0s autopkgtest [02:09:18]: starting date: 2024-03-07 0s autopkgtest [02:09:18]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [02:09:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.orpppe99/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@bos01-arm64-1.secgroup --name adt-noble-arm64-r-cran-etm-20240307-020918-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 261s autopkgtest [02:13:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 262s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 262s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [317 kB] 263s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [1817 kB] 263s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 263s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [23.8 kB] 263s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [439 kB] 263s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 263s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 263s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 263s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2118 kB] 264s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 264s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [14.6 kB] 264s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 270s Fetched 4882 kB in 3s (1716 kB/s) 270s Reading package lists... 279s Reading package lists... 280s Building dependency tree... 280s Reading state information... 281s Calculating upgrade... 282s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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:10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 282s 282s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 282s 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 282s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 282s 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 282s Reading package lists... 283s Building dependency tree... 283s Reading state information... 285s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 286s sh: Attempting to set up Debian/Ubuntu apt sources automatically 286s sh: Distribution appears to be Ubuntu 293s Reading package lists... 294s Building dependency tree... 294s Reading state information... 295s eatmydata is already the newest version (131-1). 295s dbus is already the newest version (1.14.10-4ubuntu1). 295s dbus set to manually installed. 295s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 295s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 295s 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 295s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 295s 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 295s Reading package lists... 296s Building dependency tree... 296s Reading state information... 297s rng-tools-debian is already the newest version (2.4). 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 297s Reading package lists... 298s Building dependency tree... 298s Reading state information... 300s haveged is already the newest version (1.9.14-1ubuntu1). 300s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 300s Reading package lists... 300s Building dependency tree... 300s Reading state information... 302s The following packages will be REMOVED: 302s cloud-init* python3-configobj* python3-debconf* 303s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 303s After this operation, 3248 kB disk space will be freed. 303s (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 ... 75860 files and directories currently installed.) 303s Removing cloud-init (24.1-0ubuntu1) ... 304s Removing python3-configobj (5.0.8-3) ... 305s Removing python3-debconf (1.5.86) ... 305s Processing triggers for man-db (2.12.0-3) ... 306s (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 ... 75471 files and directories currently installed.) 307s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 309s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 309s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 309s Reading package lists... 310s Building dependency tree... 310s Reading state information... 311s linux-generic is already the newest version (6.8.0-11.11+1). 311s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 312s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 312s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 312s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 312s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 312s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 313s Get:6 http://ftpmaster.internal/ubuntu noble/main Sources [1380 kB] 313s Get:7 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 315s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1418 kB] 315s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.0 MB] 320s Fetched 37.9 MB in 8s (4488 kB/s) 327s Reading package lists... 327s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 327s 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 327s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 327s 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 327s Reading package lists... 328s Building dependency tree... 328s Reading state information... 329s Calculating upgrade... 330s The following packages will be REMOVED: 330s libefiboot1 libefivar1 330s The following NEW packages will be installed: 330s libefiboot1t64 libefivar1t64 330s The following packages will be upgraded: 330s dmsetup grub-common grub2-common libdevmapper1.02.1 330s 4 upgraded, 2 newly installed, 2 to remove and 0 not upgraded. 330s Need to get 3143 kB of archives. 330s After this operation, 6144 B of additional disk space will be used. 330s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu1 [128 kB] 331s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 grub2-common arm64 2.12-1ubuntu4 [671 kB] 331s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 grub-common arm64 2.12-1ubuntu4 [2174 kB] 332s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libefivar1t64 arm64 38-3.1 [55.1 kB] 332s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libefiboot1t64 arm64 38-3.1 [40.5 kB] 332s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 dmsetup arm64 2:1.02.185-3ubuntu1 [74.5 kB] 333s Preconfiguring packages ... 333s Fetched 3143 kB in 2s (1735 kB/s) 333s (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 ... 75416 files and directories currently installed.) 333s Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu1_arm64.deb ... 333s Unpacking libdevmapper1.02.1:arm64 (2:1.02.185-3ubuntu1) over (2:1.02.185-2ubuntu1) ... 333s Preparing to unpack .../grub2-common_2.12-1ubuntu4_arm64.deb ... 333s Unpacking grub2-common (2.12-1ubuntu4) over (2.12-1ubuntu3) ... 333s Preparing to unpack .../grub-common_2.12-1ubuntu4_arm64.deb ... 333s Unpacking grub-common (2.12-1ubuntu4) over (2.12-1ubuntu3) ... 334s dpkg: libefivar1:arm64: dependency problems, but removing anyway as you requested: 334s mokutil depends on libefivar1 (>= 37). 334s libefiboot1:arm64 depends on libefivar1 (>= 38). 334s efibootmgr depends on libefivar1 (>= 38). 334s 334s (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 ... 75416 files and directories currently installed.) 334s Removing libefivar1:arm64 (38-3) ... 334s Selecting previously unselected package libefivar1t64:arm64. 334s (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 ... 75411 files and directories currently installed.) 334s Preparing to unpack .../libefivar1t64_38-3.1_arm64.deb ... 334s Unpacking libefivar1t64:arm64 (38-3.1) ... 334s dpkg: libefiboot1:arm64: dependency problems, but removing anyway as you requested: 334s efibootmgr depends on libefiboot1 (>= 38). 334s 334s (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 ... 75417 files and directories currently installed.) 334s Removing libefiboot1:arm64 (38-3) ... 334s Selecting previously unselected package libefiboot1t64:arm64. 334s (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 ... 75412 files and directories currently installed.) 334s Preparing to unpack .../libefiboot1t64_38-3.1_arm64.deb ... 334s Unpacking libefiboot1t64:arm64 (38-3.1) ... 334s Preparing to unpack .../dmsetup_2%3a1.02.185-3ubuntu1_arm64.deb ... 334s Unpacking dmsetup (2:1.02.185-3ubuntu1) over (2:1.02.185-2ubuntu1) ... 334s Setting up libefivar1t64:arm64 (38-3.1) ... 334s Setting up libdevmapper1.02.1:arm64 (2:1.02.185-3ubuntu1) ... 334s Setting up dmsetup (2:1.02.185-3ubuntu1) ... 334s Setting up libefiboot1t64:arm64 (38-3.1) ... 334s Setting up grub-common (2.12-1ubuntu4) ... 335s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 337s Setting up grub2-common (2.12-1ubuntu4) ... 337s Processing triggers for man-db (2.12.0-3) ... 338s Processing triggers for install-info (7.1-3) ... 338s Processing triggers for initramfs-tools (0.142ubuntu19) ... 339s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 339s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 366s System running in EFI mode, skipping. 366s Processing triggers for libc-bin (2.39-0ubuntu2) ... 366s Reading package lists... 367s Building dependency tree... 367s Reading state information... 368s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 369s autopkgtest [02:15:27]: rebooting testbed after setup commands that affected boot 544s autopkgtest [02:18:22]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 544s autopkgtest [02:18:22]: testbed dpkg architecture: arm64 546s autopkgtest [02:18:24]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 547s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 547s 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 547s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 547s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 547s 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 548s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 548s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 548s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 549s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 549s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 549s gpgv: issuer "tille@debian.org" 549s gpgv: Can't check signature: No public key 549s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 549s autopkgtest [02:18:27]: testing package r-cran-etm version 1.1.1-1 549s autopkgtest [02:18:27]: build not needed 551s autopkgtest [02:18:29]: test run-unit-test: preparing testbed 553s Reading package lists... 554s Building dependency tree... 554s Reading state information... 554s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 555s Starting 2 pkgProblemResolver with broken count: 0 555s Done 555s Done 556s Starting pkgProblemResolver with broken count: 0 556s Starting 2 pkgProblemResolver with broken count: 0 556s Done 558s The following additional packages will be installed: 558s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 558s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 558s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 558s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 558s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 558s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 558s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 558s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 558s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 558s r-cran-survival unzip x11-common xdg-utils zip 558s Suggested packages: 558s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 558s r-cran-rmysql r-cran-ggplot2 r-cran-geepack r-cran-getopt r-cran-rodbc 558s r-cran-foreign r-cran-inline 558s Recommended packages: 558s r-recommended r-base-dev r-doc-html r-cran-bit64 r-cran-bit r-cran-curl 558s r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-zoo r-cran-yaml 558s r-cran-knitr r-cran-rmarkdown libfile-mimeinfo-perl libnet-dbus-perl 558s libx11-protocol-perl x11-utils x11-xserver-utils 558s The following NEW packages will be installed: 558s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 558s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 558s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 558s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 558s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 558s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 558s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 558s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 558s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 558s r-cran-survival unzip x11-common xdg-utils zip 558s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 558s 1 not fully installed or removed. 