0s autopkgtest [09:55:02]: starting date: 2024-03-12 0s autopkgtest [09:55:02]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [09:55:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c3z4type/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-cran-rcpparmadillo --apt-upgrade r-cran-etm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-rcpparmadillo/0.12.8.1.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-25.secgroup --name adt-noble-s390x-r-cran-etm-20240312-095501-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 308s autopkgtest [10:00:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 308s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 309s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [449 kB] 309s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [41.4 kB] 309s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 309s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2784 kB] 310s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [585 kB] 310s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 310s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 310s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 310s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3089 kB] 310s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 310s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [37.8 kB] 310s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 312s Fetched 7120 kB in 3s (2568 kB/s) 312s Reading package lists... 320s Reading package lists... 320s Building dependency tree... 320s Reading state information... 320s Calculating upgrade... 321s The following packages will be upgraded: 321s klibc-utils libklibc python3-attr 321s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 321s Need to get 217 kB of archives. 321s After this operation, 0 B of additional disk space will be used. 321s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x klibc-utils s390x 2.0.13-4 [114 kB] 321s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libklibc s390x 2.0.13-4 [54.5 kB] 321s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x python3-attr all 23.2.0-2 [48.6 kB] 322s Fetched 217 kB in 0s (468 kB/s) 322s (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 ... 52188 files and directories currently installed.) 322s Preparing to unpack .../klibc-utils_2.0.13-4_s390x.deb ... 322s Unpacking klibc-utils (2.0.13-4) over (2.0.13-2ubuntu1) ... 322s Preparing to unpack .../libklibc_2.0.13-4_s390x.deb ... 322s Unpacking libklibc:s390x (2.0.13-4) over (2.0.13-2ubuntu1) ... 322s Preparing to unpack .../python3-attr_23.2.0-2_all.deb ... 322s Unpacking python3-attr (23.2.0-2) over (23.2.0-1) ... 322s Setting up python3-attr (23.2.0-2) ... 323s Setting up libklibc:s390x (2.0.13-4) ... 323s Setting up klibc-utils (2.0.13-4) ... 323s Processing triggers for initramfs-tools (0.142ubuntu20) ... 323s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 323s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 329s Using config file '/etc/zipl.conf' 329s Building bootmap in '/boot' 329s Adding IPL section 'ubuntu' (default) 329s Preparing boot device for LD-IPL: vda (0000). 329s Done. 330s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 330s 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 330s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 330s 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 330s Reading package lists... 331s Building dependency tree... 331s Reading state information... 332s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 332s Unknown architecture, assuming PC-style ttyS0 332s sh: Attempting to set up Debian/Ubuntu apt sources automatically 332s sh: Distribution appears to be Ubuntu 338s Reading package lists... 338s Building dependency tree... 338s Reading state information... 339s eatmydata is already the newest version (131-1). 339s dbus is already the newest version (1.14.10-4ubuntu1). 339s dbus set to manually installed. 339s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 339s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 339s 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 339s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 339s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 339s 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 340s Reading package lists... 340s Building dependency tree... 340s Reading state information... 341s rng-tools-debian is already the newest version (2.4). 341s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 341s Reading package lists... 342s Building dependency tree... 342s Reading state information... 343s haveged is already the newest version (1.9.14-1ubuntu1). 343s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 343s Reading package lists... 343s Building dependency tree... 343s Reading state information... 343s The following packages will be REMOVED: 343s cloud-init* python3-configobj* python3-debconf* 344s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 344s After this operation, 3248 kB disk space will be freed. 344s (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 ... 52188 files and directories currently installed.) 344s Removing cloud-init (24.1-0ubuntu1) ... 345s Removing python3-configobj (5.0.8-3) ... 345s Removing python3-debconf (1.5.86) ... 345s Processing triggers for man-db (2.12.0-3) ... 345s (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 ... 51799 files and directories currently installed.) 345s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 346s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 346s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 347s Reading package lists... 348s Building dependency tree... 348s Reading state information... 348s linux-generic is already the newest version (6.8.0-11.11+1). 348s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 349s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 349s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 349s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 349s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 349s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 356s Reading package lists... 356s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s 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 356s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s 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 356s Reading package lists... 357s Building dependency tree... 357s Reading state information... 358s Calculating upgrade... 358s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 358s Reading package lists... 359s Building dependency tree... 359s Reading state information... 360s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 360s autopkgtest [10:01:02]: rebooting testbed after setup commands that affected boot 378s autopkgtest [10:01:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 379s autopkgtest [10:01:21]: testbed dpkg architecture: s390x 380s autopkgtest [10:01:22]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-etm 381s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 381s 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 381s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 381s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 381s 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 383s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (dsc) [2148 B] 383s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (tar) [242 kB] 383s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-cran-etm 1.1.1-1 (diff) [3564 B] 383s gpgv: Signature made Fri Sep 18 09:39:57 2020 UTC 383s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 383s gpgv: issuer "tille@debian.org" 383s gpgv: Can't check signature: No public key 383s dpkg-source: warning: cannot verify inline signature for ./r-cran-etm_1.1.1-1.dsc: no acceptable signature found 383s autopkgtest [10:01:25]: testing package r-cran-etm version 1.1.1-1 383s autopkgtest [10:01:25]: build not needed 385s autopkgtest [10:01:27]: test run-unit-test: preparing testbed 392s Reading package lists... 393s Building dependency tree... 393s Reading state information... 393s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 394s Starting 2 pkgProblemResolver with broken count: 0 394s Done 394s Done 394s Starting pkgProblemResolver with broken count: 0 395s Starting 2 pkgProblemResolver with broken count: 0 395s Done 395s The following additional packages will be installed: 395s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 395s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 395s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 395s libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 395s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 395s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 395s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 395s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 395s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 396s r-cran-survival unzip x11-common xdg-utils zip 396s Suggested packages: 396s tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html 396s r-cran-rmysql r-cran-ggplot2 r-cran-geepack r-cran-getopt r-cran-rodbc 396s r-cran-foreign r-cran-inline 396s Recommended packages: 396s r-recommended r-base-dev r-doc-html r-cran-bit64 r-cran-bit r-cran-curl 396s r-cran-r.utils r-cran-xts r-cran-nanotime r-cran-zoo r-cran-yaml 396s r-cran-knitr r-cran-rmarkdown libfile-mimeinfo-perl libnet-dbus-perl 396s libx11-protocol-perl x11-utils x11-xserver-utils 396s The following NEW packages will be installed: 396s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 396s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 396s libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 396s libjpeg8 liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 396s libpaper-utils libpaper1 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 396s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 396s libxft2 libxrender1 libxss1 libxt6 littler r-base-core r-cran-data.table 396s r-cran-dbi r-cran-etm r-cran-kmi r-cran-lattice r-cran-littler r-cran-matrix 396s r-cran-mitools r-cran-pkgkitten r-cran-rcpp r-cran-rcpparmadillo 396s r-cran-survival unzip x11-common xdg-utils zip 396s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 396s 1 not fully installed or removed. 396s Need to get 56.2 MB of archives. 