0s autopkgtest [22:09:20]: starting date and time: 2025-03-15 22:09:20+0000 0s autopkgtest [22:09:20]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:09:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9wgohcw4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-gee --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-10.secgroup --name adt-plucky-amd64-r-cran-gee-20250315-220920-juju-7f2275-prod-proposed-migration-environment-15-689266da-affe-430e-b084-8c61e74139ce --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 51s autopkgtest [22:10:11]: testbed dpkg architecture: amd64 51s autopkgtest [22:10:11]: testbed apt version: 2.9.31ubuntu1 52s autopkgtest [22:10:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [22:10:12]: testbed release detected to be: None 53s autopkgtest [22:10:13]: updating testbed package index (apt update) 53s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 54s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 54s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 54s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 54s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 54s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 54s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 54s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 54s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 54s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 54s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 54s Fetched 1265 kB in 1s (1511 kB/s) 55s Reading package lists... 55s + lsb_release --codename --short 55s + RELEASE=plucky 55s + cat 55s + [ plucky != trusty ] 55s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 57s Calculating upgrade... 57s The following package was automatically installed and is no longer required: 57s libnl-genl-3-200 57s Use 'sudo apt autoremove' to remove it. 57s The following NEW packages will be installed: 57s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 57s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 57s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 57s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 57s The following packages will be upgraded: 57s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 57s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 57s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 57s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 57s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 57s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 57s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 57s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 57s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 57s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 57s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 57s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 57s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 57s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 57s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 57s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 57s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 57s parted pci.ids pciutils pinentry-curses python-apt-common python3 57s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 57s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 57s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 57s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 57s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 57s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 57s xz-utils 57s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 829 MB of archives. 57s After this operation, 325 MB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 58s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 58s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 58s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 58s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 58s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 58s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 58s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 58s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 58s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 58s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 58s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 58s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 58s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 58s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 58s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 58s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 58s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 58s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 58s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 58s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 58s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 58s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 58s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 58s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 58s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 58s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 59s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 59s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 59s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 59s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 59s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 59s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 59s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 59s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 59s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 59s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 59s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 59s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 59s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 59s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 59s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 59s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 59s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 59s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 59s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 59s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 59s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 59s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 59s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 59s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 59s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 59s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 59s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 59s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 59s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 59s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 59s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 59s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 59s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 59s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 59s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 59s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 59s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 59s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 59s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 59s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 59s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 59s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 59s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 59s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 59s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 59s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 59s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 59s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 59s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 59s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 59s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 59s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 59s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 59s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 59s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 59s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 59s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 59s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 59s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 59s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 59s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 59s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 59s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 59s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 59s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 59s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 59s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 59s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 59s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 60s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 60s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 60s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 60s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 60s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 60s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 60s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 78s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 78s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 78s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 78s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 78s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 78s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 78s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 78s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 79s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 79s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 83s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 83s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 83s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 83s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 83s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 83s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 83s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 83s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 83s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 83s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 83s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 83s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 83s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 83s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 84s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 84s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 84s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 84s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 84s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 84s Preconfiguring packages ... 84s Fetched 829 MB in 27s (31.1 MB/s) 84s (Reading database ... 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over (0.21.0-2ubuntu1) ... 