558s Need to get 54.3 MB of archives. 558s After this operation, 114 MB of additional disk space will be used. 558s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB] 559s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB] 559s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] 559s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B] 559s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 559s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 559s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 559s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 559s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 559s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 560s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 560s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 560s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 560s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 560s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 560s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 560s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 560s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 560s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 560s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 560s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 560s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 560s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 561s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 561s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 561s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 561s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 561s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 561s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 561s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 561s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 561s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 561s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 561s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 561s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 561s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 561s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 561s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 561s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 561s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 561s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] 561s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] 561s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB] 561s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB] 563s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB] 563s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB] 563s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB] 564s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-data.table arm64 1.14.10+dfsg-1 [1844 kB] 564s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB] 564s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 littler all 0.3.19-1 [2472 B] 564s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 564s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcpp arm64 1.0.12-1 [1971 kB] 564s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-cran-rcpparmadillo arm64 0.12.8.1.0-1 [859 kB] 564s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-etm arm64 1.1.1-1 [469 kB] 564s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dbi all 1.2.2-1 [823 kB] 564s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mitools all 2.4-2build1 [265 kB] 564s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-kmi all 0.5.5-2build1 [78.3 kB] 565s Preconfiguring packages ... 565s Fetched 54.3 MB in 6s (9677 kB/s) 565s Selecting previously unselected package zip. 565s (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 ... 75418 files and directories currently installed.) 565s Preparing to unpack .../00-zip_3.0-13_arm64.deb ... 565s Unpacking zip (3.0-13) ... 565s Selecting previously unselected package unzip. 565s Preparing to unpack .../01-unzip_6.0-28ubuntu3_arm64.deb ... 565s Unpacking unzip (6.0-28ubuntu3) ... 565s Selecting previously unselected package libpaper1:arm64. 565s Preparing to unpack .../02-libpaper1_1.1.29_arm64.deb ... 565s Unpacking libpaper1:arm64 (1.1.29) ... 565s Selecting previously unselected package libpaper-utils. 565s Preparing to unpack .../03-libpaper-utils_1.1.29_arm64.deb ... 565s Unpacking libpaper-utils (1.1.29) ... 565s Selecting previously unselected package xdg-utils. 565s Preparing to unpack .../04-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 565s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 565s Selecting previously unselected package libblas3:arm64. 565s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 565s Unpacking libblas3:arm64 (3.12.0-3) ... 565s Selecting previously unselected package fonts-dejavu-mono. 565s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 565s Unpacking fonts-dejavu-mono (2.37-8) ... 565s Selecting previously unselected package fonts-dejavu-core. 565s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 565s Unpacking fonts-dejavu-core (2.37-8) ... 566s Selecting previously unselected package fontconfig-config. 566s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 566s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 566s Selecting previously unselected package libfontconfig1:arm64. 566s Preparing to unpack .../09-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 566s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 566s Selecting previously unselected package libpixman-1-0:arm64. 566s Preparing to unpack .../10-libpixman-1-0_0.42.2-1_arm64.deb ... 566s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 566s Selecting previously unselected package libxcb-render0:arm64. 566s Preparing to unpack .../11-libxcb-render0_1.15-1_arm64.deb ... 566s Unpacking libxcb-render0:arm64 (1.15-1) ... 566s Selecting previously unselected package libxcb-shm0:arm64. 566s Preparing to unpack .../12-libxcb-shm0_1.15-1_arm64.deb ... 566s Unpacking libxcb-shm0:arm64 (1.15-1) ... 566s Selecting previously unselected package libxrender1:arm64. 566s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 566s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 566s Selecting previously unselected package libcairo2:arm64. 566s Preparing to unpack .../14-libcairo2_1.18.0-1_arm64.deb ... 566s Unpacking libcairo2:arm64 (1.18.0-1) ... 566s Selecting previously unselected package libgomp1:arm64. 566s Preparing to unpack .../15-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 566s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 566s Selecting previously unselected package libjpeg-turbo8:arm64. 566s Preparing to unpack .../16-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 566s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 567s Selecting previously unselected package libjpeg8:arm64. 567s Preparing to unpack .../17-libjpeg8_8c-2ubuntu11_arm64.deb ... 567s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 567s Selecting previously unselected package libgfortran5:arm64. 567s Preparing to unpack .../18-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 567s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 567s Selecting previously unselected package liblapack3:arm64. 567s Preparing to unpack .../19-liblapack3_3.12.0-3_arm64.deb ... 567s Unpacking liblapack3:arm64 (3.12.0-3) ... 567s Selecting previously unselected package fontconfig. 567s Preparing to unpack .../20-fontconfig_2.15.0-1ubuntu1_arm64.deb ... 567s Unpacking fontconfig (2.15.0-1ubuntu1) ... 567s Selecting previously unselected package libgraphite2-3:arm64. 567s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_arm64.deb ... 567s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 567s Selecting previously unselected package libharfbuzz0b:arm64. 567s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_arm64.deb ... 567s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 567s Selecting previously unselected package libthai-data. 567s Preparing to unpack .../23-libthai-data_0.1.29-2_all.deb ... 567s Unpacking libthai-data (0.1.29-2) ... 567s Selecting previously unselected package libdatrie1:arm64. 567s Preparing to unpack .../24-libdatrie1_0.2.13-3_arm64.deb ... 567s Unpacking libdatrie1:arm64 (0.2.13-3) ... 567s Selecting previously unselected package libthai0:arm64. 567s Preparing to unpack .../25-libthai0_0.1.29-2_arm64.deb ... 567s Unpacking libthai0:arm64 (0.1.29-2) ... 567s Selecting previously unselected package libpango-1.0-0:arm64. 567s Preparing to unpack .../26-libpango-1.0-0_1.51.0+ds-4_arm64.deb ... 567s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ... 567s Selecting previously unselected package libpangoft2-1.0-0:arm64. 567s Preparing to unpack .../27-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 567s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 567s Selecting previously unselected package libpangocairo-1.0-0:arm64. 567s Preparing to unpack .../28-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 567s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 567s Selecting previously unselected package libtcl8.6:arm64. 567s Preparing to unpack .../29-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 567s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 568s Selecting previously unselected package libdeflate0:arm64. 568s Preparing to unpack .../30-libdeflate0_1.19-1_arm64.deb ... 568s Unpacking libdeflate0:arm64 (1.19-1) ... 568s Selecting previously unselected package libjbig0:arm64. 568s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 568s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 568s Selecting previously unselected package liblerc4:arm64. 568s Preparing to unpack .../32-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 568s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 568s Selecting previously unselected package libsharpyuv0:arm64. 568s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_arm64.deb ... 568s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 568s Selecting previously unselected package libwebp7:arm64. 568s Preparing to unpack .../34-libwebp7_1.3.2-0.4_arm64.deb ... 568s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 568s Selecting previously unselected package 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590s Type 'license()' or 'licence()' for distribution details. 590s 590s R is a collaborative project with many contributors. 590s Type 'contributors()' for more information and 590s 'citation()' on how to cite R or R packages in publications. 590s 590s Type 'demo()' for some demos, 'help()' for on-line help, or 590s 'help.start()' for an HTML browser interface to help. 590s Type 'q()' to quit R. 590s 590s > ### test file for etmCIF. 