0s autopkgtest [16:21:52]: starting date: 2024-03-10 0s autopkgtest [16:21:52]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [16:21:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9ufl0oug/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-cran-rcpparmadillo --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-rcpparmadillo/0.12.8.1.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-4.secgroup --name adt-noble-ppc64el-r-cran-etm-20240310-162152-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 154s autopkgtest [16:24:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 155s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [435 kB] 155s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2613 kB] 155s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 155s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 155s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [579 kB] 155s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 155s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 155s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 155s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [2912 kB] 155s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 155s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [38.4 kB] 155s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 158s Fetched 6750 kB in 2s (3524 kB/s) 158s Reading package lists... 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Calculating upgrade... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s sh: Attempting to set up Debian/Ubuntu apt sources automatically 165s sh: Distribution appears to be Ubuntu 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 169s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1eatmydata is already the newest version (131-1). 169s dbus is already the newest version (1.14.10-4ubuntu1). 169s dbus set to manually installed. 169s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s 169s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 169s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 170s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s rng-tools-debian is already the newest version (2.4). 170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 170s haveged is already the newest version (1.9.14-1ubuntu1). 170s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s The following packages will be REMOVED: 171s cloud-init* python3-configobj* python3-debconf* 171s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 171s After this operation, 3248 kB disk space will be freed. 171s (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 ... 70101 files and directories currently installed.) 171s Removing cloud-init (24.1-0ubuntu1) ... 172s Removing python3-configobj (5.0.8-3) ... 172s Removing python3-debconf (1.5.86) ... 172s Processing triggers for man-db (2.12.0-3) ... 173s (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 ... 69712 files and directories currently installed.) 173s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 173s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 173s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s linux-generic is already the newest version (6.8.0-11.11+1). 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 175s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 175s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 175s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 175s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 179s Reading package lists... 179s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 179s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s Calculating upgrade... 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s autopkgtest [16:24:52]: rebooting testbed after setup commands that affected boot 219s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 225s autopkgtest [16:25:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 225s autopkgtest [16:25:37]: testbed dpkg architecture: ppc64el 226s autopkgtest [16:25:38]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 227s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 227s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 227s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 228s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 228s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 228s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 228s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 228s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 228s gpgv: issuer "tille@debian.org" 228s gpgv: Can't check signature: No public key 228s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 228s autopkgtest [16:25:40]: testing package r-cran-etm version 1.1.1-1 228s autopkgtest [16:25:40]: build not needed 230s autopkgtest [16:25:42]: test run-unit-test: preparing testbed 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 234s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 234s Starting 2 pkgProblemResolver with broken count: 0 234s Done 234s Done 234s Starting pkgProblemResolver with broken count: 0 234s Starting 2 pkgProblemResolver with broken count: 0 234s Done 235s The following additional packages will be installed: 235s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 235s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 235s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 235s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 235s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 235s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 235s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 235s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 235s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 235s r-cran-survival unzip x11-common xdg-utils zip 235s Suggested packages: 235s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 235s r-cran-rmysql r-cran-ggplot2 r-cran-geepack r-cran-getopt r-cran-rodbc 235s r-cran-foreign r-cran-inline 235s Recommended packages: 235s r-recommended r-base-dev r-doc-html r-cran-bit64 r-cran-bit r-cran-curl 235s r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-zoo r-cran-yaml 235s r-cran-knitr r-cran-rmarkdown libfile-mimeinfo-perl libnet-dbus-perl 235s libx11-protocol-perl x11-utils x11-xserver-utils 235s The following NEW packages will be installed: 235s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 235s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 235s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 235s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 235s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 235s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 235s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 235s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 235s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 235s r-cran-survival unzip x11-common xdg-utils zip 235s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 235s 1 not fully installed or removed. 235s Need to get 57.5 MB of archives. 235s After this operation, 126 MB of additional disk space will be used. 235s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 235s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu3 [192 kB] 235s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 235s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 235s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 235s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 236s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 236s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 236s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB] 236s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB] 236s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 236s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 236s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 236s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 236s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 237s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 237s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 237s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 237s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 237s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 238s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.15.0-1ubuntu1 [192 kB] 238s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 238s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 238s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 238s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 238s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 238s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 238s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 238s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 238s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 238s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 238s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 238s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 238s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 238s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 238s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 238s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 238s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 238s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 238s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.13-2 [916 kB] 238s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 238s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 238s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 238s Get:44 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 240s Get:45 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-lattice ppc64el 0.22-5-1 [1343 kB] 240s Get:46 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-matrix ppc64el 1.6-5-1 [4057 kB] 241s Get:47 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-survival ppc64el 3.5-8-1 [6160 kB] 241s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-data.table ppc64el 1.14.10+dfsg-1 [1909 kB] 241s Get:49 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-littler ppc64el 0.3.19-1 [95.1 kB] 241s Get:50 http://ftpmaster.internal/ubuntu noble/universe ppc64el littler all 0.3.19-1 [2472 B] 241s Get:51 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 241s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rcpp ppc64el 1.0.12-1 [1989 kB] 241s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el r-cran-rcpparmadillo ppc64el 0.12.8.1.0-1 [875 kB] 241s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-etm ppc64el 1.1.1-1 [483 kB] 241s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-dbi all 1.2.2-1 [823 kB] 241s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mitools all 2.4-2build1 [265 kB] 241s Get:57 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-kmi all 0.5.5-2build1 [78.3 kB] 242s Preconfiguring packages ... 242s Fetched 57.5 MB in 7s (8362 kB/s) 242s Selecting previously unselected package zip. 242s (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 ... 69657 files and directories currently installed.) 242s Preparing to unpack .../00-zip_3.0-13_ppc64el.deb ... 242s Unpacking zip (3.0-13) ... 242s Selecting previously unselected package unzip. 242s Preparing to unpack .../01-unzip_6.0-28ubuntu3_ppc64el.deb ... 242s Unpacking unzip (6.0-28ubuntu3) ... 242s Selecting previously unselected package libpaper1:ppc64el. 242s Preparing to unpack .../02-libpaper1_1.1.29_ppc64el.deb ... 242s Unpacking libpaper1:ppc64el (1.1.29) ... 242s Selecting previously unselected package libpaper-utils. 242s Preparing to unpack .../03-libpaper-utils_1.1.29_ppc64el.deb ... 242s Unpacking libpaper-utils (1.1.29) ... 242s Selecting previously unselected package xdg-utils. 242s Preparing to unpack .../04-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 242s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 242s Selecting previously unselected package libblas3:ppc64el. 242s Preparing to unpack .../05-libblas3_3.12.0-3_ppc64el.deb ... 242s Unpacking libblas3:ppc64el (3.12.0-3) ... 242s Selecting previously unselected package fonts-dejavu-mono. 242s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 242s Unpacking fonts-dejavu-mono (2.37-8) ... 242s Selecting previously unselected package fonts-dejavu-core. 242s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 242s Unpacking fonts-dejavu-core (2.37-8) ... 