0s autopkgtest [22:02:57]: starting date and time: 2025-03-15 22:02:57+0000 0s autopkgtest [22:02:57]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:02:57]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gb0g4d7r/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-bdsmatrix --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-6.secgroup --name adt-plucky-amd64-r-cran-bdsmatrix-20250315-220256-juju-7f2275-prod-proposed-migration-environment-15-99d624df-d29f-4fef-8b36-379d28a65073 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 41s autopkgtest [22:03:38]: testbed dpkg architecture: amd64 41s autopkgtest [22:03:38]: testbed apt version: 2.9.31ubuntu1 42s autopkgtest [22:03:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s autopkgtest [22:03:39]: testbed release detected to be: None 42s autopkgtest [22:03:39]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 42s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 42s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 42s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 42s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 42s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 42s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 42s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 42s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 42s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 43s Fetched 1265 kB in 0s (4928 kB/s) 44s Reading package lists... 44s + lsb_release --codename --short 44s + RELEASE=plucky 44s + cat 44s + [ plucky != trusty ] 44s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 44s Reading package lists... 44s Building dependency tree... 44s Reading state information... 45s Calculating upgrade... 45s Calculating upgrade... 45s The following package was automatically installed and is no longer required: 45s libnl-genl-3-200 45s Use 'sudo apt autoremove' to remove it. 46s The following NEW packages will be installed: 46s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 46s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 46s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 46s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 46s The following packages will be upgraded: 46s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 46s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 46s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 46s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 46s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 46s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 46s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 46s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 46s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 46s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 46s linux-headers-generic linux-headers-virtual linux-image-generic 46s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 46s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 46s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 46s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 46s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 46s python3.13-minimal rsync rsyslog strace xz-utils 46s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 46s Need to get 807 MB of archives. 46s After this operation, 326 MB of additional disk space will be used. 46s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 46s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 46s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 46s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 46s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 46s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 46s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 46s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 46s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 46s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 46s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 46s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 46s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 46s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 46s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 46s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 46s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 46s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 46s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 46s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 46s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 46s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 46s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 46s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 46s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 46s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 46s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 46s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 46s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 46s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 46s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 46s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 46s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 46s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 46s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 46s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 46s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 46s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 46s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 46s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 46s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 46s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 46s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 46s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 46s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 46s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 46s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 46s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 46s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 46s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 46s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 46s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 46s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 46s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 46s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 46s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 46s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 46s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 46s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 46s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 46s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 46s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 46s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 46s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 46s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 46s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 46s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 46s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 46s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 46s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 46s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 46s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 46s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 46s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 51s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 51s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 51s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 52s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 52s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 52s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 52s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 52s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 52s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 52s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 52s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 52s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 52s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 52s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 52s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 52s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 52s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 52s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 52s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 52s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 53s Preconfiguring packages ... 53s Fetched 807 MB in 7s (117 MB/s) 53s (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 ... 109138 files and directories currently installed.) 53s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 53s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 53s Setting up ncurses-bin (6.5+20250216-2) ... 