590s > ### Really simple tests and comparison with etm 590s > 590s > old <- options(digits = 5) 590s > 590s > require(etm) 590s Loading required package: etm 593s > 593s > if (!require(survival, quietly = TRUE)) { 593s + print("The following tests require the 'survival' package") 593s + } else { 593s + 593s + data(abortion) 593s + 593s + from <- rep(0, nrow(abortion)) 593s + to <- abortion$cause 593s + entry <- abortion$entry 593s + exit <- abortion$exit 593s + id <- 1:nrow(abortion) 593s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 593s + 593s + ## Computation of the CIFs with etm 593s + tra <- matrix(FALSE, 4, 4) 593s + tra[1, 2:4] <- TRUE 593s + 593s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 593s + tra, NULL, 0) 593s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 593s + tra, NULL, 0) 593s + 593s + 593s + ## Computation of the CIFs with etmCIF 593s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 593s + etype = cause, failcode = 3) 593s + 593s + ### let's do some comparisons :-) 593s + 593s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 593s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 593s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 593s + 593s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 593s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 593s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 593s + 593s + 593s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 593s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 593s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 593s + 593s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 593s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 593s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 593s + 593s + 593s + netm 593s + 593s + ## test on the summary 593s + snetm <- summary(netm) 593s + 593s + snetm 593s + 593s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 593s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 593s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 593s + 593s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 593s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 593s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 593s + 593s + scif.control <- summary(cif.control, ci.fun = "cloglog") 593s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 593s + 593s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 593s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 593s + 593s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 593s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 593s + } 594s [1] TRUE 594s > 594s > ### test with factors in the input 594s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 594s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 594s > 594s > abortion$status <- factor(abortion$status) 594s > 594s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 594s + etype = status, failcode = "spontaneous abortion") 594s > 594s > 594s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 594s [1] TRUE 594s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 594s [1] TRUE 594s > 594s > netm.factor 594s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 594s data = abortion, etype = status, failcode = "spontaneous abortion") 594s 594s Covariate: group 594s levels: 0 1 594s 594s 594s group = 0 594s time P se(P) n.event 594s CIF ETOP 43 0.040159 0.0092578 20 594s CIF life birth 43 0.799059 0.0221865 924 594s CIF spontaneous abortion 43 0.160781 0.0213261 69 594s 594s group = 1 594s time P se(P) n.event 594s CIF ETOP 42 0.28511 0.042493 38 594s CIF life birth 42 0.35257 0.042139 92 594s CIF spontaneous abortion 42 0.36232 0.049473 43 594s > 594s > summary(netm.factor) 594s 594s group=0 594s 594s CIF ETOP 594s P time var lower upper n.risk n.event 594s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 594s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 594s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 594s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 594s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 594s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 594s 594s CIF life birth 594s P time var lower upper n.risk n.event 594s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 594s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 594s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 594s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 594s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 594s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 594s 594s CIF spontaneous abortion 594s P time var lower upper n.risk n.event 594s 0.034188 6 0.00028222 0.01297 0.088523 117 4 594s 0.150468 13 0.00045513 0.11360 0.197901 645 1 594s 0.159904 26 0.00045498 0.12274 0.206925 846 1 594s 0.160781 36 0.00045480 0.12360 0.207757 876 1 594s 0.160781 40 0.00045480 0.12360 0.207757 554 0 594s 0.160781 43 0.00045480 0.12360 0.207757 6 0 594s 594s 594s group=1 594s 594s CIF ETOP 594s P time var lower upper n.risk n.event 594s 0.00000 6 0.0000000 0.00000 0.00000 35 0 594s 0.26048 13 0.0017854 0.18795 0.35425 90 0 594s 0.28115 21 0.0018028 0.20742 0.37423 93 1 594s 0.28511 34 0.0018057 0.21116 0.37806 89 0 594s 0.28511 39 0.0018057 0.21116 0.37806 59 0 594s 0.28511 42 0.0018057 0.21116 0.37806 6 0 594s 594s CIF life birth 594s P time var lower upper n.risk n.event 594s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 594s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 594s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 594s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 594s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 594s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 594s 594s CIF spontaneous abortion 594s P time var lower upper n.risk n.event 594s 0.057143 6 0.0015394 0.014605 0.20968 35 2 594s 0.333246 13 0.0025280 0.245337 0.44216 90 4 594s 0.350702 21 0.0024827 0.262769 0.45762 93 0 594s 0.358492 34 0.0024593 0.270627 0.46448 89 0 594s 0.358492 39 0.0024593 0.270627 0.46448 59 0 594s 0.362323 42 0.0024476 0.274499 0.46785 6 0 594s 594s > 594s > ### test with group as a character vector 594s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 594s > abortion$ttt <- factor(abortion$ttt) 594s > 594s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 594s + etype = status, failcode = "spontaneous abortion") 594s > 594s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 594s [1] TRUE 594s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 594s [1] TRUE 594s > 594s > netm.ttt 594s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 594s etype = status, failcode = "spontaneous abortion") 594s 594s Covariate: ttt 594s levels: control exposed 594s 594s 594s ttt = control 594s time P se(P) n.event 594s CIF ETOP 43 0.040159 0.0092578 20 594s CIF life birth 43 0.799059 0.0221865 924 594s CIF spontaneous abortion 43 0.160781 0.0213261 69 594s 594s ttt = exposed 594s time P se(P) n.event 594s CIF ETOP 42 0.28511 0.042493 38 594s CIF life birth 42 0.35257 0.042139 92 594s CIF spontaneous abortion 42 0.36232 0.049473 43 594s > 594s > summary(netm.ttt) 594s 594s ttt=control 594s 594s CIF ETOP 594s P time var lower upper n.risk n.event 594s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 594s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 594s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 594s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 594s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 594s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 594s 594s CIF life birth 594s P time var lower upper n.risk n.event 594s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 594s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 594s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 594s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 594s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 594s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 594s 594s CIF spontaneous abortion 594s P time var lower upper n.risk n.event 594s 0.034188 6 0.00028222 0.01297 0.088523 117 4 594s 0.150468 13 0.00045513 0.11360 0.197901 645 1 594s 0.159904 26 0.00045498 0.12274 0.206925 846 1 594s 0.160781 36 0.00045480 0.12360 0.207757 876 1 594s 0.160781 40 0.00045480 0.12360 0.207757 554 0 594s 0.160781 43 0.00045480 0.12360 0.207757 6 0 594s 594s 594s ttt=exposed 594s 594s CIF ETOP 594s P time var lower upper n.risk n.event 594s 0.00000 6 0.0000000 0.00000 0.00000 35 0 594s 0.26048 13 0.0017854 0.18795 0.35425 90 0 594s 0.28115 21 0.0018028 0.20742 0.37423 93 1 594s 0.28511 34 0.0018057 0.21116 0.37806 89 0 594s 0.28511 39 0.0018057 0.21116 0.37806 59 0 594s 0.28511 42 0.0018057 0.21116 0.37806 6 0 594s 594s CIF life birth 594s P time var lower upper n.risk n.event 594s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 594s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 594s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 594s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 594s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 594s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 594s 594s CIF spontaneous abortion 594s P time var lower upper n.risk n.event 594s 0.057143 6 0.0015394 0.014605 0.20968 35 2 594s 0.333246 13 0.0025280 0.245337 0.44216 90 4 594s 0.350702 21 0.0024827 0.262769 0.45762 93 0 594s 0.358492 34 0.0024593 0.270627 0.46448 89 0 594s 0.358492 39 0.0024593 0.270627 0.46448 59 0 594s 0.362323 42 0.0024476 0.274499 0.46785 6 0 594s 594s > 594s > 594s > ### A couple of comparisons with simulated data 594s > set.seed(1313) 594s > time <- rexp(100) 594s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 594s > from <- rep(11, 100) 594s > id <- 1:100 594s > cov <- rbinom(100, 1, 0.5) 594s > 594s > dat.s <- data.frame(id, time, from, to, cov) 594s > 594s > traa <- matrix(FALSE, 3, 3) 594s > traa[1, 2:3] <- TRUE 594s > 594s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 594s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 594s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 594s > 594s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 594s > 594s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 594s > 594s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 594s [1] TRUE 594s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 594s [1] TRUE 594s > 594s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 594s [1] TRUE 594s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 594s [1] TRUE 594s > 594s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 594s [1] TRUE 594s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 594s [1] TRUE 594s > 594s > test 594s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 594s 594s time P se(P) n.event 594s CIF 1 4.9088 0.809108 0.079680 45 594s CIF 2 4.9088 0.096618 0.032905 8 594s > 594s > test.c 594s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 594s 594s Covariate: cov 594s levels: 0 1 594s 594s 594s cov = 0 594s time P se(P) n.event 594s CIF 1 2.1708 0.70246 0.105797 19 594s CIF 2 2.1708 0.11144 0.053384 4 594s 594s cov = 1 594s time P se(P) n.event 594s CIF 1 4.9088 0.80787 0.094051 26 594s CIF 2 4.9088 0.08436 0.040769 4 594s > 594s > summary(test) 594s 594s 594s 594s CIF 1 594s P time var lower upper n.risk n.event 594s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 594s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 594s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 594s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 594s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 594s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 594s 594s CIF 2 594s P time var lower upper n.risk n.event 594s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 594s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 594s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 594s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 594s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 594s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 594s 594s > summary(test.c) 594s 594s cov=0 594s 594s CIF 1 594s P time var lower upper n.risk n.event 594s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 594s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 594s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 594s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 594s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 594s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 594s 594s CIF 2 594s P time var lower upper n.risk n.event 594s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 594s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 594s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 594s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 594s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 594s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 594s 594s 594s cov=1 594s 594s CIF 1 594s P time var lower upper n.risk n.event 594s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 594s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 594s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 594s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 594s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 594s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 594s 594s CIF 2 594s P time var lower upper n.risk n.event 594s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 594s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 594s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 594s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 594s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 594s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 594s 594s > 594s > options(old) 594s > 594s BEGIN TEST tests.etm.R 595s 595s R version 4.3.2 (2023-10-31) -- "Eye Holes" 595s Copyright (C) 2023 The R Foundation for Statistical Computing 595s Platform: aarch64-unknown-linux-gnu (64-bit) 595s 595s R is free software and comes with ABSOLUTELY NO WARRANTY. 