396s After this operation, 117 MB of additional disk space will be used. 396s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x zip s390x 3.0-13 [175 kB] 396s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x unzip s390x 6.0-28ubuntu3 [180 kB] 396s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libpaper1 s390x 1.1.29 [13.3 kB] 396s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libpaper-utils s390x 1.1.29 [8452 B] 396s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 396s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 396s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 396s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 396s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 396s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 396s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 396s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 396s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 396s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 396s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 396s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 396s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 396s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 396s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 396s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 397s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 397s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig s390x 2.15.0-1ubuntu1 [191 kB] 397s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 397s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 397s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libthai-data all 0.1.29-2 [158 kB] 397s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libdatrie1 s390x 0.2.13-3 [22.6 kB] 397s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libthai0 s390x 0.1.29-2 [20.6 kB] 397s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libpango-1.0-0 s390x 1.51.0+ds-4 [240 kB] 397s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libpangoft2-1.0-0 s390x 1.51.0+ds-4 [43.6 kB] 397s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libpangocairo-1.0-0 s390x 1.51.0+ds-4 [28.9 kB] 397s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libtcl8.6 s390x 8.6.13+dfsg-2 [948 kB] 397s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 397s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 397s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 397s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 397s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 397s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libxft2 s390x 2.3.6-1 [44.3 kB] 397s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 397s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libxss1 s390x 1:1.2.3-1build2 [8192 B] 397s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libtk8.6 s390x 8.6.13-2 [757 kB] 397s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libice6 s390x 2:1.0.10-1build2 [40.8 kB] 397s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libsm6 s390x 2:1.2.3-1build2 [16.9 kB] 397s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libxt6 s390x 1:1.2.1-1.1 [166 kB] 397s Get:44 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-core s390x 4.3.2-1build1 [27.1 MB] 401s Get:45 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lattice s390x 0.22-5-1 [1341 kB] 401s Get:46 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-matrix s390x 1.6-5-1 [3983 kB] 401s Get:47 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-survival s390x 3.5-8-1 [6161 kB] 402s Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-data.table s390x 1.14.10+dfsg-1 [1880 kB] 402s Get:49 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-littler s390x 0.3.19-1 [93.0 kB] 403s Get:50 http://ftpmaster.internal/ubuntu noble/universe s390x littler all 0.3.19-1 [2472 B] 403s Get:51 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 403s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcpp s390x 1.0.12-1 [1985 kB] 403s Get:53 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x r-cran-rcpparmadillo s390x 0.12.8.1.0-1 [869 kB] 403s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-etm s390x 1.1.1-1 [474 kB] 403s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-dbi all 1.2.2-1 [823 kB] 403s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mitools all 2.4-2build1 [265 kB] 403s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-kmi all 0.5.5-2build1 [78.3 kB] 404s Preconfiguring packages ... 404s Fetched 56.2 MB in 8s (7381 kB/s) 404s Selecting previously unselected package zip. 404s (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 ... 51744 files and directories currently installed.) 404s Preparing to unpack .../00-zip_3.0-13_s390x.deb ... 404s Unpacking zip (3.0-13) ... 404s Selecting previously unselected package unzip. 404s Preparing to unpack .../01-unzip_6.0-28ubuntu3_s390x.deb ... 404s Unpacking unzip (6.0-28ubuntu3) ... 404s Selecting previously unselected package libpaper1:s390x. 404s Preparing to unpack .../02-libpaper1_1.1.29_s390x.deb ... 404s Unpacking libpaper1:s390x (1.1.29) ... 404s Selecting previously unselected package libpaper-utils. 404s Preparing to unpack .../03-libpaper-utils_1.1.29_s390x.deb ... 404s Unpacking libpaper-utils (1.1.29) ... 404s Selecting previously unselected package xdg-utils. 404s Preparing to unpack .../04-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 404s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 404s Selecting previously unselected package libblas3:s390x. 404s Preparing to unpack .../05-libblas3_3.12.0-3_s390x.deb ... 404s Unpacking libblas3:s390x (3.12.0-3) ... 404s Selecting previously unselected package libfreetype6:s390x. 404s Preparing to unpack .../06-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 404s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 404s Selecting previously unselected package fonts-dejavu-mono. 404s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ... 404s Unpacking fonts-dejavu-mono (2.37-8) ... 404s Selecting previously unselected package fonts-dejavu-core. 404s Preparing to unpack .../08-fonts-dejavu-core_2.37-8_all.deb ... 404s Unpacking fonts-dejavu-core (2.37-8) ... 405s Selecting previously unselected package fontconfig-config. 405s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 405s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 405s Selecting previously unselected package libfontconfig1:s390x. 405s Preparing to unpack .../10-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 405s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 405s Selecting previously unselected package libpixman-1-0:s390x. 405s Preparing to unpack .../11-libpixman-1-0_0.42.2-1_s390x.deb ... 405s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 405s Selecting previously unselected package libxcb-render0:s390x. 405s Preparing to unpack .../12-libxcb-render0_1.15-1_s390x.deb ... 405s Unpacking libxcb-render0:s390x (1.15-1) ... 405s Selecting previously unselected package libxcb-shm0:s390x. 405s Preparing to unpack .../13-libxcb-shm0_1.15-1_s390x.deb ... 405s Unpacking libxcb-shm0:s390x (1.15-1) ... 405s Selecting previously unselected package libxrender1:s390x. 405s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 405s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 405s Selecting previously unselected package libcairo2:s390x. 405s Preparing to unpack .../15-libcairo2_1.18.0-1_s390x.deb ... 405s Unpacking libcairo2:s390x (1.18.0-1) ... 405s Selecting previously unselected package libgomp1:s390x. 405s Preparing to unpack .../16-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 405s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 405s Selecting previously unselected package libjpeg-turbo8:s390x. 405s Preparing to unpack .../17-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 405s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 405s Selecting previously unselected package libjpeg8:s390x. 405s Preparing to unpack .../18-libjpeg8_8c-2ubuntu11_s390x.deb ... 405s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 405s Selecting previously unselected package libgfortran5:s390x. 405s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 405s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 405s Selecting previously unselected package liblapack3:s390x. 405s Preparing to unpack .../20-liblapack3_3.12.0-3_s390x.deb ... 405s Unpacking liblapack3:s390x (3.12.0-3) ... 405s Selecting previously unselected package fontconfig. 405s Preparing to unpack .../21-fontconfig_2.15.0-1ubuntu1_s390x.deb ... 405s Unpacking fontconfig (2.15.0-1ubuntu1) ... 405s Selecting previously unselected package libgraphite2-3:s390x. 405s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_s390x.deb ... 405s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 405s Selecting previously unselected package libharfbuzz0b:s390x. 405s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_s390x.deb ... 405s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 405s Selecting previously unselected package libthai-data. 405s Preparing to unpack .../24-libthai-data_0.1.29-2_all.deb ... 405s Unpacking libthai-data (0.1.29-2) ... 405s Selecting previously unselected package libdatrie1:s390x. 405s Preparing to unpack .../25-libdatrie1_0.2.13-3_s390x.deb ... 405s Unpacking libdatrie1:s390x (0.2.13-3) ... 405s Selecting previously unselected package libthai0:s390x. 405s Preparing to unpack .../26-libthai0_0.1.29-2_s390x.deb ... 405s Unpacking libthai0:s390x (0.1.29-2) ... 405s Selecting previously unselected package libpango-1.0-0:s390x. 405s Preparing to unpack .../27-libpango-1.0-0_1.51.0+ds-4_s390x.deb ... 405s Unpacking libpango-1.0-0:s390x (1.51.0+ds-4) ... 405s Selecting previously unselected package libpangoft2-1.0-0:s390x. 405s Preparing to unpack .../28-libpangoft2-1.0-0_1.51.0+ds-4_s390x.deb ... 405s Unpacking libpangoft2-1.0-0:s390x (1.51.0+ds-4) ... 405s Selecting previously unselected package libpangocairo-1.0-0:s390x. 405s Preparing to unpack .../29-libpangocairo-1.0-0_1.51.0+ds-4_s390x.deb ... 405s Unpacking libpangocairo-1.0-0:s390x (1.51.0+ds-4) ... 405s Selecting previously unselected package libtcl8.6:s390x. 405s Preparing to unpack .../30-libtcl8.6_8.6.13+dfsg-2_s390x.deb ... 405s Unpacking libtcl8.6:s390x (8.6.13+dfsg-2) ... 405s Selecting previously unselected package libdeflate0:s390x. 405s Preparing to unpack .../31-libdeflate0_1.19-1_s390x.deb ... 405s Unpacking libdeflate0:s390x (1.19-1) ... 405s Selecting previously unselected package libjbig0:s390x. 405s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu1_s390x.deb ... 405s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ... 405s Selecting previously unselected package libsharpyuv0:s390x. 405s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_s390x.deb ... 405s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ... 405s Selecting previously unselected package libwebp7:s390x. 405s Preparing to unpack .../34-libwebp7_1.3.2-0.4_s390x.deb ... 405s Unpacking libwebp7:s390x (1.3.2-0.4) ... 406s Selecting previously unselected package libtiff6:s390x. 406s Preparing to unpack .../35-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ... 406s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ... 406s Selecting previously unselected package libxft2:s390x. 406s Preparing to unpack .../36-libxft2_2.3.6-1_s390x.deb ... 406s Unpacking libxft2:s390x (2.3.6-1) ... 406s Selecting previously unselected package x11-common. 406s Preparing to unpack .../37-x11-common_1%3a7.7+23ubuntu2_all.deb ... 406s Unpacking x11-common (1:7.7+23ubuntu2) ... 406s Selecting previously unselected package libxss1:s390x. 406s Preparing to unpack .../38-libxss1_1%3a1.2.3-1build2_s390x.deb ... 406s Unpacking libxss1:s390x (1:1.2.3-1build2) ... 406s Selecting previously unselected package libtk8.6:s390x. 406s Preparing to unpack .../39-libtk8.6_8.6.13-2_s390x.deb ... 406s Unpacking libtk8.6:s390x (8.6.13-2) ... 406s Selecting previously unselected package libice6:s390x. 406s Preparing to unpack .../40-libice6_2%3a1.0.10-1build2_s390x.deb ... 406s Unpacking libice6:s390x (2:1.0.10-1build2) ... 406s Selecting previously unselected package libsm6:s390x. 406s Preparing to unpack .../41-libsm6_2%3a1.2.3-1build2_s390x.deb ... 406s Unpacking libsm6:s390x (2:1.2.3-1build2) ... 406s Selecting previously unselected package libxt6:s390x. 406s Preparing to unpack .../42-libxt6_1%3a1.2.1-1.1_s390x.deb ... 406s Unpacking libxt6:s390x (1:1.2.1-1.1) ... 406s Selecting previously unselected package r-base-core. 406s Preparing to unpack .../43-r-base-core_4.3.2-1build1_s390x.deb ... 406s Unpacking r-base-core (4.3.2-1build1) ... 407s Selecting previously unselected package r-cran-lattice. 407s Preparing to unpack .../44-r-cran-lattice_0.22-5-1_s390x.deb ... 407s Unpacking r-cran-lattice (0.22-5-1) ... 407s Selecting previously unselected package r-cran-matrix. 407s Preparing to unpack .../45-r-cran-matrix_1.6-5-1_s390x.deb ... 407s Unpacking r-cran-matrix (1.6-5-1) ... 407s Selecting previously unselected package r-cran-survival. 