0s autopkgtest [15:29:25]: starting date and time: 2025-03-15 15:29:25+0000 0s autopkgtest [15:29:25]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:29:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.efinfchv/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-gee --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-43.secgroup --name adt-plucky-arm64-r-cran-gee-20250315-152924-juju-7f2275-prod-proposed-migration-environment-2-d699e726-9972-4fa7-a4b6-eed59d5c202d --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 179s autopkgtest [15:32:24]: testbed dpkg architecture: arm64 179s autopkgtest [15:32:24]: testbed apt version: 2.9.33 180s autopkgtest [15:32:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 180s autopkgtest [15:32:25]: testbed release detected to be: None 181s autopkgtest [15:32:26]: updating testbed package index (apt update) 181s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 181s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 182s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 182s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 182s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 182s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 182s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 182s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 182s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 182s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 182s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 182s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 182s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 182s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 183s Fetched 1094 kB in 1s (815 kB/s) 184s Reading package lists... 185s Reading package lists... 186s Building dependency tree... 186s Reading state information... 187s Calculating upgrade... 188s Calculating upgrade... 188s The following packages will be upgraded: 188s python3-jinja2 strace 188s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s Need to get 608 kB of archives. 188s After this operation, 11.3 kB of additional disk space will be used. 188s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 189s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 190s Fetched 608 kB in 1s (634 kB/s) 190s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 190s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 190s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 191s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 191s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 191s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 191s Setting up strace (6.13+ds-1ubuntu1) ... 191s Processing triggers for man-db (2.13.0-1) ... 192s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s Solving dependencies... 194s The following packages will be REMOVED: 194s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 194s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 194s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 194s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 195s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 195s After this operation, 267 MB disk space will be freed. 195s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 195s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 195s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 195s Removing libpython3.12t64:arm64 (3.12.9-1) ... 195s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 195s Removing libnsl2:arm64 (1.3.0-3build3) ... 195s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 195s Removing libunwind8:arm64 (1.6.2-3.1) ... 195s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 195s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 197s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 197s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 197s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 197s /etc/kernel/postrm.d/initramfs-tools: 197s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 197s /etc/kernel/postrm.d/zz-flash-kernel: 197s flash-kernel: Kernel 6.11.0-8-generic has been removed. 197s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 198s /etc/kernel/postrm.d/zz-update-grub: 198s Sourcing file `/etc/default/grub' 198s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 198s Generating grub configuration file ... 198s Found linux image: /boot/vmlinuz-6.14.0-10-generic 198s Found initrd image: /boot/initrd.img-6.14.0-10-generic 198s Warning: os-prober will not be executed to detect other bootable partitions. 198s Systems on them will not be added to the GRUB boot configuration. 198s Check GRUB_DISABLE_OS_PROBER documentation entry. 198s Adding boot menu entry for UEFI Firmware Settings ... 199s done 199s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 199s Processing triggers for libc-bin (2.41-1ubuntu1) ... 199s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81650 files and directories currently installed.) 199s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 199s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 199s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 199s autopkgtest [15:32:44]: upgrading testbed (apt dist-upgrade and autopurge) 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 201s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 202s Entering ResolveByKeep 203s 203s Calculating upgrade... 203s The following packages will be upgraded: 203s libc-bin libc-dev-bin libc6 libc6-dev locales 203s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s Need to get 9530 kB of archives. 203s After this operation, 0 B of additional disk space will be used. 203s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 205s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 205s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 209s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 209s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 214s Preconfiguring packages ... 214s Fetched 9530 kB in 11s (905 kB/s) 214s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 214s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 214s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 215s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 215s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 215s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 215s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 215s Setting up libc6:arm64 (2.41-1ubuntu2) ... 215s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 215s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 215s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 215s Setting up libc-bin (2.41-1ubuntu2) ... 215s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 215s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 215s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 216s Setting up locales (2.41-1ubuntu2) ... 216s Generating locales (this might take a while)... 219s en_US.UTF-8... done 219s Generation complete. 219s Setting up libc-dev-bin (2.41-1ubuntu2) ... 219s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 219s Processing triggers for man-db (2.13.0-1) ... 220s Processing triggers for systemd (257.3-1ubuntu3) ... 