107s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 107s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 107s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 107s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 107s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 107s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 107s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 107s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 107s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 107s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 108s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 108s Setting up media-types (13.0.0) ... 108s Installing new version of config file /etc/mime.types ... 108s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 108s Setting up ubuntu-kernel-accessories (1.549) ... 108s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 108s Setting up pci.ids (0.0~2025.03.09-1) ... 108s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 108s Setting up apt-utils (2.9.33) ... 108s Setting up libdebuginfod-common (0.192-4) ... 108s Setting up exfatprogs (1.2.8-1) ... 108s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 108s Setting up bpftool (7.6.0+6.14.0-10.10) ... 108s Setting up libestr0:amd64 (0.1.11-2) ... 108s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 108s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 108s Setting up dosfstools (4.2-1.2) ... 108s Setting up rsyslog (8.2412.0-2ubuntu2) ... 108s info: The user `syslog' is already a member of `adm'. 109s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 109s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 109s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 109s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 109s Setting up systemd (257.3-1ubuntu3) ... 109s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 109s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 109s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 110s Setting up libparted2t64:amd64 (3.6-5) ... 110s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 110s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 110s Setting up linux-headers-generic (6.14.0-10.10) ... 110s Setting up libjemalloc2:amd64 (5.3.0-3) ... 110s Setting up locales (2.41-1ubuntu1) ... 110s Installing new version of config file /etc/locale.alias ... 110s Generating locales (this might take a while)... 112s en_US.UTF-8... done 112s Generation complete. 112s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 112s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 112s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 112s Installing new version of config file /etc/apparmor.d/fusermount3 ... 112s Installing new version of config file /etc/apparmor.d/lsusb ... 112s Installing new version of config file /etc/apparmor.d/openvpn ... 113s Reloading AppArmor profiles 115s Setting up libftdi1-2:amd64 (1.5-8build1) ... 115s Setting up libglib2.0-data (2.84.0-1) ... 115s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 115s Setting up libncurses6:amd64 (6.5+20250216-2) ... 115s Setting up strace (6.13+ds-1ubuntu1) ... 115s Setting up xz-utils (5.6.4-1) ... 115s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 115s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 115s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 115s Setting up udev (257.3-1ubuntu3) ... 116s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 118s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 118s Setting up libpci3:amd64 (1:3.13.0-2) ... 118s Setting up whiptail (0.52.24-4ubuntu2) ... 118s Setting up python-apt-common (2.9.9build1) ... 118s Setting up pnp.ids (0.393-3) ... 118s Setting up libnl-3-200:amd64 (3.7.0-1) ... 118s Setting up python3.13-minimal (3.13.2-2) ... 119s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 119s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 119s Setting up libc-dev-bin (2.41-1ubuntu1) ... 119s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 119s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 119s Setting up rsync (3.4.1+ds1-3) ... 120s rsync.service is a disabled or a static unit not running, not starting it. 120s Setting up python3.13-gdbm (3.13.2-2) ... 120s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 120s Setting up systemd-resolved (257.3-1ubuntu3) ... 120s Setting up initramfs-tools-bin (0.146ubuntu1) ... 120s Setting up ncurses-term (6.5+20250216-2) ... 120s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 120s Setting up libpython3.13:amd64 (3.13.2-2) ... 120s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 120s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 120s Setting up systemd-sysv (257.3-1ubuntu3) ... 120s Setting up linux-headers-virtual (6.14.0-10.10) ... 121s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 121s Setting up python3.13 (3.13.2-2) ... 121s Setting up htop (3.4.0-2) ... 121s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 124s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 124s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 124s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 124s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 124s Setting up parted (3.6-5) ... 124s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 124s Setting up python3 (3.13.2-2) ... 124s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 124s Setting up python3-markupsafe (2.1.5-1build4) ... 124s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 126s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 126s Setting up hwdata (0.393-3) ... 126s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 127s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 127s No schema files found: doing nothing. 127s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 127s Setting up linux-perf (6.14.0-10.10) ... 127s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 127s Setting up pciutils (1:3.13.0-2) ... 127s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 127s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 127s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 127s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 127s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 127s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 127s Setting up curl (8.12.1-3ubuntu1) ... 127s Setting up linux-image-virtual (6.14.0-10.10) ... 127s Setting up initramfs-tools-core (0.146ubuntu1) ... 127s Setting up linux-tools-common (6.14.0-10.10) ... 127s Setting up python3-systemd (235-1build6) ... 127s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 127s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 127s Setting up linux-image-generic (6.14.0-10.10) ... 127s Setting up python3-dbus (1.3.2-5build5) ... 127s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 127s Setting up initramfs-tools (0.146ubuntu1) ... 127s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 127s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 127s update-initramfs: deferring update (trigger activated) 127s Setting up linux-generic (6.14.0-10.10) ... 127s Setting up ubuntu-minimal (1.549) ... 127s Setting up python3-apt (2.9.9build1) ... 127s Setting up python3-bcrypt (4.2.0-2.1build1) ... 128s Setting up python3-yaml (6.0.2-1build2) ... 128s Setting up libfwupd3:amd64 (2.0.6-4) ... 128s Setting up python3-lazr.uri (1.0.6-6) ... 128s Setting up binutils (2.44-3ubuntu1) ... 128s Setting up ubuntu-standard (1.549) ... 128s Setting up cloud-init-base (25.1-0ubuntu3) ... 129s Setting up linux-virtual (6.14.0-10.10) ... 129s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 129s Setting up python3-gi (3.50.0-4build1) ... 130s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 130s Setting up fwupd (2.0.6-4) ... 130s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 130s fwupd.service is a disabled or a static unit not running, not starting it. 130s Setting up cloud-init (25.1-0ubuntu3) ... 130s Processing triggers for man-db (2.13.0-1) ... 132s Processing triggers for dbus (1.16.2-1ubuntu1) ... 132s Processing triggers for shared-mime-info (2.4-5) ... 132s Warning: program compiled against libxml 212 using older 209 133s Processing triggers for libc-bin (2.41-1ubuntu1) ... 133s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 133s /etc/kernel/postinst.d/initramfs-tools: 133s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 133s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 144s /etc/kernel/postinst.d/zz-update-grub: 144s Sourcing file `/etc/default/grub' 144s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 144s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 144s Generating grub configuration file ... 144s Found linux image: /boot/vmlinuz-6.14.0-10-generic 144s Found initrd image: /boot/initrd.img-6.14.0-10-generic 144s Found linux image: /boot/vmlinuz-6.12.0-16-generic 144s Found initrd image: /boot/initrd.img-6.12.0-16-generic 144s Found linux image: /boot/vmlinuz-6.11.0-8-generic 144s Found initrd image: /boot/initrd.img-6.11.0-8-generic 144s Warning: os-prober will not be executed to detect other bootable partitions. 144s Systems on them will not be added to the GRUB boot configuration. 144s Check GRUB_DISABLE_OS_PROBER documentation entry. 144s Adding boot menu entry for UEFI Firmware Settings ... 144s done 145s Processing triggers for initramfs-tools (0.146ubuntu1) ... 145s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 145s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 155s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 155s + /usr/lib/apt/apt-helper analyze-pattern ?true 155s + + sed s/\./\\./g 155s uname -r 155s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 155s + apt list ?obsolete 155s + tail -n+2 155s + cut -d/ -f1 155s + grep -v ^linux-.*6\.12\.0-16-generic.* 156s + obsolete_pkgs=linux-headers-6.11.0-8-generic 156s linux-headers-6.11.0-8 156s linux-headers-6.12.0-16 156s linux-image-6.11.0-8-generic 156s linux-modules-6.11.0-8-generic 156s linux-tools-6.11.0-8-generic 156s linux-tools-6.11.0-8 156s linux-tools-6.12.0-16 156s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-headers-6.12.0-16 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 linux-tools-6.12.0-16 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 157s Solving dependencies... 157s The following packages will be REMOVED: 157s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 157s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 157s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 157s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 157s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 157s linux-tools-6.12.0-16-generic* 157s 0 upgraded, 0 newly installed, 15 to remove and 5 not upgraded. 157s After this operation, 371 MB disk space will be freed. 157s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 148643 files and directories currently installed.) 157s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 157s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 157s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 157s Removing libpython3.12t64:amd64 (3.12.9-1) ... 157s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 157s Removing libnsl2:amd64 (1.3.0-3build3) ... 157s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 157s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 158s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 160s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 160s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 162s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 162s /etc/kernel/postrm.d/initramfs-tools: 162s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 163s /etc/kernel/postrm.d/zz-update-grub: 163s Sourcing file `/etc/default/grub' 163s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 163s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 163s Generating grub configuration file ... 