407s Preparing to unpack .../46-r-cran-survival_3.5-8-1_s390x.deb ... 407s Unpacking r-cran-survival (3.5-8-1) ... 407s Selecting previously unselected package r-cran-data.table. 407s Preparing to unpack .../47-r-cran-data.table_1.14.10+dfsg-1_s390x.deb ... 407s Unpacking r-cran-data.table (1.14.10+dfsg-1) ... 407s Selecting previously unselected package r-cran-littler. 407s Preparing to unpack .../48-r-cran-littler_0.3.19-1_s390x.deb ... 407s Unpacking r-cran-littler (0.3.19-1) ... 407s Selecting previously unselected package littler. 407s Preparing to unpack .../49-littler_0.3.19-1_all.deb ... 407s Unpacking littler (0.3.19-1) ... 407s Selecting previously unselected package r-cran-pkgkitten. 407s Preparing to unpack .../50-r-cran-pkgkitten_0.2.3-1_all.deb ... 407s Unpacking r-cran-pkgkitten (0.2.3-1) ... 407s Selecting previously unselected package r-cran-rcpp. 407s Preparing to unpack .../51-r-cran-rcpp_1.0.12-1_s390x.deb ... 407s Unpacking r-cran-rcpp (1.0.12-1) ... 407s Selecting previously unselected 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Type 'license()' or 'licence()' for distribution details. 419s 419s R is a collaborative project with many contributors. 419s Type 'contributors()' for more information and 419s 'citation()' on how to cite R or R packages in publications. 419s 419s Type 'demo()' for some demos, 'help()' for on-line help, or 419s 'help.start()' for an HTML browser interface to help. 419s Type 'q()' to quit R. 419s 420s > ### test file for etmCIF. 420s > ### Really simple tests and comparison with etm 420s > 420s > old <- options(digits = 5) 420s > 420s > require(etm) 420s Loading required package: etm 421s > 421s > if (!require(survival, quietly = TRUE)) { 421s + print("The following tests require the 'survival' package") 421s + } else { 421s + 421s + data(abortion) 421s + 421s + from <- rep(0, nrow(abortion)) 421s + to <- abortion$cause 421s + entry <- abortion$entry 421s + exit <- abortion$exit 421s + id <- 1:nrow(abortion) 421s + data <- data.frame(id, from, to, entry, exit, group = abortion$group) 421s + 421s + ## Computation of the CIFs with etm 421s + tra <- matrix(FALSE, 4, 4) 421s + tra[1, 2:4] <- TRUE 421s + 421s + cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 421s + tra, NULL, 0) 421s + cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 421s + tra, NULL, 0) 421s + 421s + 421s + ## Computation of the CIFs with etmCIF 421s + netm <- etmCIF(Surv(entry, exit, cause != 0) ~ group, abortion, 421s + etype = cause, failcode = 3) 421s + 421s + ### let's do some comparisons :-) 421s + 421s + all.equal(trprob(cif.control, "0 3"), netm[[1]]$est["0", "3", ]) 421s + all.equal(trprob(cif.control, "0 2"), netm[[1]]$est["0", "2", ]) 421s + all.equal(trprob(cif.control, "0 1"), netm[[1]]$est["0", "1", ]) 421s + 421s + all.equal(trprob(cif.exposed, "0 3"), netm[[2]]$est["0", "3", ]) 421s + all.equal(trprob(cif.exposed, "0 2"), netm[[2]]$est["0", "2", ]) 421s + all.equal(trprob(cif.exposed, "0 1"), netm[[2]]$est["0", "1", ]) 421s + 421s + 421s + all.equal(trcov(cif.control, "0 3"), netm[[1]]$cov["0 3", "0 3", ]) 421s + all.equal(trcov(cif.control, "0 2"), netm[[1]]$cov["0 2", "0 2", ]) 421s + all.equal(trcov(cif.control, "0 1"), netm[[1]]$cov["0 1", "0 1", ]) 421s + 421s + all.equal(trcov(cif.exposed, "0 3"), netm[[2]]$cov["0 3", "0 3", ]) 421s + all.equal(trcov(cif.exposed, "0 2"), netm[[2]]$cov["0 2", "0 2", ]) 421s + all.equal(trcov(cif.exposed, "0 1"), netm[[2]]$cov["0 1", "0 1", ]) 421s + 421s + 421s + netm 421s + 421s + ## test on the summary 421s + snetm <- summary(netm) 421s + 421s + snetm 421s + 421s + all.equal(unname(trprob(cif.control, "0 3")), snetm[[1]][[3]]$P) 421s + all.equal(unname(trprob(cif.control, "0 2")), snetm[[1]][[2]]$P) 421s + all.equal(unname(trprob(cif.control, "0 1")), snetm[[1]][[1]]$P) 421s + 421s + all.equal(unname(trprob(cif.exposed, "0 3")), snetm[[2]][[3]]$P) 421s + all.equal(unname(trprob(cif.exposed, "0 2")), snetm[[2]][[2]]$P) 421s + all.equal(unname(trprob(cif.exposed, "0 1")), snetm[[2]][[1]]$P) 421s + 421s + scif.control <- summary(cif.control, ci.fun = "cloglog") 421s + scif.exposed <- summary(cif.exposed, ci.fun = "cloglog") 421s + 421s + all.equal(scif.control[[4]]$lower, snetm[[1]][[3]]$lower) 421s + all.equal(scif.control[[4]]$upper, snetm[[1]][[3]]$upper) 421s + 421s + all.equal(scif.exposed[[4]]$lower, snetm[[2]][[3]]$lower) 421s + all.equal(scif.exposed[[4]]$upper, snetm[[2]][[3]]$upper) 421s + } 422s [1] TRUE 422s > 422s > ### test with factors in the input 422s > abortion$status <- with(abortion, ifelse(cause == 2, "life birth", 422s + ifelse(cause == 1, "ETOP", "spontaneous abortion"))) 422s > 422s > abortion$status <- factor(abortion$status) 422s > 422s > netm.factor <- etmCIF(Surv(entry, exit, status != "cens") ~ group, abortion, 422s + etype = status, failcode = "spontaneous abortion") 422s > 422s > 422s > all.equal(trprob(cif.control, "0 3"), netm.factor[[1]]$est["0", "spontaneous abortion", ]) 422s [1] TRUE 422s > all.equal(trprob(cif.control, "0 2"), netm.factor[[1]]$est["0", "life birth", ]) 422s [1] TRUE 422s > 422s > netm.factor 422s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ group, 422s data = abortion, etype = status, failcode = "spontaneous abortion") 422s 422s Covariate: group 422s levels: 0 1 422s 422s 422s group = 0 422s time P se(P) n.event 422s CIF ETOP 43 0.040159 0.0092578 20 422s CIF life birth 43 0.799059 0.0221865 924 422s CIF spontaneous abortion 43 0.160781 0.0213261 69 422s 422s group = 1 422s time P se(P) n.event 422s CIF ETOP 42 0.28511 0.042493 38 422s CIF life birth 42 0.35257 0.042139 92 422s CIF spontaneous abortion 42 0.36232 0.049473 43 422s > 422s > summary(netm.factor) 422s 422s group=0 422s 422s CIF ETOP 422s P time var lower upper n.risk n.event 422s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 422s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 422s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 422s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 422s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 422s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 422s 422s CIF life birth 422s P time var lower upper n.risk n.event 422s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 422s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 422s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 422s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 422s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 422s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 422s 422s CIF spontaneous abortion 422s P time var lower upper n.risk n.event 422s 0.034188 6 0.00028222 0.01297 0.088523 117 4 422s 0.150468 13 0.00045513 0.11360 0.197901 645 1 422s 0.159904 26 0.00045498 0.12274 0.206925 846 1 422s 0.160781 36 0.00045480 0.12360 0.207757 876 1 422s 0.160781 40 0.00045480 0.12360 0.207757 554 0 422s 0.160781 43 0.00045480 0.12360 0.207757 6 0 422s 422s 422s group=1 422s 422s CIF ETOP 422s P time var lower upper n.risk n.event 422s 0.00000 6 0.0000000 0.00000 0.00000 35 0 422s 0.26048 13 0.0017854 0.18795 0.35425 90 0 422s 0.28115 21 0.0018028 0.20742 0.37423 93 1 422s 0.28511 34 0.0018057 0.21116 0.37806 89 0 422s 0.28511 39 0.0018057 0.21116 0.37806 59 0 422s 0.28511 42 0.0018057 0.21116 0.37806 6 0 422s 422s CIF life birth 422s P time var lower upper n.risk n.event 422s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 422s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 422s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 422s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 422s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 422s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 422s 422s CIF spontaneous abortion 422s P time var lower upper n.risk n.event 422s 0.057143 6 0.0015394 0.014605 0.20968 35 2 422s 0.333246 13 0.0025280 0.245337 0.44216 90 4 422s 0.350702 21 0.0024827 0.262769 0.45762 93 0 422s 0.358492 34 0.0024593 0.270627 0.46448 89 0 422s 0.358492 39 0.0024593 0.270627 0.46448 59 0 422s 0.362323 42 0.0024476 0.274499 0.46785 6 0 422s 422s > 422s > ### test with group as a character vector 422s > abortion$ttt <- with(abortion, ifelse(group == 0, "control", "exposed")) 422s > abortion$ttt <- factor(abortion$ttt) 422s > 422s > netm.ttt <- etmCIF(Surv(entry, exit, status != "cens") ~ ttt, abortion, 422s + etype = status, failcode = "spontaneous abortion") 422s > 422s > all.equal(trprob(cif.control, "0 3"), netm.ttt[[1]]$est["0", "spontaneous abortion", ]) 422s [1] TRUE 422s > all.equal(trprob(cif.control, "0 2"), netm.ttt[[1]]$est["0", "life birth", ]) 422s [1] TRUE 422s > 422s > netm.ttt 422s Call: etmCIF(formula = Surv(entry, exit, status != "cens") ~ ttt, data = abortion, 422s etype = status, failcode = "spontaneous abortion") 422s 422s Covariate: ttt 422s levels: control exposed 422s 422s 422s ttt = control 422s time P se(P) n.event 422s CIF ETOP 43 0.040159 0.0092578 20 422s CIF life birth 43 0.799059 0.0221865 924 422s CIF spontaneous abortion 43 0.160781 0.0213261 69 422s 422s ttt = exposed 422s time P se(P) n.event 422s CIF ETOP 42 0.28511 0.042493 38 422s CIF life birth 42 0.35257 0.042139 92 422s CIF spontaneous abortion 42 0.36232 0.049473 43 422s > 422s > summary(netm.ttt) 422s 422s ttt=control 422s 422s CIF ETOP 422s P time var lower upper n.risk n.event 422s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 422s 0.038955 13 8.4440e-05 0.024488 0.061694 645 1 422s 0.040159 26 8.5707e-05 0.025513 0.062939 846 0 422s 0.040159 36 8.5707e-05 0.025513 0.062939 876 0 422s 0.040159 40 8.5707e-05 0.025513 0.062939 554 0 422s 0.040159 43 8.5707e-05 0.025513 0.062939 6 0 422s 422s CIF life birth 422s P time var lower upper n.risk n.event 422s 0.000000 6 0.0000e+00 0.000000 0.000000 117 0 422s 0.000000 13 0.0000e+00 0.000000 0.000000 645 0 422s 0.000000 26 0.0000e+00 0.000000 0.000000 846 0 422s 0.053197 36 4.6195e-05 0.041379 0.068268 876 25 422s 0.563121 40 3.8801e-04 0.524924 0.602021 554 280 422s 0.799059 43 4.9224e-04 0.753969 0.840613 6 6 422s 422s CIF spontaneous abortion 422s P time var lower upper n.risk n.event 422s 0.034188 6 0.00028222 0.01297 0.088523 117 4 422s 0.150468 13 0.00045513 0.11360 0.197901 645 1 422s 0.159904 26 0.00045498 0.12274 0.206925 846 1 422s 0.160781 36 0.00045480 0.12360 0.207757 876 1 422s 0.160781 40 0.00045480 0.12360 0.207757 554 0 422s 0.160781 43 0.00045480 0.12360 0.207757 6 0 422s 422s 422s ttt=exposed 422s 422s CIF ETOP 422s P time var lower upper n.risk n.event 422s 0.00000 6 0.0000000 0.00000 0.00000 35 0 422s 0.26048 13 0.0017854 0.18795 0.35425 90 0 422s 0.28115 21 0.0018028 0.20742 0.37423 93 1 422s 0.28511 34 0.0018057 0.21116 0.37806 89 0 422s 0.28511 39 0.0018057 0.21116 0.37806 59 0 422s 0.28511 42 0.0018057 0.21116 0.37806 6 0 422s 422s CIF life birth 422s P time var lower upper n.risk n.event 422s 0.000000 6 0.0000e+00 0.000000 0.000000 35 0 422s 0.000000 13 0.0000e+00 0.000000 0.000000 90 0 422s 0.000000 21 0.0000e+00 0.000000 0.000000 93 0 422s 0.023073 34 9.0514e-05 0.010252 0.051504 89 2 422s 0.180156 39 8.0126e-04 0.131765 0.243663 59 13 422s 0.352565 42 1.7757e-03 0.276882 0.441775 6 6 422s 422s CIF spontaneous abortion 422s P time var lower upper n.risk n.event 422s 0.057143 6 0.0015394 0.014605 0.20968 35 2 422s 0.333246 13 0.0025280 0.245337 0.44216 90 4 422s 0.350702 21 0.0024827 0.262769 0.45762 93 0 422s 0.358492 34 0.0024593 0.270627 0.46448 89 0 422s 0.358492 39 0.0024593 0.270627 0.46448 59 0 422s 0.362323 42 0.0024476 0.274499 0.46785 6 0 422s 422s > 422s > 422s > ### A couple of comparisons with simulated data 422s > set.seed(1313) 422s > time <- rexp(100) 422s > to <- rbinom(100, 2, prob = c(1/3, 1/3, 1/3)) 422s > from <- rep(11, 100) 422s > id <- 1:100 422s > cov <- rbinom(100, 1, 0.5) 