0s autopkgtest [04:32:55]: starting date: 2024-03-12 0s autopkgtest [04:32:55]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [04:32:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4ob84014/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:perl,src:db5.3,src:gdbm,src:mmdebstrap --apt-upgrade proteinortho --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-21.secgroup --name adt-noble-amd64-proteinortho-20240312-043255-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-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/ 480s autopkgtest [04:40:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 480s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 480s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.2 kB] 480s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 480s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [447 kB] 480s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2711 kB] 480s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [388 kB] 480s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [605 kB] 480s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 480s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6228 B] 480s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [20.4 kB] 480s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 480s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1004 kB] 480s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [3230 kB] 480s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 480s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [14.4 kB] 480s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [51.5 kB] 480s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 484s Fetched 8650 kB in 1s (6587 kB/s) 484s Reading package lists... 490s Reading package lists... 490s Building dependency tree... 490s Reading state information... 490s Calculating upgrade... 491s The following packages were automatically installed and are no longer required: 491s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 491s Use 'sudo apt autoremove' to remove them. 491s The following packages will be REMOVED: 491s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 491s The following NEW packages will be installed: 491s libgdbm-compat4t64 libgdbm6t64 491s The following packages have been kept back: 491s libperl5.38 491s The following packages will be upgraded: 491s perl-base perl-modules-5.38 491s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 491s Need to get 4974 kB of archives. 491s After this operation, 4154 kB disk space will be freed. 491s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-base amd64 5.38.2-3.2 [1823 kB] 491s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgdbm6t64 amd64 1.23-5.1 [34.4 kB] 491s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgdbm-compat4t64 amd64 1.23-5.1 [6700 B] 491s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 491s Fetched 4974 kB in 0s (48.1 MB/s) 491s (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.) 491s Removing dpkg-dev (1.22.4ubuntu5) ... 491s Removing libdpkg-perl (1.22.4ubuntu5) ... 492s Removing perl (5.38.2-3) ... 492s (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 ... 71224 files and directories currently installed.) 492s Preparing to unpack .../perl-base_5.38.2-3.2_amd64.deb ... 492s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 492s Setting up perl-base (5.38.2-3.2) ... 492s dpkg: libgdbm6:amd64: dependency problems, but removing anyway as you requested: 492s python3-gdbm:amd64 depends on libgdbm6 (>= 1.16). 492s man-db depends on libgdbm6 (>= 1.16). 492s libperl5.38:amd64 depends on libgdbm6 (>= 1.21). 492s libgdbm-compat4:amd64 depends on libgdbm6 (>= 1.16). 492s 492s (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 ... 71224 files and directories currently installed.) 492s Removing libgdbm6:amd64 (1.23-5) ... 492s Selecting previously unselected package libgdbm6t64:amd64. 492s (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 ... 71219 files and directories currently installed.) 492s Preparing to unpack .../libgdbm6t64_1.23-5.1_amd64.deb ... 492s Unpacking libgdbm6t64:amd64 (1.23-5.1) ... 492s dpkg: libgdbm-compat4:amd64: dependency problems, but removing anyway as you requested: 492s libperl5.38:amd64 depends on libgdbm-compat4 (>= 1.18-3). 492s 492s (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 ... 71225 files and directories currently installed.) 492s Removing libgdbm-compat4:amd64 (1.23-5) ... 492s Selecting previously unselected package libgdbm-compat4t64:amd64. 