163s Found linux image: /boot/vmlinuz-6.14.0-10-generic 163s Found initrd image: /boot/initrd.img-6.14.0-10-generic 163s Found linux image: /boot/vmlinuz-6.12.0-16-generic 163s Found initrd image: /boot/initrd.img-6.12.0-16-generic 163s Warning: os-prober will not be executed to detect other bootable partitions. 163s Systems on them will not be added to the GRUB boot configuration. 163s Check GRUB_DISABLE_OS_PROBER documentation entry. 163s Adding boot menu entry for UEFI Firmware Settings ... 163s done 163s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 163s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 163s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 163s Processing triggers for libc-bin (2.41-1ubuntu1) ... 163s (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 ... 84830 files and directories currently installed.) 163s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 164s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 164s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 164s + grep -q trusty /etc/lsb-release 164s + [ ! -d /usr/share/doc/unattended-upgrades ] 164s + [ ! -d /usr/share/doc/lxd ] 164s + [ ! -d /usr/share/doc/lxd-client ] 164s + [ ! -d /usr/share/doc/snapd ] 164s + type iptables 164s + cat 164s + chmod 755 /etc/rc.local 164s + . /etc/rc.local 164s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 164s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 164s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 164s + uname -m 164s + [ x86_64 = ppc64le ] 164s + [ -d /run/systemd/system ] 164s + systemd-detect-virt --quiet --vm 164s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 164s + cat 164s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 164s + echo COMPRESS=lz4 164s autopkgtest [22:12:04]: upgrading testbed (apt dist-upgrade and autopurge) 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 165s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 165s Starting 2 pkgProblemResolver with broken count: 0 165s Done 165s Entering ResolveByKeep 166s 166s Calculating upgrade... 166s The following packages will be upgraded: 166s libc-bin libc-dev-bin libc6 libc6-dev locales 166s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 10.5 MB of archives. 166s After this operation, 1024 B of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 167s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 167s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 167s Preconfiguring packages ... 167s Fetched 10.5 MB in 1s (10.0 MB/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 ... 84827 files and directories currently installed.) 167s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 167s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 167s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 167s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Setting up libc6:amd64 (2.41-1ubuntu2) ... 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 ... 84827 files and directories currently installed.) 168s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 168s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 84827 files and directories currently installed.) 168s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 168s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Setting up locales (2.41-1ubuntu2) ... 169s Generating locales (this might take a while)... 171s en_US.UTF-8... done 171s Generation complete. 171s Setting up libc-dev-bin (2.41-1ubuntu2) ... 171s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 171s Processing triggers for man-db (2.13.0-1) ... 171s Processing triggers for systemd (257.3-1ubuntu3) ... 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 173s Solving dependencies... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [22:12:14]: rebooting testbed after setup commands that affected boot 197s autopkgtest [22:12:37]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 200s autopkgtest [22:12:40]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-gee 201s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (dsc) [2061 B] 201s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (tar) [53.1 kB] 201s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-gee 4.13-29-1 (diff) [3696 B] 202s gpgv: Signature made Tue Jan 28 23:41:44 2025 UTC 202s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 202s gpgv: issuer "plessy@debian.org" 202s gpgv: Can't check signature: No public key 202s dpkg-source: warning: cannot verify inline signature for ./r-cran-gee_4.13-29-1.dsc: no acceptable signature found 202s autopkgtest [22:12:42]: testing package r-cran-gee version 4.13-29-1 202s autopkgtest [22:12:42]: build not needed 205s autopkgtest [22:12:45]: test run-unit-test: preparing testbed 205s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s Starting pkgProblemResolver with broken count: 0 206s Starting 2 pkgProblemResolver with broken count: 0 206s Done 207s The following NEW packages will be installed: 207s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 207s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 207s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 207s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 207s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 207s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 207s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-gee r-cran-mass 207s unzip x11-common xdg-utils zip 207s 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. 207s Need to get 42.5 MB of archives. 207s After this operation, 87.0 MB of additional disk space will be used. 207s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 207s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 207s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 207s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 207s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 207s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 207s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 207s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 207s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 207s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 207s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 207s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 207s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 207s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 207s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 208s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 208s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 208s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 208s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 208s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 208s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 208s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 208s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 208s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 208s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 208s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 208s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 208s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 208s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 208s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 208s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 208s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 208s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 208s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 208s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 208s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 208s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 208s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 208s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 208s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 208s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 208s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 210s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gee amd64 4.13-29-1 [84.2 kB] 210s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 210s Preconfiguring packages ... 210s Fetched 42.5 MB in 3s (13.1 MB/s) 210s Selecting previously unselected package fonts-dejavu-mono. 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 ... 84827 files and directories currently installed.) 210s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 210s Unpacking fonts-dejavu-mono (2.37-8) ... 210s Selecting previously unselected package fonts-dejavu-core. 210s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 210s Unpacking fonts-dejavu-core (2.37-8) ... 211s Selecting previously unselected package fontconfig-config. 211s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 211s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 211s Selecting previously unselected package libfontconfig1:amd64. 211s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 211s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 211s Selecting previously unselected package fontconfig. 211s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 211s Unpacking fontconfig (2.15.0-2ubuntu1) ... 211s Selecting previously unselected package libblas3:amd64. 211s Preparing to unpack .../05-libblas3_3.12.1-2_amd64.deb ... 211s Unpacking libblas3:amd64 (3.12.1-2) ... 211s Selecting previously unselected package libpixman-1-0:amd64. 211s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ... 211s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 211s Selecting previously unselected package libxcb-render0:amd64. 211s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ... 211s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 211s Selecting previously unselected package libxcb-shm0:amd64. 211s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_amd64.deb ... 211s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 211s Selecting previously unselected package libxrender1:amd64. 211s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 211s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 211s Selecting previously unselected package libcairo2:amd64. 211s Preparing to unpack .../10-libcairo2_1.18.2-2_amd64.deb ... 211s Unpacking libcairo2:amd64 (1.18.2-2) ... 211s Selecting previously unselected package libdatrie1:amd64. 211s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_amd64.deb ... 211s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 211s Selecting previously unselected package libdeflate0:amd64. 211s Preparing to unpack .../12-libdeflate0_1.23-1_amd64.deb ... 211s Unpacking libdeflate0:amd64 (1.23-1) ... 211s Selecting previously unselected package libgfortran5:amd64. 211s Preparing to unpack .../13-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 211s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 211s Selecting previously unselected package libgomp1:amd64. 211s Preparing to unpack .../14-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 211s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 211s Selecting previously unselected package libgraphite2-3:amd64. 211s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 211s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 211s Selecting previously unselected package libharfbuzz0b:amd64. 