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 221s Starting pkgProblemResolver with broken count: 0 221s Starting 2 pkgProblemResolver with broken count: 0 221s Done 222s Solving dependencies... 222s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 222s autopkgtest [15:33:07]: rebooting testbed after setup commands that affected boot 246s autopkgtest [15:33:31]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 250s autopkgtest [15:33:35]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-gee 252s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (dsc) [2061 B] 252s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (tar) [53.1 kB] 252s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (diff) [3696 B] 252s gpgv: Signature made Tue Jan 28 23:41:44 2025 UTC 252s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 252s gpgv: issuer "plessy@debian.org" 252s gpgv: Can't check signature: No public key 252s dpkg-source: warning: cannot verify inline signature for ./r-cran-gee_4.13-29-1.dsc: no acceptable signature found 252s autopkgtest [15:33:37]: testing package r-cran-gee version 4.13-29-1 253s autopkgtest [15:33:38]: build not needed 254s autopkgtest [15:33:39]: test run-unit-test: preparing testbed 255s Reading package lists... 255s Building dependency tree... 255s Reading state information... 255s Starting pkgProblemResolver with broken count: 0 255s Starting 2 pkgProblemResolver with broken count: 0 255s Done 256s The following NEW packages will be installed: 256s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 256s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 256s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 256s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 256s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 256s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 256s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-gee r-cran-mass 256s unzip x11-common xdg-utils zip 256s 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. 256s Need to get 39.5 MB of archives. 256s After this operation, 81.0 MB of additional disk space will be used. 256s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 258s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 258s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 258s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 258s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 259s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 259s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 259s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 259s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 259s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 260s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 260s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 260s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 260s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 260s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 260s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 261s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 261s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 261s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 261s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 261s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 264s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 264s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 264s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 264s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 264s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 264s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 264s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 264s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 264s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 264s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 264s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 265s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 265s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 266s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 266s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 266s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 266s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 267s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 267s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 267s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 268s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 268s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 301s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gee arm64 4.13-29-1 [72.8 kB] 301s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 303s Preconfiguring packages ... 303s Fetched 39.5 MB in 46s (856 kB/s) 303s Selecting previously unselected package fonts-dejavu-mono. 303s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 303s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 303s Unpacking fonts-dejavu-mono (2.37-8) ... 303s Selecting previously unselected package fonts-dejavu-core. 303s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 303s Unpacking fonts-dejavu-core (2.37-8) ... 303s Selecting previously unselected package fontconfig-config. 303s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 303s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 303s Selecting previously unselected package libfontconfig1:arm64. 303s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 303s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 303s Selecting previously unselected package fontconfig. 303s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 303s Unpacking fontconfig (2.15.0-2ubuntu1) ... 303s Selecting previously unselected package libblas3:arm64. 303s Preparing to unpack .../05-libblas3_3.12.1-2_arm64.deb ... 303s Unpacking libblas3:arm64 (3.12.1-2) ... 304s Selecting previously unselected package libpixman-1-0:arm64. 304s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_arm64.deb ... 304s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 304s Selecting previously unselected package libxcb-render0:arm64. 304s Preparing to unpack .../07-libxcb-render0_1.17.0-2_arm64.deb ... 304s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 304s Selecting previously unselected package libxcb-shm0:arm64. 304s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_arm64.deb ... 304s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 304s Selecting previously unselected package libxrender1:arm64. 304s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 304s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 304s Selecting previously unselected package libcairo2:arm64. 304s Preparing to unpack .../10-libcairo2_1.18.2-2_arm64.deb ... 304s Unpacking libcairo2:arm64 (1.18.2-2) ... 304s Selecting previously unselected package libdatrie1:arm64. 304s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ... 304s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 304s Selecting previously unselected package libdeflate0:arm64. 304s Preparing to unpack .../12-libdeflate0_1.23-1_arm64.deb ... 304s Unpacking libdeflate0:arm64 (1.23-1) ... 