0s autopkgtest [18:02:24]: starting date and time: 2025-03-15 18:02:24+0000 0s autopkgtest [18:02:24]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:02:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.udrjf97d/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-11.secgroup --name adt-plucky-s390x-r-cran-gee-20250315-180224-juju-7f2275-prod-proposed-migration-environment-2-8a26657c-5d87-4375-8b16-1d6ce3006cef --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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/ 138s autopkgtest [18:04:42]: testbed dpkg architecture: s390x 138s autopkgtest [18:04:42]: testbed apt version: 2.9.33 138s autopkgtest [18:04:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s autopkgtest [18:04:43]: testbed release detected to be: None 140s autopkgtest [18:04:43]: updating testbed package index (apt update) 140s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 140s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 140s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 140s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 141s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 141s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 141s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 141s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 141s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 141s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 141s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 141s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 141s Fetched 1073 kB in 2s (707 kB/s) 142s Reading package lists... 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s Calculating upgrade... 143s Calculating upgrade... 143s The following packages were automatically installed and are no longer required: 143s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 143s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 143s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 143s linux-tools-6.11.0-8-generic 143s Use 'sudo apt autoremove' to remove them. 143s The following packages will be upgraded: 143s pinentry-curses python3-jinja2 strace 143s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 652 kB of archives. 143s After this operation, 27.6 kB of additional disk space will be used. 143s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 144s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 144s Fetched 652 kB in 1s (719 kB/s) 144s (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 ... 81428 files and directories currently installed.) 144s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 144s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 144s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 144s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 144s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 144s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 144s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 144s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 145s Setting up strace (6.13+ds-1ubuntu1) ... 145s Processing triggers for man-db (2.13.0-1) ... 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Solving dependencies... 146s The following packages will be REMOVED: 146s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 146s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 146s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 146s linux-tools-6.11.0-8-generic* 146s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 146s After this operation, 167 MB disk space will be freed. 146s (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 ... 81428 files and directories currently installed.) 146s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 146s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 146s Removing libpython3.12t64:s390x (3.12.9-1) ... 146s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 146s Removing libnsl2:s390x (1.3.0-3build3) ... 146s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 146s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 146s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 147s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 147s Processing triggers for libc-bin (2.41-1ubuntu1) ... 147s (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 ... 56328 files and directories currently installed.) 147s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 147s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 147s autopkgtest [18:04:51]: upgrading testbed (apt dist-upgrade and autopurge) 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 148s Starting 2 pkgProblemResolver with broken count: 0 148s Done 148s Entering ResolveByKeep 148s 148s Calculating upgrade... 148s The following packages will be upgraded: 148s libc-bin libc-dev-bin libc6 libc6-dev locales 148s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 9512 kB of archives. 148s After this operation, 8192 B of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 150s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 153s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 153s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 158s Preconfiguring packages ... 158s Fetched 9512 kB in 9s (1033 kB/s) 158s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 158s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 158s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 158s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 158s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Setting up libc6:s390x (2.41-1ubuntu2) ... 158s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 158s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 158s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Setting up libc-bin (2.41-1ubuntu2) ... 158s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 158s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 158s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Setting up locales (2.41-1ubuntu2) ... 159s Generating locales (this might take a while)... 159s en_US.UTF-8... done 159s Generation complete. 159s Setting up libc-dev-bin (2.41-1ubuntu2) ... 159s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 160s Processing triggers for man-db (2.13.0-1) ... 160s Processing triggers for systemd (257.3-1ubuntu3) ... 161s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 161s Solving dependencies... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s autopkgtest [18:05:06]: rebooting testbed after setup commands that affected boot 166s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 180s autopkgtest [18:05:24]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 183s autopkgtest [18:05:27]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-gee 185s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (dsc) [2061 B] 185s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (tar) [53.1 kB] 185s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (diff) [3696 B] 185s gpgv: Signature made Tue Jan 28 23:41:44 2025 UTC 185s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 185s gpgv: issuer "plessy@debian.org" 185s gpgv: Can't check signature: No public key 185s dpkg-source: warning: cannot verify inline signature for ./r-cran-gee_4.13-29-1.dsc: no acceptable signature found 185s autopkgtest [18:05:29]: testing package r-cran-gee version 4.13-29-1 185s autopkgtest [18:05:29]: build not needed 188s autopkgtest [18:05:32]: test run-unit-test: preparing testbed 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s Starting pkgProblemResolver with broken count: 0 188s Starting 2 pkgProblemResolver with broken count: 0 188s Done 188s The following NEW packages will be installed: 188s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 188s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 188s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 188s libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 188s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 188s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 188s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-gee r-cran-mass 188s unzip x11-common xdg-utils zip 188s 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. 188s Need to get 41.3 MB of archives. 