53s (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 ... 109138 files and directories currently installed.) 53s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 53s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 54s Setting up ncurses-base (6.5+20250216-2) ... 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 54s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 54s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 54s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 54s Setting up liblz4-1:amd64 (1.10.0-4) ... 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 54s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 54s Setting up liblzma5:amd64 (5.6.4-1) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 55s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 55s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 55s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 55s Setting up apt (2.9.33) ... 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 56s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 56s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 56s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 56s Setting up python3-minimal (3.13.2-2) ... 56s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 74s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 74s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 74s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 74s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 74s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 74s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 74s Setting up media-types (13.0.0) ... 74s Installing new version of config file /etc/mime.types ... 74s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 74s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 74s Setting up pci.ids (0.0~2025.03.09-1) ... 74s Setting up apt-utils (2.9.33) ... 74s Setting up libdebuginfod-common (0.192-4) ... 74s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 74s Setting up bpftool (7.6.0+6.14.0-10.10) ... 74s Setting up libestr0:amd64 (0.1.11-2) ... 74s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 74s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 74s Setting up dosfstools (4.2-1.2) ... 74s Setting up rsyslog (8.2412.0-2ubuntu2) ... 75s info: The user `syslog' is already a member of `adm'. 76s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 76s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 76s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 76s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 76s Setting up linux-headers-generic (6.14.0-10.10) ... 76s Setting up libjemalloc2:amd64 (5.3.0-3) ... 76s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 76s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 76s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 76s Installing new version of config file /etc/apparmor.d/openvpn ... 77s Reloading AppArmor profiles 79s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 79s No schema files found: doing nothing. 79s Setting up libglib2.0-data (2.84.0-1) ... 79s Setting up libncurses6:amd64 (6.5+20250216-2) ... 79s Setting up strace (6.13+ds-1ubuntu1) ... 79s Setting up xz-utils (5.6.4-1) ... 79s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 79s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 81s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 81s Setting up libpci3:amd64 (1:3.13.0-2) ... 81s Setting up python-apt-common (2.9.9build1) ... 81s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 81s Setting up pnp.ids (0.393-3) ... 81s Setting up libnl-3-200:amd64 (3.7.0-1) ... 81s Setting up python3.13-minimal (3.13.2-2) ... 82s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 82s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 82s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 82s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 82s Setting up rsync (3.4.1+ds1-3) ... 83s rsync.service is a disabled or a static unit not running, not starting it. 83s Setting up python3.13-gdbm (3.13.2-2) ... 83s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 83s Setting up ncurses-term (6.5+20250216-2) ... 83s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 83s Setting up libpython3.13:amd64 (3.13.2-2) ... 83s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 83s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 83s Setting up linux-headers-virtual (6.14.0-10.10) ... 83s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 83s Setting up python3.13 (3.13.2-2) ... 84s Setting up htop (3.4.0-2) ... 84s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 86s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 86s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 86s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 86s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 86s Setting up libfwupd3:amd64 (2.0.6-4) ... 86s Setting up python3 (3.13.2-2) ... 86s Setting up python3-markupsafe (2.1.5-1build4) ... 87s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 89s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 89s Setting up hwdata (0.393-3) ... 89s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 89s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 89s Setting up linux-perf (6.14.0-10.10) ... 89s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 89s Setting up python3-gi (3.50.0-4build1) ... 89s Setting up pciutils (1:3.13.0-2) ... 89s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 89s Setting up curl (8.12.1-3ubuntu1) ... 89s Setting up linux-image-virtual (6.14.0-10.10) ... 89s Setting up linux-tools-common (6.14.0-10.10) ... 89s Setting up fwupd (2.0.6-4) ... 90s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 90s fwupd.service is a disabled or a static unit not running, not starting it. 90s Setting up python3-systemd (235-1build6) ... 90s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 90s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 90s Setting up linux-image-generic (6.14.0-10.10) ... 90s Setting up python3-dbus (1.3.2-5build5) ... 90s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 90s Setting up linux-generic (6.14.0-10.10) ... 90s Setting up python3-apt (2.9.9build1) ... 90s Setting up python3-yaml (6.0.2-1build2) ... 90s Setting up python3-lazr.uri (1.0.6-6) ... 91s Setting up binutils (2.44-3ubuntu1) ... 91s Setting up cloud-init-base (25.1-0ubuntu3) ... 92s Setting up linux-virtual (6.14.0-10.10) ... 92s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 92s Setting up cloud-init (25.1-0ubuntu3) ... 92s Processing triggers for systemd (257.3-1ubuntu3) ... 92s Processing triggers for man-db (2.13.0-1) ... 94s Processing triggers for dbus (1.16.2-1ubuntu1) ... 94s Processing triggers for libc-bin (2.41-1ubuntu1) ... 94s Processing triggers for initramfs-tools (0.146ubuntu1) ... 94s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 94s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 106s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 106s /etc/kernel/postinst.d/initramfs-tools: 106s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 106s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 118s /etc/kernel/postinst.d/zz-update-grub: 118s Sourcing file `/etc/default/grub' 118s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 118s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 118s Generating grub configuration file ... 118s Found linux image: /boot/vmlinuz-6.14.0-10-generic 118s Found initrd image: /boot/initrd.img-6.14.0-10-generic 118s Found linux image: /boot/vmlinuz-6.12.0-16-generic 118s Found initrd image: /boot/initrd.img-6.12.0-16-generic 118s Found linux image: /boot/vmlinuz-6.11.0-8-generic 118s Found initrd image: /boot/initrd.img-6.11.0-8-generic 118s Warning: os-prober will not be executed to detect other bootable partitions. 118s Systems on them will not be added to the GRUB boot configuration. 118s Check GRUB_DISABLE_OS_PROBER documentation entry. 118s Adding boot menu entry for UEFI Firmware Settings ... 118s done 118s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 118s + /usr/lib/apt/apt-helper analyze-pattern ?true 118s + uname -r 118s + sed s/\./\\./g 118s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 118s + apt list ?obsolete 118s + tail -n+2 118s + cut -d/ -f1 118s + grep -v ^linux-.*6\.12\.0-16-generic.* 120s + obsolete_pkgs=linux-headers-6.11.0-8-generic 120s linux-headers-6.11.0-8 120s linux-headers-6.12.0-16 120s linux-image-6.11.0-8-generic 120s linux-modules-6.11.0-8-generic 120s linux-tools-6.11.0-8-generic 120s linux-tools-6.11.0-8 120s linux-tools-6.12.0-16 120s + 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 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Solving dependencies... 