01037861 283s [3,] -0.01037861 -0.01037861 283s [4,] -0.01037861 -0.01037861 283s [5,] -0.01037861 -0.01037861 283s [6,] -0.01037861 -0.01037861 283s [7,] -0.01037861 -0.01037861 283s [8,] -0.01037861 -0.01037861 283s [9,] -0.01037861 -0.01037861 283s [10,] -0.01037861 -0.01037861 283s [11,] -0.01037861 -0.01037861 283s [12,] -0.01037861 -0.01037861 283s [13,] -0.01037861 -0.01037861 283s [14,] -0.01037861 -0.01037861 283s [15,] -0.01037861 -0.01037861 283s [16,] -0.01037861 -0.01037861 283s [17,] -0.01037861 -0.01037861 283s [18,] -0.01037861 -0.01037861 283s [19,] 1.00000000 -0.01037861 283s [20,] -0.01037861 1.00000000 283s > 283s > summary(gee(gsind~sin(x2)+log(x3)+x4,id=id,data=testgee)) 283s (Intercept) sin(x2) log(x3) x4 283s 33.017960 1.235559 -12.033930 1.500485 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Identity 283s Variance to Mean Relation: Gaussian 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = gsind ~ sin(x2) + log(x3) + x4, id = id, data = testgee) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -14.2099238 -2.6510967 -0.4994671 2.1403832 12.8126774 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 33.017960 3.39110198 9.736646 3.03682905 10.872512 283s sin(x2) 1.235559 0.26662685 4.634036 0.44529003 2.774728 283s log(x3) -12.033930 1.43540337 -8.383657 1.33255574 -9.030714 283s x4 1.500485 0.07638601 19.643451 0.06166767 24.331791 283s 283s Estimated Scale Parameter: 17.02534 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > #summary(gee(gsind~gam(x2~x1)$fitted.values+x4,id=id,data=testgee,subset=id<20)) 283s > 283s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial)) 283s (Intercept) x2 x3 x4 283s 4.72920874 -0.34747871 -0.21939993 -0.07103635 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logit 283s Variance to Mean Relation: Binomial 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 283s family = binomial) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 4.72920874 1.03210192 4.582114 0.86323313 5.478484 283s x2 -0.34747871 0.06301385 -5.514323 0.05004796 -6.942915 283s x3 -0.21939993 0.07952035 -2.759041 0.07725222 -2.840047 283s x4 -0.07103635 0.04152051 -1.710874 0.03167549 -2.242628 283s 283s Estimated Scale Parameter: 1.009587 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > glm(lgind~x2+x3+x4,data=testgee, start=rep(0,4), # needed in R 283s + family=quasi(link=logit,variance="mu(1-mu)")) 283s 283s Call: glm(formula = lgind ~ x2 + x3 + x4, family = quasi(link = logit, 283s variance = "mu(1-mu)"), data = testgee, start = rep(0, 4)) 283s 283s Coefficients: 283s (Intercept) x2 x3 x4 283s 4.72921 -0.34748 -0.21940 -0.07104 283s 283s Degrees of Freedom: 499 Total (i.e. Null); 496 Residual 283s Null Deviance: 635.6 283s Residual Deviance: 591.4 AIC: NA 283s > 283s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial,scale.fix=TRUE)) 283s (Intercept) x2 x3 x4 283s 4.72920874 -0.34747871 -0.21939993 -0.07103635 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 283s family = binomial, scale.fix = TRUE) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 4.72920874 1.02718977 4.604026 0.86323313 5.478484 283s x2 -0.34747871 0.06271394 -5.540693 0.05004796 -6.942915 283s x3 -0.21939993 0.07914189 -2.772235 0.07725222 -2.840047 283s x4 -0.07103635 0.04132290 -1.719055 0.03167549 -2.242628 283s 283s Estimated Scale Parameter: 1 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > #glm(lgind~x2+x3+x4,data=testgee,family=binomial) 283s > 283s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="exchangeable")) 283s (Intercept) x2 x3 x4 283s 6.4719531 -0.2719330 -0.2759630 -0.1493855 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Exchangeable 283s 283s Call: 283s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 283s corstr = "exchangeable") 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.9132133 -0.4779069 0.2183723 0.4022373 0.8322064 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 6.3714080 1.01872823 6.254276 0.82259807 7.745469 283s x2 -0.2582285 0.05832328 -4.427537 0.06432493 -4.014439 283s x3 -0.2792487 0.07639349 -3.655399 0.05877904 -4.750820 283s x4 -0.1458317 0.04000757 -3.645104 0.02732683 -5.336576 283s 283s Estimated Scale Parameter: 1.008096 283s Number of Iterations: 3 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] 283s [1,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [2,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [3,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 283s [4,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 283s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 283s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 283s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [,7] [,8] [,9] [,10] [,11] [,12] 