188s After this operation, 82.6 MB of additional disk space will be used. 188s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 189s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 190s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 191s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 191s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 191s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 191s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 191s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 192s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 192s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 192s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 192s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 192s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 192s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 192s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 193s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB] 193s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 193s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 194s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 194s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 194s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 194s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 194s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 197s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 198s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 198s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB] 198s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB] 198s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB] 198s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 198s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 198s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 198s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 198s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 199s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 199s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 199s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 200s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 200s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 200s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 202s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 202s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 202s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 202s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 202s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB] 227s Get:45 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-gee s390x 4.13-29-1 [78.1 kB] 227s Get:46 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB] 228s Preconfiguring packages ... 228s Fetched 41.3 MB in 40s (1040 kB/s) 228s Selecting previously unselected package libfreetype6:s390x. 228s (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 ... 56326 files and directories currently installed.) 228s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 228s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 228s Selecting previously unselected package fonts-dejavu-mono. 228s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 228s Unpacking fonts-dejavu-mono (2.37-8) ... 228s Selecting previously unselected package fonts-dejavu-core. 228s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 228s Unpacking fonts-dejavu-core (2.37-8) ... 229s Selecting previously unselected package fontconfig-config. 229s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 229s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package libfontconfig1:s390x. 229s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 229s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package fontconfig. 229s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 229s Unpacking fontconfig (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package libblas3:s390x. 229s Preparing to unpack .../06-libblas3_3.12.1-2_s390x.deb ... 229s Unpacking libblas3:s390x (3.12.1-2) ... 229s Selecting previously unselected package libpixman-1-0:s390x. 229s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_s390x.deb ... 229s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 229s Selecting previously unselected package libxcb-render0:s390x. 229s Preparing to unpack .../08-libxcb-render0_1.17.0-2_s390x.deb ... 229s Unpacking libxcb-render0:s390x (1.17.0-2) ... 229s Selecting previously unselected package libxcb-shm0:s390x. 229s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_s390x.deb ... 229s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 229s Selecting previously unselected package libxrender1:s390x. 229s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 229s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 229s Selecting previously unselected package libcairo2:s390x. 229s Preparing to unpack .../11-libcairo2_1.18.2-2_s390x.deb ... 229s Unpacking libcairo2:s390x (1.18.2-2) ... 229s Selecting previously unselected package libdatrie1:s390x. 229s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_s390x.deb ... 229s Unpacking libdatrie1:s390x (0.2.13-3build1) ... 229s Selecting previously unselected package libdeflate0:s390x. 229s Preparing to unpack .../13-libdeflate0_1.23-1_s390x.deb ... 229s Unpacking libdeflate0:s390x (1.23-1) ... 229s Selecting previously unselected package libgfortran5:s390x. 229s Preparing to unpack .../14-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 229s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 229s Selecting previously unselected package libgomp1:s390x. 229s Preparing to unpack .../15-libgomp1_15-20250222-0ubuntu1_s390x.deb ... 229s Unpacking libgomp1:s390x (15-20250222-0ubuntu1) ... 229s Selecting previously unselected package libgraphite2-3:s390x. 229s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 229s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 229s Selecting previously unselected package libharfbuzz0b:s390x. 229s Preparing to unpack .../17-libharfbuzz0b_10.2.0-1_s390x.deb ... 229s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 229s Selecting previously unselected package x11-common. 229s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu3_all.deb ... 229s Unpacking x11-common (1:7.7+23ubuntu3) ... 229s Selecting previously unselected package libice6:s390x. 229s Preparing to unpack .../19-libice6_2%3a1.1.1-1_s390x.deb ... 229s Unpacking libice6:s390x (2:1.1.1-1) ... 229s Selecting previously unselected package libjpeg-turbo8:s390x. 229s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 229s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 229s Selecting previously unselected package libjpeg8:s390x. 229s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_s390x.deb ... 229s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 229s Selecting previously unselected package liblapack3:s390x. 229s Preparing to unpack .../22-liblapack3_3.12.1-2_s390x.deb ... 229s Unpacking liblapack3:s390x (3.12.1-2) ... 229s Selecting previously unselected package libthai-data. 229s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 229s Unpacking libthai-data (0.1.29-2build1) ... 229s Selecting previously unselected package libthai0:s390x. 229s Preparing to unpack .../24-libthai0_0.1.29-2build1_s390x.deb ... 229s Unpacking libthai0:s390x (0.1.29-2build1) ... 229s Selecting previously unselected package libpango-1.0-0:s390x. 229s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_s390x.deb ... 229s Unpacking libpango-1.0-0:s390x (1.56.2-1) ... 229s Selecting previously unselected package libpangoft2-1.0-0:s390x. 229s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_s390x.deb ... 229s Unpacking libpangoft2-1.0-0:s390x (1.56.2-1) ... 229s Selecting previously unselected package libpangocairo-1.0-0:s390x. 229s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_s390x.deb ... 229s Unpacking libpangocairo-1.0-0:s390x (1.56.2-1) ... 229s Selecting previously unselected package libpaper2:s390x. 229s Preparing to unpack .../28-libpaper2_2.2.5-0.3_s390x.deb ... 229s Unpacking libpaper2:s390x (2.2.5-0.3) ... 229s Selecting previously unselected package libpaper-utils. 229s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_s390x.deb ... 229s Unpacking libpaper-utils (2.2.5-0.3) ... 229s Selecting previously unselected package libsharpyuv0:s390x. 229s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_s390x.deb ... 229s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 229s Selecting previously unselected package libsm6:s390x. 229s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_s390x.deb ... 229s Unpacking libsm6:s390x (2:1.2.4-1) ... 