595s You are welcome to redistribute it under certain conditions. 595s Type 'license()' or 'licence()' for distribution details. 595s 595s R is a collaborative project with many contributors. 595s Type 'contributors()' for more information and 595s 'citation()' on how to cite R or R packages in publications. 595s 595s Type 'demo()' for some demos, 'help()' for on-line help, or 595s 'help.start()' for an HTML browser interface to help. 595s Type 'q()' to quit R. 595s 595s > require(etm) 595s Loading required package: etm 598s > 598s > ## Print with a bit less precision to avoid lots of notes in the comparison 598s > old <- options(digits = 4) 598s > 598s > ### Simple test 598s > 598s > time <- id <- 1:10 598s > from <- rep(0, 10) 598s > to <- rep(1, 10) 598s > 598s > data1 <- data.frame(id, from, to, time) 598s > tra1 <- matrix(FALSE, 2, 2) 598s > tra1[1, 2] <- TRUE 598s > 598s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 598s > 598s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 598s [1] TRUE 598s > 598s > etm1$cov["0 0", "0 0", ] 598s 1 2 3 4 5 6 7 8 9 10 598s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 598s > 598s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 598s [1] TRUE 598s > 598s > ### A simple test from AHR's author, where the first time is censored 598s > if (!require(survival)) { 598s + stop("This test requires the survival package") 598s + } 598s > 598s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 598s > 598s > tra <- matrix(FALSE, nrow=2, ncol=2) 598s > tra[1, 2] <- TRUE 598s > 598s > data$to[1] <- "cens" 598s > data$status[1] <- FALSE 598s > 598s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 598s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 598s Loading required package: survival 598s > 598s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 598s [1] TRUE 598s > 598s > data$to[2] <- "cens" 598s > data$status[2] <- FALSE 598s > 598s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 598s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 598s > 598s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 598s [1] TRUE 598s > 598s > ### a bit more complicated 598s > 598s > time <- id <- 1:10 598s > from <- rep(0, 10) 598s > to <- rep(c(1, 2), 5) 598s > data2 <- data.frame(id, from, to, time) 598s > 598s > tra2 <- matrix(FALSE, 3, 3) 598s > tra2[1, 2:3] <- TRUE 598s > 598s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 598s > 598s > aa <- table(time, to) 598s > 598s > cif1 <- cumsum(aa[, 1] / 10) 598s > cif2 <- cumsum(aa[, 2] / 10) 598s > surv <- cumprod((10:1 - 1) / (10:1)) 598s > 598s > all.equal(trprob(etm2, "0 1"), cif1) 598s [1] TRUE 598s > all.equal(trprob(etm2, "0 2"), cif2) 598s [1] TRUE 598s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 598s [1] TRUE 598s > 598s > ## a test on id 598s > data2$id <- letters[1:10] 598s > 598s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 598s > 598s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 598s [1] TRUE 598s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 598s [1] TRUE 598s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 598s [1] TRUE 598s > 598s > 598s > ### Test on sir.cont 598s > 598s > data(sir.cont) 598s > 598s > ## Modification for patients entering and leaving a state 598s > ## at the same date 598s > ## Change on ventilation status is considered 598s > ## to happen before end of hospital stay 598s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 598s > for (i in 2:nrow(sir.cont)) { 598s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 598s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 598s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 598s + } 598s + } 598s + } 598s > 598s > ### Computation of the transition probabilities 598s > ## Possible transitions. 598s > tra <- matrix(ncol=3,nrow=3,FALSE) 598s > tra[1, 2:3] <- TRUE 598s > tra[2, c(1, 3)] <- TRUE 598s > 598s > ## etm 598s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 598s > 598s > prob.sir 598s Multistate model with 2 transient state(s) 598s and 1 absorbing state(s) 598s 598s Possible transitions: 598s from to 598s 0 1 598s 0 2 598s 1 0 598s 1 2 598s 598s Estimate of P(1, 183) 598s 0 1 2 598s 0 0 0 1 598s 1 0 0 1 598s 2 0 0 1 598s 598s > 598s > summ.sir <- summary(prob.sir) 598s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 598s [1] TRUE 598s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 598s P time var lower upper n.risk n.event 598s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 598s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 598s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 598s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 598s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 598s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 598s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 598s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 598s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 598s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 598s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 598s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 598s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 598s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 598s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 598s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 598s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 598s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 598s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 598s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 598s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 598s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 598s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 598s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 598s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 598s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 598s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 598s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 598s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 598s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 598s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 598s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 598s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 598s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 598s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 598s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 598s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 598s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 598s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 598s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 598s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 598s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 598s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 598s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 598s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 598s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 598s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 598s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 598s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 598s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 598s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 598s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 598s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 598s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 598s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 598s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 598s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 598s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 598s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 598s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 598s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 598s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 598s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 598s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 598s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 598s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 598s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 598s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 598s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 598s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 598s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 598s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 598s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 598s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 598s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 598s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 598s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 598s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 598s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 598s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 598s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 598s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 598s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 598s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 598s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 598s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 598s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 598s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 598s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 598s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 598s > 598s > ## gonna play a bit with the state names 598s > dd <- sir.cont 598s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 598s > dd$to <- as.character(dd$to) 598s > for (i in seq_len(nrow(dd))) { 598s + dd$to[i] <- switch(dd$to[i], 598s + "0" = "initial state", 598s + "1" = "ventilation", 598s + "2" = "end of story", 598s + "cens" = "cens" 598s + ) 598s + } 598s > 598s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 599s > 599s > all.equal(test$est["initial state", "initial state", ], 599s + prob.sir$est["0", "0", ]) 599s [1] TRUE 599s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 599s [1] TRUE 599s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 599s [1] TRUE 599s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 599s [1] TRUE 599s > 599s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 599s [1] TRUE 599s > 599s > aa <- summary(test) 599s > all.equal(summ.sir[[6]], aa[[6]]) 599s [1] TRUE 599s > all.equal(summ.sir[[4]], aa[[4]]) 599s [1] TRUE 599s > 599s > ### Test on abortion data 599s > 599s > data(abortion) 599s > 599s > from <- rep(0, nrow(abortion)) 599s > to <- abortion$cause 599s > entry <- abortion$entry 599s > exit <- abortion$exit 599s > id <- 1:nrow(abortion) 599s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 599s > 599s > ## Computation of the CIFs 599s > tra <- matrix(FALSE, 4, 4) 599s > tra[1, 2:4] <- TRUE 599s > 599s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 599s + tra, NULL, 0) 599s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 599s + tra, NULL, 0) 599s > 599s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 599s [1] TRUE 599s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 599s [1] TRUE 599s > 599s > trprob(cif.control, "0 1") 599s 6 7 8 9 10 11 12 13 599s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 599s 14 17 19 21 24 25 26 30 599s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 599s 31 32 33 34 35 36 37 38 599s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 599s 39 40 41 42 