242s Selecting previously unselected package fontconfig-config. 242s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ... 242s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 242s Selecting previously unselected package libfontconfig1:ppc64el. 242s Preparing to unpack .../09-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ... 243s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ... 243s Selecting previously unselected package libpixman-1-0:ppc64el. 243s Preparing to unpack .../10-libpixman-1-0_0.42.2-1_ppc64el.deb ... 243s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 243s Selecting previously unselected package libxcb-render0:ppc64el. 243s Preparing to unpack .../11-libxcb-render0_1.15-1_ppc64el.deb ... 243s Unpacking libxcb-render0:ppc64el (1.15-1) ... 243s Selecting previously unselected package libxcb-shm0:ppc64el. 243s Preparing to unpack .../12-libxcb-shm0_1.15-1_ppc64el.deb ... 243s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 243s Selecting previously unselected package libxrender1:ppc64el. 243s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 243s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 243s Selecting previously unselected package libcairo2:ppc64el. 243s Preparing to unpack .../14-libcairo2_1.18.0-1_ppc64el.deb ... 243s Unpacking libcairo2:ppc64el (1.18.0-1) ... 243s Selecting previously unselected package libgomp1:ppc64el. 243s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 243s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 243s Selecting previously unselected package libjpeg-turbo8:ppc64el. 243s Preparing to unpack .../16-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 243s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 243s Selecting previously unselected package libjpeg8:ppc64el. 243s Preparing to unpack .../17-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 243s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 243s Selecting previously unselected package libgfortran5:ppc64el. 243s Preparing to unpack .../18-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 243s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 243s Selecting previously unselected package liblapack3:ppc64el. 243s Preparing to unpack .../19-liblapack3_3.12.0-3_ppc64el.deb ... 243s Unpacking liblapack3:ppc64el (3.12.0-3) ... 243s Selecting previously unselected package fontconfig. 243s Preparing to unpack .../20-fontconfig_2.15.0-1ubuntu1_ppc64el.deb ... 243s Unpacking fontconfig (2.15.0-1ubuntu1) ... 243s Selecting previously unselected package libgraphite2-3:ppc64el. 243s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_ppc64el.deb ... 243s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 243s Selecting previously unselected package libharfbuzz0b:ppc64el. 243s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 243s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 243s Selecting previously unselected package libthai-data. 243s Preparing to unpack .../23-libthai-data_0.1.29-2_all.deb ... 243s Unpacking libthai-data (0.1.29-2) ... 243s Selecting previously unselected package libdatrie1:ppc64el. 243s Preparing to unpack .../24-libdatrie1_0.2.13-3_ppc64el.deb ... 243s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 243s Selecting previously unselected package libthai0:ppc64el. 243s Preparing to unpack .../25-libthai0_0.1.29-2_ppc64el.deb ... 243s Unpacking libthai0:ppc64el (0.1.29-2) ... 243s Selecting previously unselected package libpango-1.0-0:ppc64el. 243s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 243s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 243s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 243s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 243s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 243s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 243s Preparing to unpack .../28-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 243s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 243s Selecting previously unselected package libtcl8.6:ppc64el. 243s Preparing to unpack .../29-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 243s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 243s Selecting previously unselected package libdeflate0:ppc64el. 243s Preparing to unpack .../30-libdeflate0_1.19-1_ppc64el.deb ... 243s Unpacking libdeflate0:ppc64el (1.19-1) ... 243s Selecting previously unselected package libjbig0:ppc64el. 243s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 243s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 243s Selecting previously unselected package liblerc4:ppc64el. 243s Preparing to unpack .../32-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 243s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 243s Selecting previously unselected package libsharpyuv0:ppc64el. 243s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 243s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 243s Selecting previously unselected package libwebp7:ppc64el. 243s Preparing to unpack .../34-libwebp7_1.3.2-0.4_ppc64el.deb ... 243s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 243s Selecting previously unselected package libtiff6:ppc64el. 243s Preparing to unpack .../35-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 243s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 243s Selecting previously unselected package libxft2:ppc64el. 243s Preparing to unpack .../36-libxft2_2.3.6-1_ppc64el.deb ... 243s Unpacking libxft2:ppc64el (2.3.6-1) ... 243s Selecting previously unselected package x11-common. 243s Preparing to unpack .../37-x11-common_1%3a7.7+23ubuntu2_all.deb ... 243s Unpacking x11-common (1:7.7+23ubuntu2) ... 243s Selecting previously unselected package libxss1:ppc64el. 243s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 243s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 243s Selecting previously unselected package libtk8.6:ppc64el. 243s Preparing to unpack .../39-libtk8.6_8.6.13-2_ppc64el.deb ... 243s Unpacking libtk8.6:ppc64el (8.6.13-2) ... 243s Selecting previously unselected package libice6:ppc64el. 243s Preparing to unpack .../40-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 243s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 243s Selecting previously unselected package libsm6:ppc64el. 243s Preparing to unpack .../41-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 243s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 243s Selecting previously unselected package libxt6:ppc64el. 243s Preparing to unpack .../42-libxt6_1%3a1.2.1-1.1_ppc64el.deb ... 243s Unpacking libxt6:ppc64el (1:1.2.1-1.1) ... 243s Selecting previously unselected package r-base-core. 243s Preparing to unpack .../43-r-base-core_4.3.2-1build1_ppc64el.deb ... 243s Unpacking r-base-core (4.3.2-1build1) ... 244s Selecting previously unselected package r-cran-lattice. 244s Preparing to unpack .../44-r-cran-lattice_0.22-5-1_ppc64el.deb ... 244s Unpacking r-cran-lattice (0.22-5-1) ... 244s Selecting previously unselected package r-cran-matrix. 244s Preparing to unpack .../45-r-cran-matrix_1.6-5-1_ppc64el.deb ... 244s Unpacking r-cran-matrix (1.6-5-1) ... 244s Selecting previously unselected package r-cran-survival. 244s Preparing to unpack .../46-r-cran-survival_3.5-8-1_ppc64el.deb ... 244s Unpacking r-cran-survival (3.5-8-1) ... 244s Selecting previously unselected package r-cran-data.table. 244s Preparing to unpack .../47-r-cran-data.table_1.14.10+dfsg-1_ppc64el.deb ... 244s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 244s Selecting previously unselected package r-cran-littler. 244s Preparing to unpack .../48-r-cran-littler_0.3.19-1_ppc64el.deb ... 244s Unpacking r-cran-littler (0.3.19-1) ... 244s Selecting previously unselected package littler. 244s Preparing to unpack .../49-littler_0.3.19-1_all.deb ... 244s Unpacking littler (0.3.19-1) ... 244s Selecting previously unselected package r-cran-pkgkitten. 244s Preparing to unpack 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(0) ... 254s autopkgtest [16:26:06]: test run-unit-test: [----------------------- 254s BEGIN TEST test.etmCIF.R 254s 254s R version 4.3.2 (2023-10-31) -- "Eye Holes" 254s Copyright (C) 2023 The R Foundation for Statistical Computing 254s Platform: powerpc64le-unknown-linux-gnu (64-bit) 254s 254s R is free software and comes with ABSOLUTELY NO WARRANTY. 254s You are welcome to redistribute it under certain conditions. 254s Type 'license()' or 'licence()' for distribution details. 254s 254s R is a collaborative project with many contributors. 254s Type 'contributors()' for more information and 254s 'citation()' on how to cite R or R packages in publications. 254s 254s Type 'demo()' for some demos, 'help()' for on-line help, or 254s 'help.start()' for an HTML browser interface to help. 254s Type 'q()' to quit R. 254s 255s > ### test file for etmCIF. 255s > ### Really simple tests and comparison with etm 255s > 255s > old <- options(digits = 5) 255s > 255s > require(etm) 255s Loading required package: etm 256s > 256s > if (!require(survival, quietly = TRUE)) { 256s + print("The following tests require the 'survival' package") 256s + } else { 256s + 256s + data(abortion) 256s + 256s + from <- rep(0, nrow(abortion)) 256s + to <- abortion$cause 256s + entry <- abortion$entry 256s + exit <- abortion$exit 256s + id <- 1:nrow(abortion) 256s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 256s + 256s + ## Computation of the CIFs with etm 256s + tra <- matrix(FALSE, 4, 4) 256s + tra[1, 2:4] <- TRUE 256s + 256s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 256s + tra, NULL, 0) 256s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 256s + tra, NULL, 0) 256s + 256s + 256s + ## Computation of the CIFs with etmCIF 256s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 256s + etype = cause, failcode = 3) 256s + 256s + ### let's do some comparisons :-) 256s + 256s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 256s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 256s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 256s + 256s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 256s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 256s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 256s + 256s + 256s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 256s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 256s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 256s + 256s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 256s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 256s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 256s + 256s + 256s + netm 256s + 256s + ## test on the summary 256s + snetm <- summary(netm) 256s + 256s + snetm 256s + 256s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 256s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 256s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 256s + 256s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 256s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 256s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 256s + 256s + scif.control <- summary(cif.control, ci.fun = "cloglog") 256s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 256s + 256s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 256s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 256s + 256s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 256s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 256s + } 256s [1] TRUE 256s > 256s > ### test with factors in the input 256s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 256s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 256s > 256s > abortion$status <- factor(abortion$status) 256s > 256s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 256s + etype = status, failcode = "spontaneous abortion") 256s > 256s > 256s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 256s [1] TRUE 256s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 256s [1] TRUE 256s > 256s > netm.factor 256s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 256s data = abortion, etype = status, failcode = "spontaneous abortion") 256s 256s Covariate: group 256s levels: 0 1 256s 256s 256s group = 0 256s time P se(P) n.event 256s CIF ETOP 43 0.040159 0.0092578 20 256s CIF life birth 43 0.799059 0.0221865 924 256s CIF spontaneous abortion 43 0.160781 0.0213261 69 256s 256s group = 1 256s time P