121s The following packages will be REMOVED: 121s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 121s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 121s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 121s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 121s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 121s linux-tools-6.12.0-16-generic* 121s 0 upgraded, 0 newly installed, 15 to remove and 5 not upgraded. 121s After this operation, 371 MB disk space will be freed. 121s (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.) 121s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 121s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 121s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 121s Removing libpython3.12t64:amd64 (3.12.9-1) ... 121s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 121s Removing libnsl2:amd64 (1.3.0-3build3) ... 121s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 122s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 122s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 124s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 125s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 127s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 127s /etc/kernel/postrm.d/initramfs-tools: 127s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 128s /etc/kernel/postrm.d/zz-update-grub: 128s Sourcing file `/etc/default/grub' 128s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 128s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 128s Generating grub configuration file ... 128s Found linux image: /boot/vmlinuz-6.14.0-10-generic 128s Found initrd image: /boot/initrd.img-6.14.0-10-generic 128s Found linux image: /boot/vmlinuz-6.12.0-16-generic 128s Found initrd image: /boot/initrd.img-6.12.0-16-generic 128s Warning: os-prober will not be executed to detect other bootable partitions. 128s Systems on them will not be added to the GRUB boot configuration. 128s Check GRUB_DISABLE_OS_PROBER documentation entry. 128s Adding boot menu entry for UEFI Firmware Settings ... 128s done 128s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 129s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 129s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 129s Processing triggers for libc-bin (2.41-1ubuntu1) ... 129s (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.) 129s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 129s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 129s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 129s + grep -q trusty /etc/lsb-release 129s + [ ! -d /usr/share/doc/unattended-upgrades ] 129s + [ ! -d /usr/share/doc/lxd ] 129s + [ ! -d /usr/share/doc/lxd-client ] 129s + [ ! -d /usr/share/doc/snapd ] 129s + type iptables 129s + cat 129s + chmod 755 /etc/rc.local 129s + . /etc/rc.local 129s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 129s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 129s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 129s + uname -m 129s + [ x86_64 = ppc64le ] 129s + [ -d /run/systemd/system ] 129s + systemd-detect-virt --quiet --vm 129s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 129s + cat 129s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 129s + echo COMPRESS=lz4 129s autopkgtest [22:05:06]: upgrading testbed (apt dist-upgrade and autopurge) 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 131s Entering ResolveByKeep 131s 131s Calculating upgrade... 131s The following packages will be upgraded: 131s libc-bin libc-dev-bin libc6 libc6-dev locales 131s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Need to get 10.5 MB of archives. 131s After this operation, 1024 B of additional disk space will be used. 131s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 131s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 131s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 132s Preconfiguring packages ... 132s Fetched 10.5 MB in 0s (44.3 MB/s) 132s (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.) 132s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 132s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 132s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 132s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 132s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 133s Setting up libc6:amd64 (2.41-1ubuntu2) ... 133s (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.) 133s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 133s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 133s Setting up libc-bin (2.41-1ubuntu2) ... 133s (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.) 133s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 133s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 133s Setting up locales (2.41-1ubuntu2) ... 134s Generating locales (this might take a while)... 135s en_US.UTF-8... done 135s Generation complete. 135s Setting up libc-dev-bin (2.41-1ubuntu2) ... 135s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 135s Processing triggers for man-db (2.13.0-1) ... 136s Processing triggers for systemd (257.3-1ubuntu3) ... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 138s Solving dependencies... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s autopkgtest [22:05:16]: rebooting testbed after setup commands that affected boot 142s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 155s autopkgtest [22:05:32]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 156s autopkgtest [22:05:33]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-bdsmatrix 157s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (dsc) [2072 B] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (tar) [48.0 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bdsmatrix 1.3-7-1 (diff) [2520 B] 157s gpgv: Signature made Tue Mar 12 13:10:28 2024 UTC 157s gpgv: using RSA key 53951D95272E0C5B82BE8C4A2CECE9350ECEBE4A 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./r-cran-bdsmatrix_1.3-7-1.dsc: no acceptable signature found 158s autopkgtest [22:05:35]: testing package r-cran-bdsmatrix version 1.3-7-1 158s autopkgtest [22:05:35]: build not needed 159s autopkgtest [22:05:36]: test run-unit-test: preparing testbed 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s The following NEW packages will be installed: 160s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 160s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 160s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 160s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 160s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 160s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 160s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-bdsmatrix unzip 160s x11-common xdg-utils zip 160s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 41.6 MB of archives. 160s After this operation, 85.9 MB of additional disk space will be used. 160s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 160s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 160s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 160s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 160s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 160s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 160s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 160s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 160s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 160s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 160s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 160s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 160s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 160s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 160s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 160s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 160s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 160s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 160s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 160s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 160s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 160s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 160s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 160s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 160s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 160s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 160s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 160s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 160s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 160s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 160s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 160s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 160s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 160s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 160s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 160s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 160s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 160s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 160s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 160s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 160s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 160s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 160s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 161s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bdsmatrix amd64 1.3-7-1 [299 kB] 161s Preconfiguring packages ... 