492s (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 ... 71220 files and directories currently installed.) 492s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_amd64.deb ... 492s Unpacking libgdbm-compat4t64:amd64 (1.23-5.1) ... 492s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 492s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 493s Setting up libgdbm6t64:amd64 (1.23-5.1) ... 493s Setting up libgdbm-compat4t64:amd64 (1.23-5.1) ... 493s Setting up perl-modules-5.38 (5.38.2-3.2) ... 493s Processing triggers for man-db (2.12.0-3) ... 494s Processing triggers for libc-bin (2.39-0ubuntu2) ... 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s 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 494s Reading package lists... 494s Building dependency tree... 494s Reading state information... 495s The following packages will be REMOVED: 495s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 495s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 495s After this operation, 50.1 MB disk space will be freed. 495s (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 ... 71226 files and directories currently installed.) 495s Removing libperl5.38:amd64 (5.38.2-3) ... 495s Removing libgdbm-compat4t64:amd64 (1.23-5.1) ... 495s Removing lto-disabled-list (47) ... 495s Removing make (4.3-4.1build1) ... 495s Removing perl-modules-5.38 (5.38.2-3.2) ... 495s Processing triggers for man-db (2.12.0-3) ... 496s Processing triggers for libc-bin (2.39-0ubuntu2) ... 496s sh: Attempting to set up Debian/Ubuntu apt sources automatically 496s sh: Distribution appears to be Ubuntu 497s Reading package lists... 497s Building dependency tree... 497s Reading state information... 497s eatmydata is already the newest version (131-1). 497s dbus is already the newest version (1.14.10-4ubuntu1). 497s dbus set to manually installed. 497s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 498s Reading package lists... 498s Building dependency tree... 498s Reading state information... 498s rng-tools-debian is already the newest version (2.4). 498s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 498s Reading package lists... 499s Building dependency tree... 499s Reading state information... 499s haveged is already the newest version (1.9.14-1ubuntu1). 499s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 499s Reading package lists... 500s Building dependency tree... 500s Reading state information... 500s The following additional packages will be installed: 500s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 500s make perl perl-modules-5.38 500s Suggested packages: 500s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 500s libterm-readline-gnu-perl | libterm-readline-perl-perl 500s libtap-harness-archive-perl 500s Recommended packages: 500s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 500s libfile-fcntllock-perl 500s The following packages will be REMOVED: 500s libdb5.3 500s The following NEW packages will be installed: 500s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 500s lto-disabled-list make perl perl-modules-5.38 500s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 500s Need to get 7375 kB/10.5 MB of archives. 500s After this operation, 54.3 MB of additional disk space will be used. 500s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5 [734 kB] 500s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libperl5.38t64 amd64 5.38.2-3.2 [4871 kB] 500s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl amd64 5.38.2-3.2 [231 kB] 500s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 500s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 make amd64 4.3-4.1build1 [180 kB] 500s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] 500s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 501s Fetched 7375 kB in 0s (64.5 MB/s) 501s dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: 501s libsasl2-modules-db:amd64 depends on libdb5.3. 501s libpython3.12-stdlib:amd64 depends on libdb5.3. 501s libpython3.11-stdlib:amd64 depends on libdb5.3. 501s libpam-modules:amd64 depends on libdb5.3. 501s iproute2 depends on libdb5.3. 501s apt-utils depends on libdb5.3. 501s 501s (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 ... 69262 files and directories currently installed.) 501s Removing libdb5.3:amd64 (5.3.28+dfsg2-4) ... 501s Selecting previously unselected package libdb5.3t64:amd64. 501s (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 ... 69256 files and directories currently installed.) 501s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_amd64.deb ... 