0s autopkgtest [18:34:23]: starting date and time: 2024-03-16 18:34:23+0000 0s autopkgtest [18:34:23]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [18:34:23]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.phmvhii3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade r-cran-gee --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-17.secgroup --name adt-noble-arm64-r-cran-gee-20240316-183423-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 139s autopkgtest [18:36:42]: testbed dpkg architecture: arm64 139s autopkgtest [18:36:42]: testbed apt version: 2.7.12 139s autopkgtest [18:36:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 141s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3682 kB] 142s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 142s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 142s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 142s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 142s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 142s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 142s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 142s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4006 kB] 142s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 142s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB] 142s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 153s Fetched 9084 kB in 5s (1765 kB/s) 153s Reading package lists... 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 162s Calculating upgrade... 164s The following packages will be REMOVED: 164s libglib2.0-0 libssl3 164s The following NEW packages will be installed: 164s libglib2.0-0t64 libssl3t64 xdg-user-dirs 164s The following packages have been kept back: 164s curl 164s The following packages will be upgraded: 164s gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common 164s 5 upgraded, 3 newly installed, 2 to remove and 1 not upgraded. 164s Need to get 4592 kB of archives. 164s After this operation, 211 kB of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB] 164s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB] 165s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 165s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 165s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB] 165s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] 165s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB] 165s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB] 166s Fetched 4592 kB in 1s (3910 kB/s) 167s (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 ... 75850 files and directories currently installed.) 167s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ... 167s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 167s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested: 167s udisks2 depends on libglib2.0-0 (>= 2.77.0). 167s shared-mime-info depends on libglib2.0-0 (>= 2.75.3). 167s python3-gi depends on libglib2.0-0 (>= 2.77.0). 167s python3-dbus depends on libglib2.0-0 (>= 2.16.0). 167s netplan.io depends on libglib2.0-0 (>= 2.70.0). 167s netplan-generator depends on libglib2.0-0 (>= 2.70.0). 167s libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0). 167s libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0). 167s libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 167s libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56). 167s libqmi-proxy depends on libglib2.0-0 (>= 2.30.0). 167s libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0). 167s libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 167s libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 167s libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3). 167s libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0). 167s libmbim-proxy depends on libglib2.0-0 (>= 2.56). 167s libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56). 167s libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3). 167s libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3). 167s libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3). 167s libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0). 167s libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0). 167s libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0). 167s libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3). 167s libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2). 167s fwupd depends on libglib2.0-0 (>= 2.79.0). 167s bolt depends on libglib2.0-0 (>= 2.56.0). 167s 167s (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 ... 75850 files and directories currently installed.) 167s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ... 167s Selecting previously unselected package libglib2.0-0t64:arm64. 168s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75825 files and directories currently installed.) 168s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ... 168s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... 168s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm' 168s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 168s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 168s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 168s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 168s wget depends on libssl3 (>= 3.0.0). 168s u-boot-tools depends on libssl3 (>= 3.0.0). 168s tnftp depends on libssl3 (>= 3.0.0). 168s tcpdump depends on libssl3 (>= 3.0.0). 168s systemd-resolved depends on libssl3 (>= 3.0.0). 168s systemd depends on libssl3 (>= 3.0.0). 168s sudo depends on libssl3 (>= 3.0.0). 168s sbsigntool depends on libssl3 (>= 3.0.0). 168s rsync depends on libssl3 (>= 3.0.0). 168s python3-cryptography depends on libssl3 (>= 3.0.0). 168s openssh-server depends on libssl3 (>= 3.0.10). 168s openssh-client depends on libssl3 (>= 3.0.10). 168s mtd-utils depends on libssl3 (>= 3.0.0). 168s mokutil depends on libssl3 (>= 3.0.0). 168s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 168s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 168s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 168s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 168s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 168s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 168s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 168s libnvme1 depends on libssl3 (>= 3.0.0). 168s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 168s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 168s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 168s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 168s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 168s kmod depends on libssl3 (>= 3.0.0). 168s dhcpcd-base depends on libssl3 (>= 3.0.0). 168s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 168s 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75850 files and directories currently installed.) 169s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 169s Selecting previously unselected package libssl3t64:arm64. 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75839 files and directories currently installed.) 169s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 169s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 169s Preparing to unpack .../libglib2.0-data_2.79.3-3ubuntu5_all.deb ... 169s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ... 169s Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... 169s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ... 169s Preparing to unpack .../readline-common_8.2-3.1_all.deb ... 169s Unpacking readline-common (8.2-3.1) over (8.2-3) ... 169s Selecting previously unselected package xdg-user-dirs. 170s Preparing to unpack .../xdg-user-dirs_0.18-1_arm64.deb ... 170s Unpacking xdg-user-dirs (0.18-1) ... 170s Setting up xdg-user-dirs (0.18-1) ... 170s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 170s Setting up libtirpc-common (1.3.4+ds-1.1) ... 170s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ... 170s No schema files found: doing nothing. 170s Setting up libglib2.0-data (2.79.3-3ubuntu5) ... 170s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ... 170s Setting up openssl (3.0.13-0ubuntu1) ... 170s Setting up readline-common (8.2-3.1) ... 170s Processing triggers for man-db (2.12.0-3) ... 171s Processing triggers for install-info (7.1-3) ... 171s Processing triggers for libc-bin (2.39-0ubuntu2) ... 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 175s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 176s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 176s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 176s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 176s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 182s Reading package lists... 182s Reading package lists... 183s Building dependency tree... 183s Reading state information... 185s Calculating upgrade... 186s The following packages have been kept back: 186s curl 186s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 186s Reading package lists... 187s Building dependency tree... 187s Reading state information... 