229s Selecting previously unselected package libtcl8.6:s390x. 229s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 229s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 229s Selecting previously unselected package libjbig0:s390x. 229s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 229s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 229s Selecting previously unselected package libwebp7:s390x. 229s Preparing to unpack .../34-libwebp7_1.5.0-0.1_s390x.deb ... 229s Unpacking libwebp7:s390x (1.5.0-0.1) ... 229s Selecting previously unselected package libtiff6:s390x. 229s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 229s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 229s Selecting previously unselected package libxft2:s390x. 229s Preparing to unpack .../36-libxft2_2.3.6-1build1_s390x.deb ... 229s Unpacking libxft2:s390x (2.3.6-1build1) ... 229s Selecting previously unselected package libxss1:s390x. 229s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_s390x.deb ... 229s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 229s Selecting previously unselected package libtk8.6:s390x. 229s Preparing to unpack .../38-libtk8.6_8.6.16-1_s390x.deb ... 229s Unpacking libtk8.6:s390x (8.6.16-1) ... 229s Selecting previously unselected package libxt6t64:s390x. 229s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 229s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 229s Selecting previously unselected package zip. 229s Preparing to unpack .../40-zip_3.0-14ubuntu2_s390x.deb ... 229s Unpacking zip (3.0-14ubuntu2) ... 229s Selecting previously unselected package unzip. 229s Preparing to unpack .../41-unzip_6.0-28ubuntu6_s390x.deb ... 229s Unpacking unzip (6.0-28ubuntu6) ... 229s Selecting previously unselected package xdg-utils. 229s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 229s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 229s Selecting previously unselected package r-base-core. 229s Preparing to unpack .../43-r-base-core_4.4.3-1_s390x.deb ... 229s Unpacking r-base-core (4.4.3-1) ... 229s Selecting previously unselected package r-cran-gee. 229s Preparing to unpack .../44-r-cran-gee_4.13-29-1_s390x.deb ... 229s Unpacking r-cran-gee (4.13-29-1) ... 229s Selecting previously unselected package r-cran-mass. 229s Preparing to unpack .../45-r-cran-mass_7.3-64-1_s390x.deb ... 229s Unpacking r-cran-mass (7.3-64-1) ... 229s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 229s Setting up libpixman-1-0:s390x (0.44.0-3) ... 229s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 229s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 230s Setting up libdatrie1:s390x (0.2.13-3build1) ... 230s Setting up libxcb-render0:s390x (1.17.0-2) ... 230s Setting up unzip (6.0-28ubuntu6) ... 230s Setting up x11-common (1:7.7+23ubuntu3) ... 230s Setting up libdeflate0:s390x (1.23-1) ... 230s Setting up libxcb-shm0:s390x (1.17.0-2) ... 230s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ... 230s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 230s Setting up zip (3.0-14ubuntu2) ... 230s Setting up libblas3:s390x (3.12.1-2) ... 230s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 230s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 230s Setting up fonts-dejavu-mono (2.37-8) ... 230s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 230s Setting up fonts-dejavu-core (2.37-8) ... 230s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 230s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 230s Setting up libwebp7:s390x (1.5.0-0.1) ... 230s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 230s Setting up libthai-data (0.1.29-2build1) ... 230s Setting up libxss1:s390x (1:1.2.3-1build3) ... 230s Setting up libpaper2:s390x (2.2.5-0.3) ... 230s Setting up xdg-utils (1.2.1-2ubuntu1) ... 230s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 230s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 230s Setting up libice6:s390x (2:1.1.1-1) ... 230s Setting up liblapack3:s390x (3.12.1-2) ... 230s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 230s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 230s Setting up libpaper-utils (2.2.5-0.3) ... 230s Setting up libthai0:s390x (0.1.29-2build1) ... 230s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 230s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 230s Setting up libsm6:s390x (2:1.2.4-1) ... 230s Setting up fontconfig (2.15.0-2ubuntu1) ... 232s Regenerating fonts cache... done. 232s Setting up libxft2:s390x (2.3.6-1build1) ... 232s Setting up libtk8.6:s390x (8.6.16-1) ... 232s Setting up libpango-1.0-0:s390x (1.56.2-1) ... 232s Setting up libcairo2:s390x (1.18.2-2) ... 232s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 232s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ... 232s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ... 232s Setting up r-base-core (4.4.3-1) ... 232s Creating config file /etc/R/Renviron with new version 232s Setting up r-cran-gee (4.13-29-1) ... 232s Setting up r-cran-mass (7.3-64-1) ... 232s Processing triggers for install-info (7.1.1-1) ... 232s Processing triggers for libc-bin (2.41-1ubuntu2) ... 232s Processing triggers for man-db (2.13.0-1) ... 234s autopkgtest [18:06:18]: test run-unit-test: [----------------------- 234s BEGIN TEST divergence.R 234s 234s R version 4.4.3 (2025-02-28) -- "Trophy Case" 234s Copyright (C) 2025 The R Foundation for Statistical Computing 234s Platform: s390x-ibm-linux-gnu 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 234s > options(digits=5) 234s > library(gee) 234s > load("data_for_gee_binomial.RData") 234s > try(gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed")) 234s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 234s running glm to get initial regression estimate 234s Error in gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed") : 234s Cgee: error: logistic model for probability has fitted value very close to 1. 234s estimates diverging; iteration terminated. 234s (Intercept) x 234s -0.1291219 0.0019241 234s > ## infinite looped in gee 4.3-14 234s > 234s > 234s > 234s BEGIN TEST tests.R 234s 234s R version 4.4.3 (2025-02-28) -- "Trophy Case" 234s Copyright (C) 2025 The R Foundation for Statistical Computing 234s Platform: s390x-ibm-linux-gnu 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 234s > 234s > # gee support @(#) tests.q 1.2 96/09/27 234s > 234s > library(gee) 234s > 234s > source("testgee.dump") 234s > 234s > myr <- gee(gsind~x2+x3+x4,id=id,data=testgee) 234s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 234s running glm to get initial regression estimate 234s (Intercept) x2 x3 x4 234s 0.8107414 2.2933133 -1.1806841 1.4415174 234s > myr 234s 234s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 234s gee S-function, version 4.13 modified 98/01/27 (1998) 234s 234s Model: 234s Link: Identity 234s Variance to Mean Relation: Gaussian 234s Correlation Structure: Independent 234s 234s Call: 234s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 234s 234s Number of observations : 500 234s 234s Maximum cluster size : 20 234s 234s 234s Coefficients: 234s (Intercept) x2 x3 x4 234s 0.8107414 2.2933133 -1.1806841 1.4415174 234s 234s Estimated Scale Parameter: 2.899625 234s Number of Iterations: 1 234s 234s Working Correlation[1:4,1:4] 234s [,1] [,2] [,3] [,4] 234s [1,] 1 0 0 0 234s [2,] 0 1 0 0 234s [3,] 0 0 1 0 234s [4,] 0 0 0 1 234s 234s 234s Returned Error Value: 234s [1] 0 234s > summary(myr) 234s 234s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 234s gee S-function, version 4.13 modified 98/01/27 (1998) 234s 234s Model: 234s Link: Identity 234s Variance to Mean Relation: Gaussian 234s Correlation Structure: Independent 234s 234s Call: 234s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 234s 234s Summary of Residuals: 234s Min 1Q Median 3Q Max 234s -5.12638044 -1.17212201 0.07530777 1.13873892 5.69264860 234s 234s 234s Coefficients: 234s Estimate Naive S.E. Naive z Robust S.E. Robust z 234s (Intercept) 0.8107414 0.75420946 1.074955 0.76905602 1.054203 234s x2 2.2933133 0.04546161 50.445055 0.04589797 49.965459 234s x3 -1.1806841 0.05974921 -19.760664 0.06847056 -17.243677 234s x4 1.4415174 0.03154513 45.696983 0.03153448 45.712418 234s 234s Estimated Scale Parameter: 2.899625 234s Number of Iterations: 1 234s 234s Working Correlation 234s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 234s running glm to get initial regression estimate 234s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 234s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 234s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 234s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 