304s Selecting previously unselected package 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306s Setting up fonts-dejavu-core (2.37-8) ... 306s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 306s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 306s Setting up libwebp7:arm64 (1.5.0-0.1) ... 306s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 306s Setting up libthai-data (0.1.29-2build1) ... 306s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 306s Setting up libpaper2:arm64 (2.2.5-0.3) ... 306s Setting up xdg-utils (1.2.1-2ubuntu1) ... 306s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 306s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 306s Setting up libice6:arm64 (2:1.1.1-1) ... 306s Setting up liblapack3:arm64 (3.12.1-2) ... 306s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 306s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 306s Setting up libpaper-utils (2.2.5-0.3) ... 306s Setting up libthai0:arm64 (0.1.29-2build1) ... 306s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 306s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 306s Setting up libsm6:arm64 (2:1.2.4-1) ... 306s Setting up fontconfig (2.15.0-2ubuntu1) ... 308s Regenerating fonts cache... done. 308s Setting up libxft2:arm64 (2.3.6-1build1) ... 308s Setting up libtk8.6:arm64 (8.6.16-1) ... 308s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 308s Setting up libcairo2:arm64 (1.18.2-2) ... 308s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 308s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 308s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 308s Setting up r-base-core (4.4.3-1) ... 308s Creating config file /etc/R/Renviron with new version 308s Setting up r-cran-gee (4.13-29-1) ... 308s Setting up r-cran-mass (7.3-64-1) ... 308s Processing triggers for install-info (7.1.1-1) ... 308s Processing triggers for libc-bin (2.41-1ubuntu2) ... 308s Processing triggers for man-db (2.13.0-1) ... 311s autopkgtest [15:34:36]: test run-unit-test: [----------------------- 311s BEGIN TEST divergence.R 311s 311s R version 4.4.3 (2025-02-28) -- "Trophy Case" 311s Copyright (C) 2025 The R Foundation for Statistical Computing 311s Platform: aarch64-unknown-linux-gnu 311s 311s R is free software and comes with ABSOLUTELY NO WARRANTY. 311s You are welcome to redistribute it under certain conditions. 311s Type 'license()' or 'licence()' for distribution details. 311s 311s R is a collaborative project with many contributors. 311s Type 'contributors()' for more information and 311s 'citation()' on how to cite R or R packages in publications. 311s 311s Type 'demo()' for some demos, 'help()' for on-line help, or 311s 'help.start()' for an HTML browser interface to help. 311s Type 'q()' to quit R. 311s 311s > options(digits=5) 311s > library(gee) 311s > load("data_for_gee_binomial.RData") 311s > try(gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed")) 311s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 311s running glm to get initial regression estimate 311s (Intercept) x 311s -0.1291219 0.0019241 311s Error in gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed") : 311s Cgee: error: logistic model for probability has fitted value very close to 1. 311s estimates diverging; iteration terminated. 311s > ## infinite looped in gee 4.3-14 311s > 311s > 311s > 311s BEGIN TEST tests.R 311s 311s R version 4.4.3 (2025-02-28) -- "Trophy Case" 311s Copyright (C) 2025 The R Foundation for Statistical Computing 311s Platform: aarch64-unknown-linux-gnu 311s 311s R is free software and comes with ABSOLUTELY NO WARRANTY. 311s You are welcome to redistribute it under certain conditions. 311s Type 'license()' or 'licence()' for distribution details. 311s 311s R is a collaborative project with many contributors. 311s Type 'contributors()' for more information and 311s 'citation()' on how to cite R or R packages in publications. 311s 311s Type 'demo()' for some demos, 'help()' for on-line help, or 311s 'help.start()' for an HTML browser interface to help. 311s Type 'q()' to quit R. 311s 311s > 311s > # gee support @(#) tests.q 1.2 96/09/27 311s > 311s > library(gee) 311s > 311s > source("testgee.dump") 311s > 311s > myr <- gee(gsind~x2+x3+x4,id=id,data=testgee) 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s (Intercept) x2 x3 x4 312s 0.8107414 2.2933133 -1.1806841 1.4415174 312s > myr 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Identity 312s Variance to Mean Relation: Gaussian 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 312s 312s Number of observations : 500 312s 312s Maximum cluster size : 20 312s 312s 312s Coefficients: 312s (Intercept) x2 x3 x4 312s 0.8107414 2.2933133 -1.1806841 1.4415174 312s 312s Estimated Scale Parameter: 2.899625 312s Number of Iterations: 1 312s 312s Working Correlation[1:4,1:4] 312s [,1] [,2] [,3] [,4] 312s [1,] 1 0 0 0 312s [2,] 0 1 0 0 312s [3,] 0 0 1 0 312s [4,] 0 0 0 1 312s 312s 312s Returned Error Value: 312s [1] 0 312s > summary(myr) 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Identity 312s Variance to Mean Relation: Gaussian 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 312s 312s Summary of Residuals: 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s Min 1Q Median 3Q Max 312s -5.12638044 -1.17212201 0.07530777 1.13873892 5.69264860 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 0.8107414 0.75420946 1.074955 0.76905602 1.054203 312s x2 2.2933133 0.04546161 50.445055 0.04589797 49.965459 312s x3 -1.1806841 0.05974921 -19.760664 0.06847056 -17.243677 312s x4 1.4415174 0.03154513 45.696983 0.03153448 45.712418 312s 312s Estimated Scale Parameter: 2.899625 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > summary(gee(gs~x2+x4,id=id,data=testgee,corstr="exchangeable")) 312s running glm to get initial regression estimate 312s (Intercept) x2 x4 312s -21.504384 4.643727 3.065537 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Identity 312s Variance to Mean Relation: Gaussian 312s Correlation Structure: Exchangeable 312s 312s Call: 312s gee(formula = gs ~ x2 + x4, id = id, data = testgee, corstr = "exchangeable") 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -32.6076365 -9.8240277 0.4309459 10.2768319 44.8278747 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) -21.675077 3.7046983 -5.85070 3.5007586 -6.191537 312s x2 4.676098 0.3786822 12.34835 0.3336659 14.014313 312s x4 3.057583 0.2632230 11.61594 0.2251384 13.580903 312s 312s Estimated Scale Parameter: 202.3612 312s Number of Iterations: 2 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] 312s [1,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [2,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [3,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 312s [4,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 312s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 312s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 312s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [,7] [,8] [,9] [,10] [,11] [,12] 312s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [7,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [8,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [9,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 312s [10,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 312s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 312s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 312s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [,13] [,14] [,15] [,16] [,17] [,18] 312s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [13,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [14,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [15,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 312s [16,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 312s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 312s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 312s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 312s [,19] [,20] 312s [1,] -0.01037861 -0.01037861 312s [2,] -0.01037861 -0.01037861 312s [3,] -0.01037861 -0.01037861 312s [4,] -0.01037861 -0.01037861 312s [5,] -0.01037861 -0.01037861 312s [6,] -0.01037861 -0.01037861 312s [7,] -0.01037861 -0.01037861 312s [8,] -0.01037861 -0.01037861 312s [9,] -0.01037861 -0.01037861 312s [10,] -0.01037861 -0.01037861 312s [11,] -0.01037861 -0.01037861 312s [12,] -0.01037861 -0.01037861 312s [13,] -0.01037861 -0.01037861 312s [14,] -0.01037861 -0.01037861 312s [15,] -0.01037861 -0.01037861 312s [16,] -0.01037861 -0.01037861 312s [17,] -0.01037861 -0.01037861 312s [18,] -0.01037861 -0.01037861 312s [19,] 1.00000000 -0.01037861 312s [20,] -0.01037861 1.00000000 312s > 312s > summary(gee(gsind~sin(x2)+log(x3)+x4,id=id,data=testgee)) 312s (Intercept) sin(x2) log(x3) x4 312s 33.017960 1.235559 -12.033930 1.500485 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Identity 312s Variance to Mean Relation: Gaussian 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = gsind ~ sin(x2) + log(x3) + x4, id = id, data = testgee) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -14.2099238 -2.6510967 -0.4994671 2.1403832 12.8126774 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust zBeginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s 312s (Intercept) 33.017960 3.39110198 9.736646 3.03682905 10.872512 312s sin(x2) 1.235559 0.26662685 4.634036 0.44529003 2.774728 312s log(x3) -12.033930 1.43540337 -8.383657 1.33255574 -9.030714 312s x4 1.500485 0.07638601 19.643451 0.06166767 24.331791 312s 312s Estimated Scale Parameter: 17.02534 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > #summary(gee(gsind~gam(x2~x1)$fitted.values+x4,id=id,data=testgee,subset=id<20)) 312s > 312s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial)) 312s (Intercept) x2 x3 x4 312s 4.72920874 -0.34747871 -0.21939993 -0.07103635 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 312s family = binomial) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 4.72920874 1.03210192 4.582114 0.86323313 5.478484 312s x2 -0.34747871 0.06301385 -5.514323 0.05004796 -6.942915 312s x3 -0.21939993 0.07952035 -2.759041 0.07725222 -2.840047 312s x4 -0.07103635 0.04152051 -1.710874 0.03167549 -2.242628 312s 312s Estimated Scale Parameter: 1.009587 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > glm(lgind~x2+x3+x4,data=testgee, start=rep(0,4), # needed in R 312s + family=quasi(link=logit,variance="mu(1-mu)")) 312s 312s Call: glm(formula = lgind ~ x2 + x3 + x4, family = quasi(link = logit, 312s variance = "mu(1-mu)"), data = testgee, start = rep(0, 4)) 312s 312s Coefficients: 312s (Intercept) x2 x3 x4 312s 4.72921 -0.34748 -0.21940 -0.07104 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s 312s Degrees of Freedom: 499 Total (i.e. Null); 496 Residual 312s Null Deviance: 635.6 312s Residual Deviance: 591.4 AIC: NA 312s > 312s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial,scale.fix=TRUE)) 312s (Intercept) x2 x3 x4 312s 4.72920874 -0.34747871 -0.21939993 -0.07103635 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 312s family = binomial, scale.fix = TRUE) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 4.72920874 1.02718977 4.604026 0.86323313 5.478484 312s x2 -0.34747871 0.06271394 -5.540693 0.05004796 -6.942915 312s x3 -0.21939993 0.07914189 -2.772235 0.07725222 -2.840047 312s x4 -0.07103635 0.04132290 -1.719055 0.03167549 -2.242628 312s 312s Estimated Scale Parameter: 1 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > #glm(lgind~x2+x3+x4,data=testgee,family=binomial) 312s > 312s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="exchangeable")) 312s (Intercept) x2 x3 x4 312s 6.4719531 -0.2719330 -0.2759630 -0.1493855 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Exchangeable 312s 312s Call: 312s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 312s corstr = "exchangeable") 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.9132133 -0.4779069 0.2183723 0.4022373 0.8322064 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 6.3714080 1.01872823 6.254276 0.82259807 7.745469 312s x2 -0.2582285 0.05832328 -4.427537 0.06432493 -4.014439 312s x3 -0.2792487 0.07639349 -3.655399 0.05877904 -4.750820 312s x4 -0.1458317 0.04000757 -3.645104 0.02732683 -5.336576 312s 312s Estimated Scale Parameter: 1.008096 312s Number of Iterations: 3 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] 312s [1,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [2,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [3,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 312s [4,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 312s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 312s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 312s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [,7] [,8] [,9] [,10] [,11] [,12] 312s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [7,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [8,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [9,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 312s [10,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 312s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 312s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 312s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [,13] [,14] [,15] [,16] [,17] [,18] 312s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [13,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [14,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [15,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 312s [16,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 312s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 312s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 312s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 312s [,19] [,20] 312s [1,] -0.02048602 -0.02048602 312s [2,] -0.02048602 -0.02048602 312s [3,] -0.02048602 -0.02048602 312s [4,] -0.02048602 -0.02048602 312s [5,] -0.02048602 -0.02048602 312s [6,] -0.02048602 -0.02048602 312s [7,] -0.02048602 -0.02048602 312s [8,] -0.02048602 -0.02048602 312s [9,] -0.02048602 -0.02048602 312s [10,] -0.02048602 -0.02048602 312s [11,] -0.02048602 -0.02048602 312s [12,] -0.02048602 -0.02048602 312s [13,] -0.02048602 -0.02048602 312s [14,] -0.02048602 -0.02048602 312s [15,] -0.02048602 -0.02048602 312s [16,] -0.02048602 -0.02048602 312s [17,] -0.02048602 -0.02048602 312s [18,] -0.02048602 -0.02048602 312s [19,] 1.00000000 -0.02048602 312s [20,] -0.02048602 1.00000000 