0s autopkgtest [02:26:01]: starting date: 2024-03-11
  0s autopkgtest [02:26:01]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline
  0s autopkgtest [02:26:01]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n8c5_25j/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:zlib --apt-upgrade bedops --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=zlib/1:1.3.dfsg-3.1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-45.secgroup --name adt-noble-amd64-bedops-20240311-022601-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/
430s autopkgtest [02:33:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup
430s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
430s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B]
430s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [433 kB]
430s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2621 kB]
430s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB]
430s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [590 kB]
430s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [374 kB]
430s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
430s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [20.4 kB]
430s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6228 B]
430s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
430s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [878 kB]
430s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [3025 kB]
430s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
430s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [50.1 kB]
430s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [13.0 kB]
430s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
433s Fetched 8182 kB in 1s (7052 kB/s)
433s Reading package lists...
437s Reading package lists...
438s Building dependency tree...
438s Reading state information...
438s Calculating upgrade...
438s The following packages will be upgraded:
438s   python3-attr zlib1g
438s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
438s Need to get 111 kB of archives.
438s After this operation, 8192 B disk space will be freed.
438s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu1 [62.7 kB]
438s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 python3-attr all 23.2.0-2 [48.6 kB]
439s Fetched 111 kB in 0s (6161 kB/s)
439s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71805 files and directories currently installed.)
439s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_amd64.deb ...
439s Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ...
439s Setting up zlib1g:amd64 (1:1.3.dfsg-3.1ubuntu1) ...
439s (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 ... 71805 files and directories currently installed.)
439s Preparing to unpack .../python3-attr_23.2.0-2_all.deb ...
439s Unpacking python3-attr (23.2.0-2) over (23.2.0-1) ...
439s Setting up python3-attr (23.2.0-2) ...
439s Processing triggers for libc-bin (2.39-0ubuntu2) ...
439s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
439s 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
439s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
439s 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
439s Reading package lists...
440s Building dependency tree...
440s Reading state information...
440s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
440s sh: Attempting to set up Debian/Ubuntu apt sources automatically
440s sh: Distribution appears to be Ubuntu
444s Reading package lists...
445s Building dependency tree...
445s Reading state information...
445s eatmydata is already the newest version (131-1).
445s dbus is already the newest version (1.14.10-4ubuntu1).
445s dbus set to manually installed.
445s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
445s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
445s 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
445s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
445s 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
445s Reading package lists...
445s Building dependency tree...
445s Reading state information...
445s rng-tools-debian is already the newest version (2.4).
445s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
446s Reading package lists...
446s Building dependency tree...
446s Reading state information...
446s haveged is already the newest version (1.9.14-1ubuntu1).
446s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
446s Reading package lists...
446s Building dependency tree...
446s Reading state information...
447s The following packages will be REMOVED:
447s   cloud-init* python3-configobj* python3-debconf*
447s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
447s After this operation, 3248 kB disk space will be freed.
447s (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 ... 71805 files and directories currently installed.)
447s Removing cloud-init (24.1-0ubuntu1) ...
447s Removing python3-configobj (5.0.8-3) ...
447s Removing python3-debconf (1.5.86) ...
448s Processing triggers for man-db (2.12.0-3) ...
448s (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 ... 71416 files and directories currently installed.)
448s Purging configuration files for cloud-init (24.1-0ubuntu1) ...
449s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
449s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
449s Reading package lists...
449s Building dependency tree...
449s Reading state information...
450s linux-generic is already the newest version (6.8.0-11.11+1).
450s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
450s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
450s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
450s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
450s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
450s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease
454s Reading package lists...
454s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
454s 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
454s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
454s 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
454s Reading package lists...
454s Building dependency tree...
454s Reading state information...
455s Calculating upgrade...
455s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
455s Reading package lists...
455s Building dependency tree...
455s Reading state information...
455s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
456s autopkgtest [02:33:37]: rebooting testbed after setup commands that affected boot
484s autopkgtest [02:34:05]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
484s autopkgtest [02:34:05]: testbed dpkg architecture: amd64
484s autopkgtest [02:34:05]: @@@@@@@@@@@@@@@@@@@@ apt-source bedops
484s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1
484s 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
484s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
484s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2
484s 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
485s Get:1 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-1 (dsc) [2178 B]
485s Get:2 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-1 (tar) [13.5 MB]
485s Get:3 http://ftpmaster.internal/ubuntu noble/universe bedops 2.4.41+dfsg-1 (diff) [10.4 kB]
486s gpgv: Signature made Mon Jul 18 09:03:24 2022 UTC
486s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
486s gpgv:                issuer "tille@debian.org"
486s gpgv: Can't check signature: No public key
486s dpkg-source: warning: cannot verify inline signature for ./bedops_2.4.41+dfsg-1.dsc: no acceptable signature found
486s autopkgtest [02:34:07]: testing package bedops version 2.4.41+dfsg-1
486s autopkgtest [02:34:07]: build not needed
486s autopkgtest [02:34:07]: test run-unit-test: preparing testbed
487s Reading package lists...
