0s autopkgtest [07:28:42]: starting date: 2024-02-18 0s autopkgtest [07:28:42]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [07:28:42]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uz387ui9/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:htslib --apt-upgrade qtltools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-1.secgroup --name adt-noble-ppc64el-qtltools-20240218-072842-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 182s autopkgtest [07:31:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 183s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 183s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [17.0 kB] 183s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [9892 B] 183s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [108 kB] 183s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [815 kB] 183s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [202 kB] 183s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 183s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1180 B] 183s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 183s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [990 kB] 183s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 183s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [8900 B] 183s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 185s Fetched 2281 kB in 1s (2099 kB/s) 185s Reading package lists... 189s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Calculating upgrade... 190s The following NEW packages will be installed: 190s apport-core-dump-handler 190s The following packages will be upgraded: 190s apport python3-apport python3-problem-report 190s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 190s Need to get 218 kB of archives. 190s After this operation, 31.7 kB of additional disk space will be used. 190s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-problem-report all 2.27.0-0ubuntu7 [21.9 kB] 190s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-apport all 2.27.0-0ubuntu7 [97.3 kB] 190s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el apport all 2.27.0-0ubuntu7 [82.4 kB] 190s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el apport-core-dump-handler all 2.27.0-0ubuntu7 [16.4 kB] 191s Fetched 218 kB in 0s (526 kB/s) 191s (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 ... 68777 files and directories currently installed.) 191s Preparing to unpack .../python3-problem-report_2.27.0-0ubuntu7_all.deb ... 191s Unpacking python3-problem-report (2.27.0-0ubuntu7) over (2.27.0-0ubuntu6) ... 191s Preparing to unpack .../python3-apport_2.27.0-0ubuntu7_all.deb ... 191s Unpacking python3-apport (2.27.0-0ubuntu7) over (2.27.0-0ubuntu6) ... 191s Preparing to unpack .../apport_2.27.0-0ubuntu7_all.deb ... 191s Unpacking apport (2.27.0-0ubuntu7) over (2.27.0-0ubuntu6) ... 191s Selecting previously unselected package apport-core-dump-handler. 191s Preparing to unpack .../apport-core-dump-handler_2.27.0-0ubuntu7_all.deb ... 191s Unpacking apport-core-dump-handler (2.27.0-0ubuntu7) ... 191s Setting up python3-problem-report (2.27.0-0ubuntu7) ... 191s Setting up python3-apport (2.27.0-0ubuntu7) ... 191s Setting up apport-core-dump-handler (2.27.0-0ubuntu7) ... 192s Setting up apport (2.27.0-0ubuntu7) ... 193s apport-autoreport.service is a disabled or a static unit not running, not starting it. 193s Processing triggers for man-db (2.12.0-3) ... 193s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 193s 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 193s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 193s 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 193s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s sh: Attempting to set up Debian/Ubuntu apt sources automatically 194s sh: Distribution appears to be Ubuntu 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 198s eatmydata is already the newest version (131-1). 198s dbus is already the newest version (1.14.10-3ubuntu1). 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 198s 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 198s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 198s 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 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 198s rng-tools-debian is already the newest version (2.4). 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s haveged is already the newest version (1.9.14-1ubuntu1). 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s The following packages will be REMOVED: 199s cloud-init* python3-configobj* python3-debconf* 199s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 199s After this operation, 3212 kB disk space will be freed. 199s (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 ... 68780 files and directories currently installed.) 199s Removing cloud-init (24.1~5g1f6eddd5-0ubuntu1) ... 200s Removing python3-configobj (5.0.8-3) ... 200s Removing python3-debconf (1.5.82) ... 200s Processing triggers for man-db (2.12.0-3) ... 200s (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 ... 68392 files and directories currently installed.) 200s Purging configuration files for cloud-init (24.1~5g1f6eddd5-0ubuntu1) ... 201s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 201s Processing triggers for rsyslog (8.2312.0-3ubuntu2) ... 201s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s linux-generic is already the newest version (6.6.0-14.14). 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 202s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 202s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 202s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 202s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 206s Reading package lists... 206s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 206s 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 206s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 206s 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 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s Calculating upgrade... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 206s Reading package lists... 207s Building dependency tree... 207s Reading state information... 207s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 207s autopkgtest [07:32:09]: rebooting testbed after setup commands that affected boot 240s autopkgtest [07:32:42]: testbed running kernel: Linux 6.6.0-14-generic #14-Ubuntu SMP Thu Nov 30 10:29:25 UTC 2023 240s autopkgtest [07:32:42]: testbed dpkg architecture: ppc64el 241s autopkgtest [07:32:43]: @@@@@@@@@@@@@@@@@@@@ apt-source qtltools 242s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 242s 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 242s W: Target Packages (main/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target CNF (main/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target Packages (restricted/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target CNF (restricted/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target Packages (universe/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target CNF (universe/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target Packages (multiverse/binary-ppc64el/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 242s W: Target CNF (multiverse/cnf/Commands-ppc64el) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 242s 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 249s Get:1 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (dsc) [2214 B] 249s Get:2 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (tar) [141 kB] 249s Get:3 http://ftpmaster.internal/ubuntu noble/universe qtltools 1.3.1+dfsg-4build1 (diff) [13.6 MB] 249s gpgv: Signature made Tue Dec 19 15:02:56 2023 UTC 249s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 249s gpgv: Can't check signature: No public key 249s dpkg-source: warning: cannot verify inline signature for ./qtltools_1.3.1+dfsg-4build1.dsc: no acceptable signature found 250s autopkgtest [07:32:52]: testing package qtltools version 1.3.1+dfsg-4build1 250s autopkgtest [07:32:52]: build not needed 271s autopkgtest [07:33:13]: test run-sample-analysis: preparing testbed 275s Reading package lists... 276s Building dependency tree... 276s Reading state information... 276s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 276s Starting 2 pkgProblemResolver with broken count: 0 276s Done 276s Done 276s Starting pkgProblemResolver with broken count: 0 276s Starting 2 pkgProblemResolver with broken count: 0 276s Done 276s The following additional packages will be installed: 276s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 276s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 276s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 276s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 276s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 276s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 276s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 276s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 276s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 276s zip 276s Suggested packages: 276s gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html tcl8.6 tk8.6 276s elpa-ess r-doc-info | r-doc-pdf r-base-html 276s Recommended packages: 276s r-bioc-qvalue r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl 276s libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils 276s The following NEW packages will be installed: 276s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 276s libboost-iostreams1.83.0 libboost-program-options1.83.0 libcairo2 libdatrie1 276s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libgsl27 276s libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0 276s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 276s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 276s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 276s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 276s qtltools qtltools-example r-base-core r-mathlib unzip x11-common xdg-utils 276s zip 276s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 276s 1 not fully installed or removed. 276s Need to get 58.8 MB of archives. 276s After this operation, 115 MB of additional disk space will be used. 276s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-2 [226 kB] 277s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-iostreams1.83.0 ppc64el 1.83.0-2ubuntu1 [340 kB] 277s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libboost-program-options1.83.0 ppc64el 1.83.0-2ubuntu1 [421 kB] 277s Get:4 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgslcblas0 ppc64el 2.7.1+dfsg-6ubuntu1 [85.3 kB] 277s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgsl27 ppc64el 2.7.1+dfsg-6ubuntu1 [1064 kB] 278s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 278s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] 278s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhts3 ppc64el 1.19+ds-1 [568 kB] 278s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-mathlib ppc64el 4.3.2-1build1 [2425 kB] 279s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el zip ppc64el 3.0-13 [192 kB] 279s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el unzip ppc64el 6.0-28ubuntu2 [191 kB] 279s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper1 ppc64el 1.1.29 [13.5 kB] 279s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libpaper-utils ppc64el 1.1.29 [8710 B] 279s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 279s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 279s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 279s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.14.2-6ubuntu1 [36.0 kB] 279s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.14.2-6ubuntu1 [184 kB] 279s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB] 