234s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 234s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 234s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 234s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 234s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 234s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 234s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 234s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 234s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 234s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 234s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 234s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 234s [1,] 0 0 0 0 0 0 0 234s [2,] 0 0 0 0 0 0 0 234s [3,] 0 0 0 0 0 0 0 234s [4,] 0 0 0 0 0 0 0 234s [5,] 0 0 0 0 0 0 0 234s [6,] 0 0 0 0 0 0 0 234s [7,] 0 0 0 0 0 0 0 234s [8,] 0 0 0 0 0 0 0 234s [9,] 0 0 0 0 0 0 0 234s [10,] 0 0 0 0 0 0 0 234s [11,] 0 0 0 0 0 0 0 234s [12,] 0 0 0 0 0 0 0 234s [13,] 0 0 0 0 0 0 0 234s [14,] 1 0 0 0 0 0 0 234s [15,] 0 1 0 0 0 0 0 234s [16,] 0 0 1 0 0 0 0 234s [17,] 0 0 0 1 0 0 0 234s [18,] 0 0 0 0 1 0 0 234s [19,] 0 0 0 0 0 1 0 234s [20,] 0 0 0 0 0 0 1 234s > summary(gee(gs~x2+x4,id=id,data=testgee,corstr="exchangeable")) 234s (Intercept) x2 x4 234s -21.504384 4.643727 3.065537 234s 234s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 234s gee S-function, version 4.13 modified 98/01/27 (1998) 234s 234s Model: 234s Link: Identity 234s Variance to Mean Relation: Gaussian 234s Correlation Structure: Exchangeable 234s 234s Call: 234s gee(formula = gs ~ x2 + x4, id = id, data = testgee, corstr = "exchangeable") 234s 234s Summary of Residuals: 234s Min 1Q Median 3Q Max 234s -32.6076365 -9.8240277 0.4309459 10.2768319 44.8278747 234s 234s 234s Coefficients: 234s Estimate Naive S.E. Naive z Robust S.E. Robust z 234s (Intercept) -21.675077 3.7046983 -5.85070 3.5007586 -6.191537 234s x2 4.676098 0.3786822 12.34835 0.3336659 14.014313 234s x4 3.057583 0.2632230 11.61594 0.2251384 13.580903 234s 234s Estimated Scale Parameter: 202.3612 234s Number of Iterations: 2 234s 234s Working Correlation 234s [,1] [,2] [,3] [,4] [,5] [,6] 234s [1,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [2,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [3,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 234s [4,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 234s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 234s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 234s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 234s [,7] [,8] [,9] [,10] [,11] [,12] 235s [1,] -0.01037861 -0.01037861Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [7,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [8,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [9,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 235s [10,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 235s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 235s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 235s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [,13] [,14] [,15] [,16] [,17] [,18] 235s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [13,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [14,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [15,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 235s [16,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 235s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 235s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 235s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 235s [,19] [,20] 235s [1,] -0.01037861 -0.01037861 235s [2,] -0.01037861 -0.01037861 235s [3,] -0.01037861 -0.01037861 235s [4,] -0.01037861 -0.01037861 235s [5,] -0.01037861 -0.01037861 235s [6,] -0.01037861 -0.01037861 235s [7,] -0.01037861 -0.01037861 235s [8,] -0.01037861 -0.01037861 235s [9,] -0.01037861 -0.01037861 235s [10,] -0.01037861 -0.01037861 235s [11,] -0.01037861 -0.01037861 235s [12,] -0.01037861 -0.01037861 235s [13,] -0.01037861 -0.01037861 235s [14,] -0.01037861 -0.01037861 235s [15,] -0.01037861 -0.01037861 235s [16,] -0.01037861 -0.01037861 235s [17,] -0.01037861 -0.01037861 235s [18,] -0.01037861 -0.01037861 235s [19,] 1.00000000 -0.01037861 235s [20,] -0.01037861 1.00000000 235s > 235s > summary(gee(gsind~sin(x2)+log(x3)+x4,id=id,data=testgee)) 235s (Intercept) sin(x2) log(x3) x4 235s 33.017960 1.235559 -12.033930 1.500485 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Identity 235s Variance to Mean Relation: Gaussian 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = gsind ~ sin(x2) + log(x3) + x4, id = id, data = testgee) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -14.2099238 -2.6510967 -0.4994671 2.1403832 12.8126774 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 33.017960 3.39110198 9.736646 3.03682905 10.872512 235s sin(x2) 1.235559 0.26662685 4.634036 0.44529003 2.774728 235s log(x3) -12.033930 1.43540337 -8.383657 1.33255574 -9.030714 235s x4 1.500485 0.07638601 19.643451 0.06166767 24.331791 235s 235s Estimated Scale Parameter: 17.02534 235s Number of Iterations: 1 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 235s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 235s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 235s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 235s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 235s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 235s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 235s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 235s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 235s [1,] 0 0 0 0 0 0 0 235s [2,] 0 0 0 0 0 0 0 235s [3,] 0 0 0 0 0 0 0 235s [4,] 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 235s [11,] 0 0 0 0 0 0 0 235s [12,] 0 0 0 0 0 0 0 235s [13,] 0 0 0 0 0 0 0 235s [14,] 1 0 0 0 0 0 0 235s [15,] 0 1 0 0 0 0 0 235s [16,] 0 0 1 0 0 0 0 235s [17,] 0 0 0 1 0 0 0 235s [18,] 0 0 0 0 1 0 0 235s [19,] 0 0 0 0 0 1 0 235s [20,] 0 0 0 0 0 0 1 235s > #summary(gee(gsind~gam(x2~x1)$fitted.values+x4,id=id,data=testgee,subset=id<20)) 235s > 235s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial)) 235s (Intercept) x2 x3 x4 235s 4.72920874 -0.34747871 -0.21939993 -0.07103635 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 235s family = binomial) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 4.72920874 1.03210192 4.582114 0.86323313 5.478484 235s x2 -0.34747871 0.06301385 -5.514323 0.05004796 -6.942915 235s x3 -0.21939993 0.07952035 -2.759041 0.07725222 -2.840047 235s x4 -0.07103635 0.04152051 -1.710874 0.03167549 -2.242628 235s 235s Estimated Scale Parameter: 1.009587 235s Number of Iterations: 1 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 235s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 235s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 235s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 235s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 235s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 235s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 235s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 235s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 235s [1,] 0 0 0 0 0 0 0 235s [2,] 0 0 0 0 0 0 0 235s [3,] 0 0 0 0 0 0 0 235s [4,] 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 235s [11,] 0 0 0 0 0 0 0 235s [12,] 0 0 0 0 0 0 0 235s [13,] 0 0 0 0 0 0 0 235s [14,] 1 0 0 0 0 0 0 235s [15,] 0 1 0 0 0 0 0 235s [16,] 0 0 1 0 0 0 0 235s [17,] 0 0 0 1 0 0 0 235s [18,] 0 0 0 0 1 0 0 235s [19,] 0 0 0 0 0 1 0 235s [20,] 0 0 0 0 0 0 1 235s > glm(lgind~x2+x3+x4,data=testgee, start=rep(0,4), # needed in R 235s + family=quasi(link=logit,variance="mu(1-mu)")) 235s 235s Call: glm(formula = lgind ~ x2 + x3 + x4, family = quasi(link = logit, 235s variance = "mu(1-mu)"), data = testgee, start = rep(0, 4)) 235s 235s Coefficients: 235s (Intercept) x2 x3 x4 235s 4.72921 -0.34748 -0.21940 -0.07104 235s 235s Degrees of Freedom: 499 Total (i.e. Null); 496 Residual 235s Null Deviance: 635.6 235s Residual Deviance: 591.4 AIC: NA 235s > 235s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial,scale.fix=TRUE)) 235s (Intercept) x2 x3 x4 235s 4.72920874 -0.34747871 -0.21939993 -0.07103635 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 235s family = binomial, scale.fix = TRUE) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 4.72920874 1.02718977 4.604026 0.86323313 5.478484 235s x2 -0.34747871 0.06271394 -5.540693 0.05004796 -6.942915 235s x3 -0.21939993 0.07914189 -2.772235 