se(P) n.event 256s CIF ETOP 42 0.28511 0.042493 38 256s CIF life birth 42 0.35257 0.042139 92 256s CIF spontaneous abortion 42 0.36232 0.049473 43 256s > 256s > summary(netm.factor) 256s 256s group=0 256s 256s CIF ETOP 256s P time var lower upper n.risk n.event 256s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 256s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 256s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 256s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 256s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 256s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 256s 256s CIF life birth 256s P time var lower upper n.risk n.event 256s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 256s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 256s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 256s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 256s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 256s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 256s 256s CIF spontaneous abortion 256s P time var lower upper n.risk n.event 256s 0.034188 6 0.00028222 0.01297 0.088523 117 4 256s 0.150468 13 0.00045513 0.11360 0.197901 645 1 256s 0.159904 26 0.00045498 0.12274 0.206925 846 1 256s 0.160781 36 0.00045480 0.12360 0.207757 876 1 256s 0.160781 40 0.00045480 0.12360 0.207757 554 0 256s 0.160781 43 0.00045480 0.12360 0.207757 6 0 256s 256s 256s group=1 256s 256s CIF ETOP 256s P time var lower upper n.risk n.event 256s 0.00000 6 0.0000000 0.00000 0.00000 35 0 256s 0.26048 13 0.0017854 0.18795 0.35425 90 0 256s 0.28115 21 0.0018028 0.20742 0.37423 93 1 256s 0.28511 34 0.0018057 0.21116 0.37806 89 0 256s 0.28511 39 0.0018057 0.21116 0.37806 59 0 256s 0.28511 42 0.0018057 0.21116 0.37806 6 0 256s 256s CIF life birth 256s P time var lower upper n.risk n.event 256s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 256s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 256s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 256s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 256s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 256s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 256s 256s CIF spontaneous abortion 256s P time var lower upper n.risk n.event 256s 0.057143 6 0.0015394 0.014605 0.20968 35 2 256s 0.333246 13 0.0025280 0.245337 0.44216 90 4 256s 0.350702 21 0.0024827 0.262769 0.45762 93 0 256s 0.358492 34 0.0024593 0.270627 0.46448 89 0 256s 0.358492 39 0.0024593 0.270627 0.46448 59 0 256s 0.362323 42 0.0024476 0.274499 0.46785 6 0 256s 256s > 256s > ### test with group as a character vector 256s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 256s > abortion$ttt <- factor(abortion$ttt) 256s > 256s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 256s + etype = status, failcode = "spontaneous abortion") 256s > 256s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 256s [1] TRUE 256s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 256s [1] TRUE 256s > 256s > netm.ttt 256s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 256s etype = status, failcode = "spontaneous abortion") 256s 256s Covariate: ttt 256s levels: control exposed 256s 256s 256s ttt = control 256s time P se(P) n.event 256s CIF ETOP 43 0.040159 0.0092578 20 256s CIF life birth 43 0.799059 0.0221865 924 256s CIF spontaneous abortion 43 0.160781 0.0213261 69 256s 256s ttt = exposed 256s time P se(P) n.event 256s CIF ETOP 42 0.28511 0.042493 38 256s CIF life birth 42 0.35257 0.042139 92 256s CIF spontaneous abortion 42 0.36232 0.049473 43 256s > 256s > summary(netm.ttt) 256s 256s ttt=control 256s 256s CIF ETOP 256s P time var lower upper n.risk n.event 256s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 256s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 256s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 256s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 256s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 256s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 256s 256s CIF life birth 256s P time var lower upper n.risk n.event 256s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 256s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 256s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 256s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 256s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 256s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 256s 256s CIF spontaneous abortion 256s P time var lower upper n.risk n.event 256s 0.034188 6 0.00028222 0.01297 0.088523 117 4 256s 0.150468 13 0.00045513 0.11360 0.197901 645 1 256s 0.159904 26 0.00045498 0.12274 0.206925 846 1 256s 0.160781 36 0.00045480 0.12360 0.207757 876 1 256s 0.160781 40 0.00045480 0.12360 0.207757 554 0 256s 0.160781 43 0.00045480 0.12360 0.207757 6 0 256s 256s 256s ttt=exposed 256s 256s CIF ETOP 256s P time var lower upper n.risk n.event 256s 0.00000 6 0.0000000 0.00000 0.00000 35 0 256s 0.26048 13 0.0017854 0.18795 0.35425 90 0 256s 0.28115 21 0.0018028 0.20742 0.37423 93 1 256s 0.28511 34 0.0018057 0.21116 0.37806 89 0 256s 0.28511 39 0.0018057 0.21116 0.37806 59 0 256s 0.28511 42 0.0018057 0.21116 0.37806 6 0 256s 256s CIF life birth 256s P time var lower upper n.risk n.event 256s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 256s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 256s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 256s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 256s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 256s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 256s 256s CIF spontaneous abortion 256s P time var lower upper n.risk n.event 256s 0.057143 6 0.0015394 0.014605 0.20968 35 2 256s 0.333246 13 0.0025280 0.245337 0.44216 90 4 256s 0.350702 21 0.0024827 0.262769 0.45762 93 0 256s 0.358492 34 0.0024593 0.270627 0.46448 89 0 256s 0.358492 39 0.0024593 0.270627 0.46448 59 0 256s 0.362323 42 0.0024476 0.274499 0.46785 6 0 256s 256s > 256s > 256s > ### A couple of comparisons with simulated data 256s > set.seed(1313) 256s > time <- rexp(100) 256s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 256s > from <- rep(11, 100) 256s > id <- 1:100 256s > cov <- rbinom(100, 1, 0.5) 256s > 256s > dat.s <- data.frame(id, time, from, to, cov) 256s > 256s > traa <- matrix(FALSE, 3, 3) 256s > traa[1, 2:3] <- TRUE 256s > 256s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 256s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 256s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 256s > 256s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 256s > 256s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 256s > 256s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 256s [1] TRUE 256s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 256s [1] TRUE 256s > 256s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 256s [1] TRUE 256s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 256s [1] TRUE 256s > 256s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 256s [1] TRUE 256s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 256s [1] TRUE 256s > 256s > test 256s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 256s 256s time P se(P) n.event 256s CIF 1 4.9088 0.809108 0.079680 45 256s CIF 2 4.9088 0.096618 0.032905 8 256s > 256s > test.c 256s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 256s 256s Covariate: cov 256s levels: 0 1 256s 256s 256s cov = 0 256s time P se(P) n.event 256s CIF 1 2.1708 0.70246 0.105797 19 256s CIF 2 2.1708 0.11144 0.053384 4 256s 256s cov = 1 256s time P se(P) n.event 256s CIF 1 4.9088 0.80787 0.094051 26 256s CIF 2 4.9088 0.08436 0.040769 4 256s > 256s > summary(test) 256s 256s 256s 256s CIF 1 256s P time var lower upper n.risk n.event 256s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 256s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 256s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 256s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 256s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 256s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 256s 256s CIF 2 256s P time var lower upper n.risk n.event 256s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 256s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 256s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 256s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 256s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 256s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 256s 256s > summary(test.c) 256s 256s cov=0 256s 256s CIF 1 256s P time var lower upper n.risk n.event 256s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 256s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 256s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 256s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 256s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 256s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 256s 256s CIF 2 256s P time var lower upper n.risk n.event 256s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 256s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 256s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 256s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 256s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 256s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 256s 256s 256s cov=1 256s 256s CIF 1 256s P time var lower upper n.risk n.event 256s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 256s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 256s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 256s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 256s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 256s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 256s 256s CIF 2 256s P time var lower upper n.risk n.event 256s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 256s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 256s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 256s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 256s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 256s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 256s 256s > 256s > options(old) 256s > 256s BEGIN TEST tests.etm.R 256s 256s R version 4.3.2 (2023-10-31) -- "Eye Holes" 256s Copyright (C) 2023 The R Foundation for Statistical Computing 256s Platform: powerpc64le-unknown-linux-gnu (64-bit) 256s 256s R is free software and comes with ABSOLUTELY NO WARRANTY. 256s You are welcome to redistribute it under certain conditions. 256s Type 'license()' or 'licence()' for distribution details. 256s 256s R is a collaborative project with many contributors. 256s Type 'contributors()' for more information and 256s 'citation()' on how to cite R or R packages in publications. 