312s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="stat_M_dep",M=1)) 312s (Intercept) x2 x3 x4 312s 6.4719531 -0.2719330 -0.2759630 -0.1493855 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Stationary M-dependent , M = 1 312s 312s Call: 312s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 312s corstr = "stat_M_dep", Mv = 1) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.8834271 -0.4920962 0.2491360 0.4108783 0.7887767 312s 312s 312s Coefficients: 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 5.4093789 0.84036337 6.436952 0.70900809 7.629502 312s x2 -0.2069859 0.04869638 -4.250540 0.05089218 -4.067147 312s x3 -0.2469902 0.06394554 -3.862508 0.04953133 -4.986545 312s x4 -0.1193671 0.03385364 -3.525976 0.02800656 -4.262113 312s 312s Estimated Scale Parameter: 0.9787236 312s Number of Iterations: 3 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] 312s [1,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 312s [2,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 312s [3,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 312s [4,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 312s [5,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 312s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 312s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 312s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [,7] [,8] [,9] [,10] [,11] [,12] 312s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [6,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [7,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 312s [8,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 312s [9,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 312s [10,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 312s [11,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 312s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 312s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 312s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [,13] [,14] [,15] [,16] [,17] [,18] 312s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [12,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [13,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 312s [14,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 312s [15,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 312s [16,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 312s [17,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 312s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 312s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 312s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 312s [,19] [,20] 312s [1,] 0.0000000 0.0000000 312s [2,] 0.0000000 0.0000000 312s [3,] 0.0000000 0.0000000 312s [4,] 0.0000000 0.0000000 312s [5,] 0.0000000 0.0000000 312s [6,] 0.0000000 0.0000000 312s [7,] 0.0000000 0.0000000 312s [8,] 0.0000000 0.0000000 312s [9,] 0.0000000 0.0000000 312s [10,] 0.0000000 0.0000000 312s [11,] 0.0000000 0.0000000 312s [12,] 0.0000000 0.0000000 312s [13,] 0.0000000 0.0000000 312s [14,] 0.0000000 0.0000000 312s [15,] 0.0000000 0.0000000 312s [16,] 0.0000000 0.0000000 312s [17,] 0.0000000 0.0000000 312s [18,] -0.3301082 0.0000000 312s [19,] 1.0000000 -0.3301082 312s [20,] -0.3301082 1.0000000 312s > 312s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial(link=probit))) 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s (Intercept) x2 x3 x4 312s 3.92612377 -0.16597664 -0.16503829 -0.09214249 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Probit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial(link = probit)) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.9259107 -0.4767799 0.2158545 0.4033760 0.8384385 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 3.92613715 0.61214299 6.413758 0.53755155 7.303741 312s x2 -0.16597696 0.03582656 -4.632790 0.04006791 -4.142391 312s x3 -0.16503933 0.04665763 -3.537242 0.03848563 -4.288336 312s x4 -0.09214252 0.02457762 -3.749042 0.01654858 -5.568001 312s 312s Estimated Scale Parameter: 1.014784 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > # next line does not work in R's glm: needs starting values for quasi 312s > #summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=quasi(link=probit,variance="mu(1-mu)"))) 312s > summary(gee(lg~x2+x3+x4, id=id, data=testgee, b=rep(0,4), family=quasi(link=probit,variance="mu(1-mu)"))) 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s user's initial regression estimate 312s [,1] 312s [1,] 0 312s [2,] 0 312s [3,] 0 312s [4,] 0 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Probit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, b = rep(0, 312s 4), family = quasi(link = probit, variance = "mu(1-mu)")) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.9259108 -0.4767799 0.2158545 0.4033761 0.8384386 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 3.92613840 0.61214303 6.413760 0.53755167 7.303741 312s x2 -0.16597699 0.03582656 -4.632791 0.04006791 -4.142392 312s x3 -0.16503949 0.04665763 -3.537245 0.03848564 -4.288340 312s x4 -0.09214246 0.02457762 -3.749040 0.01654858 -5.567998 312s 312s Estimated Scale Parameter: 1.014784 312s Number of Iterations: 4 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > 312s > logmat <- cbind(testgee[,"lg1"],testgee[,"nn"]) 312s > xmat <- cbind(testgee[,"x2"], testgee[,"x3"]) 312s > summary(gee(logmat~xmat,id = testgee[,"id"],family=binomial(link=probit))) 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s (Intercept) xmat1 xmat2 312s 0.51795625 -0.06406827 -0.04156066 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Probit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = logmat ~ xmat, id = testgee[, "id"], family = binomial(link = probit)) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s 0.5160816 1.7308948 4.6651553 7.6862003 19.5931240 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 0.51795627 0.102935017 5.031876 0.104967578 4.934441 312s xmat1 -0.06406827 0.006534226 -9.805029 0.006443532 -9.943037 312s xmat2 -0.04156066 0.008875153 -4.682810 0.010589196 -3.924817 312s 312s Estimated Scale Parameter: 0.6334804 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 312s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 312s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 312s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 312s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 312s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 312s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 312s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 312s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 312s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 312s [1,] 0 0 0 0 0 0 0 312s [2,] 0 0 0 0 0 0 0 312s [3,] 0 0 0 0 0 0 0 312s [4,] 0 0 0 0 0 0 0 312s [5,] 0 0 0 0 0 0 0 312s [6,] 0 0 0 0 0 0 0 312s [7,] 0 0 0 0 0 0 0 312s [8,] 0 0 0 0 0 0 0 312s [9,] 0 0 0 0 0 0 0 312s [10,] 0 0 0 0 0 0 0 312s [11,] 0 0 0 0 0 0 0 312s [12,] 0 0 0 0 0 0 0 312s [13,] 0 0 0 0 0 0 0 312s [14,] 1 0 0 0 0 0 0 312s [15,] 0 1 0 0 0 0 0 312s [16,] 0 0 1 0 0 0 0 312s [17,] 0 0 0 1 0 0 0 312s [18,] 0 0 0 0 1 0 0 312s [19,] 0 0 0 0 0 1 0 312s [20,] 0 0 0 0 0 0 1 312s > 312s > sub<-rep(c(FALSE,FALSE,FALSE,FALSE,TRUE),100) 312s > summary(gee(lg~x2+x4,id=id,data=testgee,family=binomial,subset=sub)) 312s (Intercept) x2 x4 312s 5.5224757 -0.3467620 -0.2667172 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logit 312s Variance to Mean Relation: Binomial 312s Correlation Structure: Independent 312s 312s Call: 312s gee(formula = lg ~ x2 + x4, id = id, data = testgee, subset = sub, 312s family = binomial) 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -0.8367702 -0.5120235 0.1897604 0.3569406 0.7244263 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive zBeginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s Robust S.E. Robust z 312s (Intercept) 5.5224757 1.5820384 3.490734 1.25770291 4.390922 312s x2 -0.3467620 0.1323609 -2.619823 0.12032183 -2.881954 312s x4 -0.2667172 0.1190969 -2.239497 0.08655567 -3.081453 312s 312s Estimated Scale Parameter: 0.9974213 312s Number of Iterations: 1 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] 312s [1,] 1 0 0 0 312s [2,] 0 1 0 0 312s [3,] 0 0 1 0 312s [4,] 0 0 0 1 312s > 312s > R <- c(1.0,0.2,0.3,0.1, 312s + 0.2,1.0,0.2,0.3, 312s + 0.3,0.2,1.0,0.2, 312s + 0.1,0.3,0.2,1.0) 312s > R <- matrix(R,nrow=4) 312s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=poisson(link=log), 312s + subset=sub,corstr="fixed",R=R)) 312s (Intercept) x2 x4 312s 2.80530150 -0.08997444 -0.04801454 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logarithm 312s Variance to Mean Relation: Poisson 312s Correlation Structure: Fixed 312s 312s Call: 312s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 312s R = R, family = poisson(link = log), corstr = "fixed") 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -7.5561190 -3.0282712 -0.7601115 2.3823498 12.5360530 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 3.02620978 0.43234114 6.999588 0.34930120 8.663611 312s x2 -0.10058734 0.04084446 -2.462692 0.04687746 -2.145751 312s x4 -0.06504106 0.03683906 -1.765546 0.03434579 -1.893713 312s 312s Estimated Scale Parameter: 3.192382 312s Number of Iterations: 3 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] 312s [1,] 1.0 0.2 0.3 0.1 312s [2,] 0.2 1.0 0.2 0.3 312s [3,] 0.3 0.2 1.0 0.2 312s [4,] 0.1 0.3 0.2 1.0 312s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=Gamma(link=log), 312s + subset=sub,corstr="fixed",R=R)) 312s (Intercept) x2 x4 312s 2.87964611 -0.08377511 -0.06186083 312s 312s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 312s gee S-function, version 4.13 modified 98/01/27 (1998) 312s 312s Model: 312s Link: Logarithm 312s Variance to Mean Relation: Gamma 312s Correlation Structure: Fixed 312s 312s Call: 312s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 312s R = R, family = Gamma(link = log), corstr = "fixed") 312s 312s Summary of Residuals: 312s Min 1Q Median 3Q Max 312s -8.3423135 -3.0545513 -0.6859899 2.2598854 12.7656153 312s 312s 312s Coefficients: 312s Estimate Naive S.E. Naive z Robust S.E. Robust z 312s (Intercept) 3.11365042 0.44562056 6.987223 0.33999983 9.157800 312s x2 -0.09008311 0.04002263 -2.250804 0.04218714 -2.135322 312s x4 -0.08356337 0.03655400 -2.286025 0.03547845 -2.355328 312s 312s Estimated Scale Parameter: 0.5550169 312s Number of Iterations: 4 312s 312s Working Correlation 312s [,1] [,2] [,3] [,4] 312s [1,] 1.0 0.2 0.3 0.1 312s [2,] 0.2 1.0 0.2 0.3 312s [3,] 0.3 0.2 1.0 0.2 312s [4,] 0.1 0.3 0.2 1.0 312s > 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 312s running glm to get initial regression estimate 312s autopkgtest [15:34:37]: test run-unit-test: -----------------------] 312s autopkgtest [15:34:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 312s run-unit-test PASS 313s autopkgtest [15:34:38]: test pkg-r-autopkgtest: preparing testbed 313s Reading package lists... 313s Building dependency tree... 313s Reading state information... 314s Starting pkgProblemResolver with broken count: 0 314s Starting 2 pkgProblemResolver with broken count: 0 314s Done 314s The following NEW packages will be installed: 314s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 314s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 314s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 314s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 314s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 314s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 314s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 314s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 314s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 314s libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 314s zlib1g-dev 315s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 315s Need to get 92.7 MB of archives. 315s After this operation, 334 MB of additional disk space will be used. 315s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 315s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 316s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 328s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 328s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 328s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 328s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 328s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 328s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 331s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 332s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 335s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 336s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 338s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 341s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 365s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 366s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 366s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 366s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 371s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 389s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 389s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 389s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 390s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 390s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 390s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 390s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 409s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 409s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 409s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 409s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 409s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 409s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 409s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 410s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 427s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 428s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 428s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 428s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 434s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 435s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 435s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 435s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 435s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 436s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 437s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 438s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 438s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 439s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 439s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 439s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 439s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 439s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 439s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 440s Fetched 92.7 MB in 2min 5s (742 kB/s) 440s Selecting previously unselected package libisl23:arm64. 