279s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB] 279s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] 279s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB] 279s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB] 279s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240201-3ubuntu1 [161 kB] 279s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 279s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 279s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240201-3ubuntu1 [572 kB] 279s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-2 [2804 kB] 280s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig ppc64el 2.14.2-6ubuntu1 [192 kB] 280s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB] 280s Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB] 280s Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai-data all 0.1.29-2 [158 kB] 280s Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el libdatrie1 ppc64el 0.2.13-3 [25.1 kB] 280s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libthai0 ppc64el 0.1.29-2 [21.4 kB] 280s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libpango-1.0-0 ppc64el 1.51.0+ds-4 [266 kB] 280s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangoft2-1.0-0 ppc64el 1.51.0+ds-4 [49.5 kB] 280s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libpangocairo-1.0-0 ppc64el 1.51.0+ds-4 [31.2 kB] 280s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libtcl8.6 ppc64el 8.6.13+dfsg-2 [1179 kB] 280s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 280s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 280s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.3 [27.9 kB] 280s Get:42 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.3 [308 kB] 280s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 280s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libxft2 ppc64el 2.3.6-1 [59.8 kB] 280s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] 280s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libxss1 ppc64el 1:1.2.3-1build2 [8982 B] 280s Get:47 http://ftpmaster.internal/ubuntu noble/main ppc64el libtk8.6 ppc64el 8.6.13-2 [916 kB] 280s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] 280s Get:49 http://ftpmaster.internal/ubuntu noble/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] 280s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el libxt6 ppc64el 1:1.2.1-1.1 [198 kB] 280s Get:51 http://ftpmaster.internal/ubuntu noble/universe ppc64el r-base-core ppc64el 4.3.2-1build1 [27.4 MB] 281s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools ppc64el 1.3.1+dfsg-4build1 [823 kB] 281s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el qtltools-example all 1.3.1+dfsg-4build1 [13.6 MB] 282s Preconfiguring packages ... 282s Fetched 58.8 MB in 6s (10.2 MB/s) 283s Selecting previously unselected package libblas3:ppc64el. 283s (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 ... 68337 files and directories currently installed.) 283s Preparing to unpack .../00-libblas3_3.12.0-2_ppc64el.deb ... 283s Unpacking libblas3:ppc64el (3.12.0-2) ... 283s Selecting previously unselected package libboost-iostreams1.83.0:ppc64el. 283s Preparing to unpack .../01-libboost-iostreams1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 283s Unpacking libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 283s Selecting previously unselected package libboost-program-options1.83.0:ppc64el. 283s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_ppc64el.deb ... 283s Unpacking libboost-program-options1.83.0:ppc64el (1.83.0-2ubuntu1) ... 283s Selecting previously unselected package libgslcblas0:ppc64el. 283s Preparing to unpack .../03-libgslcblas0_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 283s Unpacking libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 283s Selecting previously unselected package libgsl27:ppc64el. 283s Preparing to unpack .../04-libgsl27_2.7.1+dfsg-6ubuntu1_ppc64el.deb ... 283s Unpacking libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 283s Selecting previously unselected package libdeflate0:ppc64el. 283s Preparing to unpack .../05-libdeflate0_1.19-1_ppc64el.deb ... 283s Unpacking libdeflate0:ppc64el (1.19-1) ... 283s Selecting previously unselected package libhtscodecs2:ppc64el. 283s Preparing to unpack .../06-libhtscodecs2_1.6.0-1_ppc64el.deb ... 283s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ... 283s Selecting previously unselected package libhts3:ppc64el. 283s Preparing to unpack .../07-libhts3_1.19+ds-1_ppc64el.deb ... 283s Unpacking libhts3:ppc64el (1.19+ds-1) ... 283s Selecting previously unselected package r-mathlib. 283s Preparing to unpack .../08-r-mathlib_4.3.2-1build1_ppc64el.deb ... 283s Unpacking r-mathlib (4.3.2-1build1) ... 283s Selecting previously unselected package zip. 283s Preparing to unpack .../09-zip_3.0-13_ppc64el.deb ... 283s Unpacking zip (3.0-13) ... 283s Selecting previously unselected package unzip. 283s Preparing to unpack .../10-unzip_6.0-28ubuntu2_ppc64el.deb ... 283s Unpacking unzip (6.0-28ubuntu2) ... 283s Selecting previously unselected package libpaper1:ppc64el. 283s Preparing to unpack .../11-libpaper1_1.1.29_ppc64el.deb ... 283s Unpacking libpaper1:ppc64el (1.1.29) ... 283s Selecting previously unselected package libpaper-utils. 283s Preparing to unpack .../12-libpaper-utils_1.1.29_ppc64el.deb ... 283s Unpacking libpaper-utils (1.1.29) ... 283s Selecting previously unselected package xdg-utils. 283s Preparing to unpack .../13-xdg-utils_1.1.3-4.1ubuntu3_all.deb ... 283s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ... 283s Selecting previously unselected package fonts-dejavu-mono. 283s Preparing to unpack .../14-fonts-dejavu-mono_2.37-8_all.deb ... 283s Unpacking fonts-dejavu-mono (2.37-8) ... 283s Selecting previously unselected package fonts-dejavu-core. 283s Preparing to unpack .../15-fonts-dejavu-core_2.37-8_all.deb ... 283s Unpacking fonts-dejavu-core (2.37-8) ... 