488s Building dependency tree...
488s Reading state information...
488s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
488s Starting 2 pkgProblemResolver with broken count: 0
488s Done
488s  Done
489s Starting pkgProblemResolver with broken count: 0
489s Starting 2 pkgProblemResolver with broken count: 0
489s Done
489s The following additional packages will be installed:
489s   bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc
489s   libjs-underscore tcsh
489s Suggested packages:
489s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc
489s Recommended packages:
489s   javascript-common
489s The following NEW packages will be installed:
489s   bedops bedops-doc fonts-mathjax libjs-jquery libjs-mathjax libjs-sphinxdoc
489s   libjs-underscore tcsh
489s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
489s 1 not fully installed or removed.
489s Need to get 32.3 MB of archives.
489s After this operation, 89.0 MB of additional disk space will be used.
489s Get:1 http://ftpmaster.internal/ubuntu noble/universe amd64 tcsh amd64 6.24.10-3 [450 kB]
489s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 bedops amd64 2.4.41+dfsg-1 [1445 kB]
489s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
489s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
489s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-sphinxdoc all 7.2.6-4 [149 kB]
489s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
489s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
489s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 bedops-doc all 2.4.41+dfsg-1 [21.9 MB]
490s Fetched 32.3 MB in 0s (94.1 MB/s)
490s Selecting previously unselected package tcsh.
490s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 100%
(Reading database ... 71361 files and directories currently installed.)
490s Preparing to unpack .../0-tcsh_6.24.10-3_amd64.deb ...
490s Unpacking tcsh (6.24.10-3) ...
490s Selecting previously unselected package bedops.
490s Preparing to unpack .../1-bedops_2.4.41+dfsg-1_amd64.deb ...
490s Unpacking bedops (2.4.41+dfsg-1) ...
490s Selecting previously unselected package libjs-jquery.
490s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
490s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
490s Selecting previously unselected package libjs-underscore.
490s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
490s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
490s Selecting previously unselected package libjs-sphinxdoc.
490s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-4_all.deb ...
490s Unpacking libjs-sphinxdoc (7.2.6-4) ...
490s Selecting previously unselected package fonts-mathjax.
490s Preparing to unpack .../5-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
490s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
490s Selecting previously unselected package libjs-mathjax.
490s Preparing to unpack .../6-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
490s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
491s Selecting previously unselected package bedops-doc.
491s Preparing to unpack .../7-bedops-doc_2.4.41+dfsg-1_all.deb ...
491s Unpacking bedops-doc (2.4.41+dfsg-1) ...
491s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
491s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
491s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
491s Setting up tcsh (6.24.10-3) ...
491s update-alternatives: using /bin/tcsh to provide /bin/csh (csh) in auto mode
491s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
491s Setting up libjs-sphinxdoc (7.2.6-4) ...
491s Setting up bedops (2.4.41+dfsg-1) ...
491s Setting up bedops-doc (2.4.41+dfsg-1) ...
491s Setting up autopkgtest-satdep (0) ...
491s Processing triggers for debianutils (5.16) ...
492s Processing triggers for man-db (2.12.0-3) ...
494s (Reading database ... 76479 files and directories currently installed.)
494s Removing autopkgtest-satdep (0) ...
495s autopkgtest [02:34:16]: test run-unit-test: [-----------------------
495s Testing bedops
495s Testing binary [bedops] and build type []
495s make[1]: Entering directory '/tmp/autopkgtest.fHlSXM/autopkgtest_tmp/tests/bedops'
495s Missing binary [bedops] for build type []
495s Writing to [/tmp/tmp.j8Moo75Plz]
495s bedops --version
495s bedops
495s   citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
495s             https://doi.org/10.1093/bioinformatics/bts277
495s   version:  2.4.41 (typical)
495s   authors:  Shane Neph & Scott Kuehn
495s [bedops- --merge] - [Test 001] ...passed!
495s [bedops- --merge] - [Test 002] ...passed!
495s [bedops- --merge] - [Test 003] ...passed!
495s [bedops- --merge] - [Test 004] ...passed!