161s Fetched 41.6 MB in 1s (69.0 MB/s) 161s Selecting previously unselected package fonts-dejavu-mono. 161s (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.) 161s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 161s Unpacking fonts-dejavu-mono (2.37-8) ... 162s Selecting previously unselected package fonts-dejavu-core. 162s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 162s Unpacking fonts-dejavu-core (2.37-8) ... 162s Selecting previously unselected package fontconfig-config. 162s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 162s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 162s Selecting previously unselected package libfontconfig1:amd64. 162s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 162s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 162s Selecting previously unselected package fontconfig. 162s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 162s Unpacking fontconfig (2.15.0-2ubuntu1) ... 162s Selecting previously unselected package libblas3:amd64. 162s Preparing to unpack .../05-libblas3_3.12.1-2_amd64.deb ... 162s Unpacking libblas3:amd64 (3.12.1-2) ... 162s Selecting previously unselected package libpixman-1-0:amd64. 162s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ... 162s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 162s Selecting previously unselected package libxcb-render0:amd64. 162s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ... 162s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 162s Selecting previously unselected package libxcb-shm0:amd64. 162s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_amd64.deb ... 162s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 162s Selecting previously unselected package libxrender1:amd64. 162s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 162s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 162s Selecting previously unselected package libcairo2:amd64. 162s Preparing to unpack .../10-libcairo2_1.18.2-2_amd64.deb ... 162s Unpacking libcairo2:amd64 (1.18.2-2) ... 162s Selecting previously unselected package libdatrie1:amd64. 162s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_amd64.deb ... 162s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 162s Selecting previously unselected package libdeflate0:amd64. 162s Preparing to unpack .../12-libdeflate0_1.23-1_amd64.deb ... 162s Unpacking libdeflate0:amd64 (1.23-1) ... 162s Selecting previously unselected package libgfortran5:amd64. 162s Preparing to unpack .../13-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 162s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 162s Selecting previously unselected package libgomp1:amd64. 162s Preparing to unpack .../14-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 162s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 162s Selecting previously unselected package libgraphite2-3:amd64. 162s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 162s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 162s Selecting previously unselected package libharfbuzz0b:amd64. 162s Preparing to unpack .../16-libharfbuzz0b_10.2.0-1_amd64.deb ... 162s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 162s Selecting previously unselected package x11-common. 162s Preparing to unpack .../17-x11-common_1%3a7.7+23ubuntu3_all.deb ... 162s Unpacking x11-common (1:7.7+23ubuntu3) ... 162s Selecting previously unselected package libice6:amd64. 162s Preparing to unpack .../18-libice6_2%3a1.1.1-1_amd64.deb ... 162s Unpacking libice6:amd64 (2:1.1.1-1) ... 162s Selecting previously unselected package libjpeg-turbo8:amd64. 162s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 162s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 162s Selecting previously unselected package libjpeg8:amd64. 162s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_amd64.deb ... 162s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 162s Selecting previously unselected package liblapack3:amd64. 162s Preparing to unpack .../21-liblapack3_3.12.1-2_amd64.deb ... 162s Unpacking liblapack3:amd64 (3.12.1-2) ... 163s Selecting previously unselected package liblerc4:amd64. 163s Preparing to unpack .../22-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 163s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 163s Selecting previously unselected package libthai-data. 163s Preparing to unpack .../23-libthai-data_0.1.29-2build1_all.deb ... 163s Unpacking libthai-data (0.1.29-2build1) ... 163s Selecting previously unselected package libthai0:amd64. 163s Preparing to unpack .../24-libthai0_0.1.29-2build1_amd64.deb ... 163s Unpacking libthai0:amd64 (0.1.29-2build1) ... 163s Selecting previously unselected package libpango-1.0-0:amd64. 163s Preparing to unpack .../25-libpango-1.0-0_1.56.2-1_amd64.deb ... 163s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 163s Selecting previously unselected package libpangoft2-1.0-0:amd64. 163s Preparing to unpack .../26-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 163s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 163s Selecting previously unselected package libpangocairo-1.0-0:amd64. 163s Preparing to unpack .../27-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 163s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 163s Selecting previously unselected package libpaper2:amd64. 163s Preparing to unpack .../28-libpaper2_2.2.5-0.3_amd64.deb ... 163s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 163s Selecting previously unselected package libpaper-utils. 163s Preparing to unpack .../29-libpaper-utils_2.2.5-0.3_amd64.deb ... 163s Unpacking libpaper-utils (2.2.5-0.3) ... 163s Selecting previously unselected package libsharpyuv0:amd64. 163s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_amd64.deb ... 163s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 163s Selecting previously unselected package libsm6:amd64. 163s Preparing to unpack .../31-libsm6_2%3a1.2.4-1_amd64.deb ... 163s Unpacking libsm6:amd64 (2:1.2.4-1) ... 163s Selecting previously unselected package libtcl8.6:amd64. 163s Preparing to unpack .../32-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 163s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 163s Selecting previously unselected package libjbig0:amd64. 163s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 163s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 163s Selecting previously unselected package libwebp7:amd64. 163s Preparing to unpack .../34-libwebp7_1.5.0-0.1_amd64.deb ... 163s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 163s Selecting previously unselected package libtiff6:amd64. 163s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 163s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 163s Selecting previously unselected package libxft2:amd64. 163s Preparing to unpack .../36-libxft2_2.3.6-1build1_amd64.deb ... 163s Unpacking libxft2:amd64 (2.3.6-1build1) ... 163s Selecting previously unselected package libxss1:amd64. 163s Preparing to unpack .../37-libxss1_1%3a1.2.3-1build3_amd64.deb ... 163s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 163s Selecting previously unselected package libtk8.6:amd64. 163s Preparing to unpack .../38-libtk8.6_8.6.16-1_amd64.deb ... 163s Unpacking libtk8.6:amd64 (8.6.16-1) ... 163s Selecting previously unselected package libxt6t64:amd64. 163s Preparing to unpack .../39-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 163s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 163s Selecting previously unselected package zip. 163s Preparing to unpack .../40-zip_3.0-14ubuntu2_amd64.deb ... 163s Unpacking zip (3.0-14ubuntu2) ... 163s Selecting previously unselected package unzip. 163s Preparing to unpack .../41-unzip_6.0-28ubuntu6_amd64.deb ... 163s Unpacking unzip (6.0-28ubuntu6) ... 163s Selecting previously unselected package xdg-utils. 163s Preparing to unpack .../42-xdg-utils_1.2.1-2ubuntu1_all.deb ... 163s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 163s Selecting previously unselected package r-base-core. 163s Preparing to unpack .../43-r-base-core_4.4.3-1_amd64.deb ... 163s Unpacking r-base-core (4.4.3-1) ... 164s Selecting previously unselected package r-cran-bdsmatrix. 164s Preparing to unpack .../44-r-cran-bdsmatrix_1.3-7-1_amd64.deb ... 164s Unpacking r-cran-bdsmatrix (1.3-7-1) ... 