256s 256s Type 'demo()' for some demos, 'help()' for on-line help, or 256s 'help.start()' for an HTML browser interface to help. 256s Type 'q()' to quit R. 256s 256s > require(etm) 256s Loading required package: etm 258s > 258s > ## Print with a bit less precision to avoid lots of notes in the comparison 258s > old <- options(digits = 4) 258s > 258s > ### Simple test 258s > 258s > time <- id <- 1:10 258s > from <- rep(0, 10) 258s > to <- rep(1, 10) 258s > 258s > data1 <- data.frame(id, from, to, time) 258s > tra1 <- matrix(FALSE, 2, 2) 258s > tra1[1, 2] <- TRUE 258s > 258s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 258s > 258s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 258s [1] TRUE 258s > 258s > etm1$cov["0 0", "0 0", ] 258s 1 2 3 4 5 6 7 8 9 10 258s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 258s > 258s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 258s [1] TRUE 258s > 258s > ### A simple test from AHR's author, where the first time is censored 258s > if (!require(survival)) { 258s + stop("This test requires the survival package") 258s + } 258s > 258s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 258s > 258s > tra <- matrix(FALSE, nrow=2, ncol=2) 258s > tra[1, 2] <- TRUE 258s > 258s > data$to[1] <- "cens" 258s > data$status[1] <- FALSE 258s > 258s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 258s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 258s > 258s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 258s [1] TRUE 258s > 258s > data$to[2] <- "cens" 258s > data$status[2] <- FALSE 258s > 258s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 258s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 258s Loading required package: survival 258s > 258s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 258s [1] TRUE 258s > 258s > ### a bit more complicated 258s > 258s > time <- id <- 1:10 258s > from <- rep(0, 10) 258s > to <- rep(c(1, 2), 5) 258s > data2 <- data.frame(id, from, to, time) 258s > 258s > tra2 <- matrix(FALSE, 3, 3) 258s > tra2[1, 2:3] <- TRUE 258s > 258s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 258s > 258s > aa <- table(time, to) 258s > 258s > cif1 <- cumsum(aa[, 1] / 10) 258s > cif2 <- cumsum(aa[, 2] / 10) 258s > surv <- cumprod((10:1 - 1) / (10:1)) 258s > 258s > all.equal(trprob(etm2, "0 1"), cif1) 258s [1] TRUE 258s > all.equal(trprob(etm2, "0 2"), cif2) 258s [1] TRUE 258s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 258s [1] TRUE 258s > 258s > ## a test on id 258s > data2$id <- letters[1:10] 258s > 258s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 258s > 258s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 258s [1] TRUE 258s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 258s [1] TRUE 258s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 258s [1] TRUE 258s > 258s > 258s > ### Test on sir.cont 258s > 258s > data(sir.cont) 258s > 258s > ## Modification for patients entering and leaving a state 258s > ## at the same date 258s > ## Change on ventilation status is considered 258s > ## to happen before end of hospital stay 258s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 258s > for (i in 2:nrow(sir.cont)) { 258s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 258s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 258s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 258s + } 258s + } 258s + } 258s > 258s > ### Computation of the transition probabilities 258s > ## Possible transitions. 258s > tra <- matrix(ncol=3,nrow=3,FALSE) 258s > tra[1, 2:3] <- TRUE 258s > tra[2, c(1, 3)] <- TRUE 258s > 258s > ## etm 258s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 258s > 258s > prob.sir 258s Multistate model with 2 transient state(s) 258s and 1 absorbing state(s) 258s 258s Possible transitions: 258s from to 258s 0 1 258s 0 2 258s 1 0 258s 1 2 258s 258s Estimate of P(1, 183) 258s 0 1 2 258s 0 0 0 1 258s 1 0 0 1 258s 2 0 0 1 258s 258s > 258s > summ.sir <- summary(prob.sir) 258s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 258s [1] TRUE 258s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 258s P time var lower upper n.risk n.event 258s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 258s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 258s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 258s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 258s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 258s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 258s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 258s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 258s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 258s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 258s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 258s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 258s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 258s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 258s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 258s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 258s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 258s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 258s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 258s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 258s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 258s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 258s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 258s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 258s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 258s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 258s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 258s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 258s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 258s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 258s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 258s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 258s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 258s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 258s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 258s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 258s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 258s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 258s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 258s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 258s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 258s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 258s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 258s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 258s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 258s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 258s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 258s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 258s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 258s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 258s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 258s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 258s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 258s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 258s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 258s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 258s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 258s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 258s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 258s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 258s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 258s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 258s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 258s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 258s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 258s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 258s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 258s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 258s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 258s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 258s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 258s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 258s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 258s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 258s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 258s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 258s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 258s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 258s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 258s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 258s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 258s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 258s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 258s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 258s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 258s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 258s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 258s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 258s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 258s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 258s > 258s > ## gonna play a bit with the state names 258s > dd <- sir.cont 258s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 258s > dd$to <- as.character(dd$to) 258s > for (i in seq_len(nrow(dd))) { 258s + dd$to[i] <- switch(dd$to[i], 258s + "0" = "initial state", 258s + "1" = "ventilation", 258s + "2" = "end of story", 258s + "cens" = "cens" 258s + ) 258s + } 258s > 258s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 258s > 258s > all.equal(test$est["initial state", "initial state", ], 258s + prob.sir$est["0", "0", ]) 258s [1] TRUE 258s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 258s [1] TRUE 258s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 258s [1] TRUE 258s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 258s [1] TRUE 258s > 258s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 258s [1] TRUE 258s > 258s > aa <- summary(test) 258s > all.equal(summ.sir[[6]], aa[[6]]) 258s [1] TRUE 258s > all.equal(summ.sir[[4]], aa[[4]]) 258s [1] TRUE 258s > 258s > ### Test on abortion data 258s > 258s > data(abortion) 258s > 258s > from <- rep(0, nrow(abortion)) 258s > to <- abortion$cause 258s > entry <- abortion$entry 258s > exit <- abortion$exit 258s > id <- 1:nrow(abortion) 258s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 258s > 258s > ## Computation of the CIFs 258s > tra <- matrix(FALSE, 4, 4) 258s > tra[1, 2:4] <- TRUE 258s > 258s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 258s + tra, NULL, 0) 258s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 258s + tra, NULL, 0) 258s > 258s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 258s [1] TRUE 258s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 258s [1] TRUE 258s > 258s > trprob(cif.control, "0 1") 258s 6 7 8 9 10 11 12 13 258s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 258s 14 17 19 21 24 25 26 30 258s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 258s 31 32 33 34 35 36 37 38 258s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 258s 39 40 41 42 43 258s 0.040159 0.040159 0.040159 0.040159 0.040159 258s > trprob(cif.control, "0 2") 258s 6 7 8 9 10 11 12 13 258s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 258s 14 17 19 21 24 25 26 30 258s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 258s 31 32 33 34 35 36 37 38 258s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 258s 39 40 41 42 43 258s 0.322016 0.563121 0.742227 0.793893 0.799059 258s > trprob(cif.control, "0 0") 258s 6 7 8 9 10 11 12 13 258s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 258s 14 17 19 21 24 25 26 30 258s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 258s 31 32 33 34 35 36 37 38 258s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 258s 39 40 41 42 43 258s 0.477043 0.235938 0.056832 0.005167 0.000000 258s > 258s > trcov(cif.control, "0 1") 258s 6 7 8 9 10 11 12 13 258s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 258s 14 17 19 21 24 25 26 30 258s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 258s 31 32 33 34 35 36 37 38 258s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 258s 39 40 41 42 43 258s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 258s > trcov(cif.control, "0 2") 258s 6 7 8 9 10 11 12 13 258s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 258s 14 17 19 21 24 25 26 30 258s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 258s 31 32 33 34 35 36 37 38 258s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 258s 39 40 41 42 43 258s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 258s > trcov(cif.control, "0 0") 258s 6 7 8 9 10 11 12 13 258s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 258s 14 17 19 21 24 25 26 30 258s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 258s 31 32 33 34 35 36 37 38 258s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 258s 39 40 41 42 43 258s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 258s > 258s > aa <- summary(cif.control) 258s > aa$"0 1" 258s P time var lower upper n.risk n.event 258s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 258s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 258s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 258s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 258s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 258s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 258s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 258s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 258s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 258s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 258s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 258s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 258s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 