422s > 422s > dat.s <- data.frame(id, time, from, to, cov) 422s > 422s > traa <- matrix(FALSE, 3, 3) 422s > traa[1, 2:3] <- TRUE 422s > 422s > aa0 <- etm(dat.s[dat.s$cov == 0, ], c("11", "1", "2"), traa, "0", 0) 422s > aa1 <- etm(dat.s[dat.s$cov == 1, ], c("11", "1", "2"), traa, "0", 0) 422s > aa <- etm(dat.s, c("11", "1", "2"), traa, "0", 0) 422s > 422s > test <- etmCIF(Surv(time, to != 0) ~ 1, dat.s, etype = to) 422s > 422s > test.c <- etmCIF(Surv(time, to != 0) ~ cov, dat.s, etype = to) 422s > 422s > all.equal(trprob(aa, "11 1"), test[[1]]$est["0", "1", ]) 422s [1] TRUE 422s > all.equal(trprob(aa, "11 2"), test[[1]]$est["0", "2", ]) 422s [1] TRUE 422s > 422s > all.equal(trprob(aa0, "11 1"), test.c[[1]]$est["0", "1", ]) 422s [1] TRUE 422s > all.equal(trprob(aa0, "11 2"), test.c[[1]]$est["0", "2", ]) 422s [1] TRUE 422s > 422s > all.equal(trprob(aa1, "11 1"), test.c[[2]]$est["0", "1", ]) 422s [1] TRUE 422s > all.equal(trprob(aa1, "11 2"), test.c[[2]]$est["0", "2", ]) 422s [1] TRUE 422s > 422s > test 422s Call: etmCIF(formula = Surv(time, to != 0) ~ 1, data = dat.s, etype = to) 422s 422s time P se(P) n.event 422s CIF 1 4.9088 0.809108 0.079680 45 422s CIF 2 4.9088 0.096618 0.032905 8 422s > 422s > test.c 422s Call: etmCIF(formula = Surv(time, to != 0) ~ cov, data = dat.s, etype = to) 422s 422s Covariate: cov 422s levels: 0 1 422s 422s 422s cov = 0 422s time P se(P) n.event 422s CIF 1 2.1708 0.70246 0.105797 19 422s CIF 2 2.1708 0.11144 0.053384 4 422s 422s cov = 1 422s time P se(P) n.event 422s CIF 1 4.9088 0.80787 0.094051 26 422s CIF 2 4.9088 0.08436 0.040769 4 422s > 422s > summary(test) 422s 422s 422s 422s CIF 1 422s P time var lower upper n.risk n.event 422s 0.01000 0.0092099 0.0000990 0.0014147 0.068863 100 1 422s 0.11430 0.2663096 0.0010542 0.0649454 0.196993 81 1 422s 0.23451 0.7303091 0.0020436 0.1591107 0.337736 54 1 422s 0.40425 1.4299939 0.0032996 0.3020445 0.525741 29 1 422s 0.54593 2.0647206 0.0040836 0.4269008 0.673605 16 1 422s 0.80911 4.9087561 0.0063489 0.6359544 0.933733 2 1 422s 422s CIF 2 422s P time var lower upper n.risk n.event 422s 0.000000 0.0092099 0.00000000 0.000000 0.000000 100 0 422s 0.031657 0.2663096 0.00032353 0.010320 0.094942 81 0 422s 0.067029 0.7303091 0.00070366 0.030598 0.143503 54 0 422s 0.096618 1.4299939 0.00108275 0.049082 0.185474 29 0 422s 0.096618 2.0647206 0.00108275 0.049082 0.185474 16 0 422s 0.096618 4.9087561 0.00108275 0.049082 0.185474 2 0 422s 422s > summary(test.c) 422s 422s cov=0 422s 422s CIF 1 422s P time var lower upper n.risk n.event 422s 0.022222 0.0092099 0.00048285 0.0031605 0.14747 45 1 422s 0.092222 0.2982439 0.00193603 0.0355971 0.22762 36 0 422s 0.226684 0.7021938 0.00450954 0.1241760 0.39250 24 1 422s 0.378128 1.4299939 0.00760870 0.2337884 0.57145 13 1 422s 0.505736 1.6148774 0.00895330 0.3388425 0.69885 10 1 422s 0.702465 2.1708375 0.01119294 0.4944890 0.88399 3 1 422s 422s CIF 2 422s P time var lower upper n.risk n.event 422s 0.000000 0.0092099 0.0000000 0.000000 0.00000 45 0 422s 0.048441 0.2982439 0.0011168 0.012337 0.18013 36 1 422s 0.076411 0.7021938 0.0018104 0.025202 0.21928 24 0 422s 0.111440 1.4299939 0.0028499 0.042676 0.27392 13 0 422s 0.111440 1.6148774 0.0028499 0.042676 0.27392 10 0 422s 0.111440 2.1708375 0.0028499 0.042676 0.27392 3 0 422s 422s 422s cov=1 422s 422s CIF 1 422s P time var lower upper n.risk n.event 422s 0.018182 0.066692 0.00032457 0.0025813 0.12214 55 1 422s 0.112392 0.263808 0.00187215 0.0520925 0.23333 45 1 422s 0.241023 0.730309 0.00374499 0.1440057 0.38685 31 1 422s 0.401201 1.066913 0.00570788 0.2714008 0.56421 19 1 422s 0.592334 2.366275 0.00775985 0.4286230 0.76273 8 1 422s 0.807871 4.908756 0.00884554 0.6023185 0.94771 2 1 422s 422s CIF 2 422s P time var lower upper n.risk n.event 422s 0.000000 0.066692 0.00000000 0.000000 0.00000 55 0 422s 0.037434 0.263808 0.00067458 0.009494 0.14152 45 0 422s 0.059341 0.730309 0.00111295 0.019447 0.17351 31 0 422s 0.084360 1.066913 0.00166213 0.032211 0.21119 19 0 422s 0.084360 2.366275 0.00166213 0.032211 0.21119 8 0 422s 0.084360 4.908756 0.00166213 0.032211 0.21119 2 0 422s 422s > 422s > options(old) 422s > 422s BEGIN TEST tests.etm.R 422s 422s R version 4.3.2 (2023-10-31) -- "Eye Holes" 422s Copyright (C) 2023 The R Foundation for Statistical Computing 422s Platform: s390x-ibm-linux-gnu (64-bit) 422s 422s R is free software and comes with ABSOLUTELY NO WARRANTY. 422s You are welcome to redistribute it under certain conditions. 422s Type 'license()' or 'licence()' for distribution details. 422s 422s R is a collaborative project with many contributors. 422s Type 'contributors()' for more information and 422s 'citation()' on how to cite R or R packages in publications. 422s 422s Type 'demo()' for some demos, 'help()' for on-line help, or 422s 'help.start()' for an HTML browser interface to help. 422s Type 'q()' to quit R. 422s 422s > require(etm) 422s Loading required package: etm 424s > 424s > ## Print with a bit less precision to avoid lots of notes in the comparison 424s > old <- options(digits = 4) 424s > 424s > ### Simple test 424s > 425s > time <- id <- 1:10 425s > from <- rep(0, 10) 425s > to <- rep(1, 10) 425s > 425s > data1 <- data.frame(id, from, to, time) 425s > tra1 <- matrix(FALSE, 2, 2) 425s > tra1[1, 2] <- TRUE 425s > 425s > etm1 <- etm(data1, c("0", "1"), tra1, NULL, 0) 425s > 425s > all.equal(as.vector(trprob(etm1, "0 0")), cumprod((10:1 - 1) / (10:1))) 425s [1] TRUE 425s > 425s > etm1$cov["0 0", "0 0", ] 425s 1 2 3 4 5 6 7 8 9 10 425s 0.009 0.016 0.021 0.024 0.025 0.024 0.021 0.016 0.009 0.000 425s > 425s > all.equal(etm1$cov["0 0", "0 0",], trcov(etm1, "0 0")) 425s [1] TRUE 425s > 425s > ### A simple test from AHR's author, where the first time is censored 425s > if (!require(survival)) { 425s + stop("This test requires the survival package") 425s + } 425s > 425s > data <- data.frame(id=1:10, time=1:10, from=0, to=1, status=TRUE) 425s > 425s > tra <- matrix(FALSE, nrow=2, ncol=2) 425s > tra[1, 2] <- TRUE 425s > 425s > data$to[1] <- "cens" 425s > data$status[1] <- FALSE 425s > 425s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 425s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 425s > 425s Loading required package: survival 425s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 425s [1] TRUE 425s > 425s > data$to[2] <- "cens" 425s > data$status[2] <- FALSE 425s > 425s > fit.km <- survfit(Surv(time, status) ~ 1, data=data) 425s > fit.etm <- etm(data, c("0","1"), tra, "cens", s=0, t="last", covariance=FALSE) 425s > 425s > all.equal(fit.km$surv[data$status], fit.etm$est[1,1,], check.attributes = FALSE) 425s [1] TRUE 425s > 425s > ### a bit more complicated 425s > 425s > time <- id <- 1:10 425s > from <- rep(0, 10) 425s > to <- rep(c(1, 2), 5) 425s > data2 <- data.frame(id, from, to, time) 425s > 425s > tra2 <- matrix(FALSE, 3, 3) 425s > tra2[1, 2:3] <- TRUE 425s > 425s > etm2 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 425s > 425s > aa <- table(time, to) 425s > 425s > cif1 <- cumsum(aa[, 1] / 10) 425s > cif2 <- cumsum(aa[, 2] / 10) 425s > surv <- cumprod((10:1 - 1) / (10:1)) 425s > 425s > all.equal(trprob(etm2, "0 1"), cif1) 425s [1] TRUE 425s > all.equal(trprob(etm2, "0 2"), cif2) 425s [1] TRUE 425s > all.equal(as.vector(trprob(etm2, "0 0")), surv) 425s [1] TRUE 425s > 425s > ## a test on id 425s > data2$id <- letters[1:10] 425s > 425s > etm3 <- etm(data2, c("0", "1", "2"), tra2, NULL, 0) 425s > 425s > all.equal(trprob(etm2, "0 1"), trprob(etm3, "0 1")) 425s [1] TRUE 425s > all.equal(trprob(etm2, "0 2"), trprob(etm3, "0 2")) 425s [1] TRUE 425s > all.equal(trprob(etm2, "0 0"), trprob(etm3, "0 0")) 425s [1] TRUE 425s > 425s > 425s > ### Test on sir.cont 425s > 425s > data(sir.cont) 425s > 425s > ## Modification for patients entering and leaving a state 425s > ## at the same date 425s > ## Change on ventilation status is considered 425s > ## to happen before end of hospital stay 425s > sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ] 425s > for (i in 2:nrow(sir.cont)) { 425s + if (sir.cont$id[i]==sir.cont$id[i-1]) { 425s + if (sir.cont$time[i]==sir.cont$time[i-1]) { 425s + sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5 425s + } 425s + } 425s + } 425s > 425s > ### Computation of the transition probabilities 425s > ## Possible transitions. 425s > tra <- matrix(ncol=3,nrow=3,FALSE) 425s > tra[1, 2:3] <- TRUE 425s > tra[2, c(1, 3)] <- TRUE 425s > 425s > ## etm 425s > prob.sir <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1) 425s > 425s > prob.sir 425s Multistate model with 2 transient state(s) 425s and 1 absorbing state(s) 425s 425s Possible transitions: 425s from to 425s 0 1 425s 0 2 425s 1 0 425s 1 2 425s 425s Estimate of P(1, 183) 425s 0 1 2 425s 0 0 0 1 425s 1 0 0 1 425s 2 0 0 1 425s 425s > 425s > summ.sir <- summary(prob.sir) 425s > all.equal(summ.sir[['0 1']]$P, as.vector(trprob(prob.sir, "0 1"))) 425s [1] TRUE 425s > subset(summ.sir[[3]],time<183) # issue with precision on different architectures 425s P time var lower upper n.risk n.event 425s 1.5 0.0000 1.5 0.000e+00 0.00000 0.0000 394 0 425s 2 0.1187 2.0 2.641e-04 0.08683 0.1505 396 47 425s 2.5 0.1187 2.5 2.641e-04 0.08683 0.1505 364 0 425s 3 0.2454 3.0 4.465e-04 0.20398 0.2868 365 54 425s 3.5 0.2454 3.5 4.465e-04 0.20398 0.2868 328 0 425s 4 0.3806 4.0 5.416e-04 0.33501 0.4262 331 62 425s 4.5 0.3806 4.5 5.416e-04 0.33501 0.4262 280 0 425s 5 0.4792 5.0 5.480e-04 0.43333 0.5251 283 48 425s 5.5 0.4792 5.5 5.480e-04 0.43333 0.5251 248 0 425s 6 0.5693 6.0 5.141e-04 0.52482 0.6137 249 47 425s 7 0.6350 7.0 4.665e-04 0.59266 0.6773 212 36 425s 8 0.6795 8.0 4.202e-04 0.63931 0.7197 195 27 425s 8.5 0.6795 8.5 4.202e-04 0.63931 0.7197 172 0 425s 9 0.7325 9.0 3.580e-04 0.69541 0.7696 173 34 425s 10 0.7647 10.0 3.141e-04 0.72992 0.7994 148 21 425s 10.5 0.7647 10.5 3.141e-04 0.72992 0.7994 135 0 425s 11 0.7895 11.0 2.790e-04 0.75674 0.8222 136 18 425s 12 0.8138 12.0 2.420e-04 0.78330 0.8443 129 18 425s 12.5 0.8138 12.5 2.420e-04 0.78330 0.8443 117 0 425s 13 0.8294 13.0 2.182e-04 0.80045 0.8584 118 13 425s 14 0.8452 14.0 1.938e-04 0.81789 0.8725 115 14 425s 15 0.8625 15.0 1.670e-04 0.83714 0.8878 106 15 425s 16 0.8723 16.0 1.522e-04 0.84807 0.8964 93 9 425s 17 0.8852 17.0 1.330e-04 0.86256 0.9078 86 12 425s 17.5 0.8852 17.5 1.330e-04 0.86256 0.9078 77 0 425s 18 0.8960 18.0 1.168e-04 0.87484 0.9172 76 9 425s 19 0.9029 19.0 1.070e-04 0.88261 0.9232 71 7 425s 20 0.9125 20.0 9.367e-05 0.89356 0.9315 64 10 425s 21 0.9161 21.0 8.878e-05 0.89768 0.9346 57 4 425s 22 0.9226 22.0 7.996e-05 0.90504 0.9401 55 6 425s 23 0.9261 23.0 7.537e-05 0.90904 0.9431 51 4 425s 23.5 0.9261 23.5 7.537e-05 0.90904 0.9431 49 0 425s 24 0.9354 24.0 6.292e-05 0.91982 0.9509 50 9 425s 25 0.9385 25.0 5.878e-05 0.92352 0.9536 42 3 425s 26 0.9429 26.0 5.326e-05 0.92863 0.9572 39 5 425s 27 0.9477 27.0 4.749e-05 0.93417 0.9612 35 6 425s 27.5 0.9477 27.5 4.749e-05 0.93417 0.9612 29 0 425s 28 0.9531 28.0 4.093e-05 0.94059 0.9657 30 5 425s 29 0.9567 29.0 3.668e-05 0.94485 0.9686 31 4 425s 30 0.9592 30.0 3.384e-05 0.94779 0.9706 28 3 425s 30.5 0.9592 30.5 3.384e-05 0.94779 0.9706 29 0 425s 31 0.9642 31.0 2.821e-05 0.95383 0.9746 30 6 425s 32 0.9649 32.0 2.752e-05 0.95458 0.9751 25 1 425s 33 0.9669 33.0 2.533e-05 0.95708 0.9768 24 2 425s 34 0.9685 34.0 2.368e-05 0.95900 0.9781 26 2 425s 35 0.9697 35.0 2.252e-05 0.96036 0.9790 28 2 425s 36 0.9702 36.0 2.194e-05 0.96104 0.9794 26 1 425s 37 0.9718 37.0 2.043e-05 0.96290 0.9806 26 2 425s 38 0.9739 38.0 1.831e-05 0.96555 0.9823 25 4 425s 38.5 0.9739 38.5 1.831e-05 0.96555 0.9823 21 0 425s 39 0.9760 39.0 1.643e-05 0.96802 0.9839 23 3 425s 40 0.9769 40.0 1.558e-05 0.96918 0.9847 19 1 425s 41 0.9774 41.0 1.512e-05 0.96981 0.9851 22 1 425s 42 0.9779 42.0 1.476e-05 0.97032 0.9854 22 0 425s 43 0.9798 43.0 1.308e-05 0.97271 0.9869 