189s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 193s autopkgtest [18:37:36]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 193s autopkgtest [18:37:36]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-gee 195s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-gee 4.13-26-1 (dsc) [2061 B] 195s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-gee 4.13-26-1 (tar) [53.8 kB] 195s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-gee 4.13-26-1 (diff) [3608 B] 196s gpgv: Signature made Mon Jan 8 17:51:21 2024 UTC 196s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 196s gpgv: issuer "tille@debian.org" 196s gpgv: Can't check signature: No public key 196s dpkg-source: warning: cannot verify inline signature for ./r-cran-gee_4.13-26-1.dsc: no acceptable signature found 196s autopkgtest [18:37:39]: testing package r-cran-gee version 4.13-26-1 197s autopkgtest [18:37:40]: build not needed 198s autopkgtest [18:37:41]: test run-unit-test: preparing testbed 199s Reading package lists... 200s Building dependency tree... 200s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 203s The following additional packages will be installed: 203s curl fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 203s libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 203s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 203s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 203s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 203s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 203s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 203s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-gee 203s r-cran-mass unzip x11-common xdg-utils zip 204s Suggested packages: 204s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 204s Recommended packages: 204s r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl 204s libx11-protocol-perl x11-utils x11-xserver-utils 204s The following packages will be REMOVED: 204s libcurl4 libpng16-16 libpsl5 libreadline8 libtirpc3 204s The following NEW packages will be installed: 204s autopkgtest-satdep fontconfig fontconfig-config fonts-dejavu-core 204s fonts-dejavu-mono libblas3 libcairo2 libcurl4t64 libdatrie1 libdeflate0 204s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libice6 204s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 204s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 204s libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libsm6 libtcl8.6 204s libthai-data libthai0 libtiff6 libtirpc3t64 libtk8.6 libwebp7 libxcb-render0 204s libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-gee 204s r-cran-mass unzip x11-common xdg-utils zip 204s The following packages will be upgraded: 204s curl 204s 1 upgraded, 52 newly installed, 5 to remove and 0 not upgraded. 204s Need to get 38.8 MB/38.8 MB of archives. 204s After this operation, 77.0 MB of additional disk space will be used. 204s Get:1 /tmp/autopkgtest.6sYP3L/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 204s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 204s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 204s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 205s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-3 [185 kB] 205s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-3.1 [153 kB] 205s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [83.5 kB] 205s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 205s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 205s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 205s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 205s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 205s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 205s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 205s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 205s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 205s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 205s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 205s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 205s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 205s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 205s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 205s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 205s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 205s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 205s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 205s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 205s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 205s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 205s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 205s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 205s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 205s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 205s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 205s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 205s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 205s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 205s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 205s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 205s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 206s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 206s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 206s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 206s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 206s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 206s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 206s Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [168 kB] 206s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 206s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 206s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 206s Get:51 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-core arm64 4.3.3-2build1 [26.8 MB] 207s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gee arm64 4.13-26-1 [72.3 kB] 207s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 208s Preconfiguring packages ... 209s Fetched 38.8 MB in 3s (12.2 MB/s) 209s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 209s wget depends on libpsl5 (>= 0.16.0). 209s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 209s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 209s 209s (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 ... 75866 files and directories currently installed.) 209s Removing libpsl5:arm64 (0.21.2-1build1) ... 209s Selecting previously unselected package libpsl5t64:arm64. 209s (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 ... 75861 files and directories currently installed.) 209s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 209s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 209s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 209s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 210s (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 ... 75867 files and directories currently installed.) 210s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 210s Selecting previously unselected package libcurl4t64:arm64. 210s (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 ... 75862 files and directories currently installed.) 210s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 210s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 210s dpkg: libpng16-16:arm64: dependency problems, but removing anyway as you requested: 210s libplymouth5:arm64 depends on libpng16-16 (>= 1.6.2). 210s libfreetype6:arm64 depends on libpng16-16 (>= 1.6.2-1). 210s 210s (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 ... 75868 files and directories currently installed.) 210s Removing libpng16-16:arm64 (1.6.43-1) ... 210s Selecting previously unselected package libpng16-16t64:arm64. 210s (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 ... 75858 files and directories currently installed.) 210s Preparing to unpack .../libpng16-16t64_1.6.43-3_arm64.deb ... 210s Unpacking libpng16-16t64:arm64 (1.6.43-3) ... 211s dpkg: libreadline8:arm64: dependency problems, but removing anyway as you requested: 211s parted depends on libreadline8 (>= 6.0). 211s libpython3.12-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 211s libpython3.11-stdlib:arm64 depends on libreadline8 (>= 7.0~beta). 211s gpgsm depends on libreadline8 (>= 6.0). 211s gpgconf depends on libreadline8 (>= 6.0). 211s gpg depends on libreadline8 (>= 6.0). 211s gawk depends on libreadline8 (>= 6.0). 211s fdisk depends on libreadline8 (>= 6.0). 211s 211s (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 ... 75869 files and directories currently installed.) 211s Removing libreadline8:arm64 (8.2-3) ... 211s Selecting previously unselected package libreadline8t64:arm64. 211s (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 ... 75857 files and directories currently installed.) 211s Preparing to unpack .../libreadline8t64_8.2-3.1_arm64.deb ... 211s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' 211s Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' 211s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' 211s Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' 211s Unpacking libreadline8t64:arm64 (8.2-3.1) ... 211s dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: 211s lsof depends on libtirpc3 (>= 1.0.2). 211s libpython3.12-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 211s libpython3.11-stdlib:arm64 depends on libtirpc3 (>= 1.0.2). 211s libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). 211s iproute2 depends on libtirpc3 (>= 1.0.2). 211s 211s (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 ... 75877 files and directories currently installed.) 211s Removing libtirpc3:arm64 (1.3.4+ds-1build1) ... 212s Selecting previously unselected package libtirpc3t64:arm64. 212s (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 ... 