211s Preparing to unpack .../16-libharfbuzz0b_10.2.0-1_amd64.deb ... 211s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 211s Selecting previously unselected package x11-common. 211s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 211s Unpacking x11-common (1:7.7+23ubuntu3) ... 211s Selecting previously unselected package libice6:amd64. 211s Preparing to unpack .../18-libice6_2%3a1.1.1-1_amd64.deb ... 211s Unpacking libice6:amd64 (2:1.1.1-1) ... 211s Selecting previously unselected package libjpeg-turbo8:amd64. 211s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 211s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 211s Selecting previously unselected package libjpeg8:amd64. 211s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 211s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 211s Selecting previously unselected package liblapack3:amd64. 211s Preparing to unpack .../21-liblapack3_3.12.1-2_amd64.deb ... 211s Unpacking liblapack3:amd64 (3.12.1-2) ... 211s Selecting previously unselected package liblerc4:amd64. 211s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 211s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 211s Selecting previously unselected package libthai-data. 211s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 211s Unpacking libthai-data (0.1.29-2build1) ... 211s Selecting previously unselected package libthai0:amd64. 211s Preparing to unpack .../24-libthai0_0.1.29-2build1_amd64.deb ... 211s Unpacking libthai0:amd64 (0.1.29-2build1) ... 211s Selecting previously unselected package libpango-1.0-0:amd64. 211s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_amd64.deb ... 211s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 212s Selecting previously unselected package libpangoft2-1.0-0:amd64. 212s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 212s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 212s Selecting previously unselected package libpangocairo-1.0-0:amd64. 212s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 212s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 212s Selecting previously unselected package libpaper2:amd64. 212s Preparing to unpack .../28-libpaper2_2.2.5-0.3_amd64.deb ... 212s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 212s Selecting previously unselected package libpaper-utils. 212s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_amd64.deb ... 212s Unpacking libpaper-utils (2.2.5-0.3) ... 212s Selecting previously unselected package libsharpyuv0:amd64. 212s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_amd64.deb ... 212s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 212s Selecting previously unselected package libsm6:amd64. 212s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_amd64.deb ... 212s Unpacking libsm6:amd64 (2:1.2.4-1) ... 212s Selecting previously unselected package libtcl8.6:amd64. 212s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 212s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 212s Selecting previously unselected package libjbig0:amd64. 212s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 212s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 212s Selecting previously unselected package libwebp7:amd64. 212s Preparing to unpack .../34-libwebp7_1.5.0-0.1_amd64.deb ... 212s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 212s Selecting previously unselected package libtiff6:amd64. 212s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 212s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 212s Selecting previously unselected package libxft2:amd64. 212s Preparing to unpack .../36-libxft2_2.3.6-1build1_amd64.deb ... 212s Unpacking libxft2:amd64 (2.3.6-1build1) ... 212s Selecting previously unselected package libxss1:amd64. 212s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_amd64.deb ... 212s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 212s Selecting previously unselected package libtk8.6:amd64. 212s Preparing to unpack .../38-libtk8.6_8.6.16-1_amd64.deb ... 212s Unpacking libtk8.6:amd64 (8.6.16-1) ... 212s Selecting previously unselected package libxt6t64:amd64. 212s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 212s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 212s Selecting previously unselected package zip. 212s Preparing to unpack .../40-zip_3.0-14ubuntu2_amd64.deb ... 212s Unpacking zip (3.0-14ubuntu2) ... 212s Selecting previously unselected package unzip. 212s Preparing to unpack .../41-unzip_6.0-28ubuntu6_amd64.deb ... 212s Unpacking unzip (6.0-28ubuntu6) ... 212s Selecting previously unselected package xdg-utils. 212s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 212s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 212s Selecting previously unselected package r-base-core. 212s Preparing to unpack .../43-r-base-core_4.4.3-1_amd64.deb ... 212s Unpacking r-base-core (4.4.3-1) ... 212s Selecting previously unselected package r-cran-gee. 212s Preparing to unpack .../44-r-cran-gee_4.13-29-1_amd64.deb ... 212s Unpacking r-cran-gee (4.13-29-1) ... 212s Selecting previously unselected package r-cran-mass. 212s Preparing to unpack .../45-r-cran-mass_7.3-64-1_amd64.deb ... 212s Unpacking r-cran-mass (7.3-64-1) ... 213s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 213s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 213s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 213s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 213s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 213s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 213s Setting up libxcb-render0:amd64 (1.17.0-2) ... 213s Setting up unzip (6.0-28ubuntu6) ... 213s Setting up x11-common (1:7.7+23ubuntu3) ... 213s Setting up libdeflate0:amd64 (1.23-1) ... 213s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 213s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 213s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 213s Setting up zip (3.0-14ubuntu2) ... 213s Setting up libblas3:amd64 (3.12.1-2) ... 213s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 213s Setting up fonts-dejavu-mono (2.37-8) ... 213s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 213s Setting up fonts-dejavu-core (2.37-8) ... 213s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 213s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 213s Setting up libwebp7:amd64 (1.5.0-0.1) ... 213s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 213s Setting up libthai-data (0.1.29-2build1) ... 213s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 213s Setting up libpaper2:amd64 (2.2.5-0.3) ... 213s Setting up xdg-utils (1.2.1-2ubuntu1) ... 213s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 213s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 213s Setting up libice6:amd64 (2:1.1.1-1) ... 213s Setting up liblapack3:amd64 (3.12.1-2) ... 213s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 213s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 213s Setting up libpaper-utils (2.2.5-0.3) ... 213s Setting up libthai0:amd64 (0.1.29-2build1) ... 213s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 213s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 213s Setting up libsm6:amd64 (2:1.2.4-1) ... 213s Setting up fontconfig (2.15.0-2ubuntu1) ... 215s Regenerating fonts cache... done. 215s Setting up libxft2:amd64 (2.3.6-1build1) ... 215s Setting up libtk8.6:amd64 (8.6.16-1) ... 215s Setting up libpango-1.0-0:amd64 (1.56.2-1) ... 215s Setting up libcairo2:amd64 (1.18.2-2) ... 215s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 215s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... 215s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... 215s Setting up r-base-core (4.4.3-1) ... 215s Creating config file /etc/R/Renviron with new version 216s Setting up r-cran-gee (4.13-29-1) ... 216s Setting up r-cran-mass (7.3-64-1) ... 216s Processing triggers for install-info (7.1.1-1) ... 216s Processing triggers for libc-bin (2.41-1ubuntu2) ... 216s Processing triggers for man-db (2.13.0-1) ... 218s autopkgtest [22:12:58]: test run-unit-test: [----------------------- 218s BEGIN TEST divergence.R 218s 218s R version 4.4.3 (2025-02-28) -- "Trophy Case" 218s Copyright (C) 2025 The R Foundation for Statistical Computing 218s Platform: x86_64-pc-linux-gnu 218s 218s R is free software and comes with ABSOLUTELY NO WARRANTY. 218s You are welcome to redistribute it under certain conditions. 218s Type 'license()' or 'licence()' for distribution details. 218s 218s R is a collaborative project with many contributors. 218s Type 'contributors()' for more information and 218s 'citation()' on how to cite R or R packages in publications. 218s 218s Type 'demo()' for some demos, 'help()' for on-line help, or 218s 'help.start()' for an HTML browser interface to help. 218s Type 'q()' to quit R. 218s 218s > options(digits=5) 218s > library(gee) 218s > load("data_for_gee_binomial.RData") 218s > try(gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed")) 218s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 218s running glm to get initial regression estimate 218s (Intercept) x 218s -0.1291219 0.0019241 218s > ## infinite looped in gee 4.3-14 218s > 218s > 218s > 218s Error in gee(yb ~ x, family = binomial, id = id, R = R, cor = "fixed") : 218s Cgee: error: logistic model for probability has fitted value very close to 1. 218s estimates diverging; iteration terminated. 218s BEGIN TEST tests.R 218s 218s R version 4.4.3 (2025-02-28) -- "Trophy Case" 218s Copyright (C) 2025 The R Foundation for Statistical Computing 218s Platform: x86_64-pc-linux-gnu 218s 218s R is free software and comes with ABSOLUTELY NO WARRANTY. 218s You are welcome to redistribute it under certain conditions. 218s Type 'license()' or 'licence()' for distribution details. 218s 218s R is a collaborative project with many contributors. 218s Type 'contributors()' for more information and 218s 'citation()' on how to cite R or R packages in publications. 