495s [bedops- --merge] - [Test 005] ...passed!
495s [bedops- --merge] - [Test 006] ...passed!
495s [bedops- --merge] - [Test 007] ...passed!
495s [bedops- --merge] - [Test 008] ...passed!
495s [bedops- --merge] - [Test 009] ...passed!
495s [bedops- --complement] - [Test 001] ...passed!
495s [bedops- --complement] - [Test 002] ...passed!
495s [bedops- --complement] - [Test 003] ...passed!
495s [bedops- --complement] - [Test 004] ...passed!
495s [bedops- --complement] - [Test 005] ...passed!
495s [bedops- --complement] - [Test 006] ...passed!
495s [bedops- --complement] - [Test 007] ...passed!
495s [bedops- --complement] - [Test 008] ...passed!
495s [bedops- --complement] - [Test 009] ...passed!
495s [bedops- --intersection] - [Test 001] ...passed!
495s [bedops- --intersection] - [Test 002] ...passed!
495s [bedops- --intersection] - [Test 003] ...passed!
495s [bedops- --intersection] - [Test 004] ...passed!
495s [bedops- --difference] - [Test 001] ...passed!
495s [bedops- --difference] - [Test 002] ...passed!
495s [bedops- --difference] - [Test 003] ...passed!
495s [bedops- --difference] - [Test 004] ...passed!
495s [bedops- --difference] - [Test 005] ...passed!
495s [bedops- --difference] - [Test 006] ...passed!
495s [bedops- --difference] - [Test 007] ...passed!
495s [bedops- --symdiff] - [Test 001] ...passed!
495s [bedops- --symdiff] - [Test 002] ...passed!
495s [bedops- --symdiff] - [Test 003] ...passed!
495s [bedops- --symdiff] - [Test 004] ...passed!
495s [bedops- --symdiff] - [Test 005] ...passed!
495s [bedops- --element-of] - [Test 001] ...passed!
495s [bedops- --element-of] - [Test 002] ...passed!
495s [bedops- --element-of] - [Test 003] ...passed!
495s [bedops- --element-of] - [Test 004] ...passed!
495s [bedops- --not-element-of] - [Test 001] ...passed!
495s [bedops- --not-element-of] - [Test 002] ...passed!
495s [bedops- --not-element-of] - [Test 003] ...passed!
495s [bedops- --union] - [Test 001] ...passed!
495s [bedops- --union] - [Test 002] ...passed!
495s [bedops- --union] - [Test 003] ...passed!
495s [bedops- --union] - [Test 004] ...passed!
495s [bedops- --union] - [Test 005] ...passed!
495s [bedops- --union] - [Test 006] ...passed!
495s [bedops- --union] - [Test 007] ...passed!
495s [bedops- --union] - [Test 008] ...passed!
495s [bedops- --union] - [Test 009] ...passed!
495s [bedops- --partition] - [Test 001] ...passed!
495s [bedops- --partition] - [Test 002] ...passed!
495s [bedops- --partition] - [Test 003] ...passed!
495s [bedops- --partition] - [Test 004] ...passed!
495s [bedops- --partition] - [Test 005] ...passed!
495s [bedops- --chrom] - [Test 001] ...passed!
495s [bedops- --chrom] - [Test 002] ...passed!
495s [bedops- --chrom] - [Test 003] ...passed!
495s [bedops- --chrom] - [Test 004] ...passed!
495s [bedops- --chop] - [Test 001] ...passed!
495s [bedops- --chop] - [Test 002] ...passed!
495s [bedops- --chop] - [Test 003] ...passed!
495s [bedops- --chop] - [Test 004] ...passed!
495s [bedops- --chop] - [Test 005] ...passed!
495s [bedops- --stdin] - [Test 001] ...passed!
495s [bedops- --named-pipe] - [Test 001] ...passed!
496s [bedops- --ec] - [Test 001] ...passed! (not expected to pass)
496s make[1]: Leaving directory '/tmp/autopkgtest.fHlSXM/autopkgtest_tmp/tests/bedops'
496s make[1]: *** [Makefile:380: ec] Error 1
496s make: *** [Makefile:10: all] Error 2
496s Testing starch
496s Testing binary group [starch] and build type []
496s make[1]: Entering directory '/tmp/autopkgtest.fHlSXM/autopkgtest_tmp/tests/starch'
496s Missing binary [unstarch] for build type []
496s Writing to [/tmp/tmp.O0EqF4MaGr]
496s unstarch --version
496s unstarch
496s   binary version: 2.4.41 (typical) (extracts archive version: 2.2.0 or older)
496s [starch-unstarch- --signature] - [Test 001] ...passed!