258s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 258s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 258s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 258s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 258s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 258s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 258s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 258s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 258s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 258s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 258s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 258s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 258s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 258s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 258s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 258s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 258s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 258s [1] TRUE 258s > 258s > ### test on los data 258s > 258s > data(los.data) # in package changeLOS 258s > 258s > ## putting los.data in the long format (see changeLOS) 258s > my.observ <- prepare.los.data(x=los.data) 258s > 258s > tra <- matrix(FALSE, 4, 4) 258s > tra[1, 2:4] <- TRUE 258s > tra[2, 3:4] <- TRUE 258s > 258s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 258s > 258s > tr.prob 258s Multistate model with 2 transient state(s) 258s and 2 absorbing state(s) 258s 258s Possible transitions: 258s from to 258s 0 1 258s 0 2 258s 0 3 258s 1 2 258s 1 3 258s 258s Estimate of P(0, 82) 258s 0 1 2 3 258s 0 0 0 0.7474 0.2526 258s 1 0 0 0.7073 0.2927 258s 2 0 0 1.0000 0.0000 258s 3 0 0 0.0000 1.0000 258s 258s > summary(tr.prob) 258s Transition 0 0 258s P time var lower upper n.risk n.event 258s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 258s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 258s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 258s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 258s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 258s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 258s 258s Transition 0 1 258s P time var lower upper n.risk n.event 258s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 258s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 258s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 258s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 258s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 258s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 258s 258s Transition 0 2 258s P time var lower upper n.risk n.event 258s 0.08466 3 0.0001025 0.06481 0.1045 756 64 258s 0.62302 15 0.0003107 0.58847 0.6576 90 4 258s 0.69841 27 0.0002786 0.66570 0.7311 26 1 258s 0.72751 41 0.0002622 0.69578 0.7593 5 0 258s 0.74074 61 0.0002540 0.70950 0.7720 3 1 258s 0.74735 82 0.0002498 0.71638 0.7783 1 1 258s 258s Transition 0 3 258s P time var lower upper n.risk n.event 258s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 258s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 258s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 258s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 258s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 258s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 258s 258s Transition 1 1 258s P time var lower upper n.risk n.event 258s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 258s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 258s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 258s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 258s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 258s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 258s 258s Transition 1 2 258s P time var lower upper n.risk n.event 258s 0.0000 3 0.000000 0.0000 0.0000 0 0 258s 0.4107 15 0.002590 0.3110 0.5104 51 2 258s 0.6082 27 0.002254 0.5151 0.7012 23 1 258s 0.6652 41 0.002064 0.5761 0.7542 14 2 258s 0.6920 61 0.002000 0.6043 0.7796 4 0 258s 0.7073 82 0.001984 0.6200 0.7946 0 0 258s 258s Transition 1 3 258s P time var lower upper n.risk n.event 258s 0.0000 3 0.000000 0.0000 0.0000 0 0 258s 0.2027 15 0.001784 0.1199 0.2855 51 1 258s 0.2706 27 0.001968 0.1837 0.3576 23 0 258s 0.2889 41 0.001982 0.2016 0.3761 14 0 258s 0.2927 61 0.001984 0.2054 0.3800 4 0 258s 0.2927 82 0.001984 0.2054 0.3800 0 0 258s 258s > 258s > cLOS <- etm::clos(tr.prob, aw = TRUE) 258s > 258s > cLOS 258s The expected change in length of stay is: 258s 1.975 258s 258s Alternative weighting: 258s 258s Expected change in LOS with weight.1: 2.097 258s Expected change in LOS with weight.other: 1.951 258s > 258s > 258s > ### Tests on pseudo values 258s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 258s + formula = ~ 1, aw = TRUE) 274s > 274s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 274s [,1] 274s [1,] TRUE 274s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 274s [,1] 274s [1,] TRUE 274s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 274s [,1] 274s [1,] TRUE 274s > 274s > mean(t_pseudo$pseudoData$ps.e.phi) 274s [1] 1.968 274s > 274s > ### tests on etmprep 274s > 274s > ### creation of fake data in the wild format, following an illness-death model 274s > ## transition times 274s > tdisease <- c(3, 4, 3, 6, 8, 9) 274s > tdeath <- c(6, 9, 8, 6, 8, 9) 274s > 274s > ## transition status 274s > stat.disease <- c(1, 1, 1, 0, 0, 0) 274s > stat.death <- c(1, 1, 1, 1, 1, 0) 274s > 274s > ## a covariate that we want to keep in the new data 274s > set.seed(1313) 274s > cova <- rbinom(6, 1, 0.5) 274s > 274s > dat <- data.frame(tdisease, tdeath, 274s + stat.disease, stat.death, 274s + cova) 274s > 274s > ## Possible transitions 274s > tra <- matrix(FALSE, 3, 3) 274s > tra[1, 2:3] <- TRUE 274s > tra[2, 3] <- TRUE 274s > 274s > ## data preparation 274s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 274s + c(NA, "stat.disease", "stat.death"), 274s + data = dat, tra = tra, 274s + cens.name = "cens", keep = "cova") 274s > 274s > newdat 274s id entry exit from to cova 274s 1 1 0 3 0 1 1 274s 2 1 3 6 1 2 1 274s 3 2 0 4 0 1 0 274s 4 2 4 9 1 2 0 274s 5 3 0 3 0 1 1 274s 6 3 3 8 1 2 1 274s 7 4 0 6 0 2 0 274s 8 5 0 8 0 2 1 274s 9 6 0 9 0 cens 1 274s > 274s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 274s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 274s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 274s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 274s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 274s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 274s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 274s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 274s > 274s > all.equal(ref, newdat) 274s [1] TRUE 274s > 274s > 274s > ###################################### 274s > ### Test the stratified calls 274s > ###################################### 274s > 274s > if (require("kmi", quietly = TRUE)) { 274s + library(etm) 274s + 274s + data(icu.pneu) 274s + my.icu.pneu <- icu.pneu 274s + 274s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 274s + masque <- diff(my.icu.pneu$id) 274s + 274s + my.icu.pneu$from <- 0 274s + my.icu.pneu$from[c(1, masque) == 0] <- 1 274s + 274s + my.icu.pneu$to2 <- my.icu.pneu$event 274s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 274s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 274s + 274s + 274s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 274s + my.icu.pneu$to2) 274s + 274s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 274s + "to2", "age", "sex")] 274s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 274s + 274s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 274s + 274s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 274s + c("0", "1", "2"), tra_ill(), "cens", 0) 274s + 274s + all(bouh_strat[[1]]$est == bouh_female$est) 274s + 274s + ## Test the summary 274s + the_summary <- summary(bouh_strat) 274s + the_summary 274s + 274s + ## Test trprob 274s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 274s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 274s + 274s + ## Test trcov 274s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 274s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 274s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 274s + } else { 274s + print("These tests require the kmi package") 274s + } 274s [1] TRUE 274s > 274s > options(old) 274s > 274s autopkgtest [16:26:26]: test run-unit-test: -----------------------] 275s autopkgtest [16:26:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 275s run-unit-test PASS 275s autopkgtest [16:26:27]: test pkg-r-autopkgtest: preparing testbed 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 279s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 279s Starting 2 pkgProblemResolver with broken count: 0 279s Done 279s Done 279s Starting pkgProblemResolver with broken count: 0 279s Starting 2 pkgProblemResolver with broken count: 0 279s Done 279s The following additional packages will be installed: 279s build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 279s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-13 279s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 279s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-13 279s gfortran-13-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 279s icu-devtools libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin 279s libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgfortran-13-dev libicu-dev 279s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 279s liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 279s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 279s libquadmath0 libreadline-dev libstdc++-13-dev libtirpc-dev libtsan2 279s libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin 279s r-base-dev r-cran-backports r-cran-broom r-cran-cli r-cran-colorspace 279s r-cran-cpp11 r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver 279s r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 279s r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass 279s r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig 279s r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales 279s r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect 279s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto 279s zlib1g-dev 279s Suggested packages: 279s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 279s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 279s gdb-powerpc64le-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 279s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 279s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 279s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 279s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 279s r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata r-cran-caret 279s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 279s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-glmnet r-cran-gmm 279s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-knitr r-cran-ks r-cran-lavaan 279s r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans r-cran-maps 279s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 279s r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg 279s r-cran-rmarkdown r-cran-robust r-cran-robustbase r-cran-rsample 279s r-cran-sandwich r-cran-sp r-cran-spdep r-cran-spatialreg r-cran-spelling 279s r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth 279s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 279s r-cran-png r-cran-jpeg r-cran-viridis r-cran-magick r-cran-sf r-cran-bit64 279s r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units 279s r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio 279s r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms 279s r-cran-htmltools r-cran-pkgbuild r-cran-pkgload 279s Recommended packages: 279s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-cran-testthat 279s r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools 279s r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps 279s r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami 279s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 279s r-cran-progress r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql 279s r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc 279s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 279s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 279s r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-httr 279s r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms 279s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 279s The following NEW packages will be installed: 279s build-essential cpp cpp-13 cpp-13-powerpc64le-linux-gnu 279s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-13 279s g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-13 279s gcc-13-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-13 279s gfortran-13-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 279s icu-devtools libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin 279s libc6-dev libcc1-0 libcrypt-dev libgcc-13-dev libgfortran-13-dev libicu-dev 279s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 279s liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 279s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 279s libquadmath0 libreadline-dev libstdc++-13-dev libtirpc-dev libtsan2 279s libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin 279s r-base-dev r-cran-backports r-cran-broom r-cran-cli r-cran-colorspace 279s r-cran-cpp11 r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-farver 279s r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable 279s r-cran-isoband r-cran-labeling r-cran-lifecycle r-cran-magrittr r-cran-mass 279s r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig 279s r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rlang r-cran-scales 279s r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect 279s r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rpcsvc-proto 279s zlib1g-dev 280s 0 upgraded, 99 newly installed, 0 to remove and 0 not upgraded. 