0.07725222 -2.840047 235s x4 -0.07103635 0.04132290 -1.719055 0.03167549 -2.242628 235s 235s Estimated Scale Parameter: 1 235s Number of Iterations: 1 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 235s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 235s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 235s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 235s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 235s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 235s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 235s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 235s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 235s [1,] 0 0 0 0 0 0 0 235s [2,] 0 0 0 0 0 0 0 235s [3,] 0 0 0 0 0 0 0 235s [4,] 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 235s [11,] 0 0 0 0 0 0 0 235s [12,] 0 0 0 0 0 0 0 235s [13,] 0 0 0 0 0 0 0 235s [14,] 1 0 0 0 0 0 0 235s [15,] 0 1 0 0 0 0 0 235s [16,] 0 0 1 0 0 0 0 235s [17,] 0 0 0 1 0 0 0 235s [18,] 0 0 0 0 1 0 0 235s [19,] 0 0 0 0 0 1 0 235s [20,] 0 0 0 0 0 0 1 235s > #glm(lgind~x2+x3+x4,data=testgee,family=binomial) 235s > 235s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="exchangeable")) 235s (Intercept) x2 x3 x4 235s 6.4719531 -0.2719330 -0.2759630 -0.1493855 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Exchangeable 235s 235s Call: 235s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 235s corstr = "exchangeable") 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.9132133 -0.4779069 0.2183723 0.4022373 0.8322064 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 6.3714080 1.01872823 6.254276 0.82259807 7.745469 235s x2 -0.2582285 0.05832328 -4.427537 0.06432493 -4.014439 235s x3 -0.2792487 0.07639349 -3.655399 0.05877904 -4.750820 235s x4 -0.1458317 0.04000757 -3.645104 0.02732683 -5.336576 235s 235s Estimated Scale Parameter: 1.008096 235s Number of Iterations: 3 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] 235s [1,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [2,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [3,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 235s [4,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 235s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 235s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 235s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [,7] [,8] [,9] [,10] [,11] [,12] 235s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [7,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [8,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [9,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 235s [10,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 235s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 235s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 235s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [,13] [,14] [,15] [,16] [,17] [,18] 235s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [13,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [14,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [15,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 235s [16,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 235s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 235s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 235s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 235s [,19] [,20] 235s [1,] -0.02048602 -0.02048602 235s [2,] -0.02048602 -0.02048602 235s [3,] -0.02048602 -0.02048602 235s [4,] -0.02048602 -0.02048602 235s [5,] -0.02048602 -0.02048602 235s [6,] -0.02048602 -0.02048602 235s [7,] -0.02048602 -0.02048602 235s [8,] -0.02048602 -0.02048602 235s [9,] -0.02048602 -0.02048602 235s [10,] -0.02048602 -0.02048602 235s [11,] -0.02048602 -0.02048602 235s [12,] -0.02048602 -0.02048602 235s [13,] -0.02048602 -0.02048602 235s [14,] -0.02048602 -0.02048602 235s [15,] -0.02048602 -0.02048602 235s [16,] -0.02048602 -0.02048602 235s [17,] -0.02048602 -0.02048602 235s [18,] -0.02048602 -0.02048602 235s [19,] 1.00000000 -0.02048602 235s [20,] -0.02048602 1.00000000 235s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="stat_M_dep",M=1)) 235s (Intercept) x2 x3 x4 235s 6.4719531 -0.2719330 -0.2759630 -0.1493855 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Stationary M-dependent , M = 1 235s 235s Call: 235s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 235s corstr = "stat_M_dep", Mv = 1) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.8834271 -0.4920962 0.2491360 0.4108783 0.7887767 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 5.4093789 0.84036337 6.436952 0.70900809 7.629502 235s x2 -0.2069859 0.04869638 -4.250540 0.05089218 -4.067147 235s x3 -0.2469902 0.06394554 -3.862508 0.04953133 -4.986545 235s x4 -0.1193671 0.03385364 -3.525976 0.02800656 -4.262113 235s 235s Estimated Scale Parameter: 0.9787236 235s Number of Iterations: 3 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] 235s [1,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 235s [2,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 235s [3,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 235s [4,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 235s [5,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 235s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 235s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 235s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [,7] [,8] [,9] [,10] [,11] [,12] 235s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [6,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [7,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 235s [8,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 235s [9,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 235s [10,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 235s [11,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 235s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 235s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 235s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [,13] [,14] [,15] [,16] [,17] [,18] 235s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [12,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [13,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 235s [14,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 235s [15,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 235s [16,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 235s [17,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 235s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 235s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 235s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 235s [,19] [,20] 235s [1,] 0.0000000 0.0000000 235s [2,] 0.0000000 0.0000000 235s [3,] 0.0000000 0.0000000 235s [4,] 0.0000000 0.0000000 235s [5,] 0.0000000 0.0000000 235s [6,] 0.0000000 0.0000000 235s [7,] 0.0000000 0.0000000 235s [8,] 0.0000000 0.0000000 235s [9,] 0.0000000 0.0000000 235s [10,] 0.0000000 0.0000000 235s [11,] 0.0000000 0.0000000 235s [12,] 0.0000000 0.0000000 235s [13,] 0.0000000 0.0000000 235s [14,] 0.0000000 0.0000000 235s [15,] 0.0000000 0.0000000 235s [16,] 0.0000000 0.0000000 235s [17,] 0.0000000 0.0000000 235s [18,] -0.3301082 0.0000000 235s [19,] 1.0000000 -0.3301082 235s [20,] -0.3301082 1.0000000 235s > 235s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial(link=probit))) 235s (Intercept) x2 x3 x4 235s 3.92612377 -0.16597664 -0.16503829 -0.09214249 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Probit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial(link = probit)) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.9259107 -0.4767799 0.2158545 0.4033760 0.8384385 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 3.92613715 0.61214299 6.413758 0.53755155 7.303741 235s x2 -0.16597696 0.03582656 -4.632790 0.04006791 -4.142391 235s x3 -0.16503933 0.04665763 -3.537242 0.03848563 -4.288336 235s x4 -0.09214252 0.02457762 -3.749042 0.01654858 -5.568001 235s 235s Estimated Scale Parameter: 1.014784 235s Number of Iterations: 1 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 235s [1,] 1 0 0 0 0 0 0 0 0Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s 0 0 0 0 235s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 235s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 235s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 235s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 235s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 235s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 235s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 