43 599s 0.040159 0.040159 0.040159 0.040159 0.040159 599s > trprob(cif.control, "0 2") 599s 6 7 8 9 10 11 12 13 599s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 599s 14 17 19 21 24 25 26 30 599s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 599s 31 32 33 34 35 36 37 38 599s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 599s 39 40 41 42 43 599s 0.322016 0.563121 0.742227 0.793893 0.799059 599s > trprob(cif.control, "0 0") 599s 6 7 8 9 10 11 12 13 599s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 599s 14 17 19 21 24 25 26 30 599s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 599s 31 32 33 34 35 36 37 38 599s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 599s 39 40 41 42 43 599s 0.477043 0.235938 0.056832 0.005167 0.000000 599s > 599s > trcov(cif.control, "0 1") 599s 6 7 8 9 10 11 12 13 599s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 599s 14 17 19 21 24 25 26 30 599s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 599s 31 32 33 34 35 36 37 38 599s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 599s 39 40 41 42 43 599s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 599s > trcov(cif.control, "0 2") 599s 6 7 8 9 10 11 12 13 599s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 599s 14 17 19 21 24 25 26 30 599s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 599s 31 32 33 34 35 36 37 38 599s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 599s 39 40 41 42 43 599s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 599s > trcov(cif.control, "0 0") 599s 6 7 8 9 10 11 12 13 599s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 599s 14 17 19 21 24 25 26 30 599s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 599s 31 32 33 34 35 36 37 38 599s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 599s 39 40 41 42 43 599s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 599s > 599s > aa <- summary(cif.control) 599s > aa$"0 1" 599s P time var lower upper n.risk n.event 599s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 599s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 599s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 599s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 599s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 599s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 599s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 599s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 599s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 599s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 599s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 599s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 599s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 599s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 599s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 599s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 599s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 599s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 599s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 599s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 599s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 599s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 599s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 599s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 599s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 599s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 599s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 599s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 599s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 599s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 599s [1] TRUE 599s > 599s > ### test on los data 599s > 599s > data(los.data) # in package changeLOS 599s > 599s > ## putting los.data in the long format (see changeLOS) 599s > my.observ <- prepare.los.data(x=los.data) 599s > 599s > tra <- matrix(FALSE, 4, 4) 599s > tra[1, 2:4] <- TRUE 599s > tra[2, 3:4] <- TRUE 599s > 599s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 599s > 599s > tr.prob 599s Multistate model with 2 transient state(s) 599s and 2 absorbing state(s) 599s 599s Possible transitions: 599s from to 599s 0 1 599s 0 2 599s 0 3 599s 1 2 599s 1 3 599s 599s Estimate of P(0, 82) 599s 0 1 2 3 599s 0 0 0 0.7474 0.2526 599s 1 0 0 0.7073 0.2927 599s 2 0 0 1.0000 0.0000 599s 3 0 0 0.0000 1.0000 599s 599s > summary(tr.prob) 599s Transition 0 0 599s P time var lower upper n.risk n.event 599s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 599s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 599s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 599s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 599s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 599s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 599s 599s Transition 0 1 599s P time var lower upper n.risk n.event 599s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 599s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 599s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 599s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 599s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 599s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 599s 599s Transition 0 2 599s P time var lower upper n.risk n.event 599s 0.08466 3 0.0001025 0.06481 0.1045 756 64 599s 0.62302 15 0.0003107 0.58847 0.6576 90 4 599s 0.69841 27 0.0002786 0.66570 0.7311 26 1 599s 0.72751 41 0.0002622 0.69578 0.7593 5 0 599s 0.74074 61 0.0002540 0.70950 0.7720 3 1 599s 0.74735 82 0.0002498 0.71638 0.7783 1 1 599s 599s Transition 0 3 599s P time var lower upper n.risk n.event 599s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 599s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 599s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 599s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 599s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 599s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 599s 599s Transition 1 1 599s P time var lower upper n.risk n.event 599s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 599s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 599s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 599s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 599s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 599s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 599s 599s Transition 1 2 599s P time var lower upper n.risk n.event 599s 0.0000 3 0.000000 0.0000 0.0000 0 0 599s 0.4107 15 0.002590 0.3110 0.5104 51 2 599s 0.6082 27 0.002254 0.5151 0.7012 23 1 599s 0.6652 41 0.002064 0.5761 0.7542 14 2 599s 0.6920 61 0.002000 0.6043 0.7796 4 0 599s 0.7073 82 0.001984 0.6200 0.7946 0 0 599s 599s Transition 1 3 599s P time var lower upper n.risk n.event 599s 0.0000 3 0.000000 0.0000 0.0000 0 0 599s 0.2027 15 0.001784 0.1199 0.2855 51 1 599s 0.2706 27 0.001968 0.1837 0.3576 23 0 599s 0.2889 41 0.001982 0.2016 0.3761 14 0 599s 0.2927 61 0.001984 0.2054 0.3800 4 0 599s 0.2927 82 0.001984 0.2054 0.3800 0 0 599s 599s > 599s > cLOS <- etm::clos(tr.prob, aw = TRUE) 599s > 599s > cLOS 599s The expected change in length of stay is: 599s 1.975 599s 599s Alternative weighting: 599s 599s Expected change in LOS with weight.1: 2.097 599s Expected change in LOS with weight.other: 1.951 599s > 599s > 599s > ### Tests on pseudo values 599s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 599s + formula = ~ 1, aw = TRUE) 638s > 638s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 638s [,1] 638s [1,] TRUE 638s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 638s [,1] 638s [1,] TRUE 638s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 638s [,1] 638s [1,] TRUE 638s > 638s > mean(t_pseudo$pseudoData$ps.e.phi) 638s [1] 1.968 638s > 638s > ### tests on etmprep 638s > 638s > ### creation of fake data in the wild format, following an illness-death model 638s > ## transition times 638s > tdisease <- c(3, 4, 3, 6, 8, 9) 638s > tdeath <- c(6, 9, 8, 6, 8, 9) 638s > 638s > ## transition status 638s > stat.disease <- c(1, 1, 1, 0, 0, 0) 638s > stat.death <- c(1, 1, 1, 1, 1, 0) 638s > 638s > ## a covariate that we want to keep in the new data 638s > set.seed(1313) 638s > cova <- rbinom(6, 1, 0.5) 638s > 638s > dat <- data.frame(tdisease, tdeath, 638s + stat.disease, stat.death, 638s + cova) 638s > 638s > ## Possible transitions 638s > tra <- matrix(FALSE, 3, 3) 638s > tra[1, 2:3] <- TRUE 638s > tra[2, 3] <- TRUE 638s > 638s > ## data preparation 638s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 638s + c(NA, "stat.disease", "stat.death"), 638s + data = dat, tra = tra, 638s + cens.name = "cens", keep = "cova") 638s > 638s > newdat 638s id entry exit from to cova 638s 1 1 0 3 0 1 1 638s 2 1 3 6 1 2 1 638s 3 2 0 4 0 1 0 638s 4 2 4 9 1 2 0 638s 5 3 0 3 0 1 1 638s 6 3 3 8 1 2 1 638s 7 4 0 6 0 2 0 638s 8 5 0 8 0 2 1 638s 9 6 0 9 0 cens 1 638s > 638s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 638s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 638s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 638s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 638s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 638s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 638s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 638s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 638s > 638s > all.equal(ref, newdat) 638s [1] TRUE 638s > 638s > 638s > ###################################### 638s > ### Test the stratified calls 638s > ###################################### 638s > 638s > if (require("kmi", quietly = TRUE)) { 638s + library(etm) 638s + 638s + data(icu.pneu) 638s + my.icu.pneu <- icu.pneu 638s + 638s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 638s + masque <- diff(my.icu.pneu$id) 638s + 638s + my.icu.pneu$from <- 0 638s + my.icu.pneu$from[c(1, masque) == 0] <- 1 638s + 638s + my.icu.pneu$to2 <- my.icu.pneu$event 638s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 638s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 638s + 638s + 638s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 638s + my.icu.pneu$to2) 638s + 638s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 638s + "to2", "age", "sex")] 638s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 638s + 638s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 638s + 638s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 638s + c("0", "1", "2"), tra_ill(), "cens", 0) 638s + 638s + all(bouh_strat[[1]]$est == bouh_female$est) 638s + 638s + ## Test the summary 638s + the_summary <- summary(bouh_strat) 638s + the_summary 638s + 638s + ## Test trprob 638s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 638s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 638s + 638s + ## Test trcov 638s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 638s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 638s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 638s + } else { 638s + print("These tests require the kmi package") 638s + } 639s [1] TRUE 639s > 639s > options(old) 639s > 639s autopkgtest [02:19:57]: test run-unit-test: -----------------------] 640s autopkgtest [02:19:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 640s run-unit-test PASS 640s autopkgtest [02:19:58]: test pkg-r-autopkgtest: preparing testbed 642s Reading package lists... 643s Building dependency tree... 643s Reading state information... 