496s [starch-unstarch- --signature] - [Test 002] ...passed!
496s Missing binary [bedops-starch] for build type []
496s bedops-starch --version
496s starch
496s   binary version: 2.4.41 (typical) (creates archive version: 2.2.0)
496s Writing to [/tmp/tmp.O0EqF4MaGr]
496s Missing binary [bedmap] for build type []
496s bedmap --help
496s bedmap
496s   citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
496s             https://doi.org/10.1093/bioinformatics/bts277
496s   version:  2.4.41 (typical)
496s   authors:  Shane Neph & Scott Kuehn
496s                                                                                                     
496s  USAGE: bedmap [process-flags] [overlap-option] <operation(s)...> <ref-file> [map-file]             
496s      Any input file must be sorted per the sort-bed utility.                                        
496s      The program accepts BED and Starch file formats.                                               
496s      You may use '-' for a BED file to indicate the input comes from stdin.                         
496s                                                                                                     
496s      Traverse <ref-file>, while applying <operation(s)> on qualified, overlapping elements from     
496s        <map-file>.  Output is one line for each line in <ref-file>, sent to standard output.  There 
496s        is no limit on the number of operations you can specify to compute in one bedmap call.       
496s      If <map-file> is omitted, the given file is treated as both the <ref-file> and <map-file>.     
496s        This usage is more efficient than specifying the same file twice.                            
496s      Arguments may be given in any order before the input file(s).                                  
496s                                                                                                     
496s     Process Flags:                                                                                  
496s      --------                                                                                       
496s       --chrom <chromosome>  Jump to and process data for given <chromosome> only.                   
496s       --delim <delim>       Change output delimiter from '|' to <delim> between columns (e.g. '\t').
496s       --ec                  Error check all input files (slower).                                   
496s       --faster              (advanced) Strong input assumptions are made.  Compatible with:         
496s                               --bp-ovr, --range, --fraction-both, and --exact overlap options only. 
496s       --header              Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.             
496s       --help                Print this message and exit successfully.                               
496s       --min-memory          Minimize memory usage (slower).                                         
496s       --multidelim <delim>  Change delimiter of multi-value output columns from ';' to <delim>.     
496s       --prec <int>          Change the post-decimal precision of scores to <int>.  0 <= <int>.      
496s       --sci                 Use scientific notation for score outputs.                              
496s       --skip-unmapped       Print no output for a row with no mapped elements.                      
496s       --sweep-all           Ensure <map-file> is read completely (helps to prevent broken pipes).   
496s       --unmapped-val <val>  Print <val> on unmapped --echo-map* and --min/max-element* operations.  
496s                               The default is to print nothing.                                      
496s       --version             Print program information.                                              
496s                                                                                                     
496s                                                                                                     
496s     Overlap Options (At most, one may be selected.  By default, --bp-ovr 1 is used):                
496s      --------                                                                                       
496s       --bp-ovr <int>           Require <int> bp overlap between elements of input files.            
496s       --exact                  First 3 fields from <map-file> must be identical to <ref-file>'s.    
496s       --fraction-both <val>    Both --fraction-ref <val> and --fraction-map <val> must be true to   
496s                                  qualify as overlapping.  Expect 0 < val <= 1.                      
496s       --fraction-either <val>  Either --fraction-ref <val> or --fraction-map <val> must be true to  
496s                                  qualify as overlapping.  Expect 0 < val <= 1.                      
496s       --fraction-map <val>     The fraction of the element's size from <map-file> that must overlap 
496s                                  the element in <ref-file>.  Expect 0 < val <= 1.                   
496s       --fraction-ref <val>     The fraction of the element's size from <ref-file> that must overlap 
496s                                  an element in <map-file>.  Expect 0 < val <= 1.                    
496s       --range <int>            Grab <map-file> elements within <int> bp of <ref-file>'s element,    
496s                                  where 0 <= int.  --range 0 is an alias for --bp-ovr 1.             
496s                                                                                                     
496s                                                                                                     
496s     Operations:  (Any number of operations may be used any number of times.)                        
496s      ----------                                                                                     
496s       SCORE:                                                                                        
496s        <ref-file> must have at least 3 columns and <map-file> 5 columns.                            
496s                                                                                                     
496s       --cv                The result of --stdev divided by the result of --mean.
496s       --kth <val>         Generalized median. Report the value, x, such that the fraction <val>
496s                             of overlapping elements' scores from <map-file> is less than x,
496s                             and the fraction 1-<val> of scores is greater than x.  0 < val <= 1.