235s [1,] 0 0 0 0 0 0 0 235s [2,] 0 0 0 0 0 0 0 235s [3,] 0 0 0 0 0 0 0 235s [4,] 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 235s [11,] 0 0 0 0 0 0 0 235s [12,] 0 0 0 0 0 0 0 235s [13,] 0 0 0 0 0 0 0 235s [14,] 1 0 0 0 0 0 0 235s [15,] 0 1 0 0 0 0 0 235s [16,] 0 0 1 0 0 0 0 235s [17,] 0 0 0 1 0 0 0 235s [18,] 0 0 0 0 1 0 0 235s [19,] 0 0 0 0 0 1 0 235s [20,] 0 0 0 0 0 0 1 235s > # next line does not work in R's glm: needs starting values for quasi 235s > #summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=quasi(link=probit,variance="mu(1-mu)"))) 235s > summary(gee(lg~x2+x3+x4, id=id, data=testgee, b=rep(0,4), family=quasi(link=probit,variance="mu(1-mu)"))) 235s [,1] 235s [1,] 0 235s [2,] 0 235s [3,] 0 235s [4,] 0 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s user's initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 235s running glm to get initial regression estimate 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Probit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, b = rep(0, 235s 4), family = quasi(link = probit, variance = "mu(1-mu)")) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.9259108 -0.4767799 0.2158545 0.4033761 0.8384386 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 3.92613840 0.61214303 6.413760 0.53755167 7.303741 235s x2 -0.16597699 0.03582656 -4.632791 0.04006791 -4.142392 235s x3 -0.16503949 0.04665763 -3.537245 0.03848564 -4.288340 235s x4 -0.09214246 0.02457762 -3.749040 0.01654858 -5.567998 235s 235s Estimated Scale Parameter: 1.014784 235s Number of Iterations: 4 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 235s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 235s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 235s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 235s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 235s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 235s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 235s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 235s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 235s [1,] 0 0 0 0 0 0 0 235s [2,] 0 0 0 0 0 0 0 235s [3,] 0 0 0 0 0 0 0 235s [4,] 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 235s [11,] 0 0 0 0 0 0 0 235s [12,] 0 0 0 0 0 0 0 235s [13,] 0 0 0 0 0 0 0 235s [14,] 1 0 0 0 0 0 0 235s [15,] 0 1 0 0 0 0 0 235s [16,] 0 0 1 0 0 0 0 235s [17,] 0 0 0 1 0 0 0 235s [18,] 0 0 0 0 1 0 0 235s [19,] 0 0 0 0 0 1 0 235s [20,] 0 0 0 0 0 0 1 235s > 235s > logmat <- cbind(testgee[,"lg1"],testgee[,"nn"]) 235s > xmat <- cbind(testgee[,"x2"], testgee[,"x3"]) 235s > summary(gee(logmat~xmat,id = testgee[,"id"],family=binomial(link=probit))) 235s (Intercept) xmat1 xmat2 235s 0.51795625 -0.06406827 -0.04156066 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Probit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = logmat ~ xmat, id = testgee[, "id"], family = binomial(link = probit)) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s 0.5160816 1.7308948 4.6651553 7.6862003 19.5931240 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 0.51795627 0.102935017 5.031876 0.104967578 4.934441 235s xmat1 -0.06406827 0.006534226 -9.805029 0.006443532 -9.943037 235s xmat2 -0.04156066 0.008875153 -4.682810 0.010589196 -3.924817 235s 235s Estimated Scale Parameter: 0.6334804 235s Number of Iterations: 1 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 235s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 235s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 235s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 235s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 235s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 235s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 235s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 235s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 235s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 235s [1,] 0 0 0 0 0 0 0 235s [2,] 0 0 0 0 0 0 0 235s [3,] 0 0 0 0 0 0 0 235s [4,] 0 0 0 0 0 0 0 235s [5,] 0 0 0 0 0 0 0 235s [6,] 0 0 0 0 0 0 0 235s [7,] 0 0 0 0 0 0 0 235s [8,] 0 0 0 0 0 0 0 235s [9,] 0 0 0 0 0 0 0 235s [10,] 0 0 0 0 0 0 0 235s [11,] 0 0 0 0 0 0 0 235s [12,] 0 0 0 0 0 0 0 235s [13,] 0 0 0 0 0 0 0 235s [14,] 1 0 0 0 0 0 0 235s [15,] 0 1 0 0 0 0 0 235s [16,] 0 0 1 0 0 0 0 235s [17,] 0 0 0 1 0 0 0 235s [18,] 0 0 0 0 1 0 0 235s [19,] 0 0 0 0 0 1 0 235s [20,] 0 0 0 0 0 0 1 235s > 235s > sub<-rep(c(FALSE,FALSE,FALSE,FALSE,TRUE),100) 235s > summary(gee(lg~x2+x4,id=id,data=testgee,family=binomial,subset=sub)) 235s (Intercept) x2 x4 235s 5.5224757 -0.3467620 -0.2667172 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logit 235s Variance to Mean Relation: Binomial 235s Correlation Structure: Independent 235s 235s Call: 235s gee(formula = lg ~ x2 + x4, id = id, data = testgee, subset = sub, 235s family = binomial) 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -0.8367702 -0.5120235 0.1897604 0.3569406 0.7244263 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 5.5224757 1.5820384 3.490734 1.25770291 4.390922 235s x2 -0.3467620 0.1323609 -2.619823 0.12032183 -2.881954 235s x4 -0.2667172 0.1190969 -2.239497 0.08655567 -3.081453 235s 235s Estimated Scale Parameter: 0.9974213 235s Number of Iterations: 1 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] 235s [1,] 1 0 0 0 235s [2,] 0 1 0 0 235s [3,] 0 0 1 0 235s [4,] 0 0 0 1 235s > 235s > R <- c(1.0,0.2,0.3,0.1, 235s + 0.2,1.0,0.2,0.3, 235s + 0.3,0.2,1.0,0.2, 235s + 0.1,0.3,0.2,1.0) 235s > R <- matrix(R,nrow=4) 235s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=poisson(link=log), 235s + subset=sub,corstr="fixed",R=R)) 235s (Intercept) x2 x4 235s 2.80530150 -0.08997444 -0.04801454 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logarithm 235s Variance to Mean Relation: Poisson 235s Correlation Structure: Fixed 235s 235s Call: 235s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 235s R = R, family = poisson(link = log), corstr = "fixed") 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -7.5561190 -3.0282712 -0.7601115 2.3823498 12.5360530 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 3.02620978 0.43234114 6.999588 0.34930120 8.663611 235s x2 -0.10058734 0.04084446 -2.462692 0.04687746 -2.145751 235s x4 -0.06504106 0.03683906 -1.765546 0.03434579 -1.893713 235s 235s Estimated Scale Parameter: 3.192382 235s Number of Iterations: 3 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] 235s [1,] 1.0 0.2 0.3 0.1 235s [2,] 0.2 1.0 0.2 0.3 235s [3,] 0.3 0.2 1.0 0.2 235s [4,] 0.1 0.3 0.2 1.0 235s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=Gamma(link=log), 235s + subset=sub,corstr="fixed",R=R)) 235s (Intercept) x2 x4 235s 2.87964611 -0.08377511 -0.06186083 235s 235s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 235s gee S-function, version 4.13 modified 98/01/27 (1998) 235s 235s Model: 235s Link: Logarithm 235s Variance to Mean Relation: Gamma 235s Correlation Structure: Fixed 235s 235s Call: 235s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 235s R = R, family = Gamma(link = log), corstr = "fixed") 235s 235s Summary of Residuals: 235s Min 1Q Median 3Q Max 235s -8.3423135 -3.0545513 -0.6859899 2.2598854 12.7656153 235s 235s 235s Coefficients: 235s Estimate Naive S.E. Naive z Robust S.E. Robust z 235s (Intercept) 3.11365042 0.44562056 6.987223 0.33999983 9.157800 235s x2 -0.09008311 0.04002263 -2.250804 0.04218714 -2.135322 235s x4 -0.08356337 0.03655400 -2.286025 0.03547845 -2.355328 235s 235s Estimated Scale Parameter: 0.5550169 235s Number of Iterations: 4 235s 235s Working Correlation 235s [,1] [,2] [,3] [,4] 235s [1,] 1.0 0.2 0.3 0.1 235s [2,] 0.2 1.0 0.2 0.3 235s [3,] 0.3 0.2 1.0 0.2 235s [4,] 0.1 0.3 0.2 1.0 235s > 235s autopkgtest [18:06:19]: test run-unit-test: -----------------------] 235s autopkgtest [18:06:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 235s run-unit-test PASS 236s autopkgtest [18:06:20]: test pkg-r-autopkgtest: preparing testbed 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 236s Starting pkgProblemResolver with broken count: 0 236s Starting 2 pkgProblemResolver with broken count: 0 236s Done 237s The following NEW packages will be installed: 237s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu 237s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 237s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14 237s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 237s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 237s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 237s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3 237s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 237s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 237s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 237s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 237s Need to get 82.3 MB of archives. 