22 3 425s 44 0.9803 44.0 1.265e-05 0.97333 0.9873 21 1 425s 45 0.9817 45.0 1.157e-05 0.97499 0.9883 19 1 425s 46 0.9822 46.0 1.116e-05 0.97561 0.9887 17 1 425s 47 0.9831 47.0 1.037e-05 0.97683 0.9895 18 2 425s 48 0.9836 48.0 9.987e-06 0.97743 0.9898 17 1 425s 49 0.9841 49.0 9.669e-06 0.97796 0.9901 17 0 425s 50 0.9845 50.0 9.297e-06 0.97856 0.9905 17 1 425s 50.5 0.9845 50.5 9.297e-06 0.97856 0.9905 16 0 425s 51 0.9860 51.0 8.214e-06 0.98037 0.9916 17 3 425s 52 0.9870 52.0 7.513e-06 0.98159 0.9923 14 2 425s 53 0.9879 53.0 6.875e-06 0.98276 0.9930 12 1 425s 54 0.9889 54.0 6.214e-06 0.98397 0.9937 12 2 425s 55 0.9903 55.0 5.254e-06 0.98581 0.9948 10 3 425s 56 0.9913 56.0 4.667e-06 0.98703 0.9955 6 1 425s 57 0.9917 57.0 4.364e-06 0.98765 0.9958 5 1 425s 58 0.9922 58.0 4.064e-06 0.98828 0.9962 4 1 425s 59 0.9927 59.0 3.769e-06 0.98891 0.9965 3 1 425s 60 0.9932 60.0 3.488e-06 0.98953 0.9969 3 1 425s 62 0.9937 62.0 3.230e-06 0.99016 0.9972 2 0 425s 63 0.9942 63.0 2.956e-06 0.99079 0.9975 2 1 425s 68 0.9942 68.0 2.956e-06 0.99079 0.9975 1 0 425s 70 0.9946 70.0 2.694e-06 0.99143 0.9979 2 1 425s 78 0.9951 78.0 2.442e-06 0.99207 0.9982 1 0 425s 80 0.9951 80.0 2.442e-06 0.99207 0.9982 1 0 425s 85 0.9966 85.0 1.695e-06 0.99404 0.9991 2 0 425s 89 0.9966 89.0 1.695e-06 0.99404 0.9991 2 0 425s 90 0.9966 90.0 1.695e-06 0.99404 0.9991 1 0 425s 95 0.9971 95.0 1.448e-06 0.99472 0.9994 2 0 425s 100 0.9976 100.0 1.203e-06 0.99542 0.9997 3 0 425s 101 0.9981 101.0 9.592e-07 0.99613 1.0000 3 1 425s 108 0.9985 108.0 7.169e-07 0.99688 1.0000 2 1 425s 113 0.9990 113.0 4.764e-07 0.99767 1.0000 1 0 425s 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 425s 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 425s 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 425s > 425s > ## gonna play a bit with the state names 425s > dd <- sir.cont 425s > dd$from <- ifelse(dd$from == 0, "initial state", "ventilation") 425s > dd$to <- as.character(dd$to) 425s > for (i in seq_len(nrow(dd))) { 425s + dd$to[i] <- switch(dd$to[i], 425s + "0" = "initial state", 425s + "1" = "ventilation", 425s + "2" = "end of story", 425s + "cens" = "cens" 425s + ) 425s + } 425s > 425s > test <- etm(dd, c("initial state", "ventilation", "end of story"), tra, "cens", 1) 425s > 425s > all.equal(test$est["initial state", "initial state", ], 425s + prob.sir$est["0", "0", ]) 425s [1] TRUE 425s > all.equal(trprob(test, "initial state initial state"), trprob(prob.sir, "0 0")) 425s [1] TRUE 425s > all.equal(trprob(test, "initial state ventilation"), trprob(prob.sir, "0 1")) 425s [1] TRUE 425s > all.equal(trprob(test, "initial state end of story"), trprob(prob.sir, "0 2")) 425s [1] TRUE 425s > 425s > all.equal(trcov(test, "initial state end of story"), trcov(prob.sir, "0 2")) 425s [1] TRUE 425s > 425s > aa <- summary(test) 425s > all.equal(summ.sir[[6]], aa[[6]]) 425s [1] TRUE 425s > all.equal(summ.sir[[4]], aa[[4]]) 425s [1] TRUE 425s > 425s > ### Test on abortion data 425s > 425s > data(abortion) 425s > 425s > from <- rep(0, nrow(abortion)) 425s > to <- abortion$cause 425s > entry <- abortion$entry 425s > exit <- abortion$exit 425s > id <- 1:nrow(abortion) 425s > data <- data.frame(id, from, to, entry, exit, group = abortion$group) 425s > 425s > ## Computation of the CIFs 425s > tra <- matrix(FALSE, 4, 4) 425s > tra[1, 2:4] <- TRUE 425s > 425s > cif.control <- etm(data[data$group == 0, ], c("0", "1", "2", "3"), 425s + tra, NULL, 0) 425s > cif.exposed <- etm(data[data$group == 1, ], c("0", "1", "2", "3"), 425s + tra, NULL, 0) 425s > 425s > all.equal(trprob(cif.control, "0 1"), cif.control$est["0", "1", ]) 425s [1] TRUE 425s > all.equal(trcov(cif.control, c("0 1", "0 2")), cif.control$cov["0 1", "0 2", ]) 425s [1] TRUE 425s > 425s > trprob(cif.control, "0 1") 425s 6 7 8 9 10 11 12 13 425s 0.000000 0.007401 0.014881 0.026509 0.033208 0.037694 0.037694 0.038955 425s 14 17 19 21 24 25 26 30 425s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 425s 31 32 33 34 35 36 37 38 425s 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 0.040159 425s 39 40 41 42 43 425s 0.040159 0.040159 0.040159 0.040159 0.040159 425s > trprob(cif.control, "0 2") 425s 6 7 8 9 10 11 12 13 425s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 425s 14 17 19 21 24 25 26 30 425s 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003657 425s 31 32 33 34 35 36 37 38 425s 0.006371 0.008175 0.013543 0.023317 0.031260 0.053197 0.084529 0.179163 425s 39 40 41 42 43 425s 0.322016 0.563121 0.742227 0.793893 0.799059 425s > trprob(cif.control, "0 0") 425s 6 7 8 9 10 11 12 13 425s 0.965812 0.932508 0.887628 0.862433 0.838989 0.822538 0.813099 0.810578 425s 14 17 19 21 24 25 26 30 425s 0.806964 0.805874 0.803810 0.802804 0.801837 0.800883 0.799937 0.796280 425s 31 32 33 34 35 36 37 38 425s 0.793565 0.791762 0.786394 0.776620 0.768677 0.745862 0.714531 0.619897 425s 39 40 41 42 43 425s 0.477043 0.235938 0.056832 0.005167 0.000000 425s > 425s > trcov(cif.control, "0 1") 425s 6 7 8 9 10 11 12 13 425s 0.000e+00 2.719e-05 4.533e-05 6.665e-05 7.698e-05 8.304e-05 8.304e-05 8.444e-05 425s 14 17 19 21 24 25 26 30 425s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 425s 31 32 33 34 35 36 37 38 425s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 425s 39 40 41 42 43 425s 8.571e-05 8.571e-05 8.571e-05 8.571e-05 8.571e-05 425s > trcov(cif.control, "0 2") 425s 6 7 8 9 10 11 12 13 425s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 425s 14 17 19 21 24 25 26 30 425s 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 0.000e+00 3.338e-06 425s 31 32 33 34 35 36 37 38 425s 5.784e-06 7.401e-06 1.216e-05 2.072e-05 2.758e-05 4.619e-05 7.202e-05 1.461e-04 425s 39 40 41 42 43 425s 2.470e-04 3.880e-04 4.702e-04 4.903e-04 4.922e-04 425s > trcov(cif.control, "0 0") 425s 6 7 8 9 10 11 12 13 425s 2.822e-04 3.821e-04 4.527e-04 4.748e-04 4.875e-04 4.927e-04 4.941e-04 4.942e-04 425s 14 17 19 21 24 25 26 30 425s 4.941e-04 4.940e-04 4.936e-04 4.933e-04 4.931e-04 4.928e-04 4.926e-04 4.914e-04 425s 31 32 33 34 35 36 37 38 425s 4.905e-04 4.899e-04 4.880e-04 4.846e-04 4.816e-04 4.729e-04 4.601e-04 4.176e-04 425s 39 40 41 42 43 425s 3.425e-04 1.865e-04 4.797e-05 4.441e-06 0.000e+00 425s > 425s > aa <- summary(cif.control) 425s > aa$"0 1" 425s P time var lower upper n.risk n.event 425s 6 0.000000 6 0.000e+00 0.000000 0.00000 117 0 425s 7 0.007401 7 2.719e-05 0.000000 0.01762 261 2 425s 8 0.014881 8 4.533e-05 0.001685 0.02808 374 3 425s 9 0.026509 9 6.665e-05 0.010508 0.04251 458 6 425s 10 0.033208 10 7.698e-05 0.016011 0.05040 515 4 425s 11 0.037694 11 8.304e-05 0.019834 0.05555 561 3 425s 12 0.037694 12 8.304e-05 0.019834 0.05555 610 0 425s 13 0.038955 13 8.444e-05 0.020944 0.05697 645 1 425s 14 0.040159 14 8.571e-05 0.022014 0.05830 673 1 425s 17 0.040159 17 8.571e-05 0.022014 0.05830 740 0 425s 19 0.040159 19 8.571e-05 0.022014 0.05830 781 0 425s 21 0.040159 21 8.571e-05 0.022014 0.05830 799 0 425s 24 0.040159 24 8.571e-05 0.022014 0.05830 830 0 425s 25 0.040159 25 8.571e-05 0.022014 0.05830 841 0 425s 26 0.040159 26 8.571e-05 0.022014 0.05830 846 0 425s 30 0.040159 30 8.571e-05 0.022014 0.05830 875 0 425s 31 0.040159 31 8.571e-05 0.022014 0.05830 880 0 425s 32 0.040159 32 8.571e-05 0.022014 0.05830 880 0 425s 33 0.040159 33 8.571e-05 0.022014 0.05830 885 0 425s 34 0.040159 34 8.571e-05 0.022014 0.05830 885 0 425s 35 0.040159 35 8.571e-05 0.022014 0.05830 880 0 425s 36 0.040159 36 8.571e-05 0.022014 0.05830 876 0 425s 37 0.040159 37 8.571e-05 0.022014 0.05830 857 0 425s 38 0.040159 38 8.571e-05 0.022014 0.05830 823 0 425s 39 0.040159 39 8.571e-05 0.022014 0.05830 716 0 425s 40 0.040159 40 8.571e-05 0.022014 0.05830 554 0 425s 41 0.040159 41 8.571e-05 0.022014 0.05830 274 0 425s 42 0.040159 42 8.571e-05 0.022014 0.05830 66 0 425s 43 0.040159 43 8.571e-05 0.022014 0.05830 6 0 425s > all.equal(aa$"0 1"$P, as.vector(trprob(cif.control, "0 1"))) 425s [1] TRUE 425s > 425s > ### test on los data 425s > 425s > data(los.data) # in package changeLOS 425s > 425s > ## putting los.data in the long format (see changeLOS) 425s > my.observ <- prepare.los.data(x=los.data) 425s > 425s > tra <- matrix(FALSE, 4, 4) 425s > tra[1, 2:4] <- TRUE 425s > tra[2, 3:4] <- TRUE 425s > 425s > tr.prob <- etm(my.observ, c("0","1","2","3"), tra, NULL, 0) 425s > 425s > tr.prob 425s Multistate model with 2 transient state(s) 425s and 2 absorbing state(s) 425s 425s Possible transitions: 425s from to 425s 0 1 425s 0 2 425s 0 3 425s 1 2 425s 1 3 425s 425s Estimate of P(0, 82) 425s 0 1 2 3 425s 0 0 0 0.7474 0.2526 425s 1 0 0 0.7073 0.2927 425s 2 0 0 1.0000 0.0000 425s 3 0 0 0.0000 1.0000 425s 425s > summary(tr.prob) 425s Transition 0 0 425s P time var lower upper n.risk n.event 425s 0.882275 3 1.374e-04 0.8593018 0.905248 756 0 425s 0.112434 15 1.320e-04 0.0899155 0.134952 90 0 425s 0.031746 27 4.066e-05 0.0192484 0.044244 26 0 425s 0.006614 41 8.690e-06 0.0008359 0.012392 5 0 425s 0.002646 61 3.490e-06 0.0000000 0.006307 3 0 425s 0.000000 82 0.000e+00 0.0000000 0.000000 1 0 425s 425s Transition 0 1 425s P time var lower upper n.risk n.event 425s 0.017196 3 2.235e-05 0.0079289 0.02646 756 13 425s 0.063492 15 7.865e-05 0.0461099 0.08087 90 0 425s 0.030423 27 3.902e-05 0.0181805 0.04267 26 1 425s 0.015873 41 2.066e-05 0.0069637 0.02478 5 0 425s 0.005291 61 6.962e-06 0.0001197 0.01046 3 0 425s 0.000000 82 0.000e+00 0.0000000 0.00000 1 0 425s 425s Transition 0 2 425s P time var lower upper n.risk n.event 425s 0.08466 3 0.0001025 0.06481 0.1045 756 64 425s 0.62302 15 0.0003107 0.58847 0.6576 90 4 425s 0.69841 27 0.0002786 0.66570 0.7311 26 1 425s 0.72751 41 0.0002622 0.69578 0.7593 5 0 425s 0.74074 61 0.0002540 0.70950 0.7720 3 1 425s 0.74735 82 0.0002498 0.71638 0.7783 1 1 425s 425s Transition 0 3 425s P time var lower upper n.risk n.event 425s 0.01587 3 2.066e-05 0.006964 0.02478 756 12 425s 0.20106 15 2.125e-04 0.172489 0.22963 90 1 425s 0.23942 27 2.409e-04 0.208999 0.26984 26 0 425s 0.25000 41 2.480e-04 0.219133 0.28087 5 0 425s 0.25132 61 2.489e-04 0.220402 0.28224 3 0 425s 0.25265 82 2.498e-04 0.221671 0.28362 1 0 425s 425s Transition 1 1 425s P time var lower upper n.risk n.event 425s 1.00000 3 0.000e+00 1.00000 1.00000 0 0 425s 0.38661 15 2.358e-03 0.29143 0.48179 51 0 425s 0.12119 27 7.842e-04 0.06630 0.17607 23 0 425s 0.04593 41 2.405e-04 0.01554 0.07633 14 0 425s 0.01531 61 6.579e-05 0.00000 0.03121 4 0 425s 0.00000 82 0.000e+00 0.00000 0.00000 0 0 425s 425s Transition 1 2 425s P time var lower upper n.risk n.event 425s 0.0000 3 0.000000 0.0000 0.0000 0 0 425s 0.4107 15 0.002590 0.3110 0.5104 51 2 425s 0.6082 27 0.002254 0.5151 0.7012 23 1 425s 0.6652 41 0.002064 0.5761 0.7542 14 2 425s 0.6920 61 0.002000 0.6043 0.7796 4 0 425s 0.7073 82 0.001984 0.6200 0.7946 0 0 425s 425s Transition 1 3 425s P time var lower upper n.risk n.event 425s 0.0000 3 0.000000 0.0000 0.0000 0 0 425s 0.2027 15 0.001784 0.1199 0.2855 51 1 425s 0.2706 27 0.001968 0.1837 0.3576 23 0 425s 0.2889 41 0.001982 0.2016 0.3761 14 0 425s 0.2927 61 0.001984 0.2054 0.3800 4 0 425s 0.2927 82 0.001984 0.2054 0.3800 0 0 425s 425s > 425s > cLOS <- etm::clos(tr.prob, aw = TRUE) 425s > 425s > cLOS 425s The expected change in length of stay is: 425s 1.975 425s 425s Alternative weighting: 425s 425s Expected change in LOS with weight.1: 2.097 425s Expected change in LOS with weight.other: 1.951 425s > 425s > 425s > ### Tests on pseudo values 425s > t_pseudo <- closPseudo(my.observ, c("0","1","2","3"), tra, NULL, 425s + formula = ~ 1, aw = TRUE) 448s > 448s > cLOS$e.phi == t_pseudo$theta[, "e.phi"] 448s [,1] 448s [1,] TRUE 448s > cLOS$e.phi.weights.1 == t_pseudo$theta[, "e.phi.weights.1"] 448s [,1] 448s [1,] TRUE 448s > cLOS$e.phi.weights.other == t_pseudo$theta[, "e.phi.weights.other"] 448s [,1] 448s [1,] TRUE 448s > 448s > mean(t_pseudo$pseudoData$ps.e.phi) 448s [1] 