283s Selecting previously unselected package fontconfig-config. 283s Preparing to unpack .../16-fontconfig-config_2.14.2-6ubuntu1_ppc64el.deb ... 283s Unpacking fontconfig-config (2.14.2-6ubuntu1) ... 283s Selecting previously unselected package libfontconfig1:ppc64el. 283s Preparing to unpack .../17-libfontconfig1_2.14.2-6ubuntu1_ppc64el.deb ... 283s Unpacking libfontconfig1:ppc64el (2.14.2-6ubuntu1) ... 283s Selecting previously unselected package libpixman-1-0:ppc64el. 283s Preparing to unpack .../18-libpixman-1-0_0.42.2-1_ppc64el.deb ... 283s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ... 283s Selecting previously unselected package libxcb-render0:ppc64el. 283s Preparing to unpack .../19-libxcb-render0_1.15-1_ppc64el.deb ... 283s Unpacking libxcb-render0:ppc64el (1.15-1) ... 283s Selecting previously unselected package libxcb-shm0:ppc64el. 283s Preparing to unpack .../20-libxcb-shm0_1.15-1_ppc64el.deb ... 283s Unpacking libxcb-shm0:ppc64el (1.15-1) ... 283s Selecting previously unselected package libxrender1:ppc64el. 283s Preparing to unpack .../21-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ... 283s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ... 283s Selecting previously unselected package libcairo2:ppc64el. 283s Preparing to unpack .../22-libcairo2_1.18.0-1_ppc64el.deb ... 283s Unpacking libcairo2:ppc64el (1.18.0-1) ... 283s Selecting previously unselected package libgomp1:ppc64el. 283s Preparing to unpack .../23-libgomp1_14-20240201-3ubuntu1_ppc64el.deb ... 283s Unpacking libgomp1:ppc64el (14-20240201-3ubuntu1) ... 283s Selecting previously unselected package libjpeg-turbo8:ppc64el. 283s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 283s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 283s Selecting previously unselected package libjpeg8:ppc64el. 283s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 283s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 283s Selecting previously unselected package libgfortran5:ppc64el. 283s Preparing to unpack .../26-libgfortran5_14-20240201-3ubuntu1_ppc64el.deb ... 283s Unpacking libgfortran5:ppc64el (14-20240201-3ubuntu1) ... 283s Selecting previously unselected package liblapack3:ppc64el. 283s Preparing to unpack .../27-liblapack3_3.12.0-2_ppc64el.deb ... 283s Unpacking liblapack3:ppc64el (3.12.0-2) ... 283s Selecting previously unselected package fontconfig. 283s Preparing to unpack .../28-fontconfig_2.14.2-6ubuntu1_ppc64el.deb ... 283s Unpacking fontconfig (2.14.2-6ubuntu1) ... 283s Selecting previously unselected package libgraphite2-3:ppc64el. 283s Preparing to unpack .../29-libgraphite2-3_1.3.14-2_ppc64el.deb ... 283s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ... 283s Selecting previously unselected package libharfbuzz0b:ppc64el. 283s Preparing to unpack .../30-libharfbuzz0b_8.3.0-2_ppc64el.deb ... 283s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ... 283s Selecting previously unselected package libthai-data. 283s Preparing to unpack .../31-libthai-data_0.1.29-2_all.deb ... 283s Unpacking libthai-data (0.1.29-2) ... 283s Selecting previously unselected package libdatrie1:ppc64el. 283s Preparing to unpack .../32-libdatrie1_0.2.13-3_ppc64el.deb ... 283s Unpacking libdatrie1:ppc64el (0.2.13-3) ... 283s Selecting previously unselected package libthai0:ppc64el. 283s Preparing to unpack .../33-libthai0_0.1.29-2_ppc64el.deb ... 283s Unpacking libthai0:ppc64el (0.1.29-2) ... 283s Selecting previously unselected package libpango-1.0-0:ppc64el. 283s Preparing to unpack .../34-libpango-1.0-0_1.51.0+ds-4_ppc64el.deb ... 283s Unpacking libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 283s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 283s Preparing to unpack .../35-libpangoft2-1.0-0_1.51.0+ds-4_ppc64el.deb ... 283s Unpacking libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 283s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 283s Preparing to unpack .../36-libpangocairo-1.0-0_1.51.0+ds-4_ppc64el.deb ... 283s Unpacking libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 283s Selecting previously unselected package libtcl8.6:ppc64el. 283s Preparing to unpack .../37-libtcl8.6_8.6.13+dfsg-2_ppc64el.deb ... 283s Unpacking libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 284s Selecting previously unselected package libjbig0:ppc64el. 284s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 284s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 284s Selecting previously unselected package liblerc4:ppc64el. 284s Preparing to unpack .../39-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 284s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 284s Selecting previously unselected package libsharpyuv0:ppc64el. 284s Preparing to unpack .../40-libsharpyuv0_1.3.2-0.3_ppc64el.deb ... 284s Unpacking libsharpyuv0:ppc64el (1.3.2-0.3) ... 284s Selecting previously unselected package libwebp7:ppc64el. 284s Preparing to unpack .../41-libwebp7_1.3.2-0.3_ppc64el.deb ... 284s Unpacking libwebp7:ppc64el (1.3.2-0.3) ... 284s Selecting previously unselected package libtiff6:ppc64el. 284s Preparing to unpack .../42-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 284s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 284s Selecting previously unselected package libxft2:ppc64el. 284s Preparing to unpack .../43-libxft2_2.3.6-1_ppc64el.deb ... 284s Unpacking libxft2:ppc64el (2.3.6-1) ... 284s Selecting previously unselected package x11-common. 284s Preparing to unpack .../44-x11-common_1%3a7.7+23ubuntu2_all.deb ... 284s Unpacking x11-common (1:7.7+23ubuntu2) ... 284s Selecting previously unselected package libxss1:ppc64el. 284s Preparing to unpack .../45-libxss1_1%3a1.2.3-1build2_ppc64el.deb ... 284s Unpacking libxss1:ppc64el (1:1.2.3-1build2) ... 284s Selecting previously unselected package libtk8.6:ppc64el. 284s Preparing to unpack .../46-libtk8.6_8.6.13-2_ppc64el.deb ... 284s Unpacking libtk8.6:ppc64el (8.6.13-2) ... 