496s       --mad <mult=1>      The median absolute deviation of overlapping elements in <map-file>.
496s                             Multiply mad score by <mult>.  0 < mult, and mult is 1 by default.
496s       --max               The highest score from overlapping elements in <map-file>.
496s       --max-element       A (non-random) highest-scoring and overlapping element in <map-file>.
496s       --max-element-rand  A random highest-scoring and overlapping element in <map-file>.
496s       --mean              The average score from overlapping elements in <map-file>.
496s       --median            The median score from overlapping elements in <map-file>.
496s       --min               The lowest score from overlapping elements in <map-file>.
496s       --min-element       A (non-random) lowest-scoring and overlapping element in <map-file>.
496s       --min-element-rand  A random lowest-scoring and overlapping element in <map-file>.
496s       --stdev             The square root of the result of --variance.
496s       --sum               Accumulated scores from overlapping elements in <map-file>.
496s       --tmean <low> <hi>  The mean score from overlapping elements in <map-file>, after
496s                             ignoring the bottom <low> and top <hi> fractions of those scores.
496s                             0 <= low <= 1.  0 <= hi <= 1.  low+hi <= 1.
496s       --variance          The variance of scores from overlapping elements in <map-file>.
496s       --wmean             Weighted mean, scaled in proportion to the coverage of the <ref-file>
496s                             element by each overlapping <map-file> element.
496s      
496s      ----------
496s       NON-SCORE:
496s        <ref-file> must have at least 3 columns.
496s        For --echo-map-id/echo-map-id-uniq, <map-file> must have at least 4 columns.
496s        For --echo-map-score, <map-file> must have at least 5 columns.
496s        For all others, <map-file> requires at least 3 columns.
496s 
496s       --bases             The total number of overlapping bases from <map-file>.
496s       --bases-uniq        The number of distinct bases from <ref-file>'s element covered by
496s                             overlapping elements in <map-file>.
496s       --bases-uniq-f      The fraction of distinct bases from <ref-file>'s element covered by
496s                             overlapping elements in <map-file>.
496s       --count             The number of overlapping elements in <map-file>.
496s       --echo              Print each line from <ref-file>.
496s       --echo-map          List all overlapping elements from <map-file>.
496s       --echo-map-id       List IDs from all overlapping <map-file> elements.
496s       --echo-map-id-uniq  List unique IDs from overlapping <map-file> elements.
496s       --echo-map-range    Print genomic range of overlapping elements from <map-file>.
496s       --echo-map-score    List scores from overlapping <map-file> elements.
496s       --echo-map-size     List the full length of every overlapping element.
496s       --echo-overlap-size List lengths of overlaps.
496s       --echo-ref-name     Print the first 3 fields of <ref-file> using chrom:start-end format.
496s       --echo-ref-row-id   Print 'id-' followed by the line number of <ref-file>.
496s       --echo-ref-size     Print the length of each line from <ref-file>.
496s       --indicator         Print 1 if there exists an overlapping element in <map-file>, 0 otherwise.
496s 
496s 
496s [starch-starch-API- --starch_api_bedmap] - [Test 001] ...passed!
496s Missing binary [bedops-starch] for build type []
496s Writing to [/tmp/tmp.O0EqF4MaGr]
496s bedops-starch --version
496s starch
496s   binary version: 2.4.41 (typical) (creates archive version: 2.2.0)
496s Generating random intervals...
496s ./generate_random_intervals.sh /tmp/autopkgtest.fHlSXM/autopkgtest_tmp/tests/starch/data/hg38.bed 3 10000 | sort-bed - > /tmp/tmp.O0EqF4MaGr/random_intervals.bed
497s [starch-starch- --deflate_and_inflate_bzip2] - [Test 001] ...passed!
497s [starch-starch- --deflate_and_inflate_gz] - [Test 001] ...passed!
497s Removing [/tmp/tmp.O0EqF4MaGr]
497s make[1]: Leaving directory '/tmp/autopkgtest.fHlSXM/autopkgtest_tmp/tests/starch'
497s autopkgtest [02:34:18]: test run-unit-test: -----------------------]
498s run-unit-test        PASS
498s autopkgtest [02:34:19]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
498s autopkgtest [02:34:19]: @@@@@@@@@@@@@@@@@@@@ summary
498s run-unit-test        PASS
510s Creating nova instance adt-noble-amd64-bedops-20240311-022601-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240309.img (UUID cf9084ac-d9f1-45d9-9e58-3f793071bee0)...