280s 1 not fully installed or removed. 280s Need to get 128 MB of archives. 280s After this operation, 428 MB of additional disk space will be used. 280s Get:1 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-cli ppc64el 3.6.2-1 [1405 kB] 281s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-glue ppc64el 1.7.0-1 [155 kB] 281s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rlang ppc64el 1.1.3-1 [1696 kB] 282s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 282s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 282s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-isoband ppc64el 0.2.7-1 [1486 kB] 282s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mass ppc64el 7.3-60.0.1-1 [1126 kB] 283s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-nlme ppc64el 3.1.164-1 [2281 kB] 283s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-mgcv ppc64el 1.9-1-1 [3393 kB] 284s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-farver ppc64el 2.1.1-1 [1365 kB] 284s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-labeling all 0.4.3-1 [62.1 kB] 284s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-colorspace ppc64el 2.1-0+dfsg-1 [1542 kB] 284s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-munsell all 0.5.0-2build1 [208 kB] 284s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-r6 all 2.5.1-1 [99.0 kB] 284s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 284s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-viridislite all 0.4.2-2 [1088 kB] 284s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-scales all 1.3.0-1 [603 kB] 284s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-fansi ppc64el 1.0.5-1 [627 kB] 284s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-magrittr ppc64el 2.0.3-1 [154 kB] 284s Get:20 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-utf8 ppc64el 1.2.4-1 [148 kB] 284s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-vctrs ppc64el 0.6.5-1 [1399 kB] 284s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 284s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 284s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-tibble ppc64el 3.2.1+dfsg-2 [415 kB] 284s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-withr all 2.5.0-1 [225 kB] 284s Get:26 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 285s Get:27 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-backports ppc64el 1.4.1-1 [101 kB] 285s Get:28 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-generics all 0.1.3-1 [81.3 kB] 285s Get:29 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-tidyselect ppc64el 1.2.0+dfsg-1 [218 kB] 285s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-dplyr ppc64el 1.1.4-1 [1516 kB] 285s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-ellipsis ppc64el 0.3.2-2 [35.9 kB] 285s Get:32 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-purrr ppc64el 1.0.2-1 [503 kB] 285s Get:33 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-stringi ppc64el 1.8.3-1 [919 kB] 285s Get:34 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-stringr all 1.5.1-1 [290 kB] 285s Get:35 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-cpp11 all 0.4.7-1 [266 kB] 285s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-tidyr ppc64el 1.3.1-1 [1163 kB] 285s Get:37 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 285s Get:38 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-cran-geepack ppc64el 1.3.10-1 [395 kB] 285s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el dctrl-tools ppc64el 2.24-3build2 [70.6 kB] 285s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu2 [21.3 kB] 285s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 285s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 285s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1build1 [262 kB] 285s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libnsl-dev ppc64el 1.3.0-3 [79.2 kB] 285s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 285s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu2 [2102 kB] 286s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] 286s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libmpc3 ppc64el 1.3.1-1 [61.2 kB] 286s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [10.7 MB] 286s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-13 ppc64el 13.2.0-17ubuntu2 [1038 B] 286s Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] 286s Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] 286s Get:53 http://ftpmaster.internal/ubuntu noble/main ppc64el libcc1-0 ppc64el 14-20240303-1ubuntu1 [48.1 kB] 286s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libitm1 ppc64el 14-20240303-1ubuntu1 [32.4 kB] 286s Get:55 http://ftpmaster.internal/ubuntu noble/main ppc64el libatomic1 ppc64el 14-20240303-1ubuntu1 [10.7 kB] 286s Get:56 http://ftpmaster.internal/ubuntu noble/main ppc64el libasan8 ppc64el 14-20240303-1ubuntu1 [2973 kB] 287s Get:57 http://ftpmaster.internal/ubuntu noble/main ppc64el liblsan0 ppc64el 14-20240303-1ubuntu1 [1325 kB] 287s Get:58 http://ftpmaster.internal/ubuntu noble/main ppc64el libtsan2 ppc64el 14-20240303-1ubuntu1 [2734 kB] 287s Get:59 http://ftpmaster.internal/ubuntu noble/main ppc64el libubsan1 ppc64el 14-20240303-1ubuntu1 [1194 kB] 287s Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el libquadmath0 ppc64el 14-20240303-1ubuntu1 [158 kB] 287s Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcc-13-dev ppc64el 13.2.0-17ubuntu2 [1581 kB] 287s Get:62 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [20.6 MB] 289s Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-13 ppc64el 13.2.0-17ubuntu2 [477 kB] 289s Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] 289s Get:65 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] 289s Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el libstdc++-13-dev ppc64el 13.2.0-17ubuntu2 [2445 kB] 289s Get:67 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [12.2 MB] 290s Get:68 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-13 ppc64el 13.2.0-17ubuntu2 [14.5 kB] 290s Get:69 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] 290s Get:70 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] 290s Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 290s Get:72 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran-13-dev ppc64el 13.2.0-17ubuntu2 [604 kB] 290s Get:73 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran-13-powerpc64le-linux-gnu ppc64el 13.2.0-17ubuntu2 [11.2 MB] 291s Get:74 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran-13 ppc64el 13.2.0-17ubuntu2 [10.3 kB] 291s Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1030 B] 291s Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el gfortran ppc64el 4:13.2.0-7ubuntu1 [1170 B] 291s Get:77 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas-dev ppc64el 3.12.0-3 [301 kB] 291s Get:78 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack-dev ppc64el 3.12.0-3 [6100 kB] 291s Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el libncurses-dev ppc64el 6.4+20240113-1ubuntu1 [485 kB] 291s Get:80 http://ftpmaster.internal/ubuntu noble/main ppc64el libreadline-dev ppc64el 8.2-3 [226 kB] 291s Get:81 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-2ubuntu1 [357 kB] 291s Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 291s Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 291s Get:84 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-16-0 ppc64el 10.42-4ubuntu1 [245 kB] 291s Get:85 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-32-0 ppc64el 10.42-4ubuntu1 [228 kB] 291s Get:86 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-posix3 ppc64el 10.42-4ubuntu1 [7016 B] 291s Get:87 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-dev ppc64el 10.42-4ubuntu1 [794 kB] 291s Get:88 http://ftpmaster.internal/ubuntu noble/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3ubuntu1 [902 kB] 291s Get:89 http://ftpmaster.internal/ubuntu noble/main ppc64el libpng-dev ppc64el 1.6.43-1 [327 kB] 291s Get:90 http://ftpmaster.internal/ubuntu noble/main ppc64el libbz2-dev ppc64el 1.0.8-5ubuntu1 [51.2 kB] 291s Get:91 http://ftpmaster.internal/ubuntu noble/main ppc64el liblzma-dev ppc64el 5.4.5-0.3 [243 kB] 291s Get:92 http://ftpmaster.internal/ubuntu noble/main ppc64el icu-devtools ppc64el 74.2-1ubuntu1 [246 kB] 291s Get:93 http://ftpmaster.internal/ubuntu noble/main ppc64el libicu-dev ppc64el 74.2-1ubuntu1 [12.5 MB] 292s Get:94 http://ftpmaster.internal/ubuntu noble/main ppc64el libpkgconf3 ppc64el 1.8.1-2 [36.9 kB] 292s Get:95 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf-bin ppc64el 1.8.1-2 [22.0 kB] 292s Get:96 http://ftpmaster.internal/ubuntu noble/main ppc64el pkgconf ppc64el 1.8.1-2 [16.7 kB] 292s Get:97 http://ftpmaster.internal/ubuntu noble/main ppc64el pkg-config ppc64el 1.8.1-2 [7170 B] 292s Get:98 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-dev all 4.3.2-1build1 [4336 B] 292s Get:99 http://ftpmaster.internal/ubuntu noble/universe ppc64el pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 293s Fetched 128 MB in 13s (10.2 MB/s) 293s Selecting previously unselected package r-cran-cli. 293s (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 ... 73930 files and directories currently installed.) 293s Preparing to unpack .../00-r-cran-cli_3.6.2-1_ppc64el.deb ... 293s Unpacking r-cran-cli (3.6.2-1) ... 293s Selecting previously unselected package r-cran-glue. 293s Preparing to unpack .../01-r-cran-glue_1.7.0-1_ppc64el.deb ... 293s Unpacking r-cran-glue (1.7.0-1) ... 293s Selecting previously unselected package r-cran-rlang. 293s Preparing to unpack .../02-r-cran-rlang_1.1.3-1_ppc64el.deb ... 293s Unpacking r-cran-rlang (1.1.3-1) ... 293s Selecting previously unselected package r-cran-lifecycle. 293s Preparing to unpack .../03-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 293s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 293s Selecting previously unselected package r-cran-gtable. 293s Preparing to unpack .../04-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 293s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 293s Selecting previously unselected package r-cran-isoband. 293s Preparing to unpack .../05-r-cran-isoband_0.2.7-1_ppc64el.deb ... 293s Unpacking r-cran-isoband (0.2.7-1) ... 293s Selecting previously unselected package r-cran-mass. 293s Preparing to unpack .../06-r-cran-mass_7.3-60.0.1-1_ppc64el.deb ... 293s Unpacking r-cran-mass (7.3-60.0.1-1) ... 293s Selecting previously unselected package r-cran-nlme. 293s Preparing to unpack .../07-r-cran-nlme_3.1.164-1_ppc64el.deb ... 293s Unpacking r-cran-nlme (3.1.164-1) ... 293s Selecting previously unselected package r-cran-mgcv. 293s Preparing to unpack .../08-r-cran-mgcv_1.9-1-1_ppc64el.deb ... 293s Unpacking r-cran-mgcv (1.9-1-1) ... 