440s (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 ... 83923 files and directories currently installed.) 440s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 440s Unpacking libisl23:arm64 (0.27-1) ... 440s Selecting previously unselected package libmpc3:arm64. 440s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 440s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 440s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 440s Preparing to unpack .../02-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 440s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 440s Selecting previously unselected package cpp-14. 440s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 440s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 440s Selecting previously unselected package cpp-aarch64-linux-gnu. 440s Preparing to unpack .../04-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 440s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 440s Selecting previously unselected package cpp. 440s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 440s Unpacking cpp (4:14.2.0-1ubuntu1) ... 440s Selecting previously unselected package libcc1-0:arm64. 440s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package libitm1:arm64. 440s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package libasan8:arm64. 440s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package liblsan0:arm64. 440s Preparing to unpack .../09-liblsan0_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package libtsan2:arm64. 440s Preparing to unpack .../10-libtsan2_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package libubsan1:arm64. 440s Preparing to unpack .../11-libubsan1_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ... 440s Selecting previously unselected package libhwasan0:arm64. 440s Preparing to unpack .../12-libhwasan0_15-20250222-0ubuntu1_arm64.deb ... 440s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ... 441s Selecting previously unselected package libgcc-14-dev:arm64. 441s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 441s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 441s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 441s Preparing to unpack .../14-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 441s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 441s Selecting previously unselected package gcc-14. 441s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 441s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 441s Selecting previously unselected package gcc-aarch64-linux-gnu. 441s Preparing to unpack .../16-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 441s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 441s Selecting previously unselected package gcc. 441s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 441s Unpacking gcc 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... 442s Selecting previously unselected package build-essential. 442s Preparing to unpack .../23-build-essential_12.10ubuntu1_arm64.deb ... 442s Unpacking build-essential (12.10ubuntu1) ... 442s Selecting previously unselected package dctrl-tools. 442s Preparing to unpack .../24-dctrl-tools_2.24-3build3_arm64.deb ... 442s Unpacking dctrl-tools (2.24-3build3) ... 442s Selecting previously unselected package libgfortran-14-dev:arm64. 442s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 442s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 442s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 442s Preparing to unpack .../26-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 442s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 442s Selecting previously unselected package gfortran-14. 442s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 442s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 442s Selecting previously unselected package gfortran-aarch64-linux-gnu. 442s Preparing to unpack .../28-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 442s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 442s Selecting previously unselected package gfortran. 442s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 442s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 442s Selecting previously unselected package icu-devtools. 442s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_arm64.deb ... 442s Unpacking icu-devtools (76.1-1ubuntu2) ... 442s Selecting previously unselected package libblas-dev:arm64. 442s Preparing to unpack .../31-libblas-dev_3.12.1-2_arm64.deb ... 442s Unpacking libblas-dev:arm64 (3.12.1-2) ... 442s Selecting previously unselected package libbz2-dev:arm64. 442s Preparing to unpack .../32-libbz2-dev_1.0.8-6_arm64.deb ... 442s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 442s Selecting previously unselected package libdeflate-dev:arm64. 442s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 442s Unpacking libdeflate-dev:arm64 (1.23-1) ... 442s Selecting previously unselected package libicu-dev:arm64. 442s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 442s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 442s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 442s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 442s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 443s Selecting previously unselected package libjpeg8-dev:arm64. 443s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 443s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 443s Selecting previously unselected package libjpeg-dev:arm64. 443s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 443s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 443s Selecting previously unselected package liblapack-dev:arm64. 443s Preparing to unpack .../38-liblapack-dev_3.12.1-2_arm64.deb ... 443s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 443s Selecting previously unselected package libncurses-dev:arm64. 443s Preparing to unpack .../39-libncurses-dev_6.5+20250216-2_arm64.deb ... 443s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... 443s Selecting previously unselected package libpcre2-16-0:arm64. 443s Preparing to unpack .../40-libpcre2-16-0_10.45-1_arm64.deb ... 443s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 443s Selecting previously unselected package libpcre2-32-0:arm64. 443s Preparing to unpack .../41-libpcre2-32-0_10.45-1_arm64.deb ... 443s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 443s Selecting previously unselected package libpcre2-posix3:arm64. 443s Preparing to unpack .../42-libpcre2-posix3_10.45-1_arm64.deb ... 