501s Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... 501s Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... 501s Selecting previously unselected package perl-modules-5.38. 501s (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 ... 69262 files and directories currently installed.) 501s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 501s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 501s Selecting previously unselected package libgdbm-compat4t64:amd64. 501s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_amd64.deb ... 501s Unpacking libgdbm-compat4t64:amd64 (1.23-5.1) ... 501s Selecting previously unselected package libperl5.38t64:amd64. 501s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_amd64.deb ... 501s Unpacking libperl5.38t64:amd64 (5.38.2-3.2) ... 502s Selecting previously unselected package perl. 502s Preparing to unpack .../3-perl_5.38.2-3.2_amd64.deb ... 502s Unpacking perl (5.38.2-3.2) ... 502s Selecting previously unselected package libdpkg-perl. 502s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 502s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 502s Selecting previously unselected package make. 502s Preparing to unpack .../5-make_4.3-4.1build1_amd64.deb ... 502s Unpacking make (4.3-4.1build1) ... 502s Selecting previously unselected package lto-disabled-list. 502s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 502s Unpacking lto-disabled-list (47) ... 502s Selecting previously unselected package dpkg-dev. 502s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 502s Unpacking dpkg-dev (1.22.4ubuntu5) ... 502s Setting up lto-disabled-list (47) ... 502s Setting up libgdbm-compat4t64:amd64 (1.23-5.1) ... 502s Setting up make (4.3-4.1build1) ... 502s Setting up perl-modules-5.38 (5.38.2-3.2) ... 502s Setting up libperl5.38t64:amd64 (5.38.2-3.2) ... 502s Setting up perl (5.38.2-3.2) ... 502s Setting up libdpkg-perl (1.22.4ubuntu5) ... 502s Setting up dpkg-dev (1.22.4ubuntu5) ... 502s Processing triggers for man-db (2.12.0-3) ... 503s Processing triggers for libc-bin (2.39-0ubuntu2) ... 509s Reading package lists... 509s Building dependency tree... 509s Reading state information... 509s The following packages will be REMOVED: 509s cloud-init* python3-configobj* python3-debconf* 510s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 510s After this operation, 3248 kB disk space will be freed. 510s (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 ... 71807 files and directories currently installed.) 510s Removing cloud-init (24.1-0ubuntu1) ... 511s Removing python3-configobj (5.0.8-3) ... 511s Removing python3-debconf (1.5.86) ... 511s Processing triggers for man-db (2.12.0-3) ... 511s (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 ... 71418 files and directories currently installed.) 511s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 512s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 512s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 513s Reading package lists... 513s Building dependency tree... 513s Reading state information... 514s linux-generic is already the newest version (6.8.0-11.11+1). 514s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 514s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 514s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 514s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 514s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 514s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 520s Reading package lists... 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s 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 520s Reading package lists... 521s Building dependency tree... 521s Reading state information... 521s Calculating upgrade... 522s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 522s Reading package lists... 522s Building dependency tree... 522s Reading state information... 