283s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [7,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [8,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [9,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 283s [10,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 283s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 283s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 283s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [,13] [,14] [,15] [,16] [,17] [,18] 283s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [13,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [14,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [15,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 283s [16,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 283s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 283s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 283s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 283s [,19] [,20] 283s [1,] -0.02048602 -0.02048602 283s [2,] -0.02048602 -0.02048602 283s [3,] -0.02048602 -0.02048602 283s [4,] -0.02048602 -0.02048602 283s [5,] -0.02048602 -0.02048602 283s [6,] -0.02048602 -0.02048602 283s [7,] -0.02048602 -0.02048602 283s [8,] -0.02048602 -0.02048602 283s [9,] -0.02048602 -0.02048602 283s [10,] -0.02048602 -0.02048602 283s [11,] -0.02048602 -0.02048602 283s [12,] -0.02048602 -0.02048602 283s [13,] -0.02048602 -0.02048602 283s [14,] -0.02048602 -0.02048602 283s [15,] -0.02048602 -0.02048602 283s [16,] -0.02048602 -0.02048602 283s [17,] -0.02048602 -0.02048602 283s [18,] -0.02048602 -0.02048602 283s [19,] 1.00000000 -0.02048602 283s [20,] -0.02048602 1.00000000 283s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="stat_M_dep",M=1)) 283s running glm to get initial regression estimate 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s user's initial regression estimate 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s (Intercept) x2 x3 x4 283s 6.4719531 -0.2719330 -0.2759630 -0.1493855 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Stationary M-dependent , M = 1 283s 283s Call: 283s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 283s corstr = "stat_M_dep", Mv = 1) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.8834271 -0.4920962 0.2491360 0.4108783 0.7887767 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 5.4093789 0.84036337 6.436952 0.70900809 7.629502 283s x2 -0.2069859 0.04869638 -4.250540 0.05089218 -4.067147 283s x3 -0.2469902 0.06394554 -3.862508 0.04953133 -4.986545 283s x4 -0.1193671 0.03385364 -3.525976 0.02800656 -4.262113 283s 283s Estimated Scale Parameter: 0.9787236 283s Number of Iterations: 3 283s 283s Working Correlation 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s [,1] [,2] [,3] [,4] [,5] [,6] 283s [1,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 283s [2,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 283s [3,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 283s [4,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 283s [5,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 283s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 283s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 283s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [,7] [,8] [,9] [,10] [,11] [,12] 283s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [6,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [7,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 283s [8,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 283s [9,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 283s [10,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 283s [11,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 283s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 283s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 283s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [,13] [,14] [,15] [,16] [,17] [,18] 283s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [12,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [13,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 283s [14,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 283s [15,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 283s [16,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 283s [17,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 283s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 283s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 283s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 283s [,19] [,20] 283s [1,] 0.0000000 0.0000000 283s [2,] 0.0000000 0.0000000 283s [3,] 0.0000000 0.0000000 283s [4,] 0.0000000 0.0000000 283s [5,] 0.0000000 0.0000000 283s [6,] 0.0000000 0.0000000 283s [7,] 0.0000000 0.0000000 283s [8,] 0.0000000 0.0000000 283s [9,] 