1.968 448s > 448s > ### tests on etmprep 448s > 448s > ### creation of fake data in the wild format, following an illness-death model 448s > ## transition times 448s > tdisease <- c(3, 4, 3, 6, 8, 9) 448s > tdeath <- c(6, 9, 8, 6, 8, 9) 448s > 448s > ## transition status 448s > stat.disease <- c(1, 1, 1, 0, 0, 0) 448s > stat.death <- c(1, 1, 1, 1, 1, 0) 448s > 448s > ## a covariate that we want to keep in the new data 448s > set.seed(1313) 448s > cova <- rbinom(6, 1, 0.5) 448s > 448s > dat <- data.frame(tdisease, tdeath, 448s + stat.disease, stat.death, 448s + cova) 448s > 448s > ## Possible transitions 448s > tra <- matrix(FALSE, 3, 3) 448s > tra[1, 2:3] <- TRUE 448s > tra[2, 3] <- TRUE 448s > 448s > ## data preparation 448s > newdat <- etmprep(c(NA, "tdisease", "tdeath"), 448s + c(NA, "stat.disease", "stat.death"), 448s + data = dat, tra = tra, 448s + cens.name = "cens", keep = "cova") 448s > 448s > newdat 448s id entry exit from to cova 448s 1 1 0 3 0 1 1 448s 2 1 3 6 1 2 1 448s 3 2 0 4 0 1 0 448s 4 2 4 9 1 2 0 448s 5 3 0 3 0 1 1 448s 6 3 3 8 1 2 1 448s 7 4 0 6 0 2 0 448s 8 5 0 8 0 2 1 448s 9 6 0 9 0 cens 1 448s > 448s > ref <- data.frame(id = c(1, 1, 2, 2, 3, 3, 4, 5, 6), 448s + entry = c(0, 3, 0, 4, 0, 3, 0, 0, 0), 448s + exit = c(3, 6, 4, 9, 3, 8, 6, 8, 9), 448s + from = c(0, 1, 0, 1, 0, 1, 0, 0, 0), 448s + to = c(rep(c(1, 2), 3), 2, 2, "cens"), 448s + cova = c(1, 1, 0, 0, 1, 1, 0, 1, 1)) 448s > ref$from <- factor(as.character(ref$from), levels = c("0", "1", "2", "cens")) 448s > ref$to <- factor(as.character(ref$to), levels = c("0", "1", "2", "cens")) 448s > 448s > all.equal(ref, newdat) 448s [1] TRUE 448s > 448s > 448s > ###################################### 448s > ### Test the stratified calls 448s > ###################################### 448s > 448s > if (require("kmi", quietly = TRUE)) { 448s + library(etm) 448s + 448s + data(icu.pneu) 448s + my.icu.pneu <- icu.pneu 448s + 448s + my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] 448s + masque <- diff(my.icu.pneu$id) 448s + 448s + my.icu.pneu$from <- 0 448s + my.icu.pneu$from[c(1, masque) == 0] <- 1 448s + 448s + my.icu.pneu$to2 <- my.icu.pneu$event 448s + my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" 448s + my.icu.pneu$to2[c(masque, 1) == 0] <- 1 448s + 448s + 448s + my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, 448s + my.icu.pneu$to2) 448s + 448s + my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", 448s + "to2", "age", "sex")] 448s + names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") 448s + 448s + bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") 448s + 448s + bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], 448s + c("0", "1", "2"), tra_ill(), "cens", 0) 448s + 448s + all(bouh_strat[[1]]$est == bouh_female$est) 448s + 448s + ## Test the summary 448s + the_summary <- summary(bouh_strat) 448s + the_summary 448s + 448s + ## Test trprob 448s + all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) 448s + all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) 448s + 448s + ## Test trcov 448s + all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) 448s + all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) 448s + all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) 448s + } else { 448s + print("These tests require the kmi package") 448s + } 448s [1] TRUE 448s > 448s > options(old) 448s > 449s autopkgtest [10:02:31]: test run-unit-test: -----------------------] 449s run-unit-test PASS 449s autopkgtest [10:02:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 449s autopkgtest [10:02:31]: test pkg-r-autopkgtest: preparing testbed 452s Reading package lists... 452s Building dependency tree... 452s Reading state information... 452s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 452s Starting 2 pkgProblemResolver with broken count: 0 452s Done 453s Done 453s Starting pkgProblemResolver with broken count: 0 453s Starting 2 pkgProblemResolver with broken count: 0 453s Done 454s The following additional packages will be installed: 454s build-essential cpp cpp-13 cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu 454s dctrl-tools g++ g++-13 g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-13 454s gcc-13-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-13 454s gfortran-13-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 454s libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 454s libcrypt-dev libgcc-13-dev libgfortran-13-dev libicu-dev libisl23 libitm1 454s libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev 454s libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 454s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 454s libtirpc-dev libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf 454s pkgconf-bin r-base-dev r-cran-backports r-cran-broom r-cran-cli 454s r-cran-colorspace r-cran-cpp11 r-cran-dplyr r-cran-ellipsis r-cran-fansi 454s r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue 454s r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 454s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell r-cran-nlme 454s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 454s r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble 454s r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite 454s r-cran-withr rpcsvc-proto zlib1g-dev 454s Suggested packages: 454s cpp-doc gcc-13-locales cpp-13-doc debtags g++-multilib g++-13-multilib 454s gcc-13-doc gcc-multilib manpages-dev autoconf automake libtool flex bison 454s gdb gcc-doc gcc-13-multilib gdb-s390x-linux-gnu gfortran-multilib 454s gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev 454s liblapack-doc glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc 454s libstdc++-13-doc texlive-base texlive-latex-base texlive-plain-generic 454s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils 454s texlive-latex-recommended texlive-latex-extra texinfo r-cran-aer 454s r-cran-bbmle r-cran-boot r-cran-car r-cran-cardata r-cran-caret 454s r-cran-cluster r-cran-cmprsk r-cran-coda r-cran-covr r-cran-e1071 454s r-cran-emmeans r-cran-epir r-cran-gam r-cran-gee r-cran-glmnet r-cran-gmm 454s r-cran-hmisc r-cran-irlba r-cran-interp r-cran-knitr r-cran-ks r-cran-lavaan 454s r-cran-leaps r-cran-lme4 r-cran-lmtest r-cran-lsmeans r-cran-maps 454s r-cran-mclust r-cran-metafor r-cran-modeldata r-cran-multcomp r-cran-network 454s r-cran-nnet r-cran-ordinal r-cran-plm r-cran-psych r-cran-quantreg 454s r-cran-rmarkdown r-cran-robust r-cran-robustbase r-cran-rsample 454s r-cran-sandwich r-cran-sp r-cran-spdep r-cran-spatialreg r-cran-spelling 454s r-cran-survey r-cran-systemfit r-cran-tseries r-cran-zoo r-cran-kernsmooth 454s r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs 454s r-cran-png r-cran-jpeg r-cran-viridis r-cran-magick r-cran-sf r-cran-bit64 454s r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-units 454s r-cran-vdiffr r-cran-testthat r-cran-bench r-cran-blob r-cran-brio 454s r-cran-callr r-cran-crayon r-cran-evaluate r-cran-here r-cran-hms 454s r-cran-htmltools r-cran-pkgbuild r-cran-pkgload 454s Recommended packages: 454s bzip2-doc manpages manpages-dev libc-devtools libpng-tools r-cran-testthat 454s r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools 454s r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps 454s r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami 454s r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr 454s r-cran-progress r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql 454s r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-hexbin r-cran-hmisc 454s r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg 454s r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 454s r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-httr 454s r-cran-fs r-cran-usethis r-cran-bit64 r-cran-dichromat r-cran-hms 454s r-cran-mockr r-cran-formattable r-cran-readr r-cran-pkgdown r-cran-zeallot 454s The following NEW packages will be installed: 454s build-essential cpp cpp-13 cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu 454s dctrl-tools g++ g++-13 g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-13 454s gcc-13-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-13 454s gfortran-13-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 454s libatomic1 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 454s libcrypt-dev libgcc-13-dev libgfortran-13-dev libicu-dev libisl23 libitm1 454s libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev 454s libmpc3 libncurses-dev libnsl-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 454s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-13-dev 454s libtirpc-dev libubsan1 linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf 454s pkgconf-bin r-base-dev r-cran-backports r-cran-broom r-cran-cli 454s r-cran-colorspace r-cran-cpp11 r-cran-dplyr r-cran-ellipsis r-cran-fansi 454s r-cran-farver r-cran-geepack r-cran-generics r-cran-ggplot2 r-cran-glue 454s r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lifecycle 454s r-cran-magrittr r-cran-mass r-cran-mgcv r-cran-munsell r-cran-nlme 454s r-cran-pillar r-cran-pkgconfig r-cran-purrr r-cran-r6 r-cran-rcolorbrewer 454s r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble 454s r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite 454s r-cran-withr rpcsvc-proto zlib1g-dev 454s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 454s 1 not fully installed or removed. 454s Need to get 117 MB of archives. 454s After this operation, 349 MB of additional disk space will be used. 454s Get:1 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cli s390x 3.6.2-1 [1382 kB] 455s Get:2 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-glue s390x 1.7.0-1 [154 kB] 455s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rlang s390x 1.1.3-1 [1672 kB] 455s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 456s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 456s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-isoband s390x 0.2.7-1 [1481 kB] 456s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mass s390x 7.3-60.0.1-1 [1122 kB] 456s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-nlme s390x 3.1.164-1 [2268 kB] 456s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 457s Get:10 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-farver s390x 2.1.1-1 [1347 kB] 457s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-labeling all 0.4.3-1 [62.1 kB] 457s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-colorspace s390x 2.1-0+dfsg-1 [1540 kB] 457s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-munsell all 0.5.0-2build1 [208 kB] 457s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-r6 all 2.5.1-1 [99.0 kB] 457s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 457s Get:16 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-viridislite all 0.4.2-2 [1088 kB] 457s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-scales all 1.3.0-1 [603 kB] 457s Get:18 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-fansi s390x 1.0.5-1 [615 kB] 458s Get:19 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-magrittr s390x 2.0.3-1 [154 kB] 458s Get:20 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-utf8 s390x 1.2.4-1 [143 kB] 458s Get:21 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-vctrs s390x 0.6.5-1 [1448 kB] 458s Get:22 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 458s Get:23 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 458s Get:24 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tibble s390x 3.2.1+dfsg-2 [415 kB] 458s Get:25 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-withr all 2.5.0-1 [225 kB] 458s Get:26 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 458s Get:27 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-backports