237s After this operation, 279 MB of additional disk space will be used. 237s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 238s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 238s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B] 248s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 248s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 248s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB] 248s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB] 248s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB] 251s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250222-0ubuntu1 [1212 kB] 252s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB] 253s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB] 274s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB] 275s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 275s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 275s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB] 277s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB] 288s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB] 288s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 288s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 288s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 288s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB] 288s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB] 288s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB] 299s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB] 299s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B] 299s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B] 299s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB] 299s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB] 299s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB] 299s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB] 299s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB] 313s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB] 314s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 314s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 314s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB] 321s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB] 321s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 322s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 322s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B] 322s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB] 323s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB] 323s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 324s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB] 324s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB] 325s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB] 325s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB] 325s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB] 325s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] 325s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B] 325s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 325s Fetched 82.3 MB in 1min 28s (932 kB/s) 325s Selecting previously unselected package libisl23:s390x. 325s (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 ... 58603 files and directories currently installed.) 325s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ... 325s Unpacking libisl23:s390x (0.27-1) ... 325s Selecting previously unselected package libmpc3:s390x. 325s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ... 325s Unpacking libmpc3:s390x (1.3.1-1build2) ... 325s Selecting previously unselected package cpp-14-s390x-linux-gnu. 325s Preparing to unpack .../02-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 325s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 325s Selecting previously unselected package cpp-14. 325s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_s390x.deb ... 325s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 325s Selecting previously unselected package cpp-s390x-linux-gnu. 325s Preparing to unpack .../04-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 325s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 325s Selecting previously unselected package cpp. 325s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 325s Unpacking cpp (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package libcc1-0:s390x. 326s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_s390x.deb ... 326s Unpacking libcc1-0:s390x (15-20250222-0ubuntu1) ... 326s Selecting previously unselected package libitm1:s390x. 326s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_s390x.deb ... 326s Unpacking libitm1:s390x (15-20250222-0ubuntu1) ... 326s Selecting previously unselected package libasan8:s390x. 326s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_s390x.deb ... 326s Unpacking libasan8:s390x (15-20250222-0ubuntu1) ... 326s Selecting previously unselected package libubsan1:s390x. 326s Preparing to unpack .../09-libubsan1_15-20250222-0ubuntu1_s390x.deb ... 326s Unpacking libubsan1:s390x (15-20250222-0ubuntu1) ... 326s Selecting previously unselected package libgcc-14-dev:s390x. 326s Preparing to unpack .../10-libgcc-14-dev_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package gcc-14-s390x-linux-gnu. 326s Preparing to unpack .../11-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package gcc-14. 326s Preparing to unpack .../12-gcc-14_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package gcc-s390x-linux-gnu. 326s Preparing to unpack .../13-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 326s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package gcc. 326s Preparing to unpack .../14-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 326s Unpacking gcc (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package libstdc++-14-dev:s390x. 326s Preparing to unpack .../15-libstdc++-14-dev_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package g++-14-s390x-linux-gnu. 326s Preparing to unpack .../16-g++-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package g++-14. 326s Preparing to unpack .../17-g++-14_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking g++-14 (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package g++-s390x-linux-gnu. 326s Preparing to unpack .../18-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 326s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package g++. 326s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 326s Unpacking g++ (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package build-essential. 326s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ... 326s Unpacking build-essential (12.10ubuntu1) ... 326s Selecting previously unselected package dctrl-tools. 326s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ... 326s Unpacking dctrl-tools (2.24-3build3) ... 326s Selecting previously unselected package libgfortran-14-dev:s390x. 326s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package gfortran-14-s390x-linux-gnu. 326s Preparing to unpack .../23-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package gfortran-14. 326s Preparing to unpack .../24-gfortran-14_14.2.0-17ubuntu3_s390x.deb ... 326s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 326s Selecting previously unselected package gfortran-s390x-linux-gnu. 326s Preparing to unpack .../25-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 326s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package gfortran. 326s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ... 326s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package icu-devtools. 327s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ... 327s Unpacking icu-devtools (76.1-1ubuntu2) ... 327s Selecting previously unselected package libblas-dev:s390x. 327s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ... 327s Unpacking libblas-dev:s390x (3.12.1-2) ... 327s Selecting previously unselected package libbz2-dev:s390x. 327s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ... 327s Unpacking libbz2-dev:s390x (1.0.8-6) ... 327s Selecting previously unselected package libdeflate-dev:s390x. 327s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ... 327s Unpacking libdeflate-dev:s390x (1.23-1) ... 