75871 files and directories currently installed.) 212s Preparing to unpack .../00-libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... 212s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' 212s Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' 212s Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 212s Selecting previously unselected package fonts-dejavu-mono. 212s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 212s Unpacking fonts-dejavu-mono (2.37-8) ... 212s Selecting previously unselected package fonts-dejavu-core. 212s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 212s Unpacking fonts-dejavu-core (2.37-8) ... 212s Selecting previously unselected package fontconfig-config. 212s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 213s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 213s Selecting previously unselected package libfontconfig1:arm64. 213s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 213s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 213s Selecting previously unselected package fontconfig. 213s Preparing to unpack .../05-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 213s Unpacking fontconfig (2.15.0-1ubuntu1) ... 213s Selecting previously unselected package libblas3:arm64. 214s Preparing to unpack .../06-libblas3_3.12.0-3_arm64.deb ... 214s Unpacking libblas3:arm64 (3.12.0-3) ... 214s Selecting previously unselected package libpixman-1-0:arm64. 214s Preparing to unpack .../07-libpixman-1-0_0.42.2-1_arm64.deb ... 214s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 214s Selecting previously unselected package libxcb-render0:arm64. 214s Preparing to unpack .../08-libxcb-render0_1.15-1_arm64.deb ... 214s Unpacking libxcb-render0:arm64 (1.15-1) ... 214s Selecting previously unselected package libxcb-shm0:arm64. 214s Preparing to unpack .../09-libxcb-shm0_1.15-1_arm64.deb ... 214s Unpacking libxcb-shm0:arm64 (1.15-1) ... 214s Selecting previously unselected package libxrender1:arm64. 214s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 214s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 214s Selecting previously unselected package libcairo2:arm64. 214s Preparing to unpack .../11-libcairo2_1.18.0-1_arm64.deb ... 214s Unpacking libcairo2:arm64 (1.18.0-1) ... 214s Selecting previously unselected package libdatrie1:arm64. 214s Preparing to unpack .../12-libdatrie1_0.2.13-3_arm64.deb ... 214s Unpacking libdatrie1:arm64 (0.2.13-3) ... 214s Selecting previously unselected package libdeflate0:arm64. 214s Preparing to unpack .../13-libdeflate0_1.19-1_arm64.deb ... 214s Unpacking libdeflate0:arm64 (1.19-1) ... 214s Selecting previously unselected package libgfortran5:arm64. 214s Preparing to unpack .../14-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 214s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 215s Selecting previously unselected package libgomp1:arm64. 215s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 215s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 215s Selecting previously unselected package libgraphite2-3:arm64. 215s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ... 215s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 215s Selecting previously unselected package libharfbuzz0b:arm64. 215s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ... 215s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 215s Selecting previously unselected package x11-common. 215s Preparing to unpack .../18-x11-common_1%3a7.7+23ubuntu2_all.deb ... 215s Unpacking x11-common (1:7.7+23ubuntu2) ... 215s Selecting previously unselected package libice6:arm64. 215s Preparing to unpack .../19-libice6_2%3a1.0.10-1build2_arm64.deb ... 215s Unpacking libice6:arm64 (2:1.0.10-1build2) ... 215s Selecting previously unselected package libjpeg-turbo8:arm64. 215s Preparing to unpack .../20-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 215s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 215s Selecting previously unselected package libjpeg8:arm64. 215s Preparing to unpack .../21-libjpeg8_8c-2ubuntu11_arm64.deb ... 215s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 215s Selecting previously unselected package liblapack3:arm64. 215s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ... 215s Unpacking liblapack3:arm64 (3.12.0-3) ... 216s Selecting previously unselected package liblerc4:arm64. 216s Preparing to unpack .../23-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 216s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 216s Selecting previously unselected package libthai-data. 216s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 216s Unpacking libthai-data (0.1.29-2) ... 216s Selecting previously unselected package libthai0:arm64. 216s Preparing to unpack .../25-libthai0_0.1.29-2_arm64.deb ... 216s Unpacking libthai0:arm64 (0.1.29-2) ... 216s Selecting previously unselected package libpango-1.0-0:arm64. 216s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 216s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 216s Selecting previously unselected package libpangoft2-1.0-0:arm64. 216s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 216s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 216s Selecting previously unselected package libpangocairo-1.0-0:arm64. 216s Preparing to unpack .../28-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 216s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 216s Selecting previously unselected package libpaper1:arm64. 216s Preparing to unpack .../29-libpaper1_1.1.29_arm64.deb ... 216s Unpacking libpaper1:arm64 (1.1.29) ... 216s Selecting previously unselected package libpaper-utils. 216s Preparing to unpack .../30-libpaper-utils_1.1.29_arm64.deb ... 216s Unpacking libpaper-utils (1.1.29) ... 217s Selecting previously unselected package libsharpyuv0:arm64. 217s Preparing to unpack .../31-libsharpyuv0_1.3.2-0.4_arm64.deb ... 217s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 217s Selecting previously unselected package libsm6:arm64. 217s Preparing to unpack .../32-libsm6_2%3a1.2.3-1build2_arm64.deb ... 217s Unpacking libsm6:arm64 (2:1.2.3-1build2) ... 217s Selecting previously unselected package libtcl8.6:arm64. 217s Preparing to unpack .../33-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 217s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 217s Selecting previously unselected package libjbig0:arm64. 217s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 217s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 217s Selecting previously unselected package libwebp7:arm64. 217s Preparing to unpack .../35-libwebp7_1.3.2-0.4_arm64.deb ... 217s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 217s Selecting previously unselected package libtiff6:arm64. 217s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 217s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 217s Selecting previously unselected package libxft2:arm64. 217s Preparing to unpack .../37-libxft2_2.3.6-1_arm64.deb ... 217s Unpacking libxft2:arm64 (2.3.6-1) ... 217s Selecting previously unselected package libxss1:arm64. 218s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build2_arm64.deb ... 218s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 218s Selecting previously unselected package libtk8.6:arm64. 218s Preparing to unpack .../39-libtk8.6_8.6.13-2_arm64.deb ... 218s Unpacking libtk8.6:arm64 (8.6.13-2) ... 218s Selecting previously unselected package libxt6t64:arm64. 218s Preparing to unpack .../40-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... 218s Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... 218s Selecting previously unselected package zip. 218s Preparing to unpack .../41-zip_3.0-13_arm64.deb ... 218s Unpacking zip (3.0-13) ... 218s Selecting previously unselected package unzip. 218s Preparing to unpack .../42-unzip_6.0-28ubuntu3_arm64.deb ... 218s Unpacking unzip (6.0-28ubuntu3) ... 218s Selecting previously unselected package xdg-utils. 218s Preparing to unpack .../43-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 218s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 218s Selecting previously unselected package r-base-core. 218s Preparing to unpack .../44-r-base-core_4.3.3-2build1_arm64.deb ... 218s Unpacking r-base-core (4.3.3-2build1) ... 220s Selecting previously unselected package r-cran-gee. 220s Preparing to unpack .../45-r-cran-gee_4.13-26-1_arm64.deb ... 220s Unpacking r-cran-gee (4.13-26-1) ... 220s Selecting previously unselected package r-cran-mass. 220s Preparing to unpack .../46-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 220s Unpacking r-cran-mass (7.3-60.0.1-1) ... 220s Selecting previously unselected package autopkgtest-satdep. 220s Preparing to unpack .../47-1-autopkgtest-satdep.deb ... 220s Unpacking autopkgtest-satdep (0) ... 220s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 220s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 220s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 220s Setting up libpaper1:arm64 (1.1.29) ... 221s 221s Creating config file /etc/papersize with new version 221s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 221s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 221s Setting up libdatrie1:arm64 (0.2.13-3) ... 221s Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ... 221s Setting up libxcb-render0:arm64 (1.15-1) ... 221s Setting up unzip (6.0-28ubuntu3) ... 221s Setting up x11-common (1:7.7+23ubuntu2) ... 223s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 223s Setting up libdeflate0:arm64 (1.19-1) ... 