s390x 1.4.1-1 [101 kB] 458s Get:28 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-generics all 0.1.3-1 [81.3 kB] 458s Get:29 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tidyselect s390x 1.2.0+dfsg-1 [218 kB] 458s Get:30 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-dplyr s390x 1.1.4-1 [1515 kB] 458s Get:31 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-ellipsis s390x 0.3.2-2 [35.4 kB] 458s Get:32 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-purrr s390x 1.0.2-1 [501 kB] 458s Get:33 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-stringi s390x 1.8.3-1 [885 kB] 458s Get:34 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-stringr all 1.5.1-1 [290 kB] 458s Get:35 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-cpp11 all 0.4.7-1 [266 kB] 458s Get:36 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-tidyr s390x 1.3.1-1 [1157 kB] 458s Get:37 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-broom all 1.0.5+dfsg-1 [1729 kB] 459s Get:38 http://ftpmaster.internal/ubuntu noble/universe s390x r-cran-geepack s390x 1.3.10-1 [413 kB] 459s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x dctrl-tools s390x 2.24-3build2 [65.4 kB] 459s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu2 [20.2 kB] 459s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-11.11 [1590 kB] 459s Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] 459s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1build1 [225 kB] 459s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3 [73.5 kB] 459s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB] 459s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu2 [1629 kB] 459s Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libisl23 s390x 0.26-3 [722 kB] 459s Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libmpc3 s390x 1.3.1-1 [54.9 kB] 459s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [9929 kB] 460s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-17ubuntu2 [1026 B] 460s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] 460s Get:52 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] 460s Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240303-1ubuntu1 [49.9 kB] 460s Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240303-1ubuntu1 [31.1 kB] 460s Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240303-1ubuntu1 [9392 B] 460s Get:56 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240303-1ubuntu1 [2998 kB] 460s Get:57 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240303-1ubuntu1 [1186 kB] 460s Get:58 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-17ubuntu2 [1003 kB] 460s Get:59 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [19.1 MB] 462s Get:60 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-17ubuntu2 [467 kB] 462s Get:61 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] 462s Get:62 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] 462s Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-17ubuntu2 [2430 kB] 462s Get:64 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [11.3 MB] 463s Get:65 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-17ubuntu2 [14.4 kB] 463s Get:66 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] 463s Get:67 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] 463s Get:68 http://ftpmaster.internal/ubuntu noble/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 463s Get:69 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran-13-dev s390x 13.2.0-17ubuntu2 [623 kB] 463s Get:70 http://ftpmaster.internal/ubuntu noble/main s390x gfortran-13-s390x-linux-gnu s390x 13.2.0-17ubuntu2 [10.4 MB] 465s Get:71 http://ftpmaster.internal/ubuntu noble/main s390x gfortran-13 s390x 13.2.0-17ubuntu2 [10.3 kB] 465s Get:72 http://ftpmaster.internal/ubuntu noble/main s390x gfortran-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1016 B] 465s Get:73 http://ftpmaster.internal/ubuntu noble/main s390x gfortran s390x 4:13.2.0-7ubuntu1 [1174 B] 465s Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libblas-dev s390x 3.12.0-3 [239 kB] 465s Get:75 http://ftpmaster.internal/ubuntu noble/main s390x liblapack-dev s390x 3.12.0-3 [5983 kB] 465s Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libncurses-dev s390x 6.4+20240113-1ubuntu1 [412 kB] 466s Get:77 http://ftpmaster.internal/ubuntu noble/main s390x libreadline-dev s390x 8.2-3 [187 kB] 466s Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8-dev s390x 2.1.5-2ubuntu1 [264 kB] 466s Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 466s Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 466s Get:81 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-16-0 s390x 10.42-4ubuntu1 [229 kB] 466s Get:82 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-32-0 s390x 10.42-4ubuntu1 [217 kB] 466s Get:83 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-posix3 s390x 10.42-4ubuntu1 [6704 B] 466s Get:84 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-dev s390x 10.42-4ubuntu1 [805 kB] 466s Get:85 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB] 466s Get:86 http://ftpmaster.internal/ubuntu noble/main s390x libpng-dev s390x 1.6.43-1 [277 kB] 466s Get:87 http://ftpmaster.internal/ubuntu noble/main s390x libbz2-dev s390x 1.0.8-5ubuntu1 [39.4 kB] 466s Get:88 http://ftpmaster.internal/ubuntu noble/main s390x liblzma-dev s390x 5.4.5-0.3 [215 kB] 466s Get:89 http://ftpmaster.internal/ubuntu noble/main s390x icu-devtools s390x 74.2-1ubuntu1 [224 kB] 466s Get:90 http://ftpmaster.internal/ubuntu noble/main s390x libicu-dev s390x 74.2-1ubuntu1 [11.9 MB] 468s Get:91 http://ftpmaster.internal/ubuntu noble/main s390x libpkgconf3 s390x 1.8.1-2 [30.4 kB] 468s Get:92 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf-bin s390x 1.8.1-2 [20.8 kB] 468s Get:93 http://ftpmaster.internal/ubuntu noble/main s390x pkgconf s390x 1.8.1-2 [16.7 kB] 468s Get:94 http://ftpmaster.internal/ubuntu noble/main s390x pkg-config s390x 1.8.1-2 [7170 B] 468s Get:95 http://ftpmaster.internal/ubuntu noble/universe s390x r-base-dev all 4.3.2-1build1 [4336 B] 468s Get:96 http://ftpmaster.internal/ubuntu noble/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 469s Fetched 117 MB in 14s (8176 kB/s) 469s Selecting previously unselected package r-cran-cli. 469s (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 ... 56018 files and directories currently installed.) 469s Preparing to unpack .../00-r-cran-cli_3.6.2-1_s390x.deb ... 469s Unpacking r-cran-cli (3.6.2-1) ... 469s Selecting previously unselected package r-cran-glue. 469s Preparing to unpack .../01-r-cran-glue_1.7.0-1_s390x.deb ... 469s Unpacking r-cran-glue (1.7.0-1) ... 469s Selecting previously unselected package r-cran-rlang. 469s Preparing to unpack .../02-r-cran-rlang_1.1.3-1_s390x.deb ... 469s Unpacking r-cran-rlang (1.1.3-1) ... 469s Selecting previously unselected package r-cran-lifecycle. 469s Preparing to unpack .../03-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 469s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 469s Selecting previously unselected package r-cran-gtable. 469s Preparing to unpack .../04-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 469s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 470s Selecting previously unselected package r-cran-isoband. 470s Preparing to unpack .../05-r-cran-isoband_0.2.7-1_s390x.deb ... 470s Unpacking r-cran-isoband (0.2.7-1) ... 470s Selecting previously unselected package r-cran-mass. 470s Preparing to unpack .../06-r-cran-mass_7.3-60.0.1-1_s390x.deb ... 470s Unpacking r-cran-mass (7.3-60.0.1-1) ... 470s Selecting previously unselected package r-cran-nlme. 470s Preparing to unpack .../07-r-cran-nlme_3.1.164-1_s390x.deb ... 470s Unpacking r-cran-nlme (3.1.164-1) ... 470s Selecting previously unselected package r-cran-mgcv. 470s Preparing to unpack .../08-r-cran-mgcv_1.9-1-1_s390x.deb ... 470s Unpacking r-cran-mgcv (1.9-1-1) ... 470s Selecting previously unselected package r-cran-farver. 470s Preparing to unpack .../09-r-cran-farver_2.1.1-1_s390x.deb ... 470s Unpacking r-cran-farver (2.1.1-1) ... 470s Selecting previously unselected package r-cran-labeling. 470s Preparing to unpack .../10-r-cran-labeling_0.4.3-1_all.deb ... 470s Unpacking r-cran-labeling (0.4.3-1) ... 470s Selecting previously unselected package r-cran-colorspace. 470s Preparing to unpack .../11-r-cran-colorspace_2.1-0+dfsg-1_s390x.deb ... 470s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 470s Selecting previously unselected package r-cran-munsell. 470s Preparing to unpack .../12-r-cran-munsell_0.5.0-2build1_all.deb ... 470s Unpacking r-cran-munsell (0.5.0-2build1) ... 470s Selecting previously unselected package r-cran-r6. 470s Preparing to unpack .../13-r-cran-r6_2.5.1-1_all.deb ... 470s Unpacking r-cran-r6 (2.5.1-1) ... 470s Selecting previously unselected package r-cran-rcolorbrewer. 470s Preparing to unpack .../14-r-cran-rcolorbrewer_1.1-3-1build1_all.deb ... 470s Unpacking r-cran-rcolorbrewer (1.1-3-1build1) ... 470s Selecting previously unselected package r-cran-viridislite. 470s Preparing to unpack .../15-r-cran-viridislite_0.4.2-2_all.deb ... 470s Unpacking r-cran-viridislite (0.4.2-2) ... 470s Selecting previously unselected package r-cran-scales. 470s Preparing to unpack .../16-r-cran-scales_1.3.0-1_all.deb ... 470s Unpacking r-cran-scales (1.3.0-1) ... 470s Selecting previously unselected package r-cran-fansi. 470s Preparing to unpack .../17-r-cran-fansi_1.0.5-1_s390x.deb ... 470s Unpacking r-cran-fansi (1.0.5-1) ... 470s Selecting previously unselected package r-cran-magrittr. 470s Preparing to unpack .../18-r-cran-magrittr_2.0.3-1_s390x.deb ... 470s Unpacking r-cran-magrittr (2.0.3-1) ... 470s Selecting previously unselected package r-cran-utf8. 470s Preparing to unpack .../19-r-cran-utf8_1.2.4-1_s390x.deb ... 470s Unpacking r-cran-utf8 (1.2.4-1) ... 470s Selecting previously unselected package r-cran-vctrs. 470s Preparing to unpack .../20-r-cran-vctrs_0.6.5-1_s390x.deb ... 470s Unpacking r-cran-vctrs (0.6.5-1) ... 470s Selecting previously unselected package r-cran-pillar. 470s Preparing to unpack .../21-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 470s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 470s Selecting previously unselected package r-cran-pkgconfig. 470s Preparing to unpack .../22-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 470s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 470s Selecting previously unselected package r-cran-tibble. 470s Preparing to unpack .../23-r-cran-tibble_3.2.1+dfsg-2_s390x.deb ... 470s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 470s Selecting previously unselected package r-cran-withr. 470s Preparing to unpack .../24-r-cran-withr_2.5.0-1_all.deb ... 470s Unpacking r-cran-withr (2.5.0-1) ... 470s Selecting previously unselected package r-cran-ggplot2. 470s Preparing to unpack .../25-r-cran-ggplot2_3.4.4+dfsg-1_all.deb ... 470s Unpacking r-cran-ggplot2 (3.4.4+dfsg-1) ... 470s Selecting previously unselected package r-cran-backports. 470s Preparing to unpack .../26-r-cran-backports_1.4.1-1_s390x.deb ... 470s Unpacking r-cran-backports (1.4.1-1) ... 470s Selecting previously unselected package r-cran-generics. 470s Preparing to unpack .../27-r-cran-generics_0.1.3-1_all.deb ... 470s Unpacking r-cran-generics (0.1.3-1) ... 470s Selecting previously unselected package r-cran-tidyselect. 470s Preparing to unpack .../28-r-cran-tidyselect_1.2.0+dfsg-1_s390x.deb ... 470s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 470s Selecting previously unselected package r-cran-dplyr. 470s Preparing to unpack .../29-r-cran-dplyr_1.1.4-1_s390x.deb ... 470s Unpacking r-cran-dplyr (1.1.4-1) ... 471s Selecting previously unselected package r-cran-ellipsis. 