293s Selecting previously unselected package r-cran-farver. 293s Preparing to unpack .../09-r-cran-farver_2.1.1-1_ppc64el.deb ... 293s Unpacking r-cran-farver (2.1.1-1) ... 293s Selecting previously unselected package r-cran-labeling. 293s Preparing to unpack .../10-r-cran-labeling_0.4.3-1_all.deb ... 293s Unpacking r-cran-labeling (0.4.3-1) ... 293s Selecting previously unselected package r-cran-colorspace. 293s Preparing to unpack .../11-r-cran-colorspace_2.1-0+dfsg-1_ppc64el.deb ... 293s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 293s Selecting previously unselected package r-cran-munsell. 293s Preparing to unpack .../12-r-cran-munsell_0.5.0-2build1_all.deb ... 293s Unpacking r-cran-munsell (0.5.0-2build1) ... 293s Selecting previously unselected package r-cran-r6. 293s Preparing to unpack .../13-r-cran-r6_2.5.1-1_all.deb ... 293s Unpacking r-cran-r6 (2.5.1-1) ... 293s Selecting previously unselected package r-cran-rcolorbrewer. 293s Preparing to unpack .../14-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 293s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 293s Selecting previously unselected package r-cran-viridislite. 293s Preparing to unpack .../15-r-cran-viridislite_0.4.2-2_all.deb ... 293s Unpacking r-cran-viridislite (0.4.2-2) ... 293s Selecting previously unselected package r-cran-scales. 293s Preparing to unpack .../16-r-cran-scales_1.3.0-1_all.deb ... 293s Unpacking r-cran-scales (1.3.0-1) ... 293s Selecting previously unselected package r-cran-fansi. 293s Preparing to unpack .../17-r-cran-fansi_1.0.5-1_ppc64el.deb ... 293s Unpacking r-cran-fansi (1.0.5-1) ... 293s Selecting previously unselected package r-cran-magrittr. 293s Preparing to unpack .../18-r-cran-magrittr_2.0.3-1_ppc64el.deb ... 293s Unpacking r-cran-magrittr (2.0.3-1) ... 293s Selecting previously unselected package r-cran-utf8. 293s Preparing to unpack .../19-r-cran-utf8_1.2.4-1_ppc64el.deb ... 293s Unpacking r-cran-utf8 (1.2.4-1) ... 294s Selecting previously unselected package r-cran-vctrs. 294s Preparing to unpack .../20-r-cran-vctrs_0.6.5-1_ppc64el.deb ... 294s Unpacking r-cran-vctrs (0.6.5-1) ... 294s Selecting previously unselected package r-cran-pillar. 294s Preparing to unpack .../21-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 294s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 294s Selecting previously unselected package r-cran-pkgconfig. 294s Preparing to unpack .../22-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 294s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 294s Selecting previously unselected package r-cran-tibble. 294s Preparing to unpack .../23-r-cran-tibble_3.2.1+dfsg-2_ppc64el.deb ... 294s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 294s Selecting previously unselected package r-cran-withr. 294s Preparing to unpack .../24-r-cran-withr_2.5.0-1_all.deb ... 294s Unpacking r-cran-withr (2.5.0-1) ... 294s Selecting previously unselected package r-cran-ggplot2. 294s Preparing to unpack .../25-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 294s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 294s Selecting previously unselected package r-cran-backports. 294s Preparing to unpack .../26-r-cran-backports_1.4.1-1_ppc64el.deb ... 294s Unpacking r-cran-backports (1.4.1-1) ... 294s Selecting previously unselected package r-cran-generics. 294s Preparing to unpack .../27-r-cran-generics_0.1.3-1_all.deb ... 294s Unpacking r-cran-generics (0.1.3-1) ... 294s Selecting previously unselected package r-cran-tidyselect. 294s Preparing to unpack .../28-r-cran-tidyselect_1.2.0+dfsg-1_ppc64el.deb ... 294s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 294s Selecting previously unselected package r-cran-dplyr. 294s Preparing to unpack .../29-r-cran-dplyr_1.1.4-1_ppc64el.deb ... 294s Unpacking r-cran-dplyr (1.1.4-1) ... 294s Selecting previously unselected package r-cran-ellipsis. 294s Preparing to unpack .../30-r-cran-ellipsis_0.3.2-2_ppc64el.deb ... 294s Unpacking r-cran-ellipsis (0.3.2-2) ... 294s Selecting previously unselected package r-cran-purrr. 294s Preparing to unpack .../31-r-cran-purrr_1.0.2-1_ppc64el.deb ... 294s Unpacking r-cran-purrr (1.0.2-1) ... 294s Selecting previously unselected package r-cran-stringi. 294s Preparing to unpack .../32-r-cran-stringi_1.8.3-1_ppc64el.deb ... 294s Unpacking r-cran-stringi (1.8.3-1) ... 294s Selecting previously unselected package r-cran-stringr. 294s Preparing to unpack .../33-r-cran-stringr_1.5.1-1_all.deb ... 294s Unpacking r-cran-stringr (1.5.1-1) ... 294s Selecting previously unselected package r-cran-cpp11. 294s Preparing to unpack .../34-r-cran-cpp11_0.4.7-1_all.deb ... 294s Unpacking r-cran-cpp11 (0.4.7-1) ... 294s Selecting previously unselected package r-cran-tidyr. 294s Preparing to unpack .../35-r-cran-tidyr_1.3.1-1_ppc64el.deb ... 294s Unpacking r-cran-tidyr (1.3.1-1) ... 294s Selecting previously unselected package r-cran-broom. 294s Preparing to unpack .../36-r-cran-broom_1.0.5+dfsg-1_all.deb ... 294s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 294s Selecting previously unselected package r-cran-geepack. 294s Preparing to unpack .../37-r-cran-geepack_1.3.10-1_ppc64el.deb ... 294s Unpacking r-cran-geepack (1.3.10-1) ... 294s Selecting previously unselected package dctrl-tools. 294s Preparing to unpack .../38-dctrl-tools_2.24-3build2_ppc64el.deb ... 294s Unpacking dctrl-tools (2.24-3build2) ... 294s Selecting previously unselected package libc-dev-bin. 294s Preparing to unpack .../39-libc-dev-bin_2.39-0ubuntu2_ppc64el.deb ... 294s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 294s Selecting previously unselected package linux-libc-dev:ppc64el. 294s Preparing to unpack .../40-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 294s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 295s Selecting previously unselected package libcrypt-dev:ppc64el. 295s Preparing to unpack .../41-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 295s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 295s Selecting previously unselected package libtirpc-dev:ppc64el. 295s Preparing to unpack .../42-libtirpc-dev_1.3.4+ds-1build1_ppc64el.deb ... 295s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 295s Selecting previously unselected package libnsl-dev:ppc64el. 295s Preparing to unpack .../43-libnsl-dev_1.3.0-3_ppc64el.deb ... 295s Unpacking libnsl-dev:ppc64el (1.3.0-3) ... 295s Selecting previously unselected package rpcsvc-proto. 295s Preparing to unpack .../44-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 295s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 295s Selecting previously unselected package libc6-dev:ppc64el. 295s Preparing to unpack .../45-libc6-dev_2.39-0ubuntu2_ppc64el.deb ... 295s Unpacking libc6-dev:ppc64el (2.39-0ubuntu2) ... 295s Selecting previously unselected package libisl23:ppc64el. 295s Preparing to unpack .../46-libisl23_0.26-3_ppc64el.deb ... 295s Unpacking libisl23:ppc64el (0.26-3) ... 295s Selecting previously unselected package libmpc3:ppc64el. 295s Preparing to unpack .../47-libmpc3_1.3.1-1_ppc64el.deb ... 295s Unpacking libmpc3:ppc64el (1.3.1-1) ... 295s Selecting previously unselected package cpp-13-powerpc64le-linux-gnu. 295s Preparing to unpack .../48-cpp-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 295s Unpacking cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 295s Selecting previously unselected package cpp-13. 295s Preparing to unpack .../49-cpp-13_13.2.0-17ubuntu2_ppc64el.deb ... 295s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 295s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 295s Preparing to unpack .../50-cpp-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 295s Unpacking cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 295s Selecting previously unselected package cpp. 295s Preparing to unpack .../51-cpp_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 295s Unpacking cpp (4:13.2.0-7ubuntu1) ... 295s Selecting previously unselected package libcc1-0:ppc64el. 295s Preparing to unpack .../52-libcc1-0_14-20240303-1ubuntu1_ppc64el.deb ... 295s Unpacking libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 295s Selecting previously unselected package libitm1:ppc64el. 295s Preparing to unpack .../53-libitm1_14-20240303-1ubuntu1_ppc64el.deb ... 295s Unpacking libitm1:ppc64el (14-20240303-1ubuntu1) ... 295s Selecting previously unselected package libatomic1:ppc64el. 295s Preparing to unpack .../54-libatomic1_14-20240303-1ubuntu1_ppc64el.deb ... 295s Unpacking libatomic1:ppc64el (14-20240303-1ubuntu1) ... 295s Selecting previously unselected package libasan8:ppc64el. 295s Preparing to unpack .../55-libasan8_14-20240303-1ubuntu1_ppc64el.deb ... 295s Unpacking libasan8:ppc64el (14-20240303-1ubuntu1) ... 295s Selecting previously unselected package liblsan0:ppc64el. 295s Preparing to unpack .../56-liblsan0_14-20240303-1ubuntu1_ppc64el.deb ... 295s Unpacking liblsan0:ppc64el (14-20240303-1ubuntu1) ... 296s Selecting previously unselected package libtsan2:ppc64el. 296s Preparing to unpack .../57-libtsan2_14-20240303-1ubuntu1_ppc64el.deb ... 296s Unpacking libtsan2:ppc64el (14-20240303-1ubuntu1) ... 296s Selecting previously unselected package libubsan1:ppc64el. 296s Preparing to unpack .../58-libubsan1_14-20240303-1ubuntu1_ppc64el.deb ... 296s Unpacking libubsan1:ppc64el (14-20240303-1ubuntu1) ... 296s Selecting previously unselected package libquadmath0:ppc64el. 296s Preparing to unpack .../59-libquadmath0_14-20240303-1ubuntu1_ppc64el.deb ... 296s Unpacking libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 296s Selecting previously unselected package libgcc-13-dev:ppc64el. 296s Preparing to unpack .../60-libgcc-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 296s Unpacking libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 296s Selecting previously unselected package gcc-13-powerpc64le-linux-gnu. 296s Preparing to unpack .../61-gcc-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 296s Unpacking gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 296s Selecting previously unselected package gcc-13. 296s Preparing to unpack .../62-gcc-13_13.2.0-17ubuntu2_ppc64el.deb ... 296s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 296s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 296s Preparing to unpack .../63-gcc-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 296s Unpacking gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 296s Selecting previously unselected package gcc. 296s Preparing to unpack .../64-gcc_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 296s Unpacking gcc (4:13.2.0-7ubuntu1) ... 296s Selecting previously unselected package libstdc++-13-dev:ppc64el. 296s Preparing to unpack .../65-libstdc++-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 296s Unpacking libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 297s Selecting previously unselected package g++-13-powerpc64le-linux-gnu. 297s Preparing to unpack .../66-g++-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 297s Unpacking g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 297s Selecting previously unselected package g++-13. 297s Preparing to unpack .../67-g++-13_13.2.0-17ubuntu2_ppc64el.deb ... 297s Unpacking g++-13 (13.2.0-17ubuntu2) ... 297s Selecting previously unselected package g++-powerpc64le-linux-gnu. 297s Preparing to unpack .../68-g++-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 297s Unpacking g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 297s Selecting previously unselected package g++. 297s Preparing to unpack .../69-g++_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 297s Unpacking g++ (4:13.2.0-7ubuntu1) ... 297s Selecting previously unselected package build-essential. 297s Preparing to unpack .../70-build-essential_12.10ubuntu1_ppc64el.deb ... 297s Unpacking build-essential (12.10ubuntu1) ... 297s Selecting previously unselected package libgfortran-13-dev:ppc64el. 297s Preparing to unpack .../71-libgfortran-13-dev_13.2.0-17ubuntu2_ppc64el.deb ... 297s Unpacking libgfortran-13-dev:ppc64el (13.2.0-17ubuntu2) ... 297s Selecting previously unselected package gfortran-13-powerpc64le-linux-gnu. 297s Preparing to unpack .../72-gfortran-13-powerpc64le-linux-gnu_13.2.0-17ubuntu2_ppc64el.deb ... 297s Unpacking gfortran-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 297s Selecting previously unselected package gfortran-13. 297s Preparing to unpack .../73-gfortran-13_13.2.0-17ubuntu2_ppc64el.deb ... 