223s Setting up libxcb-shm0:arm64 (1.15-1) ... 223s Setting up libpaper-utils (1.1.29) ... 223s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 223s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 223s Setting up zip (3.0-13) ... 223s Setting up libblas3:arm64 (3.12.0-3) ... 223s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 223s Setting up fonts-dejavu-mono (2.37-8) ... 223s Setting up libpng16-16t64:arm64 (1.6.43-3) ... 223s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 223s Setting up fonts-dejavu-core (2.37-8) ... 223s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 223s Setting up 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(Reading database ... 77985 files and directories currently installed.) 240s Removing autopkgtest-satdep (0) ... 243s autopkgtest [18:38:26]: test run-unit-test: [----------------------- 243s BEGIN TEST divergence.R 243s 243s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 243s Copyright (C) 2024 The R Foundation for Statistical Computing 243s Platform: aarch64-unknown-linux-gnu (64-bit) 243s 243s R is free software and comes with ABSOLUTELY NO WARRANTY. 243s You are welcome to redistribute it under certain conditions. 243s Type 'license()' or 'licence()' for distribution details. 243s 243s R is a collaborative project with many contributors. 243s Type 'contributors()' for more information and 243s 'citation()' on how to cite R or R packages in publications. 243s 243s Type 'demo()' for some demos, 'help()' for on-line help, or 243s 'help.start()' for an HTML browser interface to help. 243s Type 'q()' to quit R. 243s 244s > options(digits=5) 244s > library(gee) 244s > load("data_for_gee_binomial.RData") 244s > try(gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed")) 244s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 244s running glm to get initial regression estimate 244s (Intercept) x 244s -0.1291219 0.0019241 244s Error in gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed") : 244s Cgee: error: logistic model for probability has fitted value very close to 1. 244s estimates diverging; iteration terminated. 244s > ## infinite looped in gee 4.3-14 244s > 244s > 244s > 244s BEGIN TEST tests.R 244s 244s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 244s Copyright (C) 2024 The R Foundation for Statistical Computing 244s Platform: aarch64-unknown-linux-gnu (64-bit) 244s 244s R is free software and comes with ABSOLUTELY NO WARRANTY. 244s You are welcome to redistribute it under certain conditions. 244s Type 'license()' or 'licence()' for distribution details. 244s 244s R is a collaborative project with many contributors. 244s Type 'contributors()' for more information and 244s 'citation()' on how to cite R or R packages in publications. 244s 244s Type 'demo()' for some demos, 'help()' for on-line help, or 244s 'help.start()' for an HTML browser interface to help. 244s Type 'q()' to quit R. 244s 244s > 244s > # gee support @(#) tests.q 1.2 96/09/27 244s > 244s > library(gee) 245s > 245s > source("testgee.dump") 245s > 245s > myr <- gee(gsind~x2+x3+x4,id=id,data=testgee) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x3 x4 245s 0.8107414 2.2933133 -1.1806841 1.4415174 245s > myr 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Identity 245s Variance to Mean Relation: Gaussian 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 245s 245s Number of observations : 500 245s 245s Maximum cluster size : 20 245s 245s 245s Coefficients: 245s (Intercept) x2 x3 x4 245s 0.8107414 2.2933133 -1.1806841 1.4415174 245s 245s Estimated Scale Parameter: 2.899625 245s Number of Iterations: 1 245s 245s Working Correlation[1:4,1:4] 245s [,1] [,2] [,3] [,4] 245s [1,] 1 0 0 0 245s [2,] 0 1 0 0 245s [3,] 0 0 1 0 245s [4,] 0 0 0 1 245s 245s 245s Returned Error Value: 245s [1] 0 245s > summary(myr) 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Identity 245s Variance to Mean Relation: Gaussian 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -5.12638044 -1.17212201 0.07530777 1.13873892 5.69264860 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 0.8107414 0.75420946 1.074955 0.76905602 1.054203 245s x2 2.2933133 0.04546161 50.445055 0.04589797 49.965459 245s x3 -1.1806841 0.05974921 -19.760664 0.06847056 -17.243677 245s x4 1.4415174 0.03154513 45.696983 0.03153448 45.712418 245s 245s Estimated Scale Parameter: 2.899625 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > summary(gee(gs~x2+x4,id=id,data=testgee,corstr="exchangeable")) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x4 245s -21.504384 4.643727 3.065537 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Identity 245s Variance to Mean Relation: Gaussian 245s Correlation Structure: Exchangeable 245s 245s Call: 245s gee(formula = gs ~ x2 + x4, id = id, data = testgee, corstr = "exchangeable") 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -32.6076365 -9.8240277 0.4309459 10.2768319 44.8278747 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) -21.675077 3.7046983 -5.85070 3.5007586 -6.191537 245s x2 4.676098 0.3786822 12.34835 0.3336659 14.014313 245s x4 3.057583 0.2632230 11.61594 0.2251384 13.580903 245s 245s Estimated Scale Parameter: 202.3612 245s Number of Iterations: 2 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] 245s [1,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [2,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [3,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 245s [4,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 245s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 245s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 245s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [,7] [,8] [,9] [,10] [,11] [,12] 245s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [7,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [8,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [9,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 245s [10,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 245s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 245s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 245s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [,13] [,14] [,15] [,16] [,17] [,18] 245s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [13,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [14,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [15,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 245s [16,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 245s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 245s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 245s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 245s [,19] [,20] 245s [1,] -0.01037861 -0.01037861 245s [2,] -0.01037861 -0.01037861 245s [3,] -0.01037861 -0.01037861 245s [4,] -0.01037861 -0.01037861 245s [5,] -0.01037861 -0.01037861 245s [6,] -0.01037861 -0.01037861 245s [7,] -0.01037861 -0.01037861 245s [8,] -0.01037861 -0.01037861 245s [9,] -0.01037861 -0.01037861 245s [10,] -0.01037861 -0.01037861 245s [11,] -0.01037861 -0.01037861 245s [12,] -0.01037861 -0.01037861 245s [13,] -0.01037861 -0.01037861 245s [14,] -0.01037861 -0.01037861 245s [15,] -0.01037861 -0.01037861 245s [16,] -0.01037861 -0.01037861 245s [17,] -0.01037861 -0.01037861 245s [18,] -0.01037861 -0.01037861 245s [19,] 1.00000000 -0.01037861 245s [20,] -0.01037861 1.00000000 245s > 245s > summary(gee(gsind~sin(x2)+log(x3)+x4,id=id,data=testgee)) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) sin(x2) log(x3) x4 245s 33.017960 1.235559 -12.033930 1.500485 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Identity 245s Variance to Mean Relation: Gaussian 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = gsind ~ sin(x2) + log(x3) + x4, id = id, data = testgee) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -14.2099238 -2.6510967 -0.4994671 2.1403832 12.8126774 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 33.017960 3.39110198 9.736646 3.03682905 10.872512 245s sin(x2) 1.235559 0.26662685 4.634036 0.44529003 2.774728 245s log(x3) -12.033930 1.43540337 -8.383657 1.33255574 -9.030714 245s x4 1.500485 0.07638601 19.643451 0.06166767 24.331791 245s 245s Estimated Scale Parameter: 17.02534 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > #summary(gee(gsind~gam(x2~x1)$fitted.values+x4,id=id,data=testgee,subset=id<20)) 245s > 245s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial)) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x3 x4 245s 4.72920874 -0.34747871 -0.21939993 -0.07103635 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 245s family = binomial) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 4.72920874 1.03210192 4.582114 0.86323313 5.478484 245s x2 -0.34747871 0.06301385 -5.514323 0.05004796 -6.942915 245s x3 -0.21939993 0.07952035 -2.759041 0.07725222 -2.840047 245s x4 -0.07103635 0.04152051 -1.710874 0.03167549 -2.242628 245s 245s Estimated Scale Parameter: 1.009587 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > glm(lgind~x2+x3+x4,data=testgee, start=rep(0,4), # needed in R 245s + family=quasi(link=logit,variance="mu(1-mu)")) 245s 245s Call: glm(formula = lgind ~ x2 + x3 + x4, family = quasi(link = logit, 245s variance = "mu(1-mu)"), data = testgee, start = rep(0, 4)) 245s 245s Coefficients: 245s (Intercept) x2 x3 x4 245s 4.72921 -0.34748 -0.21940 -0.07104 245s 245s Degrees of Freedom: 499 Total (i.e. Null); 496 Residual 245s Null Deviance: 635.6 245s Residual Deviance: 591.4 AIC: NA 245s > 