644s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 644s Starting 2 pkgProblemResolver with broken count: 0 644s Done 645s Done 645s Starting pkgProblemResolver with broken count: 0 646s Starting 2 pkgProblemResolver with broken count: 0 646s Done 647s The following additional packages will be installed: 647s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 647s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 647s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 647s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 647s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 647s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 647s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 647s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 647s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 647s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 647s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 647s r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-dplyr 647s r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics 647s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling 647s r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell 647s r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 647s r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 647s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 647s r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 647s Suggested packages: 647s cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib 647s manpages-dev autoconf automake libtool flex bison gdb gcc-doc 647s gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev 647s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 647s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 647s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 647s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 647s r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata r-cran-caret 647s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 647s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-glmnet r-cran-gmm 647s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-knitr r-cran-ks r-cran-lavaan 647s r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans r-cran-maps 647s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 647s r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg 647s r-cran-rmarkdown r-cran-robust r-cran-robustbase r-cran-rsample 647s r-cran-sandwich r-cran-sp r-cran-spdep r-cran-spatialreg r-cran-spelling 647s r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth 647s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 647s r-cran-png r-cran-jpeg r-cran-viridis r-cran-magick r-cran-sf r-cran-bit64 647s r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units 647s r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio 647s r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms 647s r-cran-htmltools r-cran-pkgbuild r-cran-pkgload 647s Recommended packages: 647s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-cran-testthat 647s r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools 647s r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps 647s r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami 647s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 647s r-cran-progress r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql 647s r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc 647s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 647s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 647s r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-httr 647s r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms 647s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 647s The following NEW packages will be installed: 647s build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu 647s dctrl-tools g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 647s gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-13 647s gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 647s libasan8 libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 647s libcrypt-dev libgcc-13-dev libgfortran-13-dev libhwasan0 libicu-dev libisl23 647s libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 647s liblzma-dev libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 647s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 647s libstdc++-13-dev libtirpc-dev libtsan2 libubsan1 linux-libc-dev pkg-config 647s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-backports 647s r-cran-broom r-cran-cli r-cran-colorspace r-cran-cpp11 r-cran-dplyr 647s r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-geepack r-cran-generics 647s r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling 647s r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell 647s r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 647s r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 647s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs 647s r-cran-viridislite r-cran-withr rpcsvc-proto zlib1g-dev 648s 0 upgraded, 99 newly installed, 0 to remove and 0 not upgraded. 648s 1 not fully installed or removed. 648s Need to get 123 MB of archives. 648s After this operation, 392 MB of additional disk space will be used. 648s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB] 649s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB] 649s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB] 649s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 649s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 649s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB] 649s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mass arm64 7.3-60.0.1-1 [1119 kB] 650s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-nlme arm64 3.1.164-1 [2259 kB] 650s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 650s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-farver arm64 2.1.1-1 [1336 kB] 650s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB] 650s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-colorspace arm64 2.1-0+dfsg-1 [1540 kB] 651s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] 651s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB] 651s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 651s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB] 651s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-scales all 1.3.0-1 [603 kB] 651s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB] 651s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 651s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB] 651s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 651s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 651s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 651s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB] 651s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB] 651s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 651s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-backports arm64 1.4.1-1 [101 kB] 651s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 651s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB] 651s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB] 651s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-ellipsis arm64 0.3.2-2 [35.5 kB] 651s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB] 651s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB] 651s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB] 651s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB] 651s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB] 652s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 652s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-geepack arm64 1.3.10-1 [366 kB] 652s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB] 652s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB] 652s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB] 652s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] 652s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] 652s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] 652s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB] 652s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB] 652s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB] 652s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB] 652s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB] 652s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B] 652s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] 652s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] 652s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB] 652s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB] 652s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB] 652s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB] 653s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB] 653s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB] 653s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB] 653s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB] 653s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB] 653s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB] 654s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB] 654s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] 654s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] 654s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB] 654s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB] 655s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB] 655s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] 655s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] 655s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 655s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB] 655s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB] 655s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB] 655s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B] 655s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] 655s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] 655s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] 655s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] 655s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline-dev arm64 8.2-3 [177 kB] 655s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB] 655s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 655s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 655s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB] 655s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB] 655s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B] 655s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB] 655s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB] 655s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpng-dev arm64 1.6.43-1 [266 kB] 655s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB] 655s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB] 655s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] 655s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] 656s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] 656s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB] 656s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] 656s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B] 656s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-dev all 4.3.2-1build1 [4336 B] 656s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 657s Fetched 123 MB in 8s (14.6 MB/s) 658s Selecting previously unselected package r-cran-cli. 658s (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 ... 79691 files and directories currently installed.) 658s Preparing to unpack .../00-r-cran-cli_3.6.2-1_arm64.deb ... 658s Unpacking r-cran-cli (3.6.2-1) ... 658s Selecting previously unselected package r-cran-glue. 658s Preparing to unpack .../01-r-cran-glue_1.7.0-1_arm64.deb ... 658s Unpacking r-cran-glue (1.7.0-1) ... 658s Selecting previously unselected package r-cran-rlang. 658s Preparing to unpack .../02-r-cran-rlang_1.1.3-1_arm64.deb ... 658s Unpacking r-cran-rlang (1.1.3-1) ... 658s Selecting previously unselected package r-cran-lifecycle. 658s Preparing to unpack .../03-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 658s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 658s Selecting previously unselected package r-cran-gtable. 658s Preparing to unpack .../04-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 658s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 658s Selecting previously unselected package r-cran-isoband. 658s Preparing to unpack .../05-r-cran-isoband_0.2.7-1_arm64.deb ... 658s Unpacking r-cran-isoband (0.2.7-1) ... 658s Selecting previously unselected package r-cran-mass. 658s Preparing to unpack .../06-r-cran-mass_7.3-60.0.1-1_arm64.deb ... 658s Unpacking r-cran-mass (7.3-60.0.1-1) ... 658s Selecting previously unselected package r-cran-nlme. 658s Preparing to unpack .../07-r-cran-nlme_3.1.164-1_arm64.deb ... 658s Unpacking r-cran-nlme (3.1.164-1) ... 