164s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 164s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 164s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 164s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 164s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 164s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 164s Setting up libxcb-render0:amd64 (1.17.0-2) ... 164s Setting up unzip (6.0-28ubuntu6) ... 164s Setting up x11-common (1:7.7+23ubuntu3) ... 164s Setting up libdeflate0:amd64 (1.23-1) ... 164s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 164s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 164s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 164s Setting up zip (3.0-14ubuntu2) ... 164s Setting up libblas3:amd64 (3.12.1-2) ... 164s 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 164s Setting up fonts-dejavu-mono (2.37-8) ... 164s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 164s Setting up fonts-dejavu-core (2.37-8) ... 164s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 164s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 164s Setting up libwebp7:amd64 (1.5.0-0.1) ... 164s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 164s Setting up libthai-data (0.1.29-2build1) ... 164s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 164s Setting up libpaper2:amd64 (2.2.5-0.3) ... 164s Setting up xdg-utils (1.2.1-2ubuntu1) ... 164s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 164s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 164s Setting up libice6:amd64 (2:1.1.1-1) ... 164s Setting up liblapack3:amd64 (3.12.1-2) ... 164s 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 164s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 165s Setting up libpaper-utils (2.2.5-0.3) ... 165s Setting up libthai0:amd64 (0.1.29-2build1) ... 165s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 165s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 165s Setting up libsm6:amd64 (2:1.2.4-1) ... 165s Setting up fontconfig (2.15.0-2ubuntu1) ... 167s Regenerating fonts cache... done. 167s Setting up libxft2:amd64 (2.3.6-1build1) ... 167s Setting up libtk8.6:amd64 (8.6.16-1) ... 167s Setting up libpango-1.0-0:amd64 (1.56.2-1) ... 167s Setting up libcairo2:amd64 (1.18.2-2) ... 167s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 167s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... 167s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... 167s Setting up r-base-core (4.4.3-1) ... 167s Creating config file /etc/R/Renviron with new version 167s Setting up r-cran-bdsmatrix (1.3-7-1) ... 167s Processing triggers for install-info (7.1.1-1) ... 167s Processing triggers for libc-bin (2.41-1ubuntu2) ... 167s Processing triggers for man-db (2.13.0-1) ... 169s autopkgtest [22:05:46]: test run-unit-test: [----------------------- 169s BEGIN TEST backsolvetest.R 169s 169s R version 4.4.3 (2025-02-28) -- "Trophy Case" 169s Copyright (C) 2025 The R Foundation for Statistical Computing 169s Platform: x86_64-pc-linux-gnu 169s 169s R is free software and comes with ABSOLUTELY NO WARRANTY. 169s You are welcome to redistribute it under certain conditions. 169s Type 'license()' or 'licence()' for distribution details. 169s 169s R is a collaborative project with many contributors. 169s Type 'contributors()' for more information and 169s 'citation()' on how to cite R or R packages in publications. 169s 169s Type 'demo()' for some demos, 'help()' for on-line help, or 169s 'help.start()' for an HTML browser interface to help. 169s Type 'q()' to quit R. 169s 169s > library(bdsmatrix) 169s 169s Attaching package: 'bdsmatrix' 169s 169s The following object is masked from 'package:base': 169s 169s backsolve 169s 169s > # 169s > # A test of the backsolve function 169s > # 169s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 169s > 169s > tmat <- matrix(rep(1:5,5), 5, 5) 169s > tmat <- tmat + t(tmat) 169s > diag(tmat) <- diag(tmat) + 10 169s > 169s > gt <- gchol(tmat) 169s > g1 <- as.matrix(gt) 169s > gd <- diag(sqrt(diag(gt))) 169s > gc <- gd %*% t(g1) #usual cholesky form 169s > 169s > xmat <- cbind(1:5, 11:15) 169s > 169s > s1 <- backsolve(gt, xmat, upper=TRUE) #the default 169s > aeq(gd %*% t(g1) %*% s1, xmat) 169s [1] TRUE 169s > all.equal(s1, backsolve(gc, xmat)) 169s [1] TRUE 169s > 169s > s2 <- backsolve(gt, xmat, upper=FALSE) 169s > aeq(g1 %*% gd %*% s2, xmat) 169s [1] TRUE 169s > all.equal(backsolve(gt,xmat, upper=F), backsolve(t(gc),xmat, upper=F)) 169s [1] TRUE 169s > 169s > 169s > # Now for bdsmatrix objects 169s > tmat <- bdsmatrix(c(3,2,2,4), 169s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 169s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 169s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 169s > dimnames(tmat) <- list(NULL, letters[1:13]) 169s > smat <- as.matrix(tmat) 169s > 169s > gt <- gchol(tmat) 169s > gs <- gchol(smat) 169s > 169s > xmat <- cbind(1:13, 1:13*2 + 3) 169s > 169s > s1 <- backsolve(gt, xmat) 169s > s2 <- backsolve(gs, xmat) 169s > s3 <- backsolve(gt, xmat, upper=FALSE) 169s > s4 <- backsolve(gs, xmat, upper=FALSE) 169s > 169s > aeq(s1, s2) 169s [1] TRUE 169s > aeq(s3, s4) 169s [1] TRUE 169s > 169s > g1 <- as.matrix(gt) 169s > gd <- diag(sqrt(diag(gt))) 169s > aeq(gd %*% t(g1) %*% s1, xmat) 169s [1] TRUE 169s > aeq(g1 %*% gd %*% s3, xmat) 169s [1] TRUE 169s > 169s BEGIN TEST bdstest.R 169s 169s R version 4.4.3 (2025-02-28) -- "Trophy Case" 169s Copyright (C) 2025 The R Foundation for Statistical Computing 169s Platform: x86_64-pc-linux-gnu 169s 169s R is free software and comes with ABSOLUTELY NO WARRANTY. 169s You are welcome to redistribute it under certain conditions. 169s Type 'license()' or 'licence()' for distribution details. 169s 169s R is a collaborative project with many contributors. 169s Type 'contributors()' for more information and 169s 'citation()' on how to cite R or R packages in publications. 169s 169s Type 'demo()' for some demos, 'help()' for on-line help, or 169s 'help.start()' for an HTML browser interface to help. 169s Type 'q()' to quit R. 169s 170s > # 170s > # Test out math aspects 170s > # 170s > library(bdsmatrix) 170s 170s Attaching package: 'bdsmatrix' 170s 170s The following object is masked from 'package:base': 170s 170s backsolve 170s 170s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 170s > 170s > tmat <- bdsmatrix(c(3,2,2,4), 170s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 170s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 170s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 170s > dimnames(tmat) <- list(NULL, letters[1:13]) 170s > 170s > smat <- as.matrix(tmat) 170s > 170s > aeq(smat+2.1, as.matrix(tmat+2.1)) 170s [1] TRUE 170s > aeq(smat/2.1, as.matrix(tmat/2.1)) 170s [1] TRUE 170s > aeq(smat-2.1, as.matrix(tmat-2.1)) 170s [1] TRUE 170s > aeq(smat*2.1, as.matrix(tmat*2.1)) 170s [1] TRUE 170s > aeq(round(smat,1), as.matrix(round(tmat,1))) 170s [1] TRUE 170s > aeq(exp(smat), as.matrix(exp(tmat))) 170s [1] TRUE 170s > 170s > aeq(sum(smat), sum(tmat)) 170s [1] TRUE 170s > aeq(prod(smat), prod(tmat)) 170s [1] TRUE 170s > aeq(sum(smat+3), sum(tmat+3)) 170s [1] TRUE 170s > aeq(prod(smat+2), prod(tmat+2)) 170s [1] TRUE 170s > aeq(range(smat), range(tmat)) 170s [1] TRUE 170s > aeq(max(smat), max(tmat)) 170s [1] TRUE 170s > aeq(min(smat), min(tmat)) 170s [1] TRUE 170s > 170s > aeq(smat+1:13, tmat+1:13) 170s [1] TRUE 170s > aeq(smat+1:13, 1:13 +tmat ) 170s [1] TRUE 170s > aeq(smat+tmat, 2*smat) 170s [1] TRUE 170s > all.equal(tmat+tmat, 2*tmat) 170s [1] TRUE 170s > 170s > aeq(sort(unique(c(smat))), sort(unique(tmat))) 170s [1] TRUE 170s > 170s > # 170s > # check out the alternate input style, with full blocks 170s > # 170s > rmat <- bdsmatrix(c(3,2,2,4), 170s + c(22,1,2,1,21,3,2,3,20, 19,4,4,18, 17,5,5,16, 170s + 15,6,7,8,6,14,9,10,7,9,13,11,8,10,11,12), 170s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 170s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2), 170s + dimnames=list(NULL, letters[1:13])) 170s > all.equal(rmat, tmat) 170s [1] TRUE 170s > 170s > 170s > # Do some subscripting 170s > zz <- c(1,2,7,8,9,11) 170s > aeq(smat[zz,zz], as.matrix(tmat[zz,zz])) 170s [1] TRUE 170s > 170s > all.equal(smat[zz, 8:13], tmat[zz, 8:13]) # both are matrices 170s [1] TRUE 170s > 170s > # Diagonals 170s > aeq(diag(smat), diag(tmat)) 170s [1] TRUE 170s > zz <- diag(smat) 170s > diag(smat) <- zz*2 170s > diag(tmat) <- zz*2 170s > all.equal(smat, as.matrix(tmat)) 170s [1] TRUE 170s > 170s BEGIN TEST chtest.R 170s 170s R version 4.4.3 (2025-02-28) -- "Trophy Case" 170s Copyright (C) 2025 The R Foundation for Statistical Computing 170s Platform: x86_64-pc-linux-gnu 170s 170s R is free software and comes with ABSOLUTELY NO WARRANTY. 170s You are welcome to redistribute it under certain conditions. 170s Type 'license()' or 'licence()' for distribution details. 170s 170s R is a collaborative project with many contributors. 170s Type 'contributors()' for more information and 170s 'citation()' on how to cite R or R packages in publications. 