218s 218s Type 'demo()' for some demos, 'help()' for on-line help, or 218s 'help.start()' for an HTML browser interface to help. 218s Type 'q()' to quit R. 218s 218s > 218s > # gee support @(#) tests.q 1.2 96/09/27 218s > 218s > library(gee) 218s > 218s > source("testgee.dump") 218s > 218s > myr <- gee(gsind~x2+x3+x4,id=id,data=testgee) 218s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 218s running glm to get initial regression estimate 218s (Intercept) x2 x3 x4 218s 0.8107414 2.2933133 -1.1806841 1.4415174 218s > myr 218s 218s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 218s gee S-function, version 4.13 modified 98/01/27 (1998) 218s 218s Model: 218s Link: Identity 218s Variance to Mean Relation: Gaussian 218s Correlation Structure: Independent 218s 218s Call: 218s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 218s 218s Number of observations : 500 218s 218s Maximum cluster size : 20 218s 218s 218s Coefficients: 218s (Intercept) x2 x3 x4 218s 0.8107414 2.2933133 -1.1806841 1.4415174 218s 218s Estimated Scale Parameter: 2.899625 218s Number of Iterations: 1 218s 218s Working Correlation[1:4,1:4] 218s [,1] [,2] [,3] [,4] 218s [1,] 1 0 0 0 218s [2,] 0 1 0 0 218s [3,] 0 0 1 0 218s [4,] 0 0 0 1 218s 218s 218s Returned Error Value: 218s [1] 0 218s > summary(myr) 218s 218s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 218s gee S-function, version 4.13 modified 98/01/27 (1998) 218s 218s Model: 218s Link: Identity 218s Variance to Mean Relation: Gaussian 218s Correlation Structure: Independent 218s 218s Call: 218s gee(formula = gsind ~ x2 + x3 + x4, id = id, data = testgee) 218s 218s Summary of Residuals: 218s Min 1Q Median 3Q Max 218s -5.12638044 -1.17212201 0.07530777 1.13873892 5.69264860 218s 218s 218s Coefficients: 218s Estimate Naive S.E. Naive z Robust S.E. Robust z 218s (Intercept) 0.8107414 0.75420946 1.074955 0.76905602 1.054203 218s x2 2.2933133 0.04546161 50.445055 0.04589797 49.965459 218s x3 -1.1806841 0.05974921 -19.760664 0.06847056 -17.243677 218s x4 1.4415174 0.03154513 45.696983 0.03153448 45.712418 218s 218s Estimated Scale Parameter: 2.899625 218s Number of Iterations: 1 218s 218s Working Correlation 218s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 218s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 218s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 218s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 218s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 218s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 218s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 218s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 218s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 218s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 218s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 218s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 218s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 218s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 218s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 218s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 218s [1,] 0 0 0 0 0 0 0 218s [2,] 0 0 0 0 0 0 0 218s [3,] 0 0 0 0 0 0 0 218s [4,] 0 0 0 0 0 0 0 218s [5,] 0 0 0 0 0 0 0 218s [6,] 0 0 0 0 0 0 0 219s [7,] 0Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > summary(gee(gs~x2+x4,id=id,data=testgee,corstr="exchangeable")) 219s (Intercept) x2 x4 219s -21.504384 4.643727 3.065537 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Identity 219s Variance to Mean Relation: Gaussian 219s Correlation Structure: Exchangeable 219s 219s Call: 219s gee(formula = gs ~ x2 + x4, id = id, data = testgee, corstr = "exchangeable") 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -32.6076365 -9.8240277 0.4309459 10.2768319 44.8278747 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) -21.675077 3.7046983 -5.85070 3.5007586 -6.191537 219s x2 4.676098 0.3786822 12.34835 0.3336659 14.014313 219s x4 3.057583 0.2632230 11.61594 0.2251384 13.580903 219s 219s Estimated Scale Parameter: 202.3612 219s Number of Iterations: 2 219s 219s Working Correlation 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s [,1] [,2] [,3] [,4] [,5] [,6] 219s [1,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [2,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [3,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 219s [4,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 219s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 219s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 219s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [,7] [,8] [,9] [,10] [,11] [,12] 219s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [7,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [8,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [9,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 219s [10,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 219s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 219s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 219s [13,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [14,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [15,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [16,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [,13] [,14] [,15] [,16] [,17] [,18] 219s [1,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [2,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [3,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [4,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [5,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [6,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [7,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [8,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [9,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [10,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [11,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [12,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [13,] 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [14,] -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [15,] -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 -0.01037861 219s [16,] -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 -0.01037861 219s [17,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 -0.01037861 219s [18,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 1.00000000 219s [19,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [20,] -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 -0.01037861 219s [,19] [,20] 219s [1,] -0.01037861 -0.01037861 219s [2,] -0.01037861 -0.01037861 219s [3,] -0.01037861 -0.01037861 219s [4,] -0.01037861 -0.01037861 219s [5,] -0.01037861 -0.01037861 219s [6,] -0.01037861 -0.01037861 219s [7,] -0.01037861 -0.01037861 219s [8,] -0.01037861 -0.01037861 219s [9,] -0.01037861 -0.01037861 219s [10,] -0.01037861 -0.01037861 219s [11,] -0.01037861 -0.01037861 219s [12,] -0.01037861 -0.01037861 219s [13,] -0.01037861 -0.01037861 219s [14,] -0.01037861 -0.01037861 219s [15,] -0.01037861 -0.01037861 219s [16,] -0.01037861 -0.01037861 219s [17,] -0.01037861 -0.01037861 219s [18,] -0.01037861 -0.01037861 219s [19,] 1.00000000 -0.01037861 219s [20,] -0.01037861 1.00000000 219s > 219s > summary(gee(gsind~sin(x2)+log(x3)+x4,id=id,data=testgee)) 219s (Intercept) sin(x2) log(x3) x4 219s 33.017960 1.235559 -12.033930 1.500485 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Identity 219s Variance to Mean Relation: Gaussian 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = gsind ~ sin(x2) + log(x3) + x4, id = id, data = testgee) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -14.2099238 -2.6510967 -0.4994671 2.1403832 12.8126774 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 33.017960 3.39110198 9.736646 3.03682905 10.872512 219s sin(x2) 1.235559 0.26662685 4.634036 0.44529003 2.774728 219s log(x3) -12.033930 1.43540337 -8.383657 1.33255574 -9.030714 219s x4 1.500485 0.07638601 19.643451 0.06166767 24.331791 219s 219s Estimated Scale Parameter: 17.02534 219s Number of Iterations: 1 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 219s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 219s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 219s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 219s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 219s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 219s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 219s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 219s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [16,] 0 0 0 0 0 0 0 0 0 0 0Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s 0 0 219s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 219s [1,] 0 0 0 0 0 0 0 219s [2,] 0 0 0 0 0 0 0 219s [3,] 0 0 0 0 0 0 0 219s [4,] 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > #summary(gee(gsind~gam(x2~x1)$fitted.values+x4,id=id,data=testgee,subset=id<20)) 219s > 219s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial)) 219s (Intercept) x2 x3 x4 219s 4.72920874 -0.34747871 -0.21939993 -0.07103635 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 219s family = binomial) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 4.72920874 1.03210192 4.582114 0.86323313 5.478484 219s x2 -0.34747871 0.06301385 -5.514323 0.05004796 -6.942915 219s x3 -0.21939993 0.07952035 -2.759041 0.07725222 -2.840047 219s x4 -0.07103635 0.04152051 -1.710874 0.03167549 -2.242628 219s 219s Estimated Scale Parameter: 1.009587 219s Number of Iterations: 1 219s 219s Working Correlation 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 219s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 219s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 219s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 219s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 219s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 219s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 219s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 219s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 219s [1,] 0 0 0 0 0 0 0 219s [2,] 0 0 0 0 0 0 0 219s [3,] 0 0 0 0 0 0 0 219s [4,] 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > glm(lgind~x2+x3+x4,data=testgee, start=rep(0,4), # needed in R 219s + family=quasi(link=logit,variance="mu(1-mu)")) 219s 219s Call: glm(formula = lgind ~ x2 + x3 + x4, family = quasi(link = logit, 219s variance = "mu(1-mu)"), data = testgee, start = rep(0, 4)) 219s 219s Coefficients: 219s (Intercept) x2 x3 x4 219s 4.72921 -0.34748 -0.21940 -0.07104 219s 219s Degrees of Freedom: 499 Total (i.e. Null); 496 Residual 219s Null Deviance: 635.6 219s Residual Deviance: 591.4 AIC: NA 219s > 219s > summary(gee(lgind~x2+x3+x4,id=id,data=testgee,family=binomial,scale.fix=TRUE)) 219s (Intercept) x2 x3 x4 219s 4.72920874 -0.34747871 -0.21939993 -0.07103635 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = lgind ~ x2 + x3 + x4, id = id, data = testgee, 219s family = binomial, scale.fix = TRUE) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.7537945 -0.3323381 -0.2080574 0.5160616 0.8872020 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 4.72920874 1.02718977 4.604026 0.86323313 5.478484 219s x2 -0.34747871 0.06271394 -5.540693 0.05004796 -6.942915 219s x3 -0.21939993 0.07914189 -2.772235 0.07725222 -2.840047 219s x4 -0.07103635 0.04132290 -1.719055 0.03167549 -2.242628 219s 219s Estimated Scale Parameter: 1 219s Number of Iterations: 1 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 219s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 219s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 219s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 219s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 219s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 219s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 219s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 219s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 219s [1,] 0 0 0 0 0 0 0 219s [2,] 0 0 0 0 0 0 0 219s [3,] 0 0 0 0 0 0 0 219s [4,] 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > #glm(lgind~x2+x3+x4,data=testgee,family=binomial) 219s > 219s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="exchangeable")) 219s (Intercept) x2 x3 x4 219s 6.4719531 -0.2719330 -0.2759630 -0.1493855 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Exchangeable 219s 219s Call: 219s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 219s corstr = "exchangeable") 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.9132133 -0.4779069 0.2183723 0.4022373 0.8322064 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 6.3714080 1.01872823 6.254276 0.82259807 7.745469 219s x2 -0.2582285 0.05832328 -4.427537 0.06432493 -4.014439 219s x3 -0.2792487 0.07639349 -3.655399 0.05877904 -4.750820 219s x4 -0.1458317 0.04000757 -3.645104 0.02732683 -5.336576 219s 219s Estimated Scale Parameter: 1.008096 219s Number of Iterations: 3 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] 219s [1,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [2,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [3,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 