0.0000000 0.0000000 283s [10,] 0.0000000 0.0000000 283s [11,] 0.0000000 0.0000000 283s [12,] 0.0000000 0.0000000 283s [13,] 0.0000000 0.0000000 283s [14,] 0.0000000 0.0000000 283s [15,] 0.0000000 0.0000000 283s [16,] 0.0000000 0.0000000 283s [17,] 0.0000000 0.0000000 283s [18,] -0.3301082 0.0000000 283s [19,] 1.0000000 -0.3301082 283s [20,] -0.3301082 1.0000000 283s > 283s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial(link=probit))) 283s (Intercept) x2 x3 x4 283s 3.92612377 -0.16597664 -0.16503829 -0.09214249 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Probit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial(link = probit)) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.9259107 -0.4767799 0.2158545 0.4033760 0.8384385 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 3.92613715 0.61214299 6.413758 0.53755155 7.303741 283s x2 -0.16597696 0.03582656 -4.632790 0.04006791 -4.142391 283s x3 -0.16503933 0.04665763 -3.537242 0.03848563 -4.288336 283s x4 -0.09214252 0.02457762 -3.749042 0.01654858 -5.568001 283s 283s Estimated Scale Parameter: 1.014784 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > # next line does not work in R's glm: needs starting values for quasi 283s > #summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=quasi(link=probit,variance="mu(1-mu)"))) 283s > summary(gee(lg~x2+x3+x4, id=id, data=testgee, b=rep(0,4), family=quasi(link=probit,variance="mu(1-mu)"))) 283s [,1] 283s [1,] 0 283s [2,] 0 283s [3,] 0 283s [4,] 0 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s running glm to get initial regression estimate 283s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 283s 283s Model: 283s Link: Probit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, b = rep(0, 283s 4), family = quasi(link = probit, variance = "mu(1-mu)")) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.9259108 -0.4767799 0.2158545 0.4033761 0.8384386 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 3.92613840 0.61214303 6.413760 0.53755167 7.303741 283s x2 -0.16597699 0.03582656 -4.632791 0.04006791 -4.142392 283s x3 -0.16503949 0.04665763 -3.537245 0.03848564 -4.288340 283s x4 -0.09214246 0.02457762 -3.749040 0.01654858 -5.567998 283s 283s Estimated Scale Parameter: 1.014784 283s Number of Iterations: 4 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > 283s > logmat <- cbind(testgee[,"lg1"],testgee[,"nn"]) 283s > xmat <- cbind(testgee[,"x2"], testgee[,"x3"]) 283s > summary(gee(logmat~xmat,id = testgee[,"id"],family=binomial(link=probit))) 283s (Intercept) xmat1 xmat2 283s 0.51795625 -0.06406827 -0.04156066 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Probit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = logmat ~ xmat, id = testgee[, "id"], family = binomial(link = probit)) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s 0.5160816 1.7308948 4.6651553 7.6862003 19.5931240 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 0.51795627 0.102935017 5.031876 0.104967578 4.934441 283s xmat1 -0.06406827 0.006534226 -9.805029 0.006443532 -9.943037 283s xmat2 -0.04156066 0.008875153 -4.682810 0.010589196 -3.924817 283s 283s Estimated Scale Parameter: 0.6334804 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 283s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 283s [2,] 0 1 0 0 0running glm to get initial regression estimate 283s 0 0 0 0 0 0 0 0 283s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 283s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 283s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 283s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 283s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 283s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 283s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 283s [1,] 0 0 0 0 0 0 0 283s [2,] 0 0 0 0 0 0 0 283s [3,] 0 0 0 0 0 0 0 283s [4,] 0 0 0 0 0 0 0 283s [5,] 0 0 0 0 0 0 0 283s [6,] 0 0 0 0 0 0 0 283s [7,] 0 0 0 0 0 0 0 283s [8,] 0 0 0 0 0 0 0 283s [9,] 0 0 0 0 0 0 0 283s [10,] 0 0 0 0 0 0 0 283s [11,] 0 0 0 0 0 0 0 283s [12,] 0 0 0 0 0 0 0 283s [13,] 0 0 0 0 0 0 0 283s [14,] 1 0 0 0 0 0 0 283s [15,] 0 1 0 0 0 0 0 283s [16,] 0 0 1 0 0 0 0 283s [17,] 0 0 0 1 0 0 0 283s [18,] 0 0 0 0 1 0 0 283s [19,] 0 0 0 0 0 1 0 283s [20,] 0 0 0 0 0 0 1 283s > 283s > sub<-rep(c(FALSE,FALSE,FALSE,FALSE,TRUE),100) 283s > summary(gee(lg~x2+x4,id=id,data=testgee,family=binomial,subset=sub)) 283s (Intercept) x2 x4 283s 5.5224757 -0.3467620 -0.2667172 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logit 283s Variance to Mean Relation: Binomial 283s Correlation Structure: Independent 283s 283s Call: 283s gee(formula = lg ~ x2 + x4, id = id, data = testgee, subset = sub, 283s family = binomial) 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -0.8367702 -0.5120235 0.1897604 0.3569406 0.7244263 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 5.5224757 1.5820384 3.490734 1.25770291 4.390922 283s x2 -0.3467620 0.1323609 -2.619823 0.12032183 -2.881954 283s x4 -0.2667172 0.1190969 -2.239497 0.08655567 -3.081453 283s 283s Estimated Scale Parameter: 0.9974213 283s Number of Iterations: 1 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] 283s [1,] 1 0 0 0 283s [2,] 0 1 0 0 283s [3,] 0 0 1 0 283s [4,] 0 0 0 1 283s > 283s > R <- c(1.0,0.2,0.3,0.1, 283s + 0.2,1.0,0.2,0.3, 283s + 0.3,0.2,1.0,0.2, 283s + 0.1,0.3,0.2,1.0) 283s > R <- matrix(R,nrow=4) 283s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=poisson(link=log), 283s + subset=sub,corstr="fixed",R=R)) 283s (Intercept) x2 x4 283s 2.80530150 -0.08997444 -0.04801454 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logarithm 283s Variance to Mean Relation: Poisson 283s Correlation Structure: Fixed 283s 283s Call: 283s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 283s R = R, family = poisson(link = log), corstr = "fixed") 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -7.5561190 -3.0282712 -0.7601115 2.3823498 12.5360530 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 3.02620978 0.43234114 6.999588 0.34930120 8.663611 283s x2 -0.10058734 0.04084446 -2.462692 0.04687746 -2.145751 283s x4 -0.06504106 0.03683906 -1.765546 0.03434579 -1.893713 283s 283s Estimated Scale Parameter: 3.192382 283s Number of Iterations: 3 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] 283s [1,] 1.0 0.2 0.3 0.1 283s [2,] 0.2 1.0 0.2 0.3 283s [3,] 0.3 0.2 1.0 0.2 283s [4,] 0.1 0.3 0.2 1.0 283s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=Gamma(link=log), 283s + subset=sub,corstr="fixed",R=R)) 283s (Intercept) x2 x4 283s 2.87964611 -0.08377511 -0.06186083 283s 283s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 283s gee S-function, version 4.13 modified 98/01/27 (1998) 283s 283s Model: 283s Link: Logarithm 283s Variance to Mean Relation: Gamma 283s Correlation Structure: Fixed 283s 283s Call: 283s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 283s R = R, family = Gamma(link = log), corstr = "fixed") 283s 283s Summary of Residuals: 283s Min 1Q Median 3Q Max 283s -8.3423135 -3.0545513 -0.6859899 2.2598854 12.7656153 283s 283s 283s Coefficients: 283s Estimate Naive S.E. Naive z Robust S.E. Robust z 283s (Intercept) 3.11365042 0.44562056 6.987223 0.33999983 9.157800 283s x2 -0.09008311 0.04002263 -2.250804 0.04218714 -2.135322 283s x4 -0.08356337 0.03655400 -2.286025 0.03547845 -2.355328 283s 283s Estimated Scale Parameter: 0.5550169 283s Number of Iterations: 4 283s 283s Working Correlation 283s [,1] [,2] [,3] [,4] 283s [1,] 1.0 0.2 0.3 0.1 283s [2,] 0.2 1.0 0.2 0.3 283s [3,] 0.3 0.2 1.0 0.2 283s [4,] 0.1 0.3 0.2 1.0 283s > 284s autopkgtest [16:13:27]: test run-unit-test: -----------------------] 288s autopkgtest [16:13:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 288s run-unit-test PASS 292s autopkgtest [16:13:35]: test pkg-r-autopkgtest: preparing testbed 294s Reading package lists... 295s Building dependency tree... 295s Reading state information... 295s Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 296s The following NEW packages will be installed: 296s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 296s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-14 g++-14-arm-linux-gnueabihf 296s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 296s gcc-arm-linux-gnueabihf gfortran gfortran-14 gfortran-14-arm-linux-gnueabihf 296s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 296s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-14-dev 296s libgfortran-14-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 296s libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 296s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 296s libreadline-dev libstdc++-14-dev libtirpc-dev libubsan1 linux-libc-dev 296s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 296s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 296s Need to get 78.1 MB of archives. 