297s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 297s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 297s Preparing to unpack .../74-gfortran-powerpc64le-linux-gnu_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 297s Unpacking gfortran-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 297s Selecting previously unselected package gfortran. 297s Preparing to unpack .../75-gfortran_4%3a13.2.0-7ubuntu1_ppc64el.deb ... 297s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 297s Selecting previously unselected package libblas-dev:ppc64el. 297s Preparing to unpack .../76-libblas-dev_3.12.0-3_ppc64el.deb ... 297s Unpacking libblas-dev:ppc64el (3.12.0-3) ... 297s Selecting previously unselected package liblapack-dev:ppc64el. 297s Preparing to unpack .../77-liblapack-dev_3.12.0-3_ppc64el.deb ... 297s Unpacking liblapack-dev:ppc64el (3.12.0-3) ... 298s Selecting previously unselected package libncurses-dev:ppc64el. 298s Preparing to unpack .../78-libncurses-dev_6.4+20240113-1ubuntu1_ppc64el.deb ... 298s Unpacking libncurses-dev:ppc64el (6.4+20240113-1ubuntu1) ... 298s Selecting previously unselected package libreadline-dev:ppc64el. 298s Preparing to unpack .../79-libreadline-dev_8.2-3_ppc64el.deb ... 298s Unpacking libreadline-dev:ppc64el (8.2-3) ... 298s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 298s Preparing to unpack .../80-libjpeg-turbo8-dev_2.1.5-2ubuntu1_ppc64el.deb ... 298s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-2ubuntu1) ... 298s Selecting previously unselected package libjpeg8-dev:ppc64el. 298s Preparing to unpack .../81-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 298s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 298s Selecting previously unselected package libjpeg-dev:ppc64el. 298s Preparing to unpack .../82-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 298s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 298s Selecting previously unselected package libpcre2-16-0:ppc64el. 298s Preparing to unpack .../83-libpcre2-16-0_10.42-4ubuntu1_ppc64el.deb ... 298s Unpacking libpcre2-16-0:ppc64el (10.42-4ubuntu1) ... 298s Selecting previously unselected package libpcre2-32-0:ppc64el. 298s Preparing to unpack .../84-libpcre2-32-0_10.42-4ubuntu1_ppc64el.deb ... 298s Unpacking libpcre2-32-0:ppc64el (10.42-4ubuntu1) ... 298s Selecting previously unselected package libpcre2-posix3:ppc64el. 298s Preparing to unpack .../85-libpcre2-posix3_10.42-4ubuntu1_ppc64el.deb ... 298s Unpacking libpcre2-posix3:ppc64el (10.42-4ubuntu1) ... 298s Selecting previously unselected package libpcre2-dev:ppc64el. 298s Preparing to unpack .../86-libpcre2-dev_10.42-4ubuntu1_ppc64el.deb ... 298s Unpacking libpcre2-dev:ppc64el (10.42-4ubuntu1) ... 298s Selecting previously unselected package zlib1g-dev:ppc64el. 298s Preparing to unpack .../87-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_ppc64el.deb ... 298s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 298s Selecting previously unselected package libpng-dev:ppc64el. 298s Preparing to unpack .../88-libpng-dev_1.6.43-1_ppc64el.deb ... 298s Unpacking libpng-dev:ppc64el (1.6.43-1) ... 298s Selecting previously unselected package libbz2-dev:ppc64el. 298s Preparing to unpack .../89-libbz2-dev_1.0.8-5ubuntu1_ppc64el.deb ... 298s Unpacking libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 298s Selecting previously unselected package liblzma-dev:ppc64el. 298s Preparing to unpack .../90-liblzma-dev_5.4.5-0.3_ppc64el.deb ... 298s Unpacking liblzma-dev:ppc64el (5.4.5-0.3) ... 298s Selecting previously unselected package icu-devtools. 298s Preparing to unpack .../91-icu-devtools_74.2-1ubuntu1_ppc64el.deb ... 298s Unpacking icu-devtools (74.2-1ubuntu1) ... 298s Selecting previously unselected package libicu-dev:ppc64el. 298s Preparing to unpack .../92-libicu-dev_74.2-1ubuntu1_ppc64el.deb ... 298s Unpacking libicu-dev:ppc64el (74.2-1ubuntu1) ... 298s Selecting previously unselected package libpkgconf3:ppc64el. 298s Preparing to unpack .../93-libpkgconf3_1.8.1-2_ppc64el.deb ... 298s Unpacking libpkgconf3:ppc64el (1.8.1-2) ... 298s Selecting previously unselected package pkgconf-bin. 298s Preparing to unpack .../94-pkgconf-bin_1.8.1-2_ppc64el.deb ... 298s Unpacking pkgconf-bin (1.8.1-2) ... 298s Selecting previously unselected package pkgconf:ppc64el. 298s Preparing to unpack .../95-pkgconf_1.8.1-2_ppc64el.deb ... 298s Unpacking pkgconf:ppc64el (1.8.1-2) ... 298s Selecting previously unselected package pkg-config:ppc64el. 298s Preparing to unpack .../96-pkg-config_1.8.1-2_ppc64el.deb ... 298s Unpacking pkg-config:ppc64el (1.8.1-2) ... 299s Selecting previously unselected package r-base-dev. 299s Preparing to unpack .../97-r-base-dev_4.3.2-1build1_all.deb ... 299s Unpacking r-base-dev (4.3.2-1build1) ... 299s Selecting previously unselected package pkg-r-autopkgtest. 299s Preparing to unpack .../98-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 299s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 299s Setting up r-cran-rlang (1.1.3-1) ... 299s Setting up r-cran-withr (2.5.0-1) ... 299s Setting up r-cran-backports (1.4.1-1) ... 299s Setting up r-cran-generics (0.1.3-1) ... 299s Setting up r-cran-fansi (1.0.5-1) ... 299s Setting up r-cran-mass (7.3-60.0.1-1) ... 299s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 299s Setting up r-cran-glue (1.7.0-1) ... 299s Setting up r-cran-cli (3.6.2-1) ... 299s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 299s Setting up libpcre2-16-0:ppc64el (10.42-4ubuntu1) ... 299s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 299s Setting up libpcre2-32-0:ppc64el (10.42-4ubuntu1) ... 299s Setting up r-cran-utf8 (1.2.4-1) ... 299s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 299s Setting up libpkgconf3:ppc64el (1.8.1-2) ... 299s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 299s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 299s Setting up r-cran-stringi (1.8.3-1) ... 299s Setting up r-cran-cpp11 (0.4.7-1) ... 299s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 299s Setting up r-cran-isoband (0.2.7-1) ... 299s Setting up libquadmath0:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up libmpc3:ppc64el (1.3.1-1) ... 299s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 299s Setting up libatomic1:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up r-cran-labeling (0.4.3-1) ... 299s Setting up icu-devtools (74.2-1ubuntu1) ... 299s Setting up pkgconf-bin (1.8.1-2) ... 299s Setting up r-cran-nlme (3.1.164-1) ... 299s Setting up r-cran-farver (2.1.1-1) ... 299s Setting up liblzma-dev:ppc64el (5.4.5-0.3) ... 299s Setting up libubsan1:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up r-cran-mgcv (1.9-1-1) ... 299s Setting up libpcre2-posix3:ppc64el (10.42-4ubuntu1) ... 299s Setting up libnsl-dev:ppc64el (1.3.0-3) ... 299s Setting up r-cran-viridislite (0.4.2-2) ... 299s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 299s Setting up libasan8:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up libtsan2:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up r-cran-r6 (2.5.1-1) ... 299s Setting up libisl23:ppc64el (0.26-3) ... 299s Setting up libc-dev-bin (2.39-0ubuntu2) ... 299s Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 299s Setting up r-cran-magrittr (2.0.3-1) ... 299s Setting up libcc1-0:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up r-cran-vctrs (0.6.5-1) ... 299s Setting up liblsan0:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up libblas-dev:ppc64el (3.12.0-3) ... 299s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 299s Setting up dctrl-tools (2.24-3build2) ... 299s Setting up libitm1:ppc64el (14-20240303-1ubuntu1) ... 299s Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 299s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 299s Setting up r-cran-ellipsis (0.3.2-2) ... 299s Setting up r-cran-stringr (1.5.1-1) ... 299s Setting up cpp-13 (13.2.0-17ubuntu2) ... 299s Setting up r-cran-munsell (0.5.0-2build1) ... 299s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 299s Setting up pkgconf:ppc64el (1.8.1-2) ... 299s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 299s Setting up r-cran-scales (1.3.0-1) ... 299s Setting up liblapack-dev:ppc64el (3.12.0-3) ... 299s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 299s Setting up r-cran-purrr (1.0.2-1) ... 299s Setting up pkg-config:ppc64el (1.8.1-2) ... 299s Setting up libgcc-13-dev:ppc64el (13.2.0-17ubuntu2) ... 299s Setting up cpp (4:13.2.0-7ubuntu1) ... 299s Setting up libc6-dev:ppc64el (2.39-0ubuntu2) ... 299s Setting up r-cran-dplyr (1.1.4-1) ... 299s Setting up libgfortran-13-dev:ppc64el (13.2.0-17ubuntu2) ... 299s Setting up libicu-dev:ppc64el (74.2-1ubuntu1) ... 299s Setting up libstdc++-13-dev:ppc64el (13.2.0-17ubuntu2) ... 299s Setting up libbz2-dev:ppc64el (1.0.8-5ubuntu1) ... 299s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-2ubuntu1) ... 299s Setting up libncurses-dev:ppc64el (6.4+20240113-1ubuntu1) ... 299s Setting up libpcre2-dev:ppc64el (10.42-4ubuntu1) ... 299s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 299s Setting up libreadline-dev:ppc64el (8.2-3) ... 299s Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 299s Setting up gcc-13 (13.2.0-17ubuntu2) ... 299s Setting up r-cran-tidyr (1.3.1-1) ... 299s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 299s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 299s Setting up gfortran-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 299s Setting up libpng-dev:ppc64el (1.6.43-1) ... 299s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 299s Setting up g++-13-powerpc64le-linux-gnu (13.2.0-17ubuntu2) ... 299s Setting up r-cran-broom (1.0.5+dfsg-1) ... 299s Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 299s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 299s Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 299s Setting up g++-13 (13.2.0-17ubuntu2) ... 299s Setting up r-cran-geepack (1.3.10-1) ... 299s Setting up gcc (4:13.2.0-7ubuntu1) ... 299s Setting up gfortran-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... 299s Setting up g++ (4:13.2.0-7ubuntu1) ... 299s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 299s Setting up build-essential (12.10ubuntu1) ... 299s Setting up gfortran (4:13.2.0-7ubuntu1) ... 299s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 299s 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 299s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 299s 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 299s Setting up r-base-dev (4.3.2-1build1) ... 299s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 299s Setting up autopkgtest-satdep (0) ... 299s Processing triggers for man-db (2.12.0-3) ... 300s Processing triggers for install-info (7.1-3) ... 300s Processing triggers for libc-bin (2.39-0ubuntu2) ... 303s (Reading database ... 81511 files and directories currently installed.) 303s Removing autopkgtest-satdep (0) ... 304s autopkgtest [16:26:56]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 304s autopkgtest [16:26:56]: test pkg-r-autopkgtest: [----------------------- 304s Test: Try to load the R library etm 304s 304s R version 4.3.2 (2023-10-31) -- "Eye Holes" 304s Copyright (C) 2023 The R Foundation for Statistical Computing 304s Platform: powerpc64le-unknown-linux-gnu (64-bit) 304s 304s R is free software and comes with ABSOLUTELY NO WARRANTY. 304s You are welcome to redistribute it under certain conditions. 304s Type 'license()' or 'licence()' for distribution details. 304s 304s R is a collaborative project with many contributors. 304s Type 'contributors()' for more information and 304s 'citation()' on how to cite R or R packages in publications. 304s 304s Type 'demo()' for some demos, 'help()' for on-line help, or 304s 'help.start()' for an HTML browser interface to help. 304s Type 'q()' to quit R. 304s 304s > library('etm') 305s > 305s > 305s Other tests are currently unsupported! 305s They will be progressively added. 306s autopkgtest [16:26:58]: test pkg-r-autopkgtest: -----------------------] 306s pkg-r-autopkgtest PASS 306s autopkgtest [16:26:58]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 306s autopkgtest [16:26:58]: @@@@@@@@@@@@@@@@@@@@ summary 306s run-unit-test PASS 306s pkg-r-autopkgtest PASS 325s Creating nova instance adt-noble-ppc64el-r-cran-etm-20240310-162152-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240309.img (UUID 03c4486e-34d9-4279-ba73-b318cbf3f16b)...