327s Selecting previously unselected package libicu-dev:s390x. 327s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ... 327s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ... 327s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 327s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ... 327s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 327s Selecting previously unselected package libjpeg8-dev:s390x. 327s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 327s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 327s Selecting previously unselected package libjpeg-dev:s390x. 327s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 327s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 327s Selecting previously unselected package liblapack-dev:s390x. 327s Preparing to unpack .../35-liblapack-dev_3.12.1-2_s390x.deb ... 327s Unpacking liblapack-dev:s390x (3.12.1-2) ... 327s Selecting previously unselected package libncurses-dev:s390x. 327s Preparing to unpack .../36-libncurses-dev_6.5+20250216-2_s390x.deb ... 327s Unpacking libncurses-dev:s390x (6.5+20250216-2) ... 327s Selecting previously unselected package libpcre2-16-0:s390x. 327s Preparing to unpack .../37-libpcre2-16-0_10.45-1_s390x.deb ... 327s Unpacking libpcre2-16-0:s390x (10.45-1) ... 327s Selecting previously unselected package libpcre2-32-0:s390x. 327s Preparing to unpack .../38-libpcre2-32-0_10.45-1_s390x.deb ... 327s Unpacking libpcre2-32-0:s390x (10.45-1) ... 327s Selecting previously unselected package libpcre2-posix3:s390x. 327s Preparing to unpack .../39-libpcre2-posix3_10.45-1_s390x.deb ... 327s Unpacking libpcre2-posix3:s390x (10.45-1) ... 327s Selecting previously unselected package libpcre2-dev:s390x. 327s Preparing to unpack .../40-libpcre2-dev_10.45-1_s390x.deb ... 327s Unpacking libpcre2-dev:s390x (10.45-1) ... 327s Selecting previously unselected package libpkgconf3:s390x. 327s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ... 327s Unpacking libpkgconf3:s390x (1.8.1-4) ... 327s Selecting previously unselected package zlib1g-dev:s390x. 327s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 327s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 327s Selecting previously unselected package libpng-dev:s390x. 327s Preparing to unpack .../43-libpng-dev_1.6.47-1_s390x.deb ... 327s Unpacking libpng-dev:s390x (1.6.47-1) ... 327s Selecting previously unselected package libreadline-dev:s390x. 327s Preparing to unpack .../44-libreadline-dev_8.2-6_s390x.deb ... 327s Unpacking libreadline-dev:s390x (8.2-6) ... 327s Selecting previously unselected package liblzma-dev:s390x. 327s Preparing to unpack .../45-liblzma-dev_5.6.4-1_s390x.deb ... 327s Unpacking liblzma-dev:s390x (5.6.4-1) ... 327s Selecting previously unselected package pkgconf-bin. 327s Preparing to unpack .../46-pkgconf-bin_1.8.1-4_s390x.deb ... 327s Unpacking pkgconf-bin (1.8.1-4) ... 327s Selecting previously unselected package pkgconf:s390x. 327s Preparing to unpack .../47-pkgconf_1.8.1-4_s390x.deb ... 327s Unpacking pkgconf:s390x (1.8.1-4) ... 327s Selecting previously unselected package libtirpc-dev:s390x. 327s Preparing to unpack .../48-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... 327s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ... 327s Selecting previously unselected package r-base-dev. 327s Preparing to unpack .../49-r-base-dev_4.4.3-1_all.deb ... 327s Unpacking r-base-dev (4.4.3-1) ... 327s Selecting previously unselected package pkg-r-autopkgtest. 327s Preparing to unpack .../50-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 327s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 327s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 327s Setting up libncurses-dev:s390x (6.5+20250216-2) ... 327s Setting up libreadline-dev:s390x (8.2-6) ... 327s Setting up libpcre2-16-0:s390x (10.45-1) ... 327s Setting up libpcre2-32-0:s390x (10.45-1) ... 327s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... 327s Setting up libpkgconf3:s390x (1.8.1-4) ... 327s Setting up libmpc3:s390x (1.3.1-1build2) ... 327s Setting up icu-devtools (76.1-1ubuntu2) ... 327s Setting up pkgconf-bin (1.8.1-4) ... 327s Setting up liblzma-dev:s390x (5.6.4-1) ... 327s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ... 327s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 327s Setting up libpcre2-posix3:s390x (10.45-1) ... 327s Setting up libasan8:s390x (15-20250222-0ubuntu1) ... 327s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 327s Setting up libisl23:s390x (0.27-1) ... 327s Setting up libdeflate-dev:s390x (1.23-1) ... 327s Setting up libicu-dev:s390x (76.1-1ubuntu2) ... 327s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ... 327s Setting up libblas-dev:s390x (3.12.1-2) ... 327s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode 327s Setting up dctrl-tools (2.24-3build3) ... 327s Setting up libitm1:s390x (15-20250222-0ubuntu1) ... 327s Setting up libbz2-dev:s390x (1.0.8-6) ... 327s Setting up libpcre2-dev:s390x (10.45-1) ... 327s Setting up libpng-dev:s390x (1.6.47-1) ... 327s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 327s Setting up pkgconf:s390x (1.8.1-4) ... 327s Setting up liblapack-dev:s390x (3.12.1-2) ... 327s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode 327s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 327s Setting up cpp-14 (14.2.0-17ubuntu3) ... 327s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 327s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 327s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 327s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 327s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 327s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 327s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 327s Setting up cpp (4:14.2.0-1ubuntu1) ... 327s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 327s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 327s Setting up gcc-14 (14.2.0-17ubuntu3) ... 327s Setting up g++-14 (14.2.0-17ubuntu3) ... 327s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 327s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 327s Setting up gcc (4:14.2.0-1ubuntu1) ... 327s Setting up g++ (4:14.2.0-1ubuntu1) ... 327s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 327s Setting up build-essential (12.10ubuntu1) ... 327s Setting up gfortran (4:14.2.0-1ubuntu1) ... 327s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 327s 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 327s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 327s 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 327s Setting up r-base-dev (4.4.3-1) ... 327s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 327s Processing triggers for libc-bin (2.41-1ubuntu2) ... 327s Processing triggers for man-db (2.13.0-1) ... 328s Processing triggers for install-info (7.1.1-1) ... 329s autopkgtest [18:07:53]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 329s autopkgtest [18:07:53]: test pkg-r-autopkgtest: [----------------------- 329s Test: Try to load the R library gee 329s 329s R version 4.4.3 (2025-02-28) -- "Trophy Case" 329s Copyright (C) 2025 The R Foundation for Statistical Computing 329s Platform: s390x-ibm-linux-gnu 329s 329s R is free software and comes with ABSOLUTELY NO WARRANTY. 329s You are welcome to redistribute it under certain conditions. 329s Type 'license()' or 'licence()' for distribution details. 329s 329s R is a collaborative project with many contributors. 329s Type 'contributors()' for more information and 329s 'citation()' on how to cite R or R packages in publications. 329s 329s Type 'demo()' for some demos, 'help()' for on-line help, or 329s 'help.start()' for an HTML browser interface to help. 329s Type 'q()' to quit R. 329s 329s > library('gee') 329s > 329s > 329s Other tests are currently unsupported! 329s They will be progressively added. 330s autopkgtest [18:07:54]: test pkg-r-autopkgtest: -----------------------] 330s autopkgtest [18:07:54]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 330s pkg-r-autopkgtest PASS 331s autopkgtest [18:07:55]: @@@@@@@@@@@@@@@@@@@@ summary 331s run-unit-test PASS 331s pkg-r-autopkgtest PASS 336s nova [W] Using flock in prodstack6-s390x 336s flock: timeout while waiting to get lock 336s Creating nova instance adt-plucky-s390x-r-cran-gee-20250315-180224-juju-7f2275-prod-proposed-migration-environment-2-8a26657c-5d87-4375-8b16-1d6ce3006cef from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 336s nova [W] Timed out waiting for 5840e664-d5b8-470a-bbb2-33e47ae0db20 to get deleted.