170s 170s Type 'demo()' for some demos, 'help()' for on-line help, or 170s 'help.start()' for an HTML browser interface to help. 170s Type 'q()' to quit R. 170s 170s > # 170s > # Test out the Cholesky 170s > # 170s > library(bdsmatrix) 170s 170s Attaching package: 'bdsmatrix' 170s 170s > The following object is masked from 'package:base': 170s 170s backsolve 170s 170s aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 170s > 170s > tmat <- bdsmatrix(c(3,2,2,4), 170s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 170s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 170s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 170s > dimnames(tmat) <- list(NULL, letters[1:13]) 170s > smat <- as.matrix(tmat) 170s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 170s > 170s > aeq(diag(tmat), diag(smat)) 170s [1] TRUE 170s > zz <- seq(1,13,2) 170s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 170s [1] TRUE 170s > 170s > ch0 <- chol(smat) 170s > ch1 <- gchol(smat) 170s > ch2 <- gchol(tmat) 170s > # The gchol routines use the composition LDL', where L is lower triangular 170s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 170s > # upper trangular. 170s > # The as.matrix function returns L and the diag function returns D. 170s > # Convert and compare 170s > aeq(diag(ch1), diag(ch2)) 170s [1] TRUE 170s > temp <- as.matrix(ch2) 170s > aeq(temp, as.matrix(ch1)) 170s [1] TRUE 170s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 170s > aeq(temp3, t(ch0)) 170s [1] TRUE 170s > 170s > zz0 <- solve(smat, yy) 170s > zz1 <- solve(ch1, yy) 170s > zz2 <- solve(tmat, yy) 170s > aeq(zz1, zz2) 170s [1] TRUE 170s > aeq(zz0, zz1) 170s [1] TRUE 170s > 170s > 170s BEGIN TEST chtest2.R 170s 170s R version 4.4.3 (2025-02-28) -- "Trophy Case" 170s Copyright (C) 2025 The R Foundation for Statistical Computing 170s Platform: x86_64-pc-linux-gnu 170s 170s R is free software and comes with ABSOLUTELY NO WARRANTY. 170s You are welcome to redistribute it under certain conditions. 170s Type 'license()' or 'licence()' for distribution details. 170s 170s R is a collaborative project with many contributors. 170s Type 'contributors()' for more information and 170s 'citation()' on how to cite R or R packages in publications. 170s 170s Type 'demo()' for some demos, 'help()' for on-line help, or 170s 'help.start()' for an HTML browser interface to help. 170s Type 'q()' to quit R. 170s 170s > # 170s > # Inverse of the matrix: 170s > # 170s > library(bdsmatrix) 171s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 171s > 171s > tmat <- bdsmatrix(c(3,2,2,4), 171s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 171s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 171s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 171s 171s Attaching package: 'bdsmatrix' 171s 171s The following object is masked from 'package:base': 171s 171s backsolve 171s 171s > dimnames(tmat) <- list(NULL, letters[1:13]) 171s > 171s > smat <- as.matrix(tmat) 171s > 171s > inv1 <- solve(smat) 171s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 171s > aeq(inv1, inv2) 171s [1] TRUE 171s > 171s > inv3 <- solve(gchol(tmat)) #sparse version, not all parts will be there 171s > inherits(inv3, 'bdsmatrix') #This should be true 171s [1] TRUE 171s > aeq(inv3@blocksize, tmat@blocksize) # Should be the same shape at tmat 171s [1] TRUE 171s > inv3 <- as.matrix(inv3) # What is returned should be correct 171s > aeq(inv1[1:3,1:3], inv3[1:3, 1:3]) 171s [1] TRUE 171s > aeq(inv1[4:5,4:5], inv3[4:5, 4:5]) 171s [1] TRUE 171s > aeq(inv1[6:7,6:7], inv3[6:7, 6:7]) 171s [1] TRUE 171s > aeq(inv1[8:11,8:11], inv3[8:11, 8:11]) 171s [1] TRUE 171s > aeq(inv1[,12:13], inv3[, 12:13]) # and rmat the same too 171s [1] TRUE 171s > 171s BEGIN TEST corner.R 171s 171s R version 4.4.3 (2025-02-28) -- "Trophy Case" 171s Copyright (C) 2025 The R Foundation for Statistical Computing 171s Platform: x86_64-pc-linux-gnu 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > # 171s > # Test out the behavior of a 1x1 bds corner. 171s > # Actually, the problem that motivated this occurred whenever the 171s > # rmat portion was larger than the block diagonal portion. 171s > # 171s > library(bdsmatrix) 171s 171s Attaching package: 'bdsmatrix' 171s 171s The following object is masked from 'package:base': 171s 171s backsolve 171s 171s > test1 <- bdsmatrix(blocksize=1, blocks=33, 171s + rmat=matrix(c(17,33,7,-1, -7,7,48,-7, 171s + 1, -1, -7,4),4)) 171s > 171s > test2 <- bdsmatrix(blocksize=2, blocks=c(33,17,33), 171s + rmat=matrix(c( -7,7,48,-7, 1, -1, -7,4),4)) 171s > all.equal(as.matrix(test1), as.matrix(test2)) 171s [1] TRUE 171s > 171s > g1 <- gchol(test1) 171s > g2 <- gchol(test2) 171s > all.equal(as.matrix(g1), as.matrix(g2)) 171s [1] TRUE 171s > 171s > s1 <- solve(g1, full=T) 171s > s2 <- solve(g2, full=T) 171s > all.equal(as.matrix(s1), as.matrix(s2)) 171s [1] TRUE 171s > 171s > all.equal(solve(test1), solve(test2)) 171s [1] TRUE 171s > 171s BEGIN TEST corner2.R 171s 171s R version 4.4.3 (2025-02-28) -- "Trophy Case" 171s Copyright (C) 2025 The R Foundation for Statistical Computing 171s Platform: x86_64-pc-linux-gnu 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > # 171s > # Test out the Cholesky, special case of a null block corner 171s > # In this case there is no advantage to a bdsmatrix as it consists of only 171s > # the ordinary matrix part. This case arises in coxme with an (x1+x2 | 1) 171s > # term, however, so it is nice to have it work instead of coding lots of 171s > # if/else logic in that code base. 171s > # 171s > library(bdsmatrix) 172s 172s Attaching package: 'bdsmatrix' 172s 172s The following object is masked from 'package:base': 172s 172s backsolve 172s 172s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 172s > 172s > tmat <- bdsmatrix(c(3,2,2,4), 172s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 172s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 172s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 172s > dimnames(tmat) <- list(NULL, letters[1:13]) 172s > smat <- as.matrix(tmat) 172s > tmat <- bdsmatrix(integer(0), numeric(0), rmat=smat) 172s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 172s > 172s > aeq(diag(tmat), diag(smat)) 172s [1] TRUE 172s > zz <- seq(1,13,2) 172s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 172s [1] TRUE 172s > 172s > ch0 <- chol(smat) 172s > ch1 <- gchol(smat) 172s > ch2 <- gchol(tmat) 172s > # The gchol routines use the composition LDL', where L is lower triangular 172s > # with a diagonal of 1's, and D is diagonal. chol() uses U'U where U is 172s > # upper trangular. 172s > # The as.matrix function returns L and the diag function returns D. 172s > # Convert and compare 172s > aeq(diag(ch1), diag(ch2)) 172s [1] TRUE 172s > temp <- as.matrix(ch2) 172s > aeq(temp, as.matrix(ch1)) 172s [1] TRUE 172s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 172s > aeq(temp3, t(ch0)) 172s [1] TRUE 172s > 172s > zz0 <- solve(smat, yy) 172s > zz1 <- solve(ch1, yy) 172s > zz2 <- solve(tmat, yy) 172s > aeq(zz1, zz2) 172s [1] TRUE 172s > aeq(zz0, zz1) 172s [1] TRUE 172s > 172s > inv1 <- solve(smat) 172s > inv2 <- as.matrix(solve(tmat)) # the result is a full, non-sparse matrix 172s > aeq(inv1, inv2) 172s [1] TRUE 172s > 172s > inv3 <- solve(gchol(tmat)) 172s > aeq(inv1, as.matrix(inv3)) 172s [1] TRUE 172s > 172s > gmat <- gchol(tmat) 172s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 172s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 172s [1] TRUE 172s > aeq(g2 %*% 1:13, gmat %*% 1:13) 172s [1] TRUE 172s > temp <- matrix(runif(39), nrow=3) 172s > aeq(temp %*% g2, temp %*% gmat) 172s [1] TRUE 172s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 172s [1] TRUE 172s > 172s BEGIN TEST gtest.R 172s 172s R version 4.4.3 (2025-02-28) -- "Trophy Case" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > library(bdsmatrix) 172s 172s Attaching package: 'bdsmatrix' 172s 172s The following object is masked from 'package:base': 172s 172s backsolve 172s 172s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 172s > 172s > tmat <- bdsmatrix(c(3,2,2,4), 172s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 172s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 172s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 172s > dimnames(tmat) <- list(NULL, letters[1:13]) 172s > 172s > smat <- as.matrix(tmat) 172s > 172s > # Create a matrix that is symmetric, but not positive definite 172s > # The first one, temp, has column 6 redundant with cols 1-5 172s > temp <- smat[c(1:5, 5:10), c(1:5, 5:10)] 172s > ch1 <- gchol(temp) 172s > aeq(diag(ch1)[6], 0) # Check that it has a zero in the proper place 172s [1] TRUE 172s > ginv <- solve(ch1) # see if I get a generalized inverse 172s > aeq(temp %*% ginv %*% temp, temp) 172s [1] TRUE 172s > aeq(ginv %*% temp %*% ginv, ginv) 172s [1] TRUE 172s > 172s > # Now create one that is negative definite 172s > ch2 <- gchol(smat) 172s > temp2 <- as.matrix(ch2) 172s > temp3 <- diag(ch2) * rep(c(1, -1), length=nrow(smat)) 172s > xmat <- temp2 %*% diag(temp3) %*% t(temp2) 172s > xmat <- (xmat + t(xmat))/2 #work out