219s [4,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 219s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 219s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 219s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [,7] [,8] [,9] [,10] [,11] [,12] 219s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [7,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [8,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [9,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 219s [10,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 219s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 219s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 219s [13,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [14,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [15,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [16,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [,13] [,14] [,15] [,16] [,17] [,18] 219s [1,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [2,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [3,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [4,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [5,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [6,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [7,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [8,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [9,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [10,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [11,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [12,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [13,] 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [14,] -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [15,] -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 -0.02048602 219s [16,] -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 -0.02048602 219s [17,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 -0.02048602 219s [18,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 1.00000000 219s [19,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [20,] -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 -0.02048602 219s [,19] [,20] 219s [1,] -0.02048602 -0.02048602 219s [2,] -0.02048602 -0.02048602 219s [3,] -0.02048602 -0.02048602 219s [4,] -0.02048602 -0.02048602 219s [5,] -0.02048602 -0.02048602 219s [6,] -0.02048602 -0.02048602 219s [7,] -0.02048602 -0.02048602 219s [8,] -0.02048602 -0.02048602 219s [9,] -0.02048602 -0.02048602 219s [10,] -0.02048602 -0.02048602 219s [11,] -0.02048602 -0.02048602 219s [12,] -0.02048602 -0.02048602 219s [13,] -0.02048602 -0.02048602 219s [14,] -0.02048602 -0.02048602 219s [15,] -0.02048602 -0.02048602 219s [16,] -0.02048602 -0.02048602 219s [17,] -0.02048602 -0.02048602 219s [18,] -0.02048602 -0.02048602 219s [19,] 1.00000000 -0.02048602 219s [20,] -0.02048602 1.00000000 219s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial,corstr="stat_M_dep",M=1)) 219s (Intercept) x2 x3 x4 219s 6.4719531 -0.2719330 -0.2759630 -0.1493855 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Stationary M-dependent , M = 1 219s 219s Call: 219s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial, 219s corstr = "stat_M_dep", Mv = 1) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.8834271 -0.4920962 0.2491360 0.4108783 0.7887767 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 5.4093789 0.84036337 6.436952 0.70900809 7.629502 219s x2 -0.2069859 0.04869638 -4.250540 0.05089218 -4.067147 219s x3 -0.2469902 0.06394554 -3.862508 0.04953133 -4.986545 219s x4 -0.1193671 0.03385364 -3.525976 0.02800656 -4.262113 219s 219s Estimated Scale Parameter: 0.9787236 219s Number of Iterations: 3 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] 219s [1,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 219s [2,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 219s [3,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 219s [4,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 219s [5,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 219s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 219s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 219s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [10,] 0.0000000Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [,7] [,8] [,9] [,10] [,11] [,12] 219s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [6,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [7,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 219s [8,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 219s [9,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 219s [10,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 219s [11,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 219s [12,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 219s [13,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 219s [14,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [15,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [16,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [17,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [,13] [,14] [,15] [,16] [,17] [,18] 219s [1,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [2,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [3,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [4,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [5,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [6,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [7,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [8,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [9,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [10,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [11,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [12,] -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [13,] 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 0.0000000 219s [14,] -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 0.0000000 219s [15,] 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 0.0000000 219s [16,] 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 0.0000000 219s [17,] 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 -0.3301082 219s [18,] 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 1.0000000 219s [19,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.3301082 219s [20,] 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 219s [,19] [,20] 219s [1,] 0.0000000 0.0000000 219s [2,] 0.0000000 0.0000000 219s [3,] 0.0000000 0.0000000 219s [4,] 0.0000000 0.0000000 219s [5,] 0.0000000 0.0000000 219s [6,] 0.0000000 0.0000000 219s [7,] 0.0000000 0.0000000 219s [8,] 0.0000000 0.0000000 219s [9,] 0.0000000 0.0000000 219s [10,] 0.0000000 0.0000000 219s [11,] 0.0000000 0.0000000 219s [12,] 0.0000000 0.0000000 219s [13,] 0.0000000 0.0000000 219s [14,] 0.0000000 0.0000000 219s [15,] 0.0000000 0.0000000 219s [16,] 0.0000000 0.0000000 219s [17,] 0.0000000 0.0000000 219s [18,] -0.3301082 0.0000000 219s [19,] 1.0000000 -0.3301082 219s [20,] -0.3301082 1.0000000 219s > 219s > summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=binomial(link=probit))) 219s (Intercept) x2 x3 x4 219s 3.92612377 -0.16597664 -0.16503829 -0.09214249 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Probit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, family = binomial(link = probit)) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.9259107 -0.4767799 0.2158545 0.4033760 0.8384385 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 3.92613715 0.61214299 6.413758 0.53755155 7.303741 219s x2 -0.16597696 0.03582656 -4.632790 0.04006791 -4.142391 219s x3 -0.16503933 0.04665763 -3.537242 0.03848563 -4.288336 219s x4 -0.09214252 0.02457762 -3.749042 0.01654858 -5.568001 219s 219s Estimated Scale Parameter: 1.014784 219s Number of Iterations: 1 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 219s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 219s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 219s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 219s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 219s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 219s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 219s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 219s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [20,] 0 0Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s user's initial regression estimate 219s 0 0 0 0 0 0 0 0 0 0 0 219s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 219s [1,] 0 0 0 0 0 0 0 219s [2,] 0 0 0 0 0 0 0 219s [3,] 0 0 0 0 0 0 0 219s [4,] 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > # next line does not work in R's glm: needs starting values for quasi 219s > #summary(gee(lg~x2+x3+x4,id=id,data=testgee,family=quasi(link=probit,variance="mu(1-mu)"))) 219s > summary(gee(lg~x2+x3+x4, id=id, data=testgee, b=rep(0,4), family=quasi(link=probit,variance="mu(1-mu)"))) 219s [,1] 219s [1,] 0 219s [2,] 0 219s [3,] 0 219s [4,] 0 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Probit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = lg ~ x2 + x3 + x4, id = id, data = testgee, b = rep(0, 219s 4), family = quasi(link = probit, variance = "mu(1-mu)")) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.9259108 -0.4767799 0.2158545 0.4033761 0.8384386 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 3.92613840 0.61214303 6.413760 0.53755167 7.303741 219s x2 -0.16597699 0.03582656 -4.632791 0.04006791 -4.142392 219s x3 -0.16503949 0.04665763 -3.537245 0.03848564 -4.288340 219s x4 -0.09214246 0.02457762 -3.749040 0.01654858 -5.567998 219s 219s Estimated Scale Parameter: 1.014784 219s Number of Iterations: 4 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 219s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 219s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 219s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 219s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 219s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 219s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 219s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 219s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 219s [1,] 0 0 0 0 0 0 0 219s [2,] 0 0 0 0 0 0 0 219s [3,] 0 0 0 0 0 0 0 219s [4,] 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > 219s > logmat <- cbind(testgee[,"lg1"],testgee[,"nn"]) 219s > xmat <- cbind(testgee[,"x2"], testgee[,"x3"]) 219s > summary(gee(logmat~xmat,id = testgee[,"id"],family=binomial(link=probit))) 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s (Intercept) xmat1 xmat2 219s 0.51795625 -0.06406827 -0.04156066 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Probit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = logmat ~ xmat, id = testgee[, "id"], family = binomial(link = probit)) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s 0.5160816 1.7308948 4.6651553 7.6862003 19.5931240 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 0.51795627 0.102935017 5.031876 0.104967578 4.934441 219s xmat1 -0.06406827 0.006534226 -9.805029 0.006443532 -9.943037 219s xmat2 -0.04156066 0.008875153 -4.682810 0.010589196 -3.924817 219s 219s Estimated Scale Parameter: 0.6334804 219s Number of Iterations: 1 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] 219s [1,] 1 0 0 0 0 0 0 0 0 0 0 0 0 219s [2,] 0 1 0 0 0 0 0 0 0 0 0 0 0 219s [3,] 0 0 1 0 0 0 0 0 0 0 0 0 0 219s [4,] 0 0 0 1 0 0 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 1 0 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 1 