296s After this operation, 243 MB of additional disk space will be used. 296s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-dev-bin armhf 2.41-1ubuntu2 [23.0 kB] 296s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.14.0-10.10 [1683 kB] 298s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 298s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 298s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6-dev armhf 2.41-1ubuntu2 [1396 kB] 300s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 301s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 301s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9220 kB] 311s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu3 [1030 B] 311s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 311s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 311s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250222-0ubuntu1 [38.9 kB] 311s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250222-0ubuntu1 [2955 kB] 314s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250222-0ubuntu1 [1191 kB] 315s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu3 [897 kB] 316s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [18.0 MB] 335s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu3 [506 kB] 336s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 336s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 336s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu3 [2573 kB] 339s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [10.5 MB] 350s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu3 [21.8 kB] 350s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 350s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 350s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 350s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 350s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran-14-dev armhf 14.2.0-17ubuntu3 [370 kB] 350s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9763 kB] 361s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14 armhf 14.2.0-17ubuntu3 [13.6 kB] 361s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 361s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 361s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 361s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 361s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 361s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 361s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 373s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 374s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 374s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 374s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 376s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 376s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 376s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 377s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 377s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 377s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 378s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 379s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libpng-dev armhf 1.6.47-1 [251 kB] 379s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline-dev armhf 8.2-6 [153 kB] 379s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.4-1 [166 kB] 379s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 379s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 379s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 379s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-dev all 4.4.3-1 [4176 B] 379s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 380s Fetched 78.1 MB in 1min 24s (934 kB/s) 380s Selecting previously unselected package libc-dev-bin. 380s (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 ... 66937 files and directories currently installed.) 380s Preparing to unpack .../00-libc-dev-bin_2.41-1ubuntu2_armhf.deb ... 380s Unpacking libc-dev-bin (2.41-1ubuntu2) ... 380s Selecting previously unselected package linux-libc-dev:armhf. 380s Preparing to unpack .../01-linux-libc-dev_6.14.0-10.10_armhf.deb ... 380s Unpacking linux-libc-dev:armhf (6.14.0-10.10) ... 380s Selecting previously unselected package libcrypt-dev:armhf. 380s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 380s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 380s Selecting previously unselected package rpcsvc-proto. 380s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 380s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 380s Selecting previously unselected package libc6-dev:armhf. 380s Preparing to unpack .../04-libc6-dev_2.41-1ubuntu2_armhf.deb ... 380s Unpacking libc6-dev:armhf (2.41-1ubuntu2) ... 380s Selecting previously unselected package libisl23:armhf. 380s Preparing to unpack .../05-libisl23_0.27-1_armhf.deb ... 380s Unpacking libisl23:armhf (0.27-1) ... 380s Selecting previously unselected package libmpc3:armhf. 380s Preparing to unpack .../06-libmpc3_1.3.1-1build2_armhf.deb ... 380s Unpacking libmpc3:armhf (1.3.1-1build2) ... 380s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 380s Preparing to unpack .../07-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 380s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 381s Selecting previously unselected package cpp-14. 381s Preparing to unpack .../08-cpp-14_14.2.0-17ubuntu3_armhf.deb ... 