245s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial,scale.fix=TRUE)) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x3 x4 245s 4.72920874 -0.34747871 -0.21939993 -0.07103635 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 245s family = binomial, scale.fix = TRUE) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 4.72920874 1.02718977 4.604026 0.86323313 5.478484 245s x2 -0.34747871 0.06271394 -5.540693 0.05004796 -6.942915 245s x3 -0.21939993 0.07914189 -2.772235 0.07725222 -2.840047 245s x4 -0.07103635 0.04132290 -1.719055 0.03167549 -2.242628 245s 245s Estimated Scale Parameter: 1 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > #glm(lgind~x2+x3+x4,data=testgee,family=binomial) 245s > 245s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="exchangeable")) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x3 x4 245s 6.4719531 -0.2719330 -0.2759630 -0.1493855 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Exchangeable 245s 245s Call: 245s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 245s corstr = "exchangeable") 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.9132133 -0.4779069 0.2183723 0.4022373 0.8322064 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 6.3714080 1.01872823 6.254276 0.82259807 7.745469 245s x2 -0.2582285 0.05832328 -4.427537 0.06432493 -4.014439 245s x3 -0.2792487 0.07639349 -3.655399 0.05877904 -4.750820 245s x4 -0.1458317 0.04000757 -3.645104 0.02732683 -5.336576 245s 245s Estimated Scale Parameter: 1.008096 245s Number of Iterations: 3 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] 245s [1,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [2,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [3,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 245s [4,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 245s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 245s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 245s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [,7] [,8] [,9] [,10] [,11] [,12] 245s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [7,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [8,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [9,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 245s [10,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 245s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 245s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 245s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [,13] [,14] [,15] [,16] [,17] [,18] 245s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [13,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [14,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [15,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 245s [16,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 245s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 245s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 245s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 245s [,19] [,20] 245s [1,] -0.02048602 -0.02048602 245s [2,] -0.02048602 -0.02048602 245s [3,] -0.02048602 -0.02048602 245s [4,] -0.02048602 -0.02048602 245s [5,] -0.02048602 -0.02048602 245s [6,] -0.02048602 -0.02048602 245s [7,] -0.02048602 -0.02048602 245s [8,] -0.02048602 -0.02048602 245s [9,] -0.02048602 -0.02048602 245s [10,] -0.02048602 -0.02048602 245s [11,] -0.02048602 -0.02048602 245s [12,] -0.02048602 -0.02048602 245s [13,] -0.02048602 -0.02048602 245s [14,] -0.02048602 -0.02048602 245s [15,] -0.02048602 -0.02048602 245s [16,] -0.02048602 -0.02048602 245s [17,] -0.02048602 -0.02048602 245s [18,] -0.02048602 -0.02048602 245s [19,] 1.00000000 -0.02048602 245s [20,] -0.02048602 1.00000000 245s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="stat_M_dep",M=1)) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x3 x4 245s 6.4719531 -0.2719330 -0.2759630 -0.1493855 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Stationary M-dependent , M = 1 245s 245s Call: 245s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 245s corstr = "stat_M_dep", Mv = 1) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.8834271 -0.4920962 0.2491360 0.4108783 0.7887767 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 5.4093789 0.84036337 6.436952 0.70900809 7.629502 245s x2 -0.2069859 0.04869638 -4.250540 0.05089218 -4.067147 245s x3 -0.2469902 0.06394554 -3.862508 0.04953133 -4.986545 245s x4 -0.1193671 0.03385364 -3.525976 0.02800656 -4.262113 245s 245s Estimated Scale Parameter: 0.9787236 245s Number of Iterations: 3 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] 245s [1,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 245s [2,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 245s [3,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 245s [4,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 245s [5,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 245s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 245s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 245s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [,7] [,8] [,9] [,10] [,11] [,12] 245s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [6,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [7,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 245s [8,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 245s [9,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 245s [10,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 245s [11,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 245s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 245s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 245s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [,13] [,14] [,15] [,16] [,17] [,18] 245s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [12,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [13,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 245s [14,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 245s [15,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 245s [16,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 245s [17,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 245s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 245s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 245s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 245s [,19] [,20] 245s [1,] 0.0000000 0.0000000 245s [2,] 0.0000000 0.0000000 245s [3,] 0.0000000 0.0000000 245s [4,] 0.0000000 0.0000000 245s [5,] 0.0000000 0.0000000 245s [6,] 0.0000000 0.0000000 245s [7,] 0.0000000 0.0000000 245s [8,] 0.0000000 0.0000000 245s [9,] 0.0000000 0.0000000 245s [10,] 0.0000000 0.0000000 245s [11,] 0.0000000 0.0000000 245s [12,] 0.0000000 0.0000000 245s [13,] 0.0000000 0.0000000 245s [14,] 0.0000000 0.0000000 245s [15,] 0.0000000 0.0000000 245s [16,] 0.0000000 0.0000000 245s [17,] 0.0000000 0.0000000 245s [18,] -0.3301082 0.0000000 245s [19,] 1.0000000 -0.3301082 245s [20,] -0.3301082 1.0000000 245s > 245s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial(link=probit))) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x3 x4 245s 3.92612377 -0.16597664 -0.16503829 -0.09214249 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Probit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial(link = probit)) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.9259107 -0.4767799 0.2158545 0.4033760 0.8384385 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 3.92613715 0.61214299 6.413758 0.53755155 7.303741 245s x2 -0.16597696 0.03582656 -4.632790 0.04006791 -4.142391 245s x3 -0.16503933 0.04665763 -3.537242 0.03848563 -4.288336 245s x4 -0.09214252 0.02457762 -3.749042 0.01654858 -5.568001 245s 245s Estimated Scale Parameter: 1.014784 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > # next line does not work in R's glm: needs starting values for quasi 245s > #summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=quasi(link=probit,variance="mu(1-mu)"))) 245s > summary(gee(lg~x2+x3+x4, id=id, data=testgee, b=rep(0,4), family=quasi(link=probit,variance="mu(1-mu)"))) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s user's initial regression estimate 245s [,1] 245s [1,] 0 245s [2,] 0 245s [3,] 0 245s [4,] 0 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Probit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, b = rep(0, 245s 4), family = quasi(link = probit, variance = "mu(1-mu)")) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.9259108 -0.4767799 0.2158545 0.4033761 0.8384386 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 3.92613840 0.61214303 6.413760 0.53755167 7.303741 245s x2 -0.16597699 0.03582656 -4.632791 0.04006791 -4.142392 245s x3 -0.16503949 0.04665763 -3.537245 0.03848564 -4.288340 245s x4 -0.09214246 0.02457762 -3.749040 0.01654858 -5.567998 245s 245s Estimated Scale Parameter: 1.014784 245s Number of Iterations: 4 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > 245s > logmat <- cbind(testgee[,"lg1"],testgee[,"nn"]) 245s > xmat <- cbind(testgee[,"x2"], testgee[,"x3"]) 245s > summary(gee(logmat~xmat,id = testgee[,"id"],family=binomial(link=probit))) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) xmat1 xmat2 245s 0.51795625 -0.06406827 -0.04156066 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Probit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = logmat ~ xmat, id = testgee[, "id"], family = binomial(link = probit)) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s 0.5160816 1.7308948 4.6651553 7.6862003 19.5931240 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 0.51795627 0.102935017 