round-off errors 172s > ch3 <- gchol(xmat) 172s > 172s > aeq(diag(ch3), temp3) 172s [1] TRUE 172s > aeq(as.matrix(ch3), temp2) 172s [1] TRUE 172s > 172s BEGIN TEST gtest2.R 172s 172s R version 4.4.3 (2025-02-28) -- "Trophy Case" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > library(bdsmatrix) 172s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 172s > 172s > # 172s > # Test multiplication of a vector/matrix times a gchol 172s > # 172s > tmat <- bdsmatrix(c(3,2,2,4), 172s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 172s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 172s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 172s > dimnames(tmat) <- list(NULL, letters[1:13]) 172s > 172s > gmat <- gchol(tmat) 172s > g2 <- as.matrix(gmat) %*% diag(sqrt(diag(gmat))) 172s > 172s > 172s > aeq(1:13 %*% g2, 1:13 %*% gmat) #vectors first 172s 172s Attaching package: 'bdsmatrix' 172s 172s The following object is masked from 'package:base': 172s 172s backsolve 172s 172s [1] TRUE 172s > aeq(g2 %*% 1:13, gmat %*% 1:13) 172s [1] TRUE 172s > 172s > temp <- matrix(runif(39), nrow=3) 172s > aeq(temp %*% g2, temp %*% gmat) 172s [1] TRUE 172s > aeq(g2 %*% t(temp), gmat %*% t(temp)) 172s [1] TRUE 172s > 172s BEGIN TEST matrix.R 172s 172s R version 4.4.3 (2025-02-28) -- "Trophy Case" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 173s > library(bdsmatrix) 173s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 173s > 173s > tmat <- bdsmatrix(c(3,2,2,4), 173s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 173s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 173s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 173s > dimnames(tmat) <- list(NULL, letters[1:13]) 173s > 173s > smat <- as.matrix(tmat) 173s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 173s > 173s > # matrix multiplication 173s > zz <- runif(13) 173s > aeq(zz%*% smat, zz%*% tmat) 173s 173s Attaching package: 'bdsmatrix' 173s 173s The following object is masked from 'package:base': 173s 173s backsolve 173s 173s [1] TRUE 173s > aeq(smat%*%zz, tmat%*% zz) 173s [1] TRUE 173s > 173s > xx <- matrix(1:39, ncol=3) 173s > aeq(smat %*% zz, tmat %*% zz) 173s [1] TRUE 173s > aeq(t(xx) %*% smat, t(xx) %*% tmat) 173s [1] TRUE 173s > 173s > 173s > amat <- tmat 173s > amat@offdiag <- pi 173s > bmat <- as.matrix(amat) 173s > 173s > aeq(zz%*% amat, zz%*% bmat) 173s [1] TRUE 173s > aeq(amat%*%zz, bmat%*% zz) 173s [1] TRUE 173s > 173s > 173s > # Solve the right-hand side wrt a matrix 173s > yy2 <- cbind(yy, -yy, yy+3) 173s > zz1 <- solve(smat, yy2) 173s > zz2 <- solve(tmat, yy2) 173s > aeq(zz1, zz2) 173s [1] TRUE 173s > aeq(zz2[,1], solve(tmat, yy)) 173s [1] TRUE 173s > 173s BEGIN TEST nullr.R 173s 173s R version 4.4.3 (2025-02-28) -- "Trophy Case" 173s Copyright (C) 2025 The R Foundation for Statistical Computing 173s Platform: x86_64-pc-linux-gnu 173s 173s R is free software and comes with ABSOLUTELY NO WARRANTY. 173s You are welcome to redistribute it under certain conditions. 173s Type 'license()' or 'licence()' for distribution details. 173s 173s R is a collaborative project with many contributors. 173s Type 'contributors()' for more information and 173s 'citation()' on how to cite R or R packages in publications. 173s 173s Type 'demo()' for some demos, 'help()' for on-line help, or 173s 'help.start()' for an HTML browser interface to help. 173s Type 'q()' to quit R. 173s 173s > # 173s > # Make sure things work in the simpler case of no rmat component 173s > # 173s > library(bdsmatrix) 173s 173s Attaching package: 'bdsmatrix' 173s 173s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 173s > 173s > tmat <- bdsmatrix(blocksize= c(3,2,2,4), 173s + blocks= c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 173s + 8,14,9,10,13,11,12)) 173s > dimnames(tmat) <- list(NULL, letters[1:11]) 173s > smat <- as.matrix(tmat) 173s > yy <- c(30,35,42,56,34,45,32,37,78,56,40) 173s > 173s > aeq(diag(tmat), diag(smat)) 173s [1] TRUE 173s > zz <- seq(1,11,2) 173s > aeq(as.matrix(tmat[zz,zz]), smat[zz,zz]) 173s The following object is masked from 'package:base': 173s 173s backsolve 173s 173s [1] TRUE 173s > 173s > ch0 <- chol(smat) 173s > ch1 <- gchol(smat) 173s > ch2 <- gchol(tmat) 173s > 173s > aeq(diag(ch1), diag(ch2)) 173s [1] TRUE 173s > temp <- as.matrix(ch2) 173s > aeq(temp, as.matrix(ch1)) 173s [1] TRUE 173s > temp3 <- temp %*% diag(sqrt(diag(ch2))) 173s > aeq(temp3, t(ch0)) 173s [1] TRUE 173s > 173s > zz0 <- solve(smat, yy) 173s > zz1 <- solve(ch1, yy) 173s > zz2 <- solve(tmat, yy) 173s > aeq(zz1, zz2) 173s [1] TRUE 173s > aeq(zz0, zz1) 173s [1] TRUE 173s > 173s BEGIN TEST reconcile.R 173s 173s R version 4.4.3 (2025-02-28) -- "Trophy Case" 173s Copyright (C) 2025 The R Foundation for Statistical Computing 173s Platform: x86_64-pc-linux-gnu 173s 173s R is free software and comes with ABSOLUTELY NO WARRANTY. 173s You are welcome to redistribute it under certain conditions. 173s Type 'license()' or 'licence()' for distribution details. 173s 173s R is a collaborative project with many contributors. 173s Type 'contributors()' for more information and 173s 'citation()' on how to cite R or R packages in publications. 173s 173s Type 'demo()' for some demos, 'help()' for on-line help, or 173s 'help.start()' for an HTML browser interface to help. 173s Type 'q()' to quit R. 173s 173s > # 173s > # Test cases for bdsmatrix.reconcile 173s > # 173s > library(bdsmatrix) 174s 174s Attaching package: 'bdsmatrix' 174s 174s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 174s > 174s > tmat <- bdsmatrix(c(3,2,2,4), 174s The following object is masked from 'package:base': 174s 174s backsolve 174s 174s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 174s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 174s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 174s > id <- letters[1:13] 174s > dimnames(tmat) <- list(id, id) 174s > 174s > rmat <- matrix(1:169, 13,13) 174s > rmat <- (rmat + t(rmat))/2 174s > dimnames(rmat) <- list(rev(id), rev(id)) 174s > 174s > xmat <- bdsmatrix.reconcile(list(tmat, rmat), group=id) 174s > temp <- xmat[[1]] 174s > aeq(temp@blocksize, 13) 174s [1] TRUE 174s > aeq(as.matrix(temp), as.matrix(tmat)) 174s [1] TRUE 174s > 174s > temp <- xmat[[2]] 174s > aeq(temp@blocksize, 13) 174s [1] TRUE 174s > aeq(as.matrix(temp), rmat[13:1, 13:1]) 174s [1] TRUE 174s > 174s > xmat <- bdsmatrix.reconcile(list(rmat, bdsI, tmat), group= rev(id)) 174s > temp <- xmat[[1]] 174s > aeq(as.matrix(temp), rmat) 174s [1] TRUE 174s > 174s > temp <- xmat[[2]] 174s > aeq(as.matrix(temp), diag(13)) 174s [1] TRUE 174s > 174s > temp <- xmat[[3]] 174s > aeq(as.matrix(temp), (as.matrix(tmat))[13:1,13:1]) 174s [1] TRUE 174s > 174s > # 174s > # Simplest case 174s > # 174s > xmat <- bdsmatrix.reconcile(bdsI, id) 174s > all(xmat@blocksize==1) 174s [1] TRUE 174s > aeq(as.matrix(xmat), diag(13)) 174s [1] TRUE 174s > 174s > # 174s > # The case list(tmat, tmat) will fail - can't have 2 rmats 174s > # 174s > #xmat <- bdsmatrix.reconcile(list(tmat, tmat), id) 174s > 174s > xmat <- bdsmatrix.reconcile(list(tmat, bdsI), rev(id)) 174s > temp <- xmat[[1]] 174s > aeq(as.matrix(temp), as.matrix(tmat)) 174s [1] TRUE 174s > aeq(dimnames(temp)[[1]], id) 174s [1] TRUE 174s > 174s > aeq(as.matrix(xmat[[2]]), diag(13)) 174s [1] TRUE 174s > 174s > # 174s > # Now for the hard one: 2 bdsmatrices, different orders, different 174s > # blocksize, but one contains the other 174s > # 174s > tmat <- tmat[1:11, 1:11] 174s > tord <- c(11:8, 2,1,3, 6,7,5,4) 174s > rmat <- (as.matrix(tmat))[tord, tord] 174s > rmat <- bdsmatrix(blocksize=c(4,5,2), 174s + blocks=c(rmat[1:4,1:4], rmat[5:9,5:9], rmat[10:11, 10:11]), 174s + dimnames=list(id[tord], id[tord])) 174s > 174s > aeq(as.matrix(tmat)[tord,tord], as.matrix(rmat)) 174s [1] TRUE 174s > 174s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:11]) 174s > all.equal(xmat[[2]], rmat) 174s [1] TRUE 174s > all.equal(xmat[[1]]*2, rmat) 174s [1] TRUE 174s > 174s > # Now toss out a row/col 174s > # Give it a different name, too 174s > xx <- id[tord] 174s > xx[1] <- 44 174s > dimnames(rmat) <- list(xx,xx) 174s > xmat <- bdsmatrix.reconcile(list(tmat/2, rmat), id[1:9]) 174s > all.equal(xmat[[1]]*2, xmat[[2]]) 174s [1] TRUE 174s > 174s BEGIN TEST tinv.R 174s 174s R version 4.4.3 (2025-02-28) -- "Trophy Case" 174s Copyright (C) 2025 The R Foundation for Statistical Computing 174s Platform: x86_64-pc-linux-gnu 174s 174s R is free software and comes with ABSOLUTELY NO WARRANTY. 174s You are welcome to redistribute it under certain conditions. 174s Type 'license()' or 'licence()' for distribution details. 174s 174s R is a collaborative project with many contributors. 174s Type 'contributors()' for more information and 174s 'citation()' on how to cite R or R packages in publications. 