658s Selecting previously unselected package r-cran-mgcv. 658s Preparing to unpack .../08-r-cran-mgcv_1.9-1-1_arm64.deb ... 658s Unpacking r-cran-mgcv (1.9-1-1) ... 658s Selecting previously unselected package r-cran-farver. 658s Preparing to unpack .../09-r-cran-farver_2.1.1-1_arm64.deb ... 658s Unpacking r-cran-farver (2.1.1-1) ... 659s Selecting previously unselected package r-cran-labeling. 659s Preparing to unpack .../10-r-cran-labeling_0.4.3-1_all.deb ... 659s Unpacking r-cran-labeling (0.4.3-1) ... 659s Selecting previously unselected package r-cran-colorspace. 659s Preparing to unpack .../11-r-cran-colorspace_2.1-0+dfsg-1_arm64.deb ... 659s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 659s Selecting previously unselected package r-cran-munsell. 659s Preparing to unpack .../12-r-cran-munsell_0.5.0-2build1_all.deb ... 659s Unpacking r-cran-munsell (0.5.0-2build1) ... 659s Selecting previously unselected package r-cran-r6. 659s Preparing to unpack .../13-r-cran-r6_2.5.1-1_all.deb ... 659s Unpacking r-cran-r6 (2.5.1-1) ... 659s Selecting previously unselected package r-cran-rcolorbrewer. 659s Preparing to unpack .../14-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 659s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 659s Selecting previously unselected package r-cran-viridislite. 659s Preparing to unpack .../15-r-cran-viridislite_0.4.2-2_all.deb ... 659s Unpacking r-cran-viridislite (0.4.2-2) ... 659s Selecting previously unselected package r-cran-scales. 659s Preparing to unpack .../16-r-cran-scales_1.3.0-1_all.deb ... 659s Unpacking r-cran-scales (1.3.0-1) ... 659s Selecting previously unselected package r-cran-fansi. 659s Preparing to unpack .../17-r-cran-fansi_1.0.5-1_arm64.deb ... 659s Unpacking r-cran-fansi (1.0.5-1) ... 659s Selecting previously unselected package r-cran-magrittr. 659s Preparing to unpack .../18-r-cran-magrittr_2.0.3-1_arm64.deb ... 659s Unpacking r-cran-magrittr (2.0.3-1) ... 659s Selecting previously unselected package r-cran-utf8. 659s Preparing to unpack .../19-r-cran-utf8_1.2.4-1_arm64.deb ... 659s Unpacking r-cran-utf8 (1.2.4-1) ... 659s Selecting previously unselected package r-cran-vctrs. 659s Preparing to unpack .../20-r-cran-vctrs_0.6.5-1_arm64.deb ... 659s Unpacking r-cran-vctrs (0.6.5-1) ... 659s Selecting previously unselected package r-cran-pillar. 659s Preparing to unpack .../21-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 659s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 660s Selecting previously unselected package r-cran-pkgconfig. 660s Preparing to unpack .../22-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 660s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 660s Selecting previously unselected package r-cran-tibble. 660s Preparing to unpack .../23-r-cran-tibble_3.2.1+dfsg-2_arm64.deb ... 660s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 660s Selecting previously unselected package r-cran-withr. 660s Preparing to unpack .../24-r-cran-withr_2.5.0-1_all.deb ... 660s Unpacking r-cran-withr (2.5.0-1) ... 660s Selecting previously unselected package r-cran-ggplot2. 660s Preparing to unpack .../25-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 660s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 660s Selecting previously unselected package r-cran-backports. 660s Preparing to unpack .../26-r-cran-backports_1.4.1-1_arm64.deb ... 660s Unpacking r-cran-backports (1.4.1-1) ... 660s Selecting previously unselected package r-cran-generics. 660s Preparing to unpack .../27-r-cran-generics_0.1.3-1_all.deb ... 660s Unpacking r-cran-generics (0.1.3-1) ... 660s Selecting previously unselected package r-cran-tidyselect. 660s Preparing to unpack .../28-r-cran-tidyselect_1.2.0+dfsg-1_arm64.deb ... 660s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 660s Selecting previously unselected package r-cran-dplyr. 660s Preparing to unpack .../29-r-cran-dplyr_1.1.4-1_arm64.deb ... 660s Unpacking r-cran-dplyr (1.1.4-1) ... 660s Selecting previously unselected package r-cran-ellipsis. 660s Preparing to unpack .../30-r-cran-ellipsis_0.3.2-2_arm64.deb ... 660s Unpacking r-cran-ellipsis (0.3.2-2) ... 661s Selecting previously unselected package r-cran-purrr. 661s Preparing to unpack .../31-r-cran-purrr_1.0.2-1_arm64.deb ... 661s Unpacking r-cran-purrr (1.0.2-1) ... 661s Selecting previously unselected package r-cran-stringi. 661s Preparing to unpack .../32-r-cran-stringi_1.8.3-1_arm64.deb ... 661s Unpacking r-cran-stringi (1.8.3-1) ... 661s Selecting previously unselected package r-cran-stringr. 661s Preparing to unpack .../33-r-cran-stringr_1.5.1-1_all.deb ... 661s Unpacking r-cran-stringr (1.5.1-1) ... 661s Selecting previously unselected package r-cran-cpp11. 661s Preparing to unpack .../34-r-cran-cpp11_0.4.7-1_all.deb ... 661s Unpacking r-cran-cpp11 (0.4.7-1) ... 661s Selecting previously unselected package r-cran-tidyr. 661s Preparing to unpack .../35-r-cran-tidyr_1.3.1-1_arm64.deb ... 661s Unpacking r-cran-tidyr (1.3.1-1) ... 661s Selecting previously unselected package r-cran-broom. 661s Preparing to unpack .../36-r-cran-broom_1.0.5+dfsg-1_all.deb ... 661s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 661s Selecting previously unselected package r-cran-geepack. 661s Preparing to unpack .../37-r-cran-geepack_1.3.10-1_arm64.deb ... 661s Unpacking r-cran-geepack (1.3.10-1) ... 661s Selecting previously unselected package dctrl-tools. 661s Preparing to unpack .../38-dctrl-tools_2.24-3build2_arm64.deb ... 661s Unpacking dctrl-tools (2.24-3build2) ... 661s Selecting previously unselected package libc-dev-bin. 661s Preparing to unpack .../39-libc-dev-bin_2.39-0ubuntu2_arm64.deb ... 661s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 661s Selecting previously unselected package linux-libc-dev:arm64. 661s Preparing to unpack .../40-linux-libc-dev_6.8.0-11.11_arm64.deb ... 661s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ... 662s Selecting previously unselected package libcrypt-dev:arm64. 662s Preparing to unpack .../41-libcrypt-dev_1%3a4.4.36-4_arm64.deb ... 662s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ... 662s Selecting previously unselected package libtirpc-dev:arm64. 662s Preparing to unpack .../42-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ... 662s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 662s Selecting previously unselected package libnsl-dev:arm64. 662s Preparing to unpack .../43-libnsl-dev_1.3.0-3_arm64.deb ... 662s Unpacking libnsl-dev:arm64 (1.3.0-3) ... 662s Selecting previously unselected package rpcsvc-proto. 662s Preparing to unpack .../44-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ... 662s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 662s Selecting previously unselected package libc6-dev:arm64. 662s Preparing to unpack .../45-libc6-dev_2.39-0ubuntu2_arm64.deb ... 662s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ... 662s Selecting previously unselected package libisl23:arm64. 662s Preparing to unpack .../46-libisl23_0.26-3_arm64.deb ... 662s Unpacking libisl23:arm64 (0.26-3) ... 663s Selecting previously unselected package libmpc3:arm64. 663s Preparing to unpack .../47-libmpc3_1.3.1-1_arm64.deb ... 663s Unpacking libmpc3:arm64 (1.3.1-1) ... 663s Selecting previously unselected package cpp-13-aarch64-linux-gnu. 663s Preparing to unpack .../48-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 663s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 663s Selecting previously unselected package cpp-13. 663s Preparing to unpack .../49-cpp-13_13.2.0-17ubuntu2_arm64.deb ... 663s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 663s Selecting previously unselected package cpp-aarch64-linux-gnu. 663s Preparing to unpack .../50-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 663s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 663s Selecting previously unselected package cpp. 663s Preparing to unpack .../51-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ... 663s Unpacking cpp (4:13.2.0-7ubuntu1) ... 663s Selecting previously unselected package libcc1-0:arm64. 663s Preparing to unpack .../52-libcc1-0_14-20240303-1ubuntu1_arm64.deb ... 663s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ... 663s Selecting previously unselected package libitm1:arm64. 663s Preparing to unpack .../53-libitm1_14-20240303-1ubuntu1_arm64.deb ... 663s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ... 663s Selecting previously unselected package libatomic1:arm64. 663s Preparing to unpack .../54-libatomic1_14-20240303-1ubuntu1_arm64.deb ... 663s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ... 663s Selecting previously unselected package libasan8:arm64. 663s Preparing to unpack .../55-libasan8_14-20240303-1ubuntu1_arm64.deb ... 663s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ... 664s Selecting previously unselected package liblsan0:arm64. 664s Preparing to unpack .../56-liblsan0_14-20240303-1ubuntu1_arm64.deb ... 664s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ... 664s Selecting previously unselected package libtsan2:arm64. 664s Preparing to unpack .../57-libtsan2_14-20240303-1ubuntu1_arm64.deb ... 664s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ... 664s Selecting previously unselected package libubsan1:arm64. 664s Preparing to unpack .../58-libubsan1_14-20240303-1ubuntu1_arm64.deb ... 664s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ... 664s Selecting previously unselected package libhwasan0:arm64. 664s Preparing to unpack .../59-libhwasan0_14-20240303-1ubuntu1_arm64.deb ... 664s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ... 664s Selecting previously unselected package libgcc-13-dev:arm64. 664s Preparing to unpack .../60-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ... 664s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 665s Selecting previously unselected package gcc-13-aarch64-linux-gnu. 665s Preparing to unpack .../61-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 665s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 665s Selecting previously unselected package gcc-13. 665s Preparing to unpack .../62-gcc-13_13.2.0-17ubuntu2_arm64.deb ... 665s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 665s Selecting previously unselected package gcc-aarch64-linux-gnu. 665s Preparing to unpack .../63-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 665s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 666s Selecting previously unselected package gcc. 666s Preparing to unpack .../64-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ... 666s Unpacking gcc (4:13.2.0-7ubuntu1) ... 666s Selecting previously unselected package libstdc++-13-dev:arm64. 666s Preparing to unpack .../65-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ... 666s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 666s Selecting previously unselected package g++-13-aarch64-linux-gnu. 666s Preparing to unpack .../66-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 666s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 667s Selecting previously unselected package g++-13. 667s Preparing to unpack .../67-g++-13_13.2.0-17ubuntu2_arm64.deb ... 667s Unpacking g++-13 (13.2.0-17ubuntu2) ... 667s Selecting previously unselected package g++-aarch64-linux-gnu. 667s Preparing to unpack .../68-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 667s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 667s Selecting previously unselected package g++. 667s Preparing to unpack .../69-g++_4%3a13.2.0-7ubuntu1_arm64.deb ... 667s Unpacking g++ (4:13.2.0-7ubuntu1) ... 667s Selecting previously unselected package build-essential. 667s Preparing to unpack .../70-build-essential_12.10ubuntu1_arm64.deb ... 667s Unpacking build-essential (12.10ubuntu1) ... 667s Selecting previously unselected package libgfortran-13-dev:arm64. 667s Preparing to unpack .../71-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ... 667s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 667s Selecting previously unselected package gfortran-13-aarch64-linux-gnu. 667s Preparing to unpack .../72-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ... 667s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 667s Selecting previously unselected package gfortran-13. 667s Preparing to unpack .../73-gfortran-13_13.2.0-17ubuntu2_arm64.deb ... 