5.031876 0.104967578 4.934441 245s xmat1 -0.06406827 0.006534226 -9.805029 0.006443532 -9.943037 245s xmat2 -0.04156066 0.008875153 -4.682810 0.010589196 -3.924817 245s 245s Estimated Scale Parameter: 0.6334804 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 245s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 245s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 245s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 245s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 245s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 245s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 245s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 245s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 245s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 245s [1,] 0 0 0 0 0 0 0 245s [2,] 0 0 0 0 0 0 0 245s [3,] 0 0 0 0 0 0 0 245s [4,] 0 0 0 0 0 0 0 245s [5,] 0 0 0 0 0 0 0 245s [6,] 0 0 0 0 0 0 0 245s [7,] 0 0 0 0 0 0 0 245s [8,] 0 0 0 0 0 0 0 245s [9,] 0 0 0 0 0 0 0 245s [10,] 0 0 0 0 0 0 0 245s [11,] 0 0 0 0 0 0 0 245s [12,] 0 0 0 0 0 0 0 245s [13,] 0 0 0 0 0 0 0 245s [14,] 1 0 0 0 0 0 0 245s [15,] 0 1 0 0 0 0 0 245s [16,] 0 0 1 0 0 0 0 245s [17,] 0 0 0 1 0 0 0 245s [18,] 0 0 0 0 1 0 0 245s [19,] 0 0 0 0 0 1 0 245s [20,] 0 0 0 0 0 0 1 245s > 245s > sub<-rep(c(FALSE,FALSE,FALSE,FALSE,TRUE),100) 245s > summary(gee(lg~x2+x4,id=id,data=testgee,family=binomial,subset=sub)) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x4 245s 5.5224757 -0.3467620 -0.2667172 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logit 245s Variance to Mean Relation: Binomial 245s Correlation Structure: Independent 245s 245s Call: 245s gee(formula = lg ~ x2 + x4, id = id, data = testgee, subset = sub, 245s family = binomial) 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -0.8367702 -0.5120235 0.1897604 0.3569406 0.7244263 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 5.5224757 1.5820384 3.490734 1.25770291 4.390922 245s x2 -0.3467620 0.1323609 -2.619823 0.12032183 -2.881954 245s x4 -0.2667172 0.1190969 -2.239497 0.08655567 -3.081453 245s 245s Estimated Scale Parameter: 0.9974213 245s Number of Iterations: 1 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] 245s [1,] 1 0 0 0 245s [2,] 0 1 0 0 245s [3,] 0 0 1 0 245s [4,] 0 0 0 1 245s > 245s > R <- c(1.0,0.2,0.3,0.1, 245s + 0.2,1.0,0.2,0.3, 245s + 0.3,0.2,1.0,0.2, 245s + 0.1,0.3,0.2,1.0) 245s > R <- matrix(R,nrow=4) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=poisson(link=log), 245s + subset=sub,corstr="fixed",R=R)) 245s running glm to get initial regression estimate 245s (Intercept) x2 x4 245s 2.80530150 -0.08997444 -0.04801454 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logarithm 245s Variance to Mean Relation: Poisson 245s Correlation Structure: Fixed 245s 245s Call: 245s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 245s R = R, family = poisson(link = log), corstr = "fixed") 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -7.5561190 -3.0282712 -0.7601115 2.3823498 12.5360530 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 3.02620978 0.43234114 6.999588 0.34930120 8.663611 245s x2 -0.10058734 0.04084446 -2.462692 0.04687746 -2.145751 245s x4 -0.06504106 0.03683906 -1.765546 0.03434579 -1.893713 245s 245s Estimated Scale Parameter: 3.192382 245s Number of Iterations: 3 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] 245s [1,] 1.0 0.2 0.3 0.1 245s [2,] 0.2 1.0 0.2 0.3 245s [3,] 0.3 0.2 1.0 0.2 245s [4,] 0.1 0.3 0.2 1.0 245s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=Gamma(link=log), 245s + subset=sub,corstr="fixed",R=R)) 245s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 245s running glm to get initial regression estimate 245s (Intercept) x2 x4 245s 2.87964611 -0.08377511 -0.06186083 245s 245s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 245s gee S-function, version 4.13 modified 98/01/27 (1998) 245s 245s Model: 245s Link: Logarithm 245s Variance to Mean Relation: Gamma 245s Correlation Structure: Fixed 245s 245s Call: 245s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 245s R = R, family = Gamma(link = log), corstr = "fixed") 245s 245s Summary of Residuals: 245s Min 1Q Median 3Q Max 245s -8.3423135 -3.0545513 -0.6859899 2.2598854 12.7656153 245s 245s 245s Coefficients: 245s Estimate Naive S.E. Naive z Robust S.E. Robust z 245s (Intercept) 3.11365042 0.44562056 6.987223 0.33999983 9.157800 245s x2 -0.09008311 0.04002263 -2.250804 0.04218714 -2.135322 245s x4 -0.08356337 0.03655400 -2.286025 0.03547845 -2.355328 245s 245s Estimated Scale Parameter: 0.5550169 245s Number of Iterations: 4 245s 245s Working Correlation 245s [,1] [,2] [,3] [,4] 245s [1,] 1.0 0.2 0.3 0.1 245s [2,] 0.2 1.0 0.2 0.3 245s [3,] 0.3 0.2 1.0 0.2 245s [4,] 0.1 0.3 0.2 1.0 245s > 246s autopkgtest [18:38:29]: test run-unit-test: -----------------------] 246s run-unit-test PASS 246s autopkgtest [18:38:29]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 247s autopkgtest [18:38:30]: test pkg-r-autopkgtest: preparing testbed 249s Reading package lists... 250s Building dependency tree... 250s Reading state information... 251s Starting pkgProblemResolver with broken count: 0 251s Starting 2 pkgProblemResolver with broken count: 0 251s Done 253s The following additional packages will be installed: 253s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 253s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 253s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 253s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 253s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 253s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 253s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 253s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 253s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 253s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 253s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 253s Suggested packages: 253s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 253s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 253s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 253s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 253s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 253s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 253s texlive-latex-recommended texlive-latex-extra texinfo 253s Recommended packages: 253s bzip2-doc manpages manpages-dev libc-devtools libpng-tools 253s The following NEW packages will be installed: 253s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu 253s cpp-aarch64-linux-gnu dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu 253s g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu 253s gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu 253s gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev 253s libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev 253s libgfortran-13-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 253s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 253s libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 253s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 253s libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest 253s pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 253s 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. 253s Need to get 92.8 MB/92.8 MB of archives. 253s After this operation, 343 MB of additional disk space will be used. 253s Get:1 /tmp/autopkgtest.6sYP3L/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 254s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 254s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 254s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 254s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [201 kB] 254s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 254s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 254s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 254s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 254s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 254s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 255s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 255s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 255s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 255s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 255s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 255s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 255s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 255s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 255s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 255s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 255s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 255s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 255s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 256s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 256s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 256s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 256s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 256s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 257s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 257s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 257s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 257s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 257s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 257s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 257s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 