523s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 523s autopkgtest [04:41:38]: rebooting testbed after setup commands that affected boot 573s autopkgtest [04:42:28]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 573s autopkgtest [04:42:28]: testbed dpkg architecture: amd64 574s autopkgtest [04:42:29]: @@@@@@@@@@@@@@@@@@@@ apt-source proteinortho 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 574s 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 575s Get:1 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] 575s Get:2 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (tar) [376 kB] 575s Get:3 http://ftpmaster.internal/ubuntu noble/universe proteinortho 6.3.1+dfsg-1 (diff) [7248 B] 575s gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 575s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 575s gpgv: issuer "tille@debian.org" 575s gpgv: Can't check signature: No public key 575s dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found 575s autopkgtest [04:42:30]: testing package proteinortho version 6.3.1+dfsg-1 575s autopkgtest [04:42:30]: build not needed 575s autopkgtest [04:42:30]: test run-unit-test: preparing testbed 577s Reading package lists... 577s Building dependency tree... 577s Reading state information... 578s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 578s Starting 2 pkgProblemResolver with broken count: 0 578s Done 578s Done 578s Starting pkgProblemResolver with broken count: 0 579s Starting 2 pkgProblemResolver with broken count: 0 579s Done 579s The following additional packages will be installed: 579s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 579s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 579s Recommended packages: 579s med-config 579s The following NEW packages will be installed: 579s diamond-aligner libblas3 libgfortran5 libgomp1 liblapack3 libmbedcrypto7 579s libmbedtls14 libmbedx509-1 ncbi-blast+ ncbi-data proteinortho 579s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 579s 1 not fully installed or removed. 579s Need to get 24.2 MB of archives. 579s After this operation, 95.5 MB of additional disk space will be used. 579s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 579s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 579s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 579s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 579s Get:5 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 580s Get:6 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedcrypto7 amd64 2.28.7-1ubuntu1 [206 kB] 580s Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedx509-1 amd64 2.28.7-1ubuntu1 [46.4 kB] 580s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedtls14 amd64 2.28.7-1ubuntu1 [82.1 kB] 580s Get:9 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.6 MB] 580s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 diamond-aligner amd64 2.1.9-1 [2504 kB] 580s Get:11 http://ftpmaster.internal/ubuntu noble/universe amd64 proteinortho amd64 6.3.1+dfsg-1 [358 kB] 581s Fetched 24.2 MB in 1s (37.9 MB/s) 581s Selecting previously unselected package libgomp1:amd64. 581s (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 ... 71363 files and directories currently installed.) 581s Preparing to unpack .../00-libgomp1_14-20240303-1ubuntu1_amd64.deb ... 581s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ... 581s Selecting previously unselected package libblas3:amd64. 581s Preparing to unpack .../01-libblas3_3.12.0-3_amd64.deb ... 581s Unpacking libblas3:amd64 (3.12.0-3) ... 581s Selecting previously unselected package libgfortran5:amd64. 581s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 581s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 581s Selecting previously unselected package liblapack3:amd64. 581s Preparing to unpack .../03-liblapack3_3.12.0-3_amd64.deb ... 581s Unpacking liblapack3:amd64 (3.12.0-3) ... 581s Selecting previously unselected package ncbi-data. 581s Preparing to unpack .../04-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 581s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 581s Selecting previously unselected package libmbedcrypto7:amd64. 581s Preparing to unpack .../05-libmbedcrypto7_2.28.7-1ubuntu1_amd64.deb ... 581s Unpacking libmbedcrypto7:amd64 (2.28.7-1ubuntu1) ... 581s Selecting previously unselected package libmbedx509-1:amd64. 581s Preparing to unpack .../06-libmbedx509-1_2.28.7-1ubuntu1_amd64.deb ... 581s Unpacking libmbedx509-1:amd64 (2.28.7-1ubuntu1) ... 581s Selecting previously unselected package libmbedtls14:amd64. 581s Preparing to unpack .../07-libmbedtls14_2.28.7-1ubuntu1_amd64.deb ... 581s Unpacking libmbedtls14:amd64 (2.28.7-1ubuntu1) ... 581s Selecting previously unselected package ncbi-blast+. 581s Preparing to unpack .../08-ncbi-blast+_2.12.0+ds-4_amd64.deb ... 581s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 582s Selecting previously unselected package diamond-aligner. 582s Preparing to unpack .../09-diamond-aligner_2.1.9-1_amd64.deb ... 582s Unpacking diamond-aligner (2.1.9-1) ... 582s Selecting previously unselected package proteinortho. 582s Preparing to unpack .../10-proteinortho_6.3.1+dfsg-1_amd64.deb ... 