284s Selecting previously unselected package libice6:ppc64el. 284s Preparing to unpack .../47-libice6_2%3a1.0.10-1build2_ppc64el.deb ... 284s Unpacking libice6:ppc64el (2:1.0.10-1build2) ... 284s Selecting previously unselected package libsm6:ppc64el. 284s Preparing to unpack .../48-libsm6_2%3a1.2.3-1build2_ppc64el.deb ... 284s Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... 284s Selecting previously unselected package libxt6:ppc64el. 284s Preparing to unpack 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284s Setting up libpaper1:ppc64el (1.1.29) ... 284s 284s Creating config file /etc/papersize with new version 284s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 284s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ... 284s Setting up libdatrie1:ppc64el (0.2.13-3) ... 284s Setting up libgslcblas0:ppc64el (2.7.1+dfsg-6ubuntu1) ... 284s Setting up libxcb-render0:ppc64el (1.15-1) ... 284s Setting up unzip (6.0-28ubuntu2) ... 284s Setting up x11-common (1:7.7+23ubuntu2) ... 285s Setting up libdeflate0:ppc64el (1.19-1) ... 285s Setting up libgsl27:ppc64el (2.7.1+dfsg-6ubuntu1) ... 285s Setting up libxcb-shm0:ppc64el (1.15-1) ... 285s Setting up libpaper-utils (1.1.29) ... 285s Setting up libgomp1:ppc64el (14-20240201-3ubuntu1) ... 285s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 285s Setting up zip (3.0-13) ... 285s Setting up libblas3:ppc64el (3.12.0-2) ... 285s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 285s Setting up libboost-iostreams1.83.0:ppc64el (1.83.0-2ubuntu1) ... 285s Setting up fonts-dejavu-mono (2.37-8) ... 285s Setting up libtcl8.6:ppc64el (8.6.13+dfsg-2) ... 285s Setting up fonts-dejavu-core (2.37-8) ... 285s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 285s Setting up libgfortran5:ppc64el (14-20240201-3ubuntu1) ... 285s Setting up libwebp7:ppc64el (1.3.2-0.3) ... 285s Setting up r-mathlib (4.3.2-1build1) ... 285s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ... 285s Setting up libthai-data (0.1.29-2) ... 285s Setting up libxss1:ppc64el (1:1.2.3-1build2) ... 285s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 285s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 285s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 285s Setting up libice6:ppc64el (2:1.0.10-1build2) ... 285s Setting up liblapack3:ppc64el (3.12.0-2) ... 285s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 285s Setting up libhts3:ppc64el (1.19+ds-1) ... 285s Setting up fontconfig-config (2.14.2-6ubuntu1) ... 285s Setting up libthai0:ppc64el (0.1.29-2) ... 285s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 285s Setting up libfontconfig1:ppc64el (2.14.2-6ubuntu1) ... 285s Setting up libsm6:ppc64el (2:1.2.3-1build2) ... 285s Setting up fontconfig (2.14.2-6ubuntu1) ... 287s Regenerating fonts cache... done. 287s Setting up libxft2:ppc64el (2.3.6-1) ... 287s Setting up libtk8.6:ppc64el (8.6.13-2) ... 287s Setting up libpango-1.0-0:ppc64el (1.51.0+ds-4) ... 287s Setting up libcairo2:ppc64el (1.18.0-1) ... 287s Setting up libxt6:ppc64el (1:1.2.1-1.1) ... 287s Setting up libpangoft2-1.0-0:ppc64el (1.51.0+ds-4) ... 287s Setting up libpangocairo-1.0-0:ppc64el (1.51.0+ds-4) ... 287s Setting up r-base-core (4.3.2-1build1) ... 287s 287s Creating config file /etc/R/Renviron with new version 287s Setting up qtltools (1.3.1+dfsg-4build1) ... 287s Setting up autopkgtest-satdep (0) ... 287s Processing triggers for man-db (2.12.0-3) ... 288s Processing triggers for install-info (7.1-3) ... 288s Processing triggers for libc-bin (2.38-3ubuntu1) ... 292s (Reading database ... 70432 files and directories currently installed.) 292s Removing autopkgtest-satdep (0) ... 292s autopkgtest [07:33:34]: test run-sample-analysis: [----------------------- 293s ./genes.50percent.chr22.bed.gz 293s ./genes.50percent.chr22.bed.gz.tbi 293s ./genes.covariates.pc50.txt.gz 293s ./genes.simulated.chr22.bed.gz 293s ./genes.simulated.chr22.bed.gz.tbi 293s ./genotypes.chr22.vcf.gz 293s ./genotypes.chr22.vcf.gz.tbi 293s 293s QTLtools 293s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 293s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 293s * Webpage : https://qtltools.github.io/qtltools/ 293s * Version : 1.3.1 293s * Date : 18/02/2024 - 07:33:35 293s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 293s 293s CONDUCT PCA ON DATA 293s 293s Initialize random number generator 293s * Built-in seed is 15112011 293s * First Integer = 30553 293s * First Double = 0.0126695 293s 293s Reading sample list from [genes.50percent.chr22.bed.gz] 293s * #samples = 358 293s 293s Merging sample sets from all input files 293s * #files = 1 293s * #samples in all files = 358 293s 293s Reading phenotype data in [genes.50percent.chr22.bed.gz] 293s * 358 samples included 294s * 608 phenotypes included 294s 294s Calculating PCA with a matrix 358 x 608 294s * Calculated mean and sd 294s * 0 sd==0 columns removed 294s * Variables centered 294s * Variables scaled to unit variance 294s * Running SVD 294s * SVD complete 294s * Calculated sd and var for PCs 294s * Calculated cumulative var for PCs 294s * Done! 294s 294s Running time: 0 seconds 294s 294s QTLtools 294s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 294s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 294s * Webpage : https://qtltools.github.io/qtltools/ 294s * Version : 1.3.1 294s * Date : 18/02/2024 - 07:33:36 294s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 294s 294s MAPPING QTL IN CIS 294s * TASK: Report all nominal associations with p <= 0.01 294s * Linear model: Phe ~ Var + Cov 294s * Cis-window size is 1000000 bp 294s * Region = [chr22:17000000-18000000] 294s 294s Initialize random number generator 294s * Built-in seed is 15112011 294s * First Integer = 30553 294s * First Double = 0.0126695 294s 294s Reading sample list from [genes.50percent.chr22.bed.gz] 294s * #samples = 358 294s 294s Read sample list from [genotypes.chr22.vcf.gz] 294s * #samples = 358 294s 294s