257s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 257s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 257s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 257s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 257s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 257s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 257s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 258s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 258s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 258s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 258s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 258s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 258s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 258s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 258s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 258s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 258s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 258s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 258s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng-dev arm64 1.6.43-3 [267 kB] 258s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-3.1 [177 kB] 258s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 258s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 258s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 258s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 258s Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-base-dev all 4.3.3-2build1 [4334 B] 258s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 260s Fetched 92.8 MB in 5s (19.6 MB/s) 260s Selecting previously unselected package libc-dev-bin. 260s (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 ... 77985 files and directories currently installed.) 260s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 260s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 260s Selecting previously unselected package linux-libc-dev:arm64. 260s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_arm64.deb ... 260s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 261s Selecting previously unselected package libcrypt-dev:arm64. 261s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 261s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 261s Selecting previously unselected package libtirpc-dev:arm64. 261s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... 261s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 261s Selecting previously unselected package libnsl-dev:arm64. 261s Preparing to unpack .../04-libnsl-dev_1.3.0-3_arm64.deb ... 261s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 261s Selecting previously unselected package rpcsvc-proto. 261s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 261s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 261s Selecting previously unselected package libc6-dev:arm64. 261s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_arm64.deb ... 261s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 262s Selecting previously unselected package libisl23:arm64. 262s Preparing to unpack .../07-libisl23_0.26-3_arm64.deb ... 262s Unpacking libisl23:arm64 (0.26-3) ... 262s Selecting previously unselected package libmpc3:arm64. 262s Preparing to unpack .../08-libmpc3_1.3.1-1_arm64.deb ... 262s Unpacking libmpc3:arm64 (1.3.1-1) ... 262s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 262s Preparing to unpack .../09-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 262s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 263s Selecting previously unselected package cpp-13. 263s Preparing to unpack .../10-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 263s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 263s Selecting previously unselected package cpp-aarch64-linux-gnu. 263s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 263s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 263s Selecting previously unselected package cpp. 263s Preparing to unpack .../12-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 263s Unpacking cpp (4:13.2.0-7ubuntu1) ... 263s Selecting previously unselected package libcc1-0:arm64. 263s Preparing to unpack .../13-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 263s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 263s Selecting previously unselected package libitm1:arm64. 263s Preparing to unpack .../14-libitm1_14-20240303-1ubuntu1_arm64.deb ... 263s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 263s Selecting previously unselected package libatomic1:arm64. 263s Preparing to unpack .../15-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 263s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 263s Selecting previously unselected package libasan8:arm64. 263s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_arm64.deb ... 263s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 264s Selecting previously unselected package liblsan0:arm64. 264s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 264s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 264s Selecting previously unselected package libtsan2:arm64. 264s Preparing to unpack .../18-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 264s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 264s Selecting previously unselected package libubsan1:arm64. 264s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 264s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 264s Selecting previously unselected package libhwasan0:arm64. 264s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 264s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 265s Selecting previously unselected package libgcc-13-dev:arm64. 265s Preparing to unpack .../21-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 265s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 265s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 265s Preparing to unpack .../22-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 265s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 267s Selecting previously unselected package gcc-13. 267s Preparing to unpack .../23-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 267s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 267s Selecting previously unselected package gcc-aarch64-linux-gnu. 267s Preparing to unpack .../24-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 267s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 267s Selecting previously unselected package gcc. 267s Preparing to unpack .../25-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 267s Unpacking gcc (4:13.2.0-7ubuntu1) ... 267s Selecting previously unselected package libstdc++-13-dev:arm64. 267s Preparing to unpack .../26-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 267s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 268s Selecting previously unselected package g++-13-aarch64-linux-gnu. 268s Preparing to unpack .../27-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 268s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 269s Selecting previously unselected package g++-13. 269s Preparing to unpack .../28-g++-13_13.2.0-17ubuntu2_arm64.deb ... 269s Unpacking g++-13 (13.2.0-17ubuntu2) ... 269s Selecting previously unselected package g++-aarch64-linux-gnu. 269s Preparing to unpack .../29-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 269s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 269s Selecting previously unselected package g++. 269s Preparing to unpack .../30-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 269s Unpacking g++ (4:13.2.0-7ubuntu1) ... 269s Selecting previously unselected package build-essential. 269s Preparing to unpack .../31-build-essential_12.10ubuntu1_arm64.deb ... 269s Unpacking build-essential (12.10ubuntu1) ... 269s Selecting previously unselected package dctrl-tools. 269s Preparing to unpack .../32-dctrl-tools_2.24-3build2_arm64.deb ... 269s Unpacking dctrl-tools (2.24-3build2) ... 269s Selecting previously unselected package libgfortran-13-dev:arm64. 269s Preparing to unpack .../33-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 269s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 269s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 269s Preparing to unpack .../34-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 269s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 270s Selecting previously unselected package gfortran-13. 270s Preparing to unpack .../35-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 270s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 270s Selecting previously unselected package gfortran-aarch64-linux-gnu. 270s Preparing to unpack .../36-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 270s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 270s Selecting previously unselected package gfortran. 271s Preparing to unpack .../37-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 271s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 271s Selecting previously unselected package icu-devtools. 271s Preparing to unpack .../38-icu-devtools_74.2-1ubuntu1_arm64.deb ... 271s Unpacking icu-devtools (74.2-1ubuntu1) ... 271s Selecting previously unselected package libblas-dev:arm64. 271s Preparing to unpack .../39-libblas-dev_3.12.0-3_arm64.deb ... 271s Unpacking libblas-dev:arm64 (3.12.0-3) ... 271s Selecting previously unselected package libbz2-dev:arm64. 