471s Preparing to unpack .../30-r-cran-ellipsis_0.3.2-2_s390x.deb ... 471s Unpacking r-cran-ellipsis (0.3.2-2) ... 471s Selecting previously unselected package r-cran-purrr. 471s Preparing to unpack .../31-r-cran-purrr_1.0.2-1_s390x.deb ... 471s Unpacking r-cran-purrr (1.0.2-1) ... 471s Selecting previously unselected package r-cran-stringi. 471s Preparing to unpack .../32-r-cran-stringi_1.8.3-1_s390x.deb ... 471s Unpacking r-cran-stringi (1.8.3-1) ... 471s Selecting previously unselected package r-cran-stringr. 471s Preparing to unpack .../33-r-cran-stringr_1.5.1-1_all.deb ... 471s Unpacking r-cran-stringr (1.5.1-1) ... 471s Selecting previously unselected package r-cran-cpp11. 471s Preparing to unpack .../34-r-cran-cpp11_0.4.7-1_all.deb ... 471s Unpacking r-cran-cpp11 (0.4.7-1) ... 471s Selecting previously unselected package r-cran-tidyr. 471s Preparing to unpack .../35-r-cran-tidyr_1.3.1-1_s390x.deb ... 471s Unpacking r-cran-tidyr (1.3.1-1) ... 471s Selecting previously unselected package r-cran-broom. 471s Preparing to unpack .../36-r-cran-broom_1.0.5+dfsg-1_all.deb ... 471s Unpacking r-cran-broom (1.0.5+dfsg-1) ... 471s Selecting previously unselected package r-cran-geepack. 471s Preparing to unpack .../37-r-cran-geepack_1.3.10-1_s390x.deb ... 471s Unpacking r-cran-geepack (1.3.10-1) ... 471s Selecting previously unselected package dctrl-tools. 471s Preparing to unpack .../38-dctrl-tools_2.24-3build2_s390x.deb ... 471s Unpacking dctrl-tools (2.24-3build2) ... 471s Selecting previously unselected package libc-dev-bin. 471s Preparing to unpack .../39-libc-dev-bin_2.39-0ubuntu2_s390x.deb ... 471s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 471s Selecting previously unselected package linux-libc-dev:s390x. 471s Preparing to unpack .../40-linux-libc-dev_6.8.0-11.11_s390x.deb ... 471s Unpacking linux-libc-dev:s390x (6.8.0-11.11) ... 471s Selecting previously unselected package libcrypt-dev:s390x. 471s Preparing to unpack .../41-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... 471s Unpacking libcrypt-dev:s390x (1:4.4.36-4) ... 471s Selecting previously unselected package libtirpc-dev:s390x. 471s Preparing to unpack .../42-libtirpc-dev_1.3.4+ds-1build1_s390x.deb ... 471s Unpacking libtirpc-dev:s390x (1.3.4+ds-1build1) ... 472s Selecting previously unselected package libnsl-dev:s390x. 472s Preparing to unpack .../43-libnsl-dev_1.3.0-3_s390x.deb ... 472s Unpacking libnsl-dev:s390x (1.3.0-3) ... 472s Selecting previously unselected package rpcsvc-proto. 472s Preparing to unpack .../44-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ... 472s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 472s Selecting previously unselected package libc6-dev:s390x. 472s Preparing to unpack .../45-libc6-dev_2.39-0ubuntu2_s390x.deb ... 472s Unpacking libc6-dev:s390x (2.39-0ubuntu2) ... 472s Selecting previously unselected package libisl23:s390x. 472s Preparing to unpack .../46-libisl23_0.26-3_s390x.deb ... 472s Unpacking libisl23:s390x (0.26-3) ... 472s Selecting previously unselected package libmpc3:s390x. 472s Preparing to unpack .../47-libmpc3_1.3.1-1_s390x.deb ... 472s Unpacking libmpc3:s390x (1.3.1-1) ... 472s Selecting previously unselected package cpp-13-s390x-linux-gnu. 472s Preparing to unpack .../48-cpp-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 472s Unpacking cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 472s Selecting previously unselected package cpp-13. 472s Preparing to unpack .../49-cpp-13_13.2.0-17ubuntu2_s390x.deb ... 472s Unpacking cpp-13 (13.2.0-17ubuntu2) ... 472s Selecting previously unselected package cpp-s390x-linux-gnu. 472s Preparing to unpack .../50-cpp-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 472s Unpacking cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 472s Selecting previously unselected package cpp. 472s Preparing to unpack .../51-cpp_4%3a13.2.0-7ubuntu1_s390x.deb ... 472s Unpacking cpp (4:13.2.0-7ubuntu1) ... 472s Selecting previously unselected package libcc1-0:s390x. 472s Preparing to unpack .../52-libcc1-0_14-20240303-1ubuntu1_s390x.deb ... 472s Unpacking libcc1-0:s390x (14-20240303-1ubuntu1) ... 472s Selecting previously unselected package libitm1:s390x. 472s Preparing to unpack .../53-libitm1_14-20240303-1ubuntu1_s390x.deb ... 472s Unpacking libitm1:s390x (14-20240303-1ubuntu1) ... 472s Selecting previously unselected package libatomic1:s390x. 472s Preparing to unpack .../54-libatomic1_14-20240303-1ubuntu1_s390x.deb ... 472s Unpacking libatomic1:s390x (14-20240303-1ubuntu1) ... 472s Selecting previously unselected package libasan8:s390x. 472s Preparing to unpack .../55-libasan8_14-20240303-1ubuntu1_s390x.deb ... 472s Unpacking libasan8:s390x (14-20240303-1ubuntu1) ... 472s Selecting previously unselected package libubsan1:s390x. 472s Preparing to unpack .../56-libubsan1_14-20240303-1ubuntu1_s390x.deb ... 472s Unpacking libubsan1:s390x (14-20240303-1ubuntu1) ... 472s Selecting previously unselected package libgcc-13-dev:s390x. 472s Preparing to unpack .../57-libgcc-13-dev_13.2.0-17ubuntu2_s390x.deb ... 472s Unpacking libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... 472s Selecting previously unselected package gcc-13-s390x-linux-gnu. 472s Preparing to unpack .../58-gcc-13-s390x-linux-gnu_13.2.0-17ubuntu2_s390x.deb ... 472s Unpacking gcc-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 473s Selecting previously unselected package gcc-13. 473s Preparing to unpack .../59-gcc-13_13.2.0-17ubuntu2_s390x.deb ... 473s Unpacking gcc-13 (13.2.0-17ubuntu2) ... 473s Selecting previously unselected package gcc-s390x-linux-gnu. 473s Preparing to unpack .../60-gcc-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... 473s Unpacking gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 473s Selecting previously unselected package gcc. 473s Preparing to unpack .../61-gcc_4%3a13.2.0-7ubuntu1_s390x.deb ... 473s Unpacking gcc (4:13.2.0-7ubuntu1) ... 473s Selecting previously unselected package libstdc++-13-dev:s390x. 473s Preparing to unpack .../62-libstdc++-13-dev_13.2.0-17ubuntu2_s390x.deb ... 473s Unpacking libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... 474s Selecting previously unselected package g++-13-s390x-linux-gnu. 474s 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libblas-dev:s390x. 474s Preparing to unpack .../73-libblas-dev_3.12.0-3_s390x.deb ... 474s Unpacking libblas-dev:s390x (3.12.0-3) ... 474s Selecting previously unselected package liblapack-dev:s390x. 474s Preparing to unpack .../74-liblapack-dev_3.12.0-3_s390x.deb ... 474s Unpacking liblapack-dev:s390x (3.12.0-3) ... 475s Selecting previously unselected package libncurses-dev:s390x. 475s Preparing to unpack .../75-libncurses-dev_6.4+20240113-1ubuntu1_s390x.deb ... 475s Unpacking libncurses-dev:s390x (6.4+20240113-1ubuntu1) ... 475s Selecting previously unselected package libreadline-dev:s390x. 475s Preparing to unpack .../76-libreadline-dev_8.2-3_s390x.deb ... 475s Unpacking libreadline-dev:s390x (8.2-3) ... 475s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 475s Preparing to unpack .../77-libjpeg-turbo8-dev_2.1.5-2ubuntu1_s390x.deb ... 475s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-2ubuntu1) ... 475s Selecting previously unselected package libjpeg8-dev:s390x. 475s 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476s Setting up r-cran-viridislite (0.4.2-2) ... 476s Setting up libcrypt-dev:s390x (1:4.4.36-4) ... 476s Setting up libasan8:s390x (14-20240303-1ubuntu1) ... 476s Setting up r-cran-r6 (2.5.1-1) ... 476s Setting up libisl23:s390x (0.26-3) ... 476s Setting up libc-dev-bin (2.39-0ubuntu2) ... 476s Setting up r-cran-magrittr (2.0.3-1) ... 476s Setting up libcc1-0:s390x (14-20240303-1ubuntu1) ... 476s Setting up r-cran-vctrs (0.6.5-1) ... 476s Setting up libblas-dev:s390x (3.12.0-3) ... 476s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode 476s Setting up dctrl-tools (2.24-3build2) ... 476s Setting up libitm1:s390x (14-20240303-1ubuntu1) ... 476s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 476s Setting up r-cran-ellipsis (0.3.2-2) ... 476s Setting up r-cran-stringr (1.5.1-1) ... 476s Setting up r-cran-munsell (0.5.0-2build1) ... 476s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 476s Setting up pkgconf:s390x (1.8.1-2) ... 476s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... 476s Setting up cpp-13-s390x-linux-gnu (13.2.0-17ubuntu2) ... 476s Setting up r-cran-scales (1.3.0-1) ... 476s Setting up liblapack-dev:s390x (3.12.0-3) ... 476s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode 476s Setting up r-cran-purrr (1.0.2-1) ... 476s Setting up pkg-config:s390x (1.8.1-2) ... 476s Setting up libgcc-13-dev:s390x (13.2.0-17ubuntu2) ... 476s Setting up libc6-dev:s390x (2.39-0ubuntu2) ... 476s Setting up r-cran-dplyr (1.1.4-1) ... 476s Setting up libgfortran-13-dev:s390x (13.2.0-17ubuntu2) ... 476s Setting up libicu-dev:s390x (74.2-1ubuntu1) ... 476s Setting up libstdc++-13-dev:s390x (13.2.0-17ubuntu2) ... 476s Setting up libbz2-dev:s390x (1.0.8-5ubuntu1) ... 476s Setting up libjpeg-turbo8-dev:s390x (2.1.5-2ubuntu1) ... 476s Setting up libncurses-dev:s390x 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476s Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... 476s Setting up gcc (4:13.2.0-7ubuntu1) ... 476s Setting up r-cran-broom (1.0.5+dfsg-1) ... 476s Setting up gfortran-13 (13.2.0-17ubuntu2) ... 476s Setting up g++ (4:13.2.0-7ubuntu1) ... 476s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 476s Setting up build-essential (12.10ubuntu1) ... 476s Setting up r-cran-geepack (1.3.10-1) ... 476s Setting up gfortran (4:13.2.0-7ubuntu1) ... 476s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 476s 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 476s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 476s 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 476s Setting up r-base-dev (4.3.2-1build1) ... 476s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 476s Setting up autopkgtest-satdep (0) ... 476s Processing triggers for man-db (2.12.0-3) ... 477s Processing triggers for install-info (7.1-3) ... 477s Processing triggers for libc-bin (2.39-0ubuntu2) ... 480s (Reading database ... 63560 files and directories currently installed.) 480s Removing autopkgtest-satdep (0) ... 481s autopkgtest [10:03:03]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 481s autopkgtest [10:03:03]: test pkg-r-autopkgtest: [----------------------- 481s Test: Try to load the R library etm 481s 481s R version 4.3.2 (2023-10-31) -- "Eye Holes" 481s Copyright (C) 2023 The R Foundation for Statistical Computing 481s Platform: s390x-ibm-linux-gnu (64-bit) 481s 481s R is free software and comes with ABSOLUTELY NO WARRANTY. 481s You are welcome to redistribute it under certain conditions. 481s Type 'license()' or 'licence()' for distribution details. 481s 481s R is a collaborative project with many contributors. 481s Type 'contributors()' for more information and 481s 'citation()' on how to cite R or R packages in publications. 481s 481s Type 'demo()' for some demos, 'help()' for on-line help, or 481s 'help.start()' for an HTML browser interface to help. 481s Type 'q()' to quit R. 481s 482s > library('etm') 484s > 484s > 484s Other tests are currently unsupported! 484s They will be progressively added. 484s autopkgtest [10:03:06]: test pkg-r-autopkgtest: -----------------------] 485s autopkgtest [10:03:07]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 485s pkg-r-autopkgtest PASS 485s autopkgtest [10:03:07]: @@@@@@@@@@@@@@@@@@@@ summary 485s run-unit-test PASS 485s pkg-r-autopkgtest PASS 514s Creating nova instance adt-noble-s390x-r-cran-etm-20240312-095501-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240309.img (UUID 15f62ec0-c004-41c2-ab66-72a4ef6796cc)...