Reading sample list from [genes.covariates.pc50.txt.gz] 294s * #samples = 358 294s 294s Merging sample sets from all input files 294s * #files = 3 294s * #samples in all files = 358 294s 294s Reading phenotype data in [genes.50percent.chr22.bed.gz] 294s * target region [chr22:17000000-18000000] 294s * 8 phenotypes included 294s * 3 phenotypes are on the negative strand 294s 294s Reading genotype data in [genotypes.chr22.vcf.gz] 294s * File format detected: VCF 294s * target region [chr22:16000000-19000000] 294s * 6404 variants included 294s 294s Reading covariates in [genes.covariates.pc50.txt.gz] 294s * 53 covariates included 294s 294s Residualize phenotypes for covariates 294s * #covariates = 53 294s 294s Processing phenotype [ENSG00000237438.2] [1/8] 294s * #variants in cis = 5095 294s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 294s 294s Processing phenotype [ENSG00000273203.1] [2/8] 294s * #variants in cis = 5170 294s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 294s 294s Processing phenotype [ENSG00000273442.1] [3/8] 294s * #variants in cis = 5188 294s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 294s 294s Processing phenotype [ENSG00000177663.9] [4/8] 294s * #variants in cis = 5193 294s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 294s 294s Processing phenotype [ENSG00000183307.3] [5/8] 294s * #variants in cis = 5230 294s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 294s 294s Processing phenotype [ENSG00000069998.8] [6/8] 294s * #variants in cis = 5291 294s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 294s 294s Processing phenotype [ENSG00000093072.11] [7/8] 294s * #variants in cis = 5293 294s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 294s 294s Processing phenotype [ENSG00000099954.14] [8/8] 294s * #variants in cis = 5435 294s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 294s 294s Running time: 0 seconds 294s 294s QTLtools 294s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 294s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 294s * Webpage : https://qtltools.github.io/qtltools/ 294s * Version : 1.3.1 294s * Date : 18/02/2024 - 07:33:36 294s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 294s 294s MAPPING QTL IN CIS 294s * TASK: Perform 1000 permutations 294s * Linear model: Phe ~ Var + Cov 294s * Cis-window size is 1000000 bp 294s * Region = [chr22:17000000-18000000] 294s 294s Initialize random number generator 294s * Built-in seed is 15112011 294s * First Integer = 30553 294s * First Double = 0.0126695 294s 294s Reading sample list from [genes.50percent.chr22.bed.gz] 294s * #samples = 358 294s 294s Read sample list from [genotypes.chr22.vcf.gz] 294s * #samples = 358 294s 294s Reading sample list from [genes.covariates.pc50.txt.gz] 294s * #samples = 358 294s 294s Merging sample sets from all input files 294s * #files = 3 294s * #samples in all files = 358 294s 294s Reading phenotype data in [genes.50percent.chr22.bed.gz] 294s * target region [chr22:17000000-18000000] 294s * 8 phenotypes included 294s * 3 phenotypes are on the negative strand 294s 294s Reading genotype data in [genotypes.chr22.vcf.gz] 294s * File format detected: VCF 294s * target region [chr22:16000000-19000000] 294s * 6404 variants included 294s 294s Reading covariates in [genes.covariates.pc50.txt.gz] 294s * 53 covariates included 294s 294s Residualize phenotypes for covariates 294s * #covariates = 53 295s 295s Processing phenotype [ENSG00000237438.2] [1/8] 295s * #variants in cis = 5095 296s * Best hit: [id=22_17542810, d=25350, pv=1.1864e-25, s=-0.7518] 296s * Beta parameters: [s1=1.00995, s2=621.053] 296s * Adjusted p-values: [emp=0.000999001, beta=1.28062e-20] 296s 296s Processing phenotype [ENSG00000273203.1] [2/8] 296s * #variants in cis = 5170 297s * Best hit: [id=22_17517388, d=-31323, pv=5.86611e-06, s=-0.1406] 297s * Beta parameters: [s1=1.11817, s2=641.379] 297s * Adjusted p-values: [emp=0.00799201, beta=0.00751892] 297s 297s Processing phenotype [ENSG00000273442.1] [3/8] 297s * #variants in cis = 5188 298s * Best hit: [id=22_17553526, d=-8065, pv=0.000244522, s=0.1340] 298s * Beta parameters: [s1=1.08364, s2=467.63] 298s * Adjusted p-values: [emp=0.297702, beta=0.293948] 298s 298s Processing phenotype [ENSG00000177663.9] [4/8] 298s * #variants in cis = 5193 299s * Best hit: [id=22_17513703, d=-52141, pv=8.03358e-14, s=-0.2096] 299s * Beta parameters: [s1=0.989061, s2=704.553] 299s * Adjusted p-values: [emp=0.000999001, beta=7.91291e-10] 299s 299s Processing phenotype [ENSG00000183307.3] [5/8] 299s * #variants in cis = 5230 300s * Best hit: [id=22_17587975, d=14282, pv=1.56789e-07, s=-0.0078] 300s * Beta parameters: [s1=1.01322, s2=559.49] 300s * Adjusted p-values: [emp=0.000999001, beta=0.00050707] 300s 300s Processing phenotype [ENSG00000069998.8] [6/8] 300s * #variants in cis = 5291 301s * Best hit: [id=22_17620429, d=25748, pv=1.37287e-14, s=-1.5147] 301s * Beta parameters: [s1=1.02312, s2=563.339] 301s * Adjusted p-values: [emp=0.000999001, beta=2.56935e-10] 301s 301s Processing phenotype [ENSG00000093072.11] [7/8] 301s * #variants in cis = 5293 302s * Best hit: [id=22_17699630, d=3249, pv=0.000578649, s=0.6404] 302s * Beta parameters: [s1=0.957514, s2=559.397] 302s * Adjusted p-values: [emp=0.574426, beta=0.562826] 302s 302s Processing phenotype [ENSG00000099954.14] [8/8] 302s * #variants in cis = 5435 304s * Best hit: [id=22_17175937, d=-664900, pv=0.000866455, s=0.0067] 304s * Beta parameters: [s1=0.938041, s2=226.852] 304s * Adjusted p-values: [emp=0.842158, beta=0.84836] 304s 304s Running time: 9 seconds 304s 304s QTLtools 304s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 304s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 304s * Webpage : https://qtltools.github.io/qtltools/ 304s * Version : 1.3.1 304s * Date : 18/02/2024 - 07:33:46 304s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 304s 304s MAPPING QTL IN TRANS 304s * TASK: Perform a full nominal