271s Preparing to unpack .../40-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 271s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 271s Selecting previously unselected package libicu-dev:arm64. 271s Preparing to unpack .../41-libicu-dev_74.2-1ubuntu1_arm64.deb ... 271s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 272s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 272s Preparing to unpack .../42-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 272s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 272s Selecting previously unselected package libjpeg8-dev:arm64. 272s Preparing to unpack .../43-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 272s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 272s Selecting previously unselected package libjpeg-dev:arm64. 272s Preparing to unpack .../44-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 272s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 273s Selecting previously unselected package liblapack-dev:arm64. 273s Preparing to unpack .../45-liblapack-dev_3.12.0-3_arm64.deb ... 273s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 273s Selecting previously unselected package libncurses-dev:arm64. 273s Preparing to unpack .../46-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 273s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 273s Selecting previously unselected package libpcre2-16-0:arm64. 273s Preparing to unpack .../47-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 273s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 273s Selecting previously unselected package libpcre2-32-0:arm64. 273s Preparing to unpack .../48-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 273s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 274s Selecting previously unselected package libpcre2-posix3:arm64. 274s Preparing to unpack .../49-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 274s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 274s Selecting previously unselected package libpcre2-dev:arm64. 274s Preparing to unpack .../50-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 274s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 274s Selecting previously unselected package libpkgconf3:arm64. 274s Preparing to unpack .../51-libpkgconf3_1.8.1-2_arm64.deb ... 274s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 274s Selecting previously unselected package zlib1g-dev:arm64. 274s Preparing to unpack .../52-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 274s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 274s Selecting previously unselected package libpng-dev:arm64. 274s Preparing to unpack .../53-libpng-dev_1.6.43-3_arm64.deb ... 274s Unpacking libpng-dev:arm64 (1.6.43-3) ... 274s Selecting previously unselected package libreadline-dev:arm64. 274s Preparing to unpack .../54-libreadline-dev_8.2-3.1_arm64.deb ... 274s Unpacking libreadline-dev:arm64 (8.2-3.1) ... 274s Selecting previously unselected package pkgconf-bin. 274s Preparing to unpack .../55-pkgconf-bin_1.8.1-2_arm64.deb ... 274s Unpacking pkgconf-bin (1.8.1-2) ... 275s Selecting previously unselected package pkgconf:arm64. 275s Preparing to unpack .../56-pkgconf_1.8.1-2_arm64.deb ... 275s Unpacking pkgconf:arm64 (1.8.1-2) ... 275s Selecting previously unselected package pkg-config:arm64. 275s Preparing to unpack .../57-pkg-config_1.8.1-2_arm64.deb ... 275s Unpacking pkg-config:arm64 (1.8.1-2) ... 275s Selecting previously unselected package liblzma-dev:arm64. 275s Preparing to unpack .../58-liblzma-dev_5.4.5-0.3_arm64.deb ... 275s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 275s Selecting previously unselected package r-base-dev. 275s Preparing to unpack .../59-r-base-dev_4.3.3-2build1_all.deb ... 275s Unpacking r-base-dev (4.3.3-2build1) ... 275s Selecting previously unselected package pkg-r-autopkgtest. 275s Preparing to unpack .../60-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 275s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 275s Selecting previously unselected package autopkgtest-satdep. 275s Preparing to unpack .../61-2-autopkgtest-satdep.deb ... 275s Unpacking autopkgtest-satdep (0) ... 275s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 275s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 275s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 275s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... 275s Setting up libpkgconf3:arm64 (1.8.1-2) ... 275s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 275s Setting up libmpc3:arm64 (1.3.1-1) ... 275s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 275s Setting up icu-devtools (74.2-1ubuntu1) ... 275s Setting up pkgconf-bin (1.8.1-2) ... 275s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 275s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 275s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 275s Setting up libnsl-dev:arm64 (1.3.0-3) ... 275s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 275s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 275s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 275s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 275s Setting up libisl23:arm64 (0.26-3) ... 275s Setting up libc-dev-bin (2.39-0ubuntu2) ... 275s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 275s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 275s Setting up libblas-dev:arm64 (3.12.0-3) ... 275s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 275s Setting up dctrl-tools (2.24-3build2) ... 275s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 275s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 275s Setting up pkgconf:arm64 (1.8.1-2) ... 275s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 275s Setting up liblapack-dev:arm64 (3.12.0-3) ... 275s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 275s Setting up pkg-config:arm64 (1.8.1-2) ... 275s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 275s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 275s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 275s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 275s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 275s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 276s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 276s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 276s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 276s Setting up cpp-13 (13.2.0-17ubuntu2) ... 276s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 276s Setting up libreadline-dev:arm64 (8.2-3.1) ... 276s Setting up gcc-13 (13.2.0-17ubuntu2) ... 276s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 276s Setting up cpp (4:13.2.0-7ubuntu1) ... 276s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 276s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 276s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 276s Setting up g++-13 (13.2.0-17ubuntu2) ... 276s Setting up libpng-dev:arm64 (1.6.43-3) ... 276s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 276s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 276s Setting up gcc (4:13.2.0-7ubuntu1) ... 276s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 276s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 276s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 276s Setting up gfortran (4:13.2.0-7ubuntu1) ... 276s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 276s 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 276s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 276s 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 276s Setting up g++ (4:13.2.0-7ubuntu1) ... 276s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 276s Setting up build-essential (12.10ubuntu1) ... 276s Setting up r-base-dev (4.3.3-2build1) ... 276s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 276s Setting up autopkgtest-satdep (0) ... 276s Processing triggers for man-db (2.12.0-3) ... 278s Processing triggers for install-info (7.1-3) ... 278s Processing triggers for libc-bin (2.39-0ubuntu2) ... 287s (Reading database ... 81544 files and directories currently installed.) 287s Removing autopkgtest-satdep (0) ... 288s autopkgtest [18:39:11]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 288s autopkgtest [18:39:11]: test pkg-r-autopkgtest: [----------------------- 288s Test: Try to load the R library gee 289s 289s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 289s Copyright (C) 2024 The R Foundation for Statistical Computing 289s Platform: aarch64-unknown-linux-gnu (64-bit) 289s 289s R is free software and comes with ABSOLUTELY NO WARRANTY. 289s You are welcome to redistribute it under certain conditions. 289s Type 'license()' or 'licence()' for distribution details. 289s 289s R is a collaborative project with many contributors. 289s Type 'contributors()' for more information and 289s 'citation()' on how to cite R or R packages in publications. 289s 289s Type 'demo()' for some demos, 'help()' for on-line help, or 289s 'help.start()' for an HTML browser interface to help. 289s Type 'q()' to quit R. 289s 289s > library('gee') 289s > 289s > 289s Other tests are currently unsupported! 289s They will be progressively added. 290s autopkgtest [18:39:13]: test pkg-r-autopkgtest: -----------------------] 290s pkg-r-autopkgtest PASS 290s autopkgtest [18:39:13]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 291s autopkgtest [18:39:14]: @@@@@@@@@@@@@@@@@@@@ summary 291s run-unit-test PASS 291s pkg-r-autopkgtest PASS 301s Creating nova instance adt-noble-arm64-r-cran-gee-20240316-183423-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...