443s Unpacking libpcre2-posix3:arm64 (10.45-1) ... 443s Selecting previously unselected package libpcre2-dev:arm64. 443s Preparing to unpack .../43-libpcre2-dev_10.45-1_arm64.deb ... 443s Unpacking libpcre2-dev:arm64 (10.45-1) ... 443s Selecting previously unselected package libpkgconf3:arm64. 443s Preparing to unpack .../44-libpkgconf3_1.8.1-4_arm64.deb ... 443s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 443s Selecting previously unselected package zlib1g-dev:arm64. 443s Preparing to unpack .../45-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 443s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 443s Selecting previously unselected package libpng-dev:arm64. 443s Preparing to unpack .../46-libpng-dev_1.6.47-1_arm64.deb ... 443s Unpacking libpng-dev:arm64 (1.6.47-1) ... 443s Selecting previously unselected package libreadline-dev:arm64. 443s Preparing to unpack .../47-libreadline-dev_8.2-6_arm64.deb ... 443s Unpacking libreadline-dev:arm64 (8.2-6) ... 443s Selecting previously unselected package liblzma-dev:arm64. 443s Preparing to unpack .../48-liblzma-dev_5.6.4-1_arm64.deb ... 443s Unpacking liblzma-dev:arm64 (5.6.4-1) ... 443s Selecting previously unselected package pkgconf-bin. 443s Preparing to unpack .../49-pkgconf-bin_1.8.1-4_arm64.deb ... 443s Unpacking pkgconf-bin (1.8.1-4) ... 443s Selecting previously unselected package pkgconf:arm64. 443s Preparing to unpack .../50-pkgconf_1.8.1-4_arm64.deb ... 443s Unpacking pkgconf:arm64 (1.8.1-4) ... 443s Selecting previously unselected package libtirpc-dev:arm64. 443s Preparing to unpack .../51-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... 443s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 443s Selecting previously unselected package r-base-dev. 443s Preparing to unpack .../52-r-base-dev_4.4.3-1_all.deb ... 443s Unpacking r-base-dev (4.4.3-1) ... 443s Selecting previously unselected package pkg-r-autopkgtest. 443s Preparing to unpack .../53-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 443s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 443s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 443s Setting up libncurses-dev:arm64 (6.5+20250216-2) ... 443s Setting up libreadline-dev:arm64 (8.2-6) ... 443s Setting up libpcre2-16-0:arm64 (10.45-1) ... 443s Setting up libpcre2-32-0:arm64 (10.45-1) ... 443s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 443s Setting up libpkgconf3:arm64 (1.8.1-4) ... 443s Setting up libmpc3:arm64 (1.3.1-1build2) ... 443s Setting up icu-devtools (76.1-1ubuntu2) ... 443s Setting up pkgconf-bin (1.8.1-4) ... 443s Setting up liblzma-dev:arm64 (5.6.4-1) ... 443s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ... 443s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 443s Setting up libpcre2-posix3:arm64 (10.45-1) ... 443s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ... 443s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ... 443s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ... 443s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 443s Setting up libisl23:arm64 (0.27-1) ... 443s Setting up libdeflate-dev:arm64 (1.23-1) ... 443s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ... 443s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ... 443s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ... 443s Setting up libblas-dev:arm64 (3.12.1-2) ... 443s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 443s Setting up dctrl-tools (2.24-3build3) ... 443s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ... 443s Setting up libbz2-dev:arm64 (1.0.8-6) ... 443s Setting up libpcre2-dev:arm64 (10.45-1) ... 443s Setting up libpng-dev:arm64 (1.6.47-1) ... 443s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 443s Setting up pkgconf:arm64 (1.8.1-4) ... 443s Setting up liblapack-dev:arm64 (3.12.1-2) ... 443s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 443s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 443s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 443s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 443s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 443s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 443s Setting up cpp-14 (14.2.0-17ubuntu3) ... 443s Setting up cpp (4:14.2.0-1ubuntu1) ... 443s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 443s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 443s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 443s Setting up gcc-14 (14.2.0-17ubuntu3) ... 443s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 443s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 443s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 443s Setting up g++-14 (14.2.0-17ubuntu3) ... 443s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 443s Setting up gcc (4:14.2.0-1ubuntu1) ... 443s Setting up g++ (4:14.2.0-1ubuntu1) ... 443s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 443s Setting up build-essential (12.10ubuntu1) ... 443s Setting up gfortran (4:14.2.0-1ubuntu1) ... 443s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 443s 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 443s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 443s 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 443s Setting up r-base-dev (4.4.3-1) ... 443s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 443s Processing triggers for libc-bin (2.41-1ubuntu2) ... 443s Processing triggers for man-db (2.13.0-1) ... 444s Processing triggers for install-info (7.1.1-1) ... 446s autopkgtest [15:36:51]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 446s autopkgtest [15:36:51]: test pkg-r-autopkgtest: [----------------------- 446s Test: Try to load the R library gee 446s 446s R version 4.4.3 (2025-02-28) -- "Trophy Case" 446s Copyright (C) 2025 The R Foundation for Statistical Computing 446s Platform: aarch64-unknown-linux-gnu 446s 446s R is free software and comes with ABSOLUTELY NO WARRANTY. 446s You are welcome to redistribute it under certain conditions. 446s Type 'license()' or 'licence()' for distribution details. 446s 446s R is a collaborative project with many contributors. 446s Type 'contributors()' for more information and 446s 'citation()' on how to cite R or R packages in publications. 446s 446s Type 'demo()' for some demos, 'help()' for on-line help, or 446s 'help.start()' for an HTML browser interface to help. 446s Type 'q()' to quit R. 446s 446s > library('gee') 446s > 446s > 446s Other tests are currently unsupported! 446s They will be progressively added. 446s autopkgtest [15:36:51]: test pkg-r-autopkgtest: -----------------------] 447s pkg-r-autopkgtest PASS 447s autopkgtest [15:36:52]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 447s autopkgtest [15:36:52]: @@@@@@@@@@@@@@@@@@@@ summary 447s run-unit-test PASS 447s pkg-r-autopkgtest PASS 453s nova [W] Using flock in prodstack6-arm64 453s flock: timeout while waiting to get lock 453s Creating nova instance adt-plucky-arm64-r-cran-gee-20250315-152924-juju-7f2275-prod-proposed-migration-environment-2-d699e726-9972-4fa7-a4b6-eed59d5c202d from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 453s nova [W] Timed out waiting for 82d30770-9d27-47a8-8d06-e15b1e192c08 to get deleted.