pass, do not adjust p-values 304s * Cis-window size is 5000000 bp 304s * #bins = 1000 304s * threshold = 1e-05 304s 304s Initialize random number generator 304s * Built-in seed is 15112011 304s * First Integer = 30553 304s * First Double = 0.0126695 304s 304s Read sample list from [genotypes.chr22.vcf.gz] 304s * #samples = 358 304s 304s Checking sample list in [genes.simulated.chr22.bed.gz] 304s * #samples = 358 304s 304s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 304s * 358 samples included 304s * 608 phenotypes included 304s * 275 phenotypes is on the negative strand 304s 304s Calculate correlation threshold 304s * thres = 1e-05 304s * corr = 0.2311 304s 304s Sweep through genotype data in [genotypes.chr22.vcf.gz] 304s * #variants=1950 #multi_allelic=0 #not_processed=0 #hits=101/1000000 speed=3.89MT/s 304s * #variants=4001 #multi_allelic=0 #not_processed=0 #hits=153/2000000 speed=3.86MT/s 305s * #variants=6187 #multi_allelic=0 #not_processed=0 #hits=244/3000000 speed=3.76MT/s 305s * #variants=8537 #multi_allelic=0 #not_processed=0 #hits=285/4000000 speed=3.77MT/s 305s * #variants=11025 #multi_allelic=0 #not_processed=0 #hits=312/5000000 speed=3.76MT/s 305s * #variants=13621 #multi_allelic=0 #not_processed=0 #hits=320/6000000 speed=3.70MT/s 306s * #variants=16217 #multi_allelic=0 #not_processed=0 #hits=342/7000000 speed=3.72MT/s 306s * #variants=18755 #multi_allelic=0 #not_processed=0 #hits=401/8000000 speed=3.73MT/s 306s * #variants=21237 #multi_allelic=0 #not_processed=0 #hits=402/9000000 speed=3.79MT/s 306s * #variants=23680 #multi_allelic=0 #not_processed=0 #hits=455/10000000 speed=3.75MT/s 307s * #variants=26171 #multi_allelic=0 #not_processed=0 #hits=463/11000000 speed=3.75MT/s 307s * #variants=28609 #multi_allelic=0 #not_processed=0 #hits=469/12000000 speed=3.72MT/s 307s * #variants=30861 #multi_allelic=0 #not_processed=0 #hits=973/13000000 speed=3.82MT/s 307s * #variants=32932 #multi_allelic=0 #not_processed=0 #hits=979/14000000 speed=3.88MT/s 308s * #variants=34974 #multi_allelic=0 #not_processed=0 #hits=1085/15000000 speed=3.88MT/s 308s * #variants=37021 #multi_allelic=0 #not_processed=0 #hits=1086/16000000 speed=3.88MT/s 308s * #variants=39122 #multi_allelic=0 #not_processed=0 #hits=1089/17000000 speed=3.83MT/s 309s * #variants=41334 #multi_allelic=0 #not_processed=0 #hits=1089/18000000 speed=3.82MT/s 309s * #variants=43627 #multi_allelic=0 #not_processed=0 #hits=1096/19000000 speed=3.80MT/s 309s * #variants=45897 #multi_allelic=0 #not_processed=0 #hits=1153/20000000 speed=3.79MT/s 309s * #variants=48114 #multi_allelic=0 #not_processed=0 #hits=1243/21000000 speed=3.79MT/s 310s * #variants=50410 #multi_allelic=0 #not_processed=0 #hits=1249/22000000 speed=3.77MT/s 310s * #variants=52820 #multi_allelic=0 #not_processed=0 #hits=1259/23000000 speed=3.75MT/s 310s * #variants=55279 #multi_allelic=0 #not_processed=0 #hits=1498/24000000 speed=3.73MT/s 310s * #variants=57789 #multi_allelic=0 #not_processed=0 #hits=1724/25000000 speed=3.72MT/s 311s * #variants=60201 #multi_allelic=0 #not_processed=0 #hits=2168/26000000 speed=3.79MT/s 311s * #variants=62476 #multi_allelic=0 #not_processed=0 #hits=2452/27000000 speed=3.76MT/s 311s * #variants=64608 #multi_allelic=0 #not_processed=0 #hits=2544/28000000 speed=3.83MT/s 311s * #variants=66709 #multi_allelic=0 #not_processed=0 #hits=2684/29000000 speed=3.80MT/s 312s * #variants=68871 #multi_allelic=0 #not_processed=0 #hits=2688/30000000 speed=3.83MT/s 312s * #variants=71070 #multi_allelic=0 #not_processed=0 #hits=2720/31000000 speed=3.83MT/s 312s * #variants=73151 #multi_allelic=0 #not_processed=0 #hits=2891/32000000 speed=3.83MT/s 313s * #variants=75122 #multi_allelic=0 #not_processed=0 #hits=3110/33000000 speed=3.86MT/s 313s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=3209/34000000 speed=3.88MT/s 313s * #variants=78989 #multi_allelic=0 #not_processed=0 #hits=3218/35000000 speed=3.94MT/s 313s * #variants=80903 #multi_allelic=0 #not_processed=0 #hits=3250/36000000 speed=3.89MT/s 314s * #variants=82811 #multi_allelic=0 #not_processed=0 #hits=3463/37000000 speed=3.94MT/s 314s * #variants=84694 #multi_allelic=0 #not_processed=0 #hits=4035/38000000 speed=3.86MT/s 314s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=4036/38425275 speed=3.94MT/s 314s 314s Running time: 10 seconds 314s 314s QTLtools 314s * Authors : Olivier DELANEAU / Halit ONGEN / Emmanouil DERMITZAKIS 314s * Contact : olivier.delaneau@gmail.com / halit.ongen@unige.ch / Emmanouil.Dermitzakis@unige.ch 314s * Webpage : https://qtltools.github.io/qtltools/ 314s * Version : 1.3.1 314s * Date : 18/02/2024 - 07:33:56 314s * Citation: A complete tool set for molecular QTL discovery and analysis, https://doi.org/10.1038/ncomms15452 314s 314s MAPPING QTL IN TRANS 314s * TASK: Permute randomly chosen phenotypes 1000 times and test 314s * Cis-window size is 5000000 bp 314s * #bins = 1000 314s * threshold = 1e-05 314s 314s Initialize random number generator 314s * Built-in seed is 15112011 314s * First Integer = 30553 314s * First Double = 0.0126695 314s 314s Read sample list from [genotypes.chr22.vcf.gz] 314s * #samples = 358 314s 314s Checking sample list in [genes.simulated.chr22.bed.gz] 314s * #samples = 358 314s 314s Reading phenotype data in [genes.simulated.chr22.bed.gz] from line 0 to 0 314s * 358 samples included 314s * 608 phenotypes included 314s * 275 phenotypes is on the negative strand 314s 314s Normal transform phenotypes 314s 314s Calculate correlation threshold 314s * thres = 1e-05 314s * corr = 0.2311 314s 314s Sweep through genotype data in [genotypes.chr22.vcf.gz] 314s * #variants=1177 #multi_allelic=0 #not_processed=0 #hits=28/1000000 speed=4.07MT/s 315s * #variants=2383 #multi_allelic=0 #not_processed=0 #hits=38/2000000 speed=4.00MT/s 315s * #variants=3633 #multi_allelic=0 #not_processed=0 #hits=53/3000000 speed=3.97MT/s 315s * #variants=4928 #multi_allelic=0 #not_processed=0 #hits=53/4000000 speed=3.89MT/s 315s * #variants=6269 #multi_allelic=0 #not_processed=0 #hits=71/5000000 speed=3.88MT/s 316s * #variants=7675 #multi_allelic=0 #not_processed=0 #hits=72/6000000 speed=3.77MT/s 316s * #variants=9151 #multi_allelic=0 #not_processed=0 #hits=88/7000000 speed=3.69MT/s 316s * #variants=10663 #multi_allelic=0 #not_processed=0 #hits=96/8000000 speed=3.64MT/s 316s * #variants=12202 #multi_allelic=0 #not_processed=0 #hits=96/9000000 speed=3.61MT/s 317s * #variants=13804 #multi_allelic=0 #not_processed=0 #hits=96/10000000 speed=3.68MT/s 317s * #variants=15381 #multi_allelic=0 #not_processed=0 #hits=120/11000000 speed=3.70MT/s 317s * #variants=16946 #multi_allelic=0 #not_processed=0 #hits=123/12000000 speed=3.72MT/s 317s * #variants=18483 #multi_allelic=0 #not_processed=0 #hits=129/13000000 speed=3.72MT/s 318s * #variants=19995 #multi_allelic=0 #not_processed=0 #hits=131/14000000 speed=3.75MT/s 318s * #variants=21489 #multi_allelic=0 #not_processed=0 #hits=132/15000000 speed=3.75MT/s 318s * #variants=22947 #multi_allelic=0 #not_processed=0 #hits=151/16000000 speed=3.75MT/s 319s * #variants=24445 #multi_allelic=0 #not_processed=0 #hits=168/17000000 speed=3.73MT/s 319s * #variants=25965 #multi_allelic=0 #not_processed=0 #hits=175/18000000 speed=3.66MT/s 319s * #variants=27472 #multi_allelic=0 #not_processed=0 #hits=179/19000000 speed=3.75MT/s 319s * #variants=28933 #multi_allelic=0 #not_processed=0 #hits=181/20000000 speed=3.79MT/s 320s * #variants=30325 #multi_allelic=0 #not_processed=0 #hits=181/21000000 speed=3.85MT/s 320s * #variants=31617 #multi_allelic=0 #not_processed=0 #hits=182/22000000 speed=3.95MT/s 320s * #variants=32875 #multi_allelic=0 #not_processed=0 #hits=190/23000000 speed=3.97MT/s 320s * #variants=34127 #multi_allelic=0 #not_processed=0 #hits=192/24000000 speed=3.97MT/s 321s * #variants=35392 #multi_allelic=0 #not_processed=0 #hits=206/25000000 speed=3.95MT/s 321s * #variants=36652 #multi_allelic=0 #not_processed=0 #hits=206/26000000 speed=3.97MT/s 321s * #variants=37940 #multi_allelic=0 #not_processed=0 #hits=213/27000000 speed=3.91MT/s 321s * #variants=39255 #multi_allelic=0 #not_processed=0 #hits=238/28000000 speed=3.91MT/s 322s * #variants=40602 #multi_allelic=0 #not_processed=0 #hits=239/29000000 speed=3.88MT/s 322s * #variants=41998 #multi_allelic=0 #not_processed=0 #hits=245/30000000 speed=3.82MT/s 322s * #variants=43398 #multi_allelic=0 #not_processed=0 #hits=245/31000000 speed=3.85MT/s 322s * #variants=44803 #multi_allelic=0 #not_processed=0 #hits=260/32000000 speed=3.85MT/s 323s * #variants=46187 #multi_allelic=0 #not_processed=0 #hits=261/33000000 speed=3.86MT/s 323s * #variants=47545 #multi_allelic=0 #not_processed=0 #hits=268/34000000 speed=3.86MT/s 323s * #variants=48904 #multi_allelic=0 #not_processed=0 #hits=280/35000000 speed=3.86MT/s 323s * #variants=50309 #multi_allelic=0 #not_processed=0 #hits=306/36000000 speed=3.82MT/s 324s * #variants=51731 #multi_allelic=0 #not_processed=0 #hits=314/37000000 speed=3.82MT/s 324s * #variants=53171 #multi_allelic=0 #not_processed=0 #hits=320/38000000 speed=3.82MT/s 324s * #variants=54621 #multi_allelic=0 #not_processed=0 #hits=323/39000000 speed=3.80MT/s 325s * #variants=56099 #multi_allelic=0 #not_processed=0 #hits=323/40000000 speed=3.79MT/s 325s * #variants=57584 #multi_allelic=0 #not_processed=0 #hits=340/41000000 speed=3.77MT/s 325s * #variants=59032 #multi_allelic=0 #not_processed=0 #hits=344/42000000 speed=3.86MT/s 325s * #variants=60437 #multi_allelic=0 #not_processed=0 #hits=345/43000000 speed=3.91MT/s 326s * #variants=61810 #multi_allelic=0 #not_processed=0 #hits=357/44000000 speed=3.89MT/s 326s * #variants=63129 #multi_allelic=0 #not_processed=0 #hits=384/45000000 speed=3.94MT/s 326s * #variants=64409 #multi_allelic=0 #not_processed=0 #hits=391/46000000 speed=4.02MT/s 326s * #variants=65679 #multi_allelic=0 #not_processed=0 #hits=430/47000000 speed=4.02MT/s 327s * #variants=66953 #multi_allelic=0 #not_processed=0 #hits=436/48000000 speed=4.02MT/s 327s * #variants=68247 #multi_allelic=0 #not_processed=0 #hits=446/49000000 speed=4.03MT/s 327s * #variants=69595 #multi_allelic=0 #not_processed=0 #hits=460/50000000 speed=3.94MT/s 327s * #variants=70918 #multi_allelic=0 #not_processed=0 #hits=481/51000000 speed=3.89MT/s 328s * #variants=72211 #multi_allelic=0 #not_processed=0 #hits=492/52000000 speed=4.00MT/s 328s * #variants=73449 #multi_allelic=0 #not_processed=0 #hits=492/53000000 speed=3.94MT/s 328s * #variants=74662 #multi_allelic=0 #not_processed=0 #hits=500/54000000 speed=4.07MT/s 328s * #variants=75863 #multi_allelic=0 #not_processed=0 #hits=506/55000000 speed=4.02MT/s 330s * #variants=77058 #multi_allelic=0 #not_processed=0 #hits=513/56000000 speed=4.03MT/s 330s * #variants=78253 #multi_allelic=0 #not_processed=0 #hits=515/57000000 speed=4.05MT/s 330s * #variants=79446 #multi_allelic=0 #not_processed=0 #hits=530/58000000 speed=3.89MT/s 330s * #variants=80634 #multi_allelic=0 #not_processed=0 #hits=581/59000000 speed=4.00MT/s 330s * #variants=81817 #multi_allelic=0 #not_processed=0 #hits=594/60000000 speed=4.00MT/s 330s * #variants=82993 #multi_allelic=0 #not_processed=0 #hits=598/61000000 speed=4.02MT/s 330s * #variants=84160 #multi_allelic=0 #not_processed=0 #hits=599/62000000 speed=4.03MT/s 330s * #variants=85304 #multi_allelic=0 #not_processed=0 #hits=609/63000000 speed=4.08MT/s 330s * #variants=85485 #multi_allelic=0 #not_processed=0 #hits=609/63157827 speed=4.15MT/s 330s 330s Running time: 16 seconds 331s autopkgtest [07:34:13]: test run-sample-analysis: -----------------------] 331s autopkgtest [07:34:13]: test run-sample-analysis: - - - - - - - - - - results - - - - - - - - - - 331s run-sample-analysis PASS 332s autopkgtest [07:34:14]: @@@@@@@@@@@@@@@@@@@@ summary 332s run-sample-analysis PASS 344s Creating nova instance adt-noble-ppc64el-qtltools-20240218-072842-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240217.img (UUID 3a5f9ddc-1783-4d29-b4f2-fff36e098426)...