582s Unpacking proteinortho (6.3.1+dfsg-1) ... 582s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 582s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 582s Setting up diamond-aligner (2.1.9-1) ... 582s Setting up libblas3:amd64 (3.12.0-3) ... 582s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 582s Setting up libmbedcrypto7:amd64 (2.28.7-1ubuntu1) ... 582s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 582s Setting up liblapack3:amd64 (3.12.0-3) ... 582s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 582s Setting up libmbedx509-1:amd64 (2.28.7-1ubuntu1) ... 582s Setting up libmbedtls14:amd64 (2.28.7-1ubuntu1) ... 582s Setting up ncbi-blast+ (2.12.0+ds-4) ... 582s Setting up proteinortho (6.3.1+dfsg-1) ... 582s Setting up autopkgtest-satdep (0) ... 582s Processing triggers for man-db (2.12.0-3) ... 582s Processing triggers for libc-bin (2.39-0ubuntu2) ... 586s (Reading database ... 71697 files and directories currently installed.) 586s Removing autopkgtest-satdep (0) ... 586s autopkgtest [04:42:41]: test run-unit-test: [----------------------- 586s ***************************************************************** 586s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 586s ***************************************************************** 586s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 586s Checking input files. 586s Checking input files. 586s Checking test/C_clean.faa... ok 586s Checking test/C2.faa... ok 586s Checking test/E.faa... ok 586s Checking test/L.faa... ok 586s Checking test/M.faa... ok 586s Checking test/C.faa... 586s  [WARNING] input 'test/C.faa' contains a gene-name with a comma, this causes problems with the proteinortho.tsv output, I will clean the file ('test/C_clean.faa') and restart the analysis !!! 586s The line is: 586s C_10,test 586s ok 586s Checking test/M.faa... ok 586s Checking test/L.faa... ok 586s Checking test/C2.faa... ok 586s Checking test/C_clean.faa... ok 586s 586s **Step 1** 587s Generating indices anyway (forced). 587s Building database for 'test/C_clean.faa' (218 sequences) 587s Generating indices anyway (forced). 587s Building database for 'test/L.faa' (80 sequences) 587s Generating indices anyway (forced). 587s Building database for 'test/M.faa' (80 sequences) 587s Generating indices anyway (forced). 587s Building database for 'test/C2.faa' (4 sequences) 587s Generating indices anyway (forced). 587s Building database for 'test/E.faa' (72 sequences) 587s 587s **Step 2** using blastp+ 591s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 591s [OUTPUT] -> written to test_blastp.blast-graph 591s 591s **Step 3** 592s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 592s Reading test_blastp.blast-graph 592s 5 species 592s 112 paired proteins 592s 147 bidirectional edges 592s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 592s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.tsv 592s You can extract the fasta files of each orthology group with 592s proteinortho_grab_proteins.pl -tofiles test_blastp.proteinortho.tsv 'test/C_clean.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 'test/E.faa' 592s (Careful: This will generate a file foreach line in the file test_blastp.proteinortho.tsv). 592s [OUTPUT] -> Orthologous pairs are written to test_blastp.proteinortho-graph 593s # test_blastp.proteinortho.tsv statistics: 593s # number of groups that contains at least p% species: 593s # p species groups genes in groups 593s 0% 0 32 (100%) 112 (100%) 593s 20% 1 32 (100%) 112 (100%) 593s 40% 2 32 (100%) 112 (100%) 593s 60% 3 17 (53.12%) 74 (66.07%) 593s 80% 4 11 (34.37%) 51 (45.53%) 593s 100% 5 1 (3.12%) 5 (4.46%) 593s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 593s # number of groups for each input species: 593s L.faa 32 100% 593s M.faa 32 100% 593s E.faa 15 46.87% 593s C_clean.faa 13 40.62% 593s C2.faa 1 3.12% 593s 593s [OUTPUT] -> Summary is written to test_blastp.proteinortho-graph.summary 593s 593s [OUTPUT] -> Orthologous groups are written to test_blastp.proteinortho.html 593s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 593s proteinortho2xml.pl test_blastp.proteinortho.tsv >test_blastp.proteinortho.tsv.xml 593s 593s All finished. 593s ***************************************************************** 593s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 593s ***************************************************************** 593s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 593s Checking input files. 