174s 174s Type 'demo()' for some demos, 'help()' for on-line help, or 174s 'help.start()' for an HTML browser interface to help. 174s Type 'q()' to quit R. 174s 174s > library(bdsmatrix) 174s 174s Attaching package: 'bdsmatrix' 174s 174s The following object is masked from 'package:base': 174s 174s backsolve 174s 174s > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y)) 174s > 174s > tmat <- bdsmatrix(c(3,2,2,4), 174s + c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), 174s + matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, 174s + 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) 174s > dimnames(tmat) <- list(NULL, letters[1:13]) 174s > 174s > smat <- as.matrix(tmat) 174s > yy <- c(30,35,42,56,34,45,32,37,78,56,40,52,39) 174s > # look at inverses more closely 174s > # (I needed this when some of the other tests weren't being passed, 174s > # to figure out where in the decomposition/inversion/multiply process 174s > # the flaw was). 174s > 174s > ch1 <- gchol(smat) 174s > ch2 <- gchol(tmat) 174s > 174s > inv1 <- solve(as.matrix(ch1)) 174s > inv2 <- solve(ch2,full=F) #inverse of the cholesky, not of tmat 174s > aeq(inv1, as.matrix(inv2)) 174s [1] TRUE 174s > 174s > # Full matrix tests 174s > inv3 <- solve(smat) 174s > inv4 <- solve(tmat) 174s > inv5 <- solve(gchol(smat), full=T) 174s > aeq(inv3, inv4) 174s [1] TRUE 174s > aeq(inv3, inv5) 174s [1] TRUE 174s > 174s > # The following test is false by design: when called with a bdsmatrix 174s > # object that has an rmat portion, the true inverse is dense. But 174s > # coxme only needs the trace for one calcluation; solve(gchol(tmat)) 174s > # cheats and only returns the block diagonal portion of the inverse. 174s > #inv6 <- solve(gchol(tmat), full=T) 174s > #aeq(inv3, inv6) 174s > 174s > # 174s > # Now test the solution to a partial solve 174s > # We want to be able to transform a matrix to uncorrelated form 174s > # If tmat= LDL', and A is general, I want (D^{-1/2}) L^{-1} A 174s > # 174s > amat <- matrix(runif(5*nrow(tmat)), nrow=nrow(tmat)) 174s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), amat) 174s > xx2 <- solve(ch2, amat, full=F) 174s > aeq(xx1, xx2) 174s [1] TRUE 174s > 174s > xx1 <- diag(1/sqrt(diag(ch1))) %*% solve(as.matrix(ch1), yy) 174s > xx2 <- solve(ch2, yy, full=F) 174s > aeq(xx1, xx2) 174s [1] TRUE 174s > 174s autopkgtest [22:05:51]: test run-unit-test: -----------------------] 175s run-unit-test PASS 175s autopkgtest [22:05:52]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 175s autopkgtest [22:05:52]: test pkg-r-autopkgtest: preparing testbed 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 176s The following NEW packages will be installed: 176s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 176s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 176s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 176s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 176s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 176s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 176s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 176s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 176s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 176s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 176s r-base-dev zlib1g-dev 176s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 103 MB of archives. 176s After this operation, 363 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 176s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 176s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 176s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 176s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 176s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 176s Get:7 http://ftpmaster.internal/ubuntu plucky/main 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Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 181s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 181s Setting up libncurses-dev:amd64 (6.5+20250216-2) ... 181s Setting up libreadline-dev:amd64 (8.2-6) ... 181s Setting up libpcre2-16-0:amd64 (10.45-1) ... 181s Setting up libpcre2-32-0:amd64 (10.45-1) ... 181s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 181s Setting up libpkgconf3:amd64 (1.8.1-4) ... 181s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ... 181s Setting up libmpc3:amd64 (1.3.1-1build2) ... 181s Setting up icu-devtools (76.1-1ubuntu2) ... 181s Setting up pkgconf-bin (1.8.1-4) ... 181s Setting up liblzma-dev:amd64 (5.6.4-1) ... 181s Setting up libubsan1:amd64 (15-20250222-0ubuntu1) ... 181s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 181s Setting up libpcre2-posix3:amd64 (10.45-1) ... 181s Setting up libhwasan0:amd64 (15-20250222-0ubuntu1) ... 181s Setting up libasan8:amd64 (15-20250222-0ubuntu1) ... 181s Setting up libtsan2:amd64 (15-20250222-0ubuntu1) ... 181s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 181s Setting up libisl23:amd64 (0.27-1) ... 181s Setting up libdeflate-dev:amd64 (1.23-1) ... 181s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 181s Setting up libcc1-0:amd64 (15-20250222-0ubuntu1) ... 181s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ... 181s Setting up libblas-dev:amd64 (3.12.1-2) ... 181s 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 181s Setting up dctrl-tools (2.24-3build3) ... 181s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ... 181s Setting up libbz2-dev:amd64 (1.0.8-6) ... 181s Setting up libpcre2-dev:amd64 (10.45-1) ... 181s Setting up libpng-dev:amd64 (1.6.47-1) ... 181s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 181s Setting up pkgconf:amd64 (1.8.1-4) ... 181s Setting up liblapack-dev:amd64 (3.12.1-2) ... 181s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 181s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 181s Setting up cpp-14 (14.2.0-17ubuntu3) ... 181s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 181s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 181s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 181s Setting up libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 181s Setting up cpp (4:14.2.0-1ubuntu1) ... 181s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 181s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 181s Setting up gcc-14 (14.2.0-17ubuntu3) ... 181s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 181s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 181s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 181s Setting up g++-14 (14.2.0-17ubuntu3) ... 181s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 181s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 181s Setting up gcc (4:14.2.0-1ubuntu1) ... 181s Setting up g++ (4:14.2.0-1ubuntu1) ... 181s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 181s Setting up build-essential (12.10ubuntu1) ... 181s Setting up gfortran (4:14.2.0-1ubuntu1) ... 181s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 181s 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 181s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 181s 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 181s Setting up r-base-dev (4.4.3-1) ... 181s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 181s Processing triggers for libc-bin (2.41-1ubuntu2) ... 181s Processing triggers for man-db (2.13.0-1) ... 182s Processing triggers for install-info (7.1.1-1) ... 183s autopkgtest [22:06:00]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 183s autopkgtest [22:06:00]: test pkg-r-autopkgtest: [----------------------- 183s Test: Try to load the R library bdsmatrix 183s 183s R version 4.4.3 (2025-02-28) -- "Trophy Case" 183s Copyright (C) 2025 The R Foundation for Statistical Computing 183s Platform: x86_64-pc-linux-gnu 183s 183s R is free software and comes with ABSOLUTELY NO WARRANTY. 183s You are welcome to redistribute it under certain conditions. 183s Type 'license()' or 'licence()' for distribution details. 183s 183s R is a collaborative project with many contributors. 183s Type 'contributors()' for more information and 183s 'citation()' on how to cite R or R packages in publications. 183s 183s Type 'demo()' for some demos, 'help()' for on-line help, or 183s 'help.start()' for an HTML browser interface to help. 183s Type 'q()' to quit R. 183s 183s > library('bdsmatrix') 183s 183s Attaching package: ‘bdsmatrix’ 183s 183s The following object is masked from ‘package:base’: 183s 183s backsolve 183s 183s > 183s > 183s Other tests are currently unsupported! 183s They will be progressively added. 184s autopkgtest [22:06:01]: test pkg-r-autopkgtest: -----------------------] 184s pkg-r-autopkgtest PASS 184s autopkgtest [22:06:01]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 184s autopkgtest [22:06:01]: @@@@@@@@@@@@@@@@@@@@ summary 184s run-unit-test PASS 184s pkg-r-autopkgtest PASS 200s nova [W] Skipping flock for amd64 200s Creating nova instance adt-plucky-amd64-r-cran-bdsmatrix-20250315-220256-juju-7f2275-prod-proposed-migration-environment-15-99d624df-d29f-4fef-8b36-379d28a65073 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 200s nova [W] Timed out waiting for 961ce1ad-3512-48b8-a9a7-37a87ef085c8 to get deleted.