381s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 381s Selecting previously unselected package cpp-arm-linux-gnueabihf. 381s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 381s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 381s Selecting previously unselected package cpp. 381s Preparing to unpack .../10-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 381s Unpacking cpp (4:14.2.0-1ubuntu1) ... 381s Selecting previously unselected package libcc1-0:armhf. 381s Preparing to unpack .../11-libcc1-0_15-20250222-0ubuntu1_armhf.deb ... 381s Unpacking libcc1-0:armhf (15-20250222-0ubuntu1) ... 381s Selecting previously unselected package libasan8:armhf. 381s Preparing to unpack .../12-libasan8_15-20250222-0ubuntu1_armhf.deb ... 381s Unpacking libasan8:armhf (15-20250222-0ubuntu1) ... 381s Selecting previously unselected package libubsan1:armhf. 381s Preparing to unpack .../13-libubsan1_15-20250222-0ubuntu1_armhf.deb ... 381s Unpacking libubsan1:armhf (15-20250222-0ubuntu1) ... 381s Selecting previously unselected package libgcc-14-dev:armhf. 381s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_armhf.deb ... 381s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 381s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 381s Preparing to unpack .../15-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 381s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 381s Selecting previously unselected package gcc-14. 381s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_armhf.deb ... 381s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 381s Selecting previously unselected package gcc-arm-linux-gnueabihf. 381s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 381s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 381s Selecting previously unselected package gcc. 381s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 381s Unpacking gcc (4:14.2.0-1ubuntu1) ... 382s Selecting previously unselected package libstdc++-14-dev:armhf. 382s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_armhf.deb ... 382s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 382s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 382s Preparing to unpack .../20-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 382s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 382s Selecting previously unselected package g++-14. 382s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_armhf.deb ... 382s Unpacking g++-14 (14.2.0-17ubuntu3) ... 382s Selecting previously unselected package g++-arm-linux-gnueabihf. 382s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 382s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 382s Selecting previously unselected package g++. 382s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 382s Unpacking g++ (4:14.2.0-1ubuntu1) ... 382s Selecting previously unselected package build-essential. 382s Preparing to unpack .../24-build-essential_12.10ubuntu1_armhf.deb ... 382s Unpacking build-essential (12.10ubuntu1) ... 382s Selecting previously unselected package dctrl-tools. 382s Preparing to unpack .../25-dctrl-tools_2.24-3build3_armhf.deb ... 382s Unpacking dctrl-tools (2.24-3build3) ... 382s Selecting previously unselected package libgfortran-14-dev:armhf. 382s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_armhf.deb ... 382s Unpacking libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 382s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 382s Preparing to unpack .../27-gfortran-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 382s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 382s Selecting previously unselected package gfortran-14. 382s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_armhf.deb ... 382s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 382s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 382s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 382s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 382s Selecting previously unselected package gfortran. 382s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 382s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 382s Selecting previously unselected package icu-devtools. 382s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_armhf.deb ... 382s Unpacking icu-devtools (76.1-1ubuntu2) ... 382s Selecting previously unselected package libblas-dev:armhf. 382s Preparing to unpack .../32-libblas-dev_3.12.1-2_armhf.deb ... 382s Unpacking libblas-dev:armhf (3.12.1-2) ... 382s Selecting previously unselected package libbz2-dev:armhf. 383s Preparing to unpack .../33-libbz2-dev_1.0.8-6_armhf.deb ... 383s Unpacking libbz2-dev:armhf (1.0.8-6) ... 383s Selecting previously unselected package libdeflate-dev:armhf. 383s Preparing to unpack .../34-libdeflate-dev_1.23-1_armhf.deb ... 