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 1 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 1 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 0 1 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 0 0 1 0 0 0 219s [11,] 0 0 0 0 0 0 0 0 0 0 1 0 0 219s [12,] 0 0 0 0 0 0 0 0 0 0 0 1 0 219s [13,] 0 0 0 0 0 0 0 0 0 0 0 0 1 219s [14,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [15,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [16,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [17,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [18,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [19,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [20,] 0 0 0 0 0 0 0 0 0 0 0 0 0 219s [,14] [,15] [,16] [,17] [,18] [,19] [,20] 219s [1,] 0 0 0 0 0 0 0 219s [2,] 0 0 0 0 0 0 0 219s [3,] 0 0 0 0 0 0 0 219s [4,] 0 0 0 0 0 0 0 219s [5,] 0 0 0 0 0 0 0 219s [6,] 0 0 0 0 0 0 0 219s [7,] 0 0 0 0 0 0 0 219s [8,] 0 0 0 0 0 0 0 219s [9,] 0 0 0 0 0 0 0 219s [10,] 0 0 0 0 0 0 0 219s [11,] 0 0 0 0 0 0 0 219s [12,] 0 0 0 0 0 0 0 219s [13,] 0 0 0 0 0 0 0 219s [14,] 1 0 0 0 0 0 0 219s [15,] 0 1 0 0 0 0 0 219s [16,] 0 0 1 0 0 0 0 219s [17,] 0 0 0 1 0 0 0 219s [18,] 0 0 0 0 1 0 0 219s [19,] 0 0 0 0 0 1 0 219s [20,] 0 0 0 0 0 0 1 219s > 219s > sub<-rep(c(FALSE,FALSE,FALSE,FALSE,TRUE),100) 219s > summary(gee(lg~x2+x4,id=id,data=testgee,family=binomial,subset=sub)) 219s (Intercept) x2 x4 219s 5.5224757 -0.3467620 -0.2667172 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logit 219s Variance to Mean Relation: Binomial 219s Correlation Structure: Independent 219s 219s Call: 219s gee(formula = lg ~ x2 + x4, id = id, data = testgee, subset = sub, 219s family = binomial) 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -0.8367702 -0.5120235 0.1897604 0.3569406 0.7244263 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 5.5224757 1.5820384 3.490734 1.25770291 4.390922 219s x2 -0.3467620 0.1323609 -2.619823 0.12032183 -2.881954 219s x4 -0.2667172 0.1190969 -2.239497 0.08655567 -3.081453 219s 219s Estimated Scale Parameter: 0.9974213 219s Number of Iterations: 1 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] 219s [1,] 1 0 0 0 219s [2,] 0 1 0 0 219s [3,] 0 0 1 0 219s [4,] 0 0 0 1 219s > 219s > R <- c(1.0,0.2,0.3,0.1, 219s + 0.2,1.0,0.2,0.3, 219s + 0.3,0.2,1.0,0.2, 219s + 0.1,0.3,0.2,1.0) 219s > R <- matrix(R,nrow=4) 219s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=poisson(link=log), 219s + subset=sub,corstr="fixed",R=R)) 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s (Intercept) x2 x4 219s 2.80530150 -0.08997444 -0.04801454 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logarithm 219s Variance to Mean Relation: Poisson 219s Correlation Structure: Fixed 219s 219s Call: 219s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 219s R = R, family = poisson(link = log), corstr = "fixed") 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -7.5561190 -3.0282712 -0.7601115 2.3823498 12.5360530 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept) 3.02620978 0.43234114 6.999588 0.34930120 8.663611 219s x2 -0.10058734 0.04084446 -2.462692 0.04687746 -2.145751 219s x4 -0.06504106 0.03683906 -1.765546 0.03434579 -1.893713 219s 219s Estimated Scale Parameter: 3.192382 219s Number of Iterations: 3 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] 219s [1,] 1.0 0.2 0.3 0.1 219s [2,] 0.2 1.0 0.2 0.3 219s [3,] 0.3 0.2 1.0 0.2 219s [4,] 0.1 0.3 0.2 1.0 219s > summary(gee(lg1~x2+x4,id=id,data=testgee,family=Gamma(link=log), 219s + subset=sub,corstr="fixed",R=R)) 219s (Intercept) x2 x4 219s 2.87964611 -0.08377511 -0.06186083 219s 219s GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA 219s gee S-function, version 4.13 modified 98/01/27 (1998) 219s 219s Model: 219s Link: Logarithm 219s Variance to Mean Relation: Gamma 219s Correlation Structure: Fixed 219s 219s Call: 219s gee(formula = lg1 ~ x2 + x4, id = id, data = testgee, subset = sub, 219s R = R, family = Gamma(link = log), corstr = "fixed") 219s 219s Summary of Residuals: 219s Min 1Q Median 3Q Max 219s -8.3423135 -3.0545513 -0.6859899 2.2598854 12.7656153 219s 219s 219s Coefficients: 219s Estimate Naive S.E. Naive z Robust S.E. Robust z 219s (Intercept)running glm to get initial regression estimate 219s Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 219s running glm to get initial regression estimate 219s 3.11365042 0.44562056 6.987223 0.33999983 9.157800 219s x2 -0.09008311 0.04002263 -2.250804 0.04218714 -2.135322 219s x4 -0.08356337 0.03655400 -2.286025 0.03547845 -2.355328 219s 219s Estimated Scale Parameter: 0.5550169 219s Number of Iterations: 4 219s 219s Working Correlation 219s [,1] [,2] [,3] [,4] 219s [1,] 1.0 0.2 0.3 0.1 219s [2,] 0.2 1.0 0.2 0.3 219s [3,] 0.3 0.2 1.0 0.2 219s [4,] 0.1 0.3 0.2 1.0 219s > 219s autopkgtest [22:12:59]: test run-unit-test: -----------------------] 219s run-unit-test PASS 219s autopkgtest [22:12:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 220s autopkgtest [22:13:00]: test pkg-r-autopkgtest: preparing testbed 220s Reading package lists... 220s Building dependency tree... 220s Reading state information... 221s Starting pkgProblemResolver with broken count: 0 221s Starting 2 pkgProblemResolver with broken count: 0 221s Done 221s The following NEW packages will be installed: 221s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 221s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 221s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 221s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 221s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 221s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 221s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 221s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 221s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 221s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 221s r-base-dev zlib1g-dev 221s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 221s Need to get 103 MB of archives. 221s After this operation, 363 MB of additional disk space will be used. 221s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 222s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 222s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 223s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 223s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 223s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 223s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 223s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 223s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 223s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 223s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 223s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 223s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 223s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 223s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 223s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 225s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 225s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 225s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 225s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 225s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 226s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 226s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 226s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 226s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 226s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 226s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 226s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 226s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 226s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 226s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 226s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 226s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 226s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 226s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 226s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 227s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 227s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 227s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 227s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 227s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 227s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 227s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 227s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 227s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 227s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 227s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 227s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 227s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 227s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB] 227s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 227s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 227s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 227s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 227s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 228s Fetched 103 MB in 6s (16.5 MB/s) 228s Selecting previously unselected package libisl23:amd64. 228s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 87145 files and directories currently installed.) 228s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 228s Unpacking libisl23:amd64 (0.27-1) ... 228s Selecting previously unselected package libmpc3:amd64. 228s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 228s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 228s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 228s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 228s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 228s Selecting previously unselected package cpp-14. 228s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 228s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 228s Selecting previously unselected package cpp-x86-64-linux-gnu. 228s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 228s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 228s Selecting previously unselected package cpp. 228s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 228s Unpacking cpp (4:14.2.0-1ubuntu1) ... 228s Selecting previously unselected package libcc1-0:amd64. 228s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_amd64.deb ... 228s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ... 228s Selecting previously unselected package libitm1:amd64. 228s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_amd64.deb ... 228s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 228s Selecting previously unselected package libasan8:amd64. 228s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_amd64.deb ... 228s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 228s Selecting previously unselected package liblsan0:amd64. 228s Preparing to unpack .../09-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 228s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 228s Selecting previously unselected package libtsan2:amd64. 228s Preparing to unpack .../10-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 228s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 229s Selecting previously unselected package libubsan1:amd64. 229s Preparing to unpack .../11-libubsan1_15-20250222-0ubuntu1_amd64.deb ... 229s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ... 