667s Unpacking gfortran-13 (13.2.0-17ubuntu2) ... 667s Selecting previously unselected package gfortran-aarch64-linux-gnu. 667s Preparing to unpack .../74-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ... 667s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 667s Selecting previously unselected package gfortran. 668s Preparing to unpack .../75-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ... 668s Unpacking gfortran (4:13.2.0-7ubuntu1) ... 668s Selecting previously unselected package libblas-dev:arm64. 668s Preparing to unpack .../76-libblas-dev_3.12.0-3_arm64.deb ... 668s Unpacking libblas-dev:arm64 (3.12.0-3) ... 668s Selecting previously unselected package liblapack-dev:arm64. 668s Preparing to unpack .../77-liblapack-dev_3.12.0-3_arm64.deb ... 668s Unpacking liblapack-dev:arm64 (3.12.0-3) ... 668s Selecting previously unselected package libncurses-dev:arm64. 668s Preparing to unpack .../78-libncurses-dev_6.4+20240113-1ubuntu1_arm64.deb ... 668s Unpacking libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 668s Selecting previously unselected package libreadline-dev:arm64. 668s Preparing to unpack .../79-libreadline-dev_8.2-3_arm64.deb ... 668s Unpacking libreadline-dev:arm64 (8.2-3) ... 668s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 668s Preparing to unpack .../80-libjpeg-turbo8-dev_2.1.5-2ubuntu1_arm64.deb ... 668s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 668s Selecting previously unselected package libjpeg8-dev:arm64. 668s Preparing to unpack .../81-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 668s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 668s Selecting previously unselected package libjpeg-dev:arm64. 668s Preparing to unpack .../82-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 668s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 668s Selecting previously unselected package libpcre2-16-0:arm64. 668s Preparing to unpack .../83-libpcre2-16-0_10.42-4ubuntu1_arm64.deb ... 668s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 668s Selecting previously unselected package libpcre2-32-0:arm64. 669s Preparing to unpack .../84-libpcre2-32-0_10.42-4ubuntu1_arm64.deb ... 669s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 669s Selecting previously unselected package libpcre2-posix3:arm64. 669s Preparing to unpack .../85-libpcre2-posix3_10.42-4ubuntu1_arm64.deb ... 669s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 669s Selecting previously unselected package libpcre2-dev:arm64. 669s Preparing to unpack .../86-libpcre2-dev_10.42-4ubuntu1_arm64.deb ... 669s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu1) ... 669s Selecting previously unselected package zlib1g-dev:arm64. 669s Preparing to unpack .../87-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_arm64.deb ... 669s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 669s Selecting previously unselected package libpng-dev:arm64. 669s Preparing to unpack .../88-libpng-dev_1.6.43-1_arm64.deb ... 669s Unpacking libpng-dev:arm64 (1.6.43-1) ... 669s Selecting previously unselected package libbz2-dev:arm64. 669s Preparing to unpack .../89-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ... 669s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 669s Selecting previously unselected package liblzma-dev:arm64. 669s Preparing to unpack .../90-liblzma-dev_5.4.5-0.3_arm64.deb ... 669s Unpacking liblzma-dev:arm64 (5.4.5-0.3) ... 669s Selecting previously unselected package icu-devtools. 669s Preparing to unpack .../91-icu-devtools_74.2-1ubuntu1_arm64.deb ... 669s Unpacking icu-devtools (74.2-1ubuntu1) ... 669s Selecting previously unselected package libicu-dev:arm64. 669s Preparing to unpack .../92-libicu-dev_74.2-1ubuntu1_arm64.deb ... 669s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ... 670s Selecting previously unselected package libpkgconf3:arm64. 670s Preparing to unpack .../93-libpkgconf3_1.8.1-2_arm64.deb ... 670s Unpacking libpkgconf3:arm64 (1.8.1-2) ... 670s Selecting previously unselected package pkgconf-bin. 670s Preparing to unpack .../94-pkgconf-bin_1.8.1-2_arm64.deb ... 670s Unpacking pkgconf-bin (1.8.1-2) ... 670s Selecting previously unselected package pkgconf:arm64. 670s Preparing to unpack .../95-pkgconf_1.8.1-2_arm64.deb ... 670s Unpacking pkgconf:arm64 (1.8.1-2) ... 670s Selecting previously unselected package pkg-config:arm64. 670s Preparing to unpack .../96-pkg-config_1.8.1-2_arm64.deb ... 670s Unpacking pkg-config:arm64 (1.8.1-2) ... 670s Selecting previously unselected package r-base-dev. 670s Preparing to unpack .../97-r-base-dev_4.3.2-1build1_all.deb ... 670s Unpacking r-base-dev (4.3.2-1build1) ... 670s Selecting previously unselected package pkg-r-autopkgtest. 670s Preparing to unpack .../98-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 670s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 670s Setting up r-cran-rlang (1.1.3-1) ... 670s Setting up r-cran-withr (2.5.0-1) ... 670s Setting up r-cran-backports (1.4.1-1) ... 670s Setting up r-cran-generics (0.1.3-1) ... 670s Setting up r-cran-fansi (1.0.5-1) ... 670s Setting up r-cran-mass (7.3-60.0.1-1) ... 670s Setting up linux-libc-dev:arm64 (6.8.0-11.11) ... 670s Setting up r-cran-glue (1.7.0-1) ... 670s Setting up r-cran-cli (3.6.2-1) ... 670s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 670s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu1) ... 670s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 670s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu1) ... 670s Setting up r-cran-utf8 (1.2.4-1) ... 670s Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... 670s Setting up libpkgconf3:arm64 (1.8.1-2) ... 670s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 670s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 670s Setting up r-cran-stringi (1.8.3-1) ... 670s Setting up r-cran-cpp11 (0.4.7-1) ... 670s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 670s Setting up r-cran-isoband (0.2.7-1) ... 670s Setting up libmpc3:arm64 (1.3.1-1) ... 670s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 670s Setting up libatomic1:arm64 (14-20240303-1ubuntu1) ... 670s Setting up r-cran-labeling (0.4.3-1) ... 670s Setting up icu-devtools (74.2-1ubuntu1) ... 670s Setting up pkgconf-bin (1.8.1-2) ... 670s Setting up r-cran-nlme (3.1.164-1) ... 670s Setting up r-cran-farver (2.1.1-1) ... 670s Setting up liblzma-dev:arm64 (5.4.5-0.3) ... 670s Setting up libubsan1:arm64 (14-20240303-1ubuntu1) ... 670s Setting up r-cran-mgcv (1.9-1-1) ... 670s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu1) ... 670s Setting up libnsl-dev:arm64 (1.3.0-3) ... 670s Setting up r-cran-viridislite (0.4.2-2) ... 670s Setting up libhwasan0:arm64 (14-20240303-1ubuntu1) ... 670s Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... 670s Setting up libasan8:arm64 (14-20240303-1ubuntu1) ... 670s Setting up libtsan2:arm64 (14-20240303-1ubuntu1) ... 670s Setting up r-cran-r6 (2.5.1-1) ... 670s Setting up libisl23:arm64 (0.26-3) ... 670s Setting up libc-dev-bin (2.39-0ubuntu2) ... 670s Setting up r-cran-magrittr (2.0.3-1) ... 670s Setting up libcc1-0:arm64 (14-20240303-1ubuntu1) ... 670s Setting up r-cran-vctrs (0.6.5-1) ... 670s Setting up liblsan0:arm64 (14-20240303-1ubuntu1) ... 670s Setting up libblas-dev:arm64 (3.12.0-3) ... 670s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 670s Setting up dctrl-tools (2.24-3build2) ... 670s Setting up libitm1:arm64 (14-20240303-1ubuntu1) ... 670s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 670s Setting up r-cran-ellipsis (0.3.2-2) ... 670s Setting up r-cran-stringr (1.5.1-1) ... 670s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 670s Setting up r-cran-munsell (0.5.0-2build1) ... 670s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 670s Setting up pkgconf:arm64 (1.8.1-2) ... 670s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 670s Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 670s Setting up r-cran-scales (1.3.0-1) ... 670s Setting up liblapack-dev:arm64 (3.12.0-3) ... 670s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 670s Setting up r-cran-purrr (1.0.2-1) ... 670s Setting up pkg-config:arm64 (1.8.1-2) ... 670s Setting up libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ... 670s Setting up libc6-dev:arm64 (2.39-0ubuntu2) ... 670s Setting up r-cran-dplyr (1.1.4-1) ... 670s Setting up libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ... 670s Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... 670s Setting up libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ... 670s Setting up libbz2-dev:arm64 (1.0.8-5ubuntu1) ... 670s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... 670s Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... 670s Setting up libpcre2-dev:arm64 (10.42-4ubuntu1) ... 670s Setting up cpp-13 (13.2.0-17ubuntu2) ... 670s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 670s Setting up gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 670s Setting up libreadline-dev:arm64 (8.2-3) ... 670s Setting up gcc-13 (13.2.0-17ubuntu2) ... 670s Setting up r-cran-tidyr (1.3.1-1) ... 670s Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3ubuntu1) ... 670s Setting up cpp (4:13.2.0-7ubuntu1) ... 670s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 670s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 670s Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 670s Setting up g++-13 (13.2.0-17ubuntu2) ... 670s Setting up libpng-dev:arm64 (1.6.43-1) ... 670s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 670s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ... 670s Setting up gcc (4:13.2.0-7ubuntu1) ... 670s Setting up r-cran-broom (1.0.5+dfsg-1) ... 670s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 670s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 670s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 670s Setting up r-cran-geepack (1.3.10-1) ... 670s Setting up gfortran (4:13.2.0-7ubuntu1) ... 670s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 670s 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 670s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 670s 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 670s Setting up g++ (4:13.2.0-7ubuntu1) ... 670s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 670s Setting up build-essential (12.10ubuntu1) ... 670s Setting up r-base-dev (4.3.2-1build1) ... 670s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 670s Setting up autopkgtest-satdep (0) ... 670s Processing triggers for man-db (2.12.0-3) ... 672s Processing triggers for install-info (7.1-3) ... 672s Processing triggers for libc-bin (2.39-0ubuntu2) ... 678s (Reading database ... 87237 files and directories currently installed.) 678s Removing autopkgtest-satdep (0) ... 679s autopkgtest [02:20:37]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 679s autopkgtest [02:20:37]: test pkg-r-autopkgtest: [----------------------- 680s Test: Try to load the R library etm 680s 680s R version 4.3.2 (2023-10-31) -- "Eye Holes" 680s Copyright (C) 2023 The R Foundation for Statistical Computing 680s Platform: aarch64-unknown-linux-gnu (64-bit) 680s 680s R is free software and comes with ABSOLUTELY NO WARRANTY. 680s You are welcome to redistribute it under certain conditions. 680s Type 'license()' or 'licence()' for distribution details. 680s 680s R is a collaborative project with many contributors. 680s Type 'contributors()' for more information and 680s 'citation()' on how to cite R or R packages in publications. 680s 680s Type 'demo()' for some demos, 'help()' for on-line help, or 680s 'help.start()' for an HTML browser interface to help. 680s Type 'q()' to quit R. 680s 680s > library('etm') 683s > 683s > 683s Other tests are currently unsupported! 683s They will be progressively added. 684s autopkgtest [02:20:42]: test pkg-r-autopkgtest: -----------------------] 684s autopkgtest [02:20:42]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 684s pkg-r-autopkgtest PASS 685s autopkgtest [02:20:43]: @@@@@@@@@@@@@@@@@@@@ summary 685s run-unit-test PASS 685s pkg-r-autopkgtest PASS 700s Creating nova instance adt-noble-arm64-r-cran-etm-20240307-020918-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240306.img (UUID fe83f9af-4e32-48b1-9e6a-30d9e6eedf79)...