383s Unpacking libdeflate-dev:armhf (1.23-1) ... 383s Selecting previously unselected package libicu-dev:armhf. 383s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_armhf.deb ... 383s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 383s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 383s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 383s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 383s Selecting previously unselected package libjpeg8-dev:armhf. 383s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 383s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 383s Selecting previously unselected package libjpeg-dev:armhf. 383s 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.../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 384s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 384s Setting up linux-libc-dev:armhf (6.14.0-10.10) ... 384s Setting up libpcre2-16-0:armhf (10.45-1) ... 384s Setting up libpcre2-32-0:armhf (10.45-1) ... 384s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ... 384s Setting up libpkgconf3:armhf (1.8.1-4) ... 384s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 384s Setting up libmpc3:armhf (1.3.1-1build2) ... 384s Setting up icu-devtools (76.1-1ubuntu2) ... 384s Setting up pkgconf-bin (1.8.1-4) ... 384s Setting up liblzma-dev:armhf (5.6.4-1) ... 384s Setting up libubsan1:armhf (15-20250222-0ubuntu1) ... 384s Setting up libpcre2-posix3:armhf (10.45-1) ... 384s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 384s Setting up libasan8:armhf (15-20250222-0ubuntu1) ... 384s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 384s Setting up libisl23:armhf (0.27-1) ... 384s Setting up libc-dev-bin (2.41-1ubuntu2) ... 384s Setting up libdeflate-dev:armhf (1.23-1) ... 384s Setting up libcc1-0:armhf (15-20250222-0ubuntu1) ... 384s Setting up libblas-dev:armhf (3.12.1-2) ... 384s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 384s Setting up dctrl-tools (2.24-3build3) ... 384s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 384s Setting up libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 384s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 384s Setting up pkgconf:armhf (1.8.1-4) ... 384s Setting up liblapack-dev:armhf (3.12.1-2) ... 384s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 384s Setting up cpp-14 (14.2.0-17ubuntu3) ... 384s Setting up libc6-dev:armhf (2.41-1ubuntu2) ... 384s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 384s 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(4:14.2.0-1ubuntu1) ... 384s Setting up libpng-dev:armhf (1.6.47-1) ... 384s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 384s Setting up gcc (4:14.2.0-1ubuntu1) ... 384s Setting up g++ (4:14.2.0-1ubuntu1) ... 384s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 384s Setting up build-essential (12.10ubuntu1) ... 384s Setting up gfortran (4:14.2.0-1ubuntu1) ... 384s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 384s 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 384s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 384s 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 384s Setting up r-base-dev (4.4.3-1) ... 384s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 384s Processing triggers for libc-bin (2.41-1ubuntu2) ... 384s Processing triggers for man-db (2.13.0-1) ... 385s Processing triggers for install-info (7.1.1-1) ... 393s autopkgtest [16:15:16]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 393s autopkgtest [16:15:16]: test pkg-r-autopkgtest: [----------------------- 395s Test: Try to load the R library gee 395s 395s R version 4.4.3 (2025-02-28) -- "Trophy Case" 395s Copyright (C) 2025 The R Foundation for Statistical Computing 395s Platform: arm-unknown-linux-gnueabihf (32-bit) 395s 395s R is free software and comes with ABSOLUTELY NO WARRANTY. 395s You are welcome to redistribute it under certain conditions. 395s Type 'license()' or 'licence()' for distribution details. 395s 395s R is a collaborative project with many contributors. 395s Type 'contributors()' for more information and 395s 'citation()' on how to cite R or R packages in publications. 395s 395s Type 'demo()' for some demos, 'help()' for on-line help, or 395s 'help.start()' for an HTML browser interface to help. 395s Type 'q()' to quit R. 395s 395s > library('gee') 395s > 395s > 395s Other tests are currently unsupported! 395s They will be progressively added. 395s autopkgtest [16:15:18]: test pkg-r-autopkgtest: -----------------------] 399s autopkgtest [16:15:22]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 399s pkg-r-autopkgtest PASS 403s autopkgtest [16:15:26]: @@@@@@@@@@@@@@@@@@@@ summary 403s run-unit-test PASS 403s pkg-r-autopkgtest PASS