229s Selecting previously unselected package libhwasan0:amd64. 229s Preparing to unpack .../12-libhwasan0_15-20250222-0ubuntu1_amd64.deb ... 229s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ... 229s Selecting previously unselected package libquadmath0:amd64. 229s Preparing to unpack .../13-libquadmath0_15-20250222-0ubuntu1_amd64.deb ... 229s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ... 229s Selecting previously unselected package libgcc-14-dev:amd64. 229s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 229s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 229s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 229s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 229s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 229s Selecting previously unselected package gcc-14. 229s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 229s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 229s Selecting previously unselected package gcc-x86-64-linux-gnu. 229s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 229s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 229s Selecting previously unselected package gcc. 229s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 229s Unpacking gcc (4:14.2.0-1ubuntu1) ... 229s Selecting previously unselected package libstdc++-14-dev:amd64. 229s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 229s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 229s Selecting previously unselected package g++-14-x86-64-linux-gnu. 229s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 229s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 230s Selecting previously unselected package g++-14. 230s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_amd64.deb ... 230s Unpacking g++-14 (14.2.0-17ubuntu3) ... 230s Selecting previously unselected package g++-x86-64-linux-gnu. 230s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 230s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 230s Selecting previously unselected package g++. 230s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 230s Unpacking g++ (4:14.2.0-1ubuntu1) ... 230s Selecting previously unselected package build-essential. 230s Preparing to unpack .../24-build-essential_12.10ubuntu1_amd64.deb ... 230s Unpacking build-essential (12.10ubuntu1) ... 230s Selecting previously unselected package dctrl-tools. 230s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ... 230s Unpacking dctrl-tools (2.24-3build3) ... 230s Selecting previously unselected package libgfortran-14-dev:amd64. 230s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ... 230s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 230s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 230s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 230s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 230s Selecting previously unselected package gfortran-14. 230s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_amd64.deb ... 230s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 230s Selecting previously unselected package gfortran-x86-64-linux-gnu. 230s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 230s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 230s Selecting previously unselected package gfortran. 230s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 230s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 230s Selecting previously unselected package icu-devtools. 230s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ... 230s Unpacking icu-devtools (76.1-1ubuntu2) ... 230s Selecting previously unselected package libblas-dev:amd64. 230s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... 230s Unpacking libblas-dev:amd64 (3.12.1-2) ... 230s Selecting previously unselected package libbz2-dev:amd64. 230s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 230s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 230s Selecting previously unselected package libdeflate-dev:amd64. 230s Preparing to unpack .../34-libdeflate-dev_1.23-1_amd64.deb ... 230s Unpacking libdeflate-dev:amd64 (1.23-1) ... 230s Selecting previously unselected package libicu-dev:amd64. 230s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 230s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 231s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 231s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 231s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 231s Selecting previously unselected package libjpeg8-dev:amd64. 231s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 231s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 231s Selecting previously unselected package libjpeg-dev:amd64. 231s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 231s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 231s Selecting previously unselected package liblapack-dev:amd64. 231s Preparing to unpack .../39-liblapack-dev_3.12.1-2_amd64.deb ... 231s Unpacking liblapack-dev:amd64 (3.12.1-2) ... 231s Selecting previously unselected package libncurses-dev:amd64. 231s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_amd64.deb ... 231s Unpacking libncurses-dev:amd64 (6.5+20250216-2) ... 231s Selecting previously unselected package libpcre2-16-0:amd64. 231s Preparing to unpack .../41-libpcre2-16-0_10.45-1_amd64.deb ... 231s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 231s Selecting previously unselected package libpcre2-32-0:amd64. 231s Preparing to unpack .../42-libpcre2-32-0_10.45-1_amd64.deb ... 231s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 231s Selecting previously unselected package libpcre2-posix3:amd64. 231s Preparing to unpack .../43-libpcre2-posix3_10.45-1_amd64.deb ... 231s Unpacking libpcre2-posix3:amd64 (10.45-1) ... 231s Selecting previously unselected package libpcre2-dev:amd64. 231s Preparing to unpack .../44-libpcre2-dev_10.45-1_amd64.deb ... 231s Unpacking libpcre2-dev:amd64 (10.45-1) ... 231s Selecting previously unselected package libpkgconf3:amd64. 231s Preparing to unpack .../45-libpkgconf3_1.8.1-4_amd64.deb ... 231s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 231s Selecting previously unselected package zlib1g-dev:amd64. 231s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 231s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 231s Selecting previously unselected package libpng-dev:amd64. 231s Preparing to unpack .../47-libpng-dev_1.6.47-1_amd64.deb ... 231s Unpacking libpng-dev:amd64 (1.6.47-1) ... 231s Selecting previously unselected package libreadline-dev:amd64. 231s Preparing to unpack .../48-libreadline-dev_8.2-6_amd64.deb ... 231s Unpacking libreadline-dev:amd64 (8.2-6) ... 232s Selecting previously unselected package liblzma-dev:amd64. 232s Preparing to unpack .../49-liblzma-dev_5.6.4-1_amd64.deb ... 232s Unpacking liblzma-dev:amd64 (5.6.4-1) ... 232s Selecting previously unselected package pkgconf-bin. 232s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_amd64.deb ... 232s Unpacking pkgconf-bin (1.8.1-4) ... 232s Selecting previously unselected package pkgconf:amd64. 232s Preparing to unpack .../51-pkgconf_1.8.1-4_amd64.deb ... 232s Unpacking pkgconf:amd64 (1.8.1-4) ... 232s Selecting previously unselected package libtirpc-dev:amd64. 232s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... 232s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 232s Selecting previously unselected package r-base-dev. 232s Preparing to unpack .../53-r-base-dev_4.4.3-1_all.deb ... 232s Unpacking r-base-dev (4.4.3-1) ... 232s Selecting previously unselected package pkg-r-autopkgtest. 232s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 232s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 232s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 232s Setting up libncurses-dev:amd64 (6.5+20250216-2) ... 232s Setting up libreadline-dev:amd64 (8.2-6) ... 232s Setting up libpcre2-16-0:amd64 (10.45-1) ... 232s Setting up libpcre2-32-0:amd64 (10.45-1) ... 232s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 232s Setting up libpkgconf3:amd64 (1.8.1-4) ... 232s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ... 232s Setting up libmpc3:amd64 (1.3.1-1build2) ... 232s Setting up icu-devtools (76.1-1ubuntu2) ... 232s Setting up pkgconf-bin (1.8.1-4) ... 232s Setting up liblzma-dev:amd64 (5.6.4-1) ... 232s Setting up libubsan1:amd64 (15-20250222-0ubuntu1) ... 232s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 232s Setting up libpcre2-posix3:amd64 (10.45-1) ... 232s Setting up libhwasan0:amd64 (15-20250222-0ubuntu1) ... 232s Setting up libasan8:amd64 (15-20250222-0ubuntu1) ... 232s Setting up libtsan2:amd64 (15-20250222-0ubuntu1) ... 232s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 232s Setting up libisl23:amd64 (0.27-1) ... 232s Setting up libdeflate-dev:amd64 (1.23-1) ... 232s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 232s Setting up libcc1-0:amd64 (15-20250222-0ubuntu1) ... 232s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ... 232s Setting up libblas-dev:amd64 (3.12.1-2) ... 232s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 232s Setting up dctrl-tools (2.24-3build3) ... 232s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ... 232s Setting up libbz2-dev:amd64 (1.0.8-6) ... 232s Setting up libpcre2-dev:amd64 (10.45-1) ... 232s Setting up libpng-dev:amd64 (1.6.47-1) ... 232s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 232s Setting up pkgconf:amd64 (1.8.1-4) ... 232s Setting up liblapack-dev:amd64 (3.12.1-2) ... 232s update-alternatives: using 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232s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 232s Setting up gcc (4:14.2.0-1ubuntu1) ... 232s Setting up g++ (4:14.2.0-1ubuntu1) ... 232s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 232s Setting up build-essential (12.10ubuntu1) ... 232s Setting up gfortran (4:14.2.0-1ubuntu1) ... 232s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 232s 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 232s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 232s 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 232s Setting up r-base-dev (4.4.3-1) ... 232s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 232s Processing triggers for libc-bin (2.41-1ubuntu2) ... 232s Processing triggers for man-db (2.13.0-1) ... 233s Processing triggers for install-info (7.1.1-1) ... 234s autopkgtest [22:13:14]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 234s autopkgtest [22:13:14]: test pkg-r-autopkgtest: [----------------------- 234s Test: Try to load the R library gee 234s 234s R version 4.4.3 (2025-02-28) -- "Trophy Case" 234s Copyright (C) 2025 The R Foundation for Statistical Computing 234s Platform: x86_64-pc-linux-gnu 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 234s > library('gee') 234s > 234s > 235s Other tests are currently unsupported! 235s They will be progressively added. 235s autopkgtest [22:13:15]: test pkg-r-autopkgtest: -----------------------] 235s pkg-r-autopkgtest PASS 235s autopkgtest [22:13:15]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 236s autopkgtest [22:13:16]: @@@@@@@@@@@@@@@@@@@@ summary 236s run-unit-test PASS 236s pkg-r-autopkgtest PASS 253s nova [W] Skipping flock for amd64 253s Creating nova instance adt-plucky-amd64-r-cran-gee-20250315-220920-juju-7f2275-prod-proposed-migration-environment-15-689266da-affe-430e-b084-8c61e74139ce from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 253s nova [W] Timed out waiting for d08114c0-9d27-4f70-9e91-d6633c2d9773 to get deleted.