593s Checking test/C_clean.faa... ok 593s Checking test/C2.faa... ok 593s Checking test/E.faa... ok 593s Checking test/L.faa... ok 593s Checking test/M.faa... ok 593s 593s **Step 1** 593s Generating indices anyway (forced). 593s Building database for 'test/C2.faa' (2 sequences) 593s Generating indices anyway (forced). 593s Building database for 'test/M.faa' (40 sequences) 593s Generating indices anyway (forced). 593s Building database for 'test/L.faa' (40 sequences) 593s Generating indices anyway (forced). 593s Building database for 'test/C_clean.faa' (109 sequences) 593s Generating indices anyway (forced). 593s Building database for 'test/E.faa' (72 sequences) 593s 593s **Step 2** using blastp+ with : synteny 598s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 598s [OUTPUT] -> written to test_synteny.blast-graph 598s 598s **Step 3** 598s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 598s Reading test_synteny.blast-graph 598s 5 species 598s 112 paired proteins 598s 147 bidirectional edges 599s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components 599s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.tsv 599s You can extract the fasta files of each orthology group with 599s proteinortho_grab_proteins.pl -tofiles test_synteny.proteinortho.tsv 'test/C2.faa' 'test/M.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 599s (Careful: This will generate a file foreach line in the file test_synteny.proteinortho.tsv). 599s Adding singles... 599s [OUTPUT] -> Orthologous pairs are written to test_synteny.proteinortho-graph 599s # test_synteny.proteinortho.tsv statistics: 599s # number of groups that contains at least p% species: 599s # p species groups genes in groups 599s 0% 0 182 (100%) 262 (100%) 599s 20% 1 182 (100%) 262 (100%) 599s 40% 2 32 (17.58%) 112 (42.74%) 599s 60% 3 17 (9.34%) 74 (28.24%) 599s 80% 4 11 (6.04%) 51 (19.46%) 599s 100% 5 1 (0.54%) 5 (1.9%) 599s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 599s # groups that contains only one species: 599s single 5 150 (82.41%) 150 (57.25%) 599s # number of groups for each input species: 599s L.faa 32 100% 599s M.faa 32 100% 599s E.faa 15 46.87% 599s C_clean.faa 13 40.62% 599s C2.faa 1 3.12% 599s 599s [OUTPUT] -> Summary is written to test_synteny.proteinortho-graph.summary 599s 599s [OUTPUT] -> Orthologous groups are written to test_synteny.proteinortho.html 599s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 599s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 599s 599s 599s Clustering by gene-order (POFF mode) 599s Reading test_synteny.ffadj-graph 599s 5 species 599s 105 paired proteins 599s 106 bidirectional edges 600s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Reading test_synteny.ffadj-graph 600s 5 species 600s 105 paired proteins 600s 106 bidirectional edges 601s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (33@lapack* + 0@power) connected components Clustering: working on (32@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (31@lapack* + 0@power) connected components Clustering: working on (30@lapack* + 0@power) connected components Clustering: working on (29@lapack* + 0@power) connected components Clustering: working on (28@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 601s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.tsv 601s You can extract the fasta files of each orthology group with 601s proteinortho_grab_proteins.pl -tofiles test_synteny.poff.tsv 'test/C2.faa' 'test/M.faa' 'test/L.faa' 'test/C_clean.faa' 'test/E.faa' 601s (Careful: This will generate a file foreach line in the file test_synteny.poff.tsv). 601s Adding singles... 601s [OUTPUT] -> Orthologous pairs written to test_synteny.poff-graph 601s # test_synteny.poff.tsv statistics: 601s # number of groups that contains at least p% species: 601s # p species groups genes in groups 601s 0% 0 195 (100%) 262 (100%) 601s 20% 1 195 (100%) 262 (100%) 601s 40% 2 37 (18.97%) 104 (39.69%) 601s 60% 3 17 (8.71%) 64 (24.42%) 601s 80% 4 10 (5.12%) 43 (16.41%) 601s 100% 5 1 (0.51%) 5 (1.9%) 601s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 601s # groups that contains only one species: 601s single 5 158 (81.02%) 158 (60.3%) 601s # number of groups for each input species: 601s L.faa 37 100% 601s M.faa 37 100% 601s E.faa 14 37.83% 601s C_clean.faa 13 35.13% 601s C2.faa 1 2.7% 601s 601s [OUTPUT] -> Summary is written to test_synteny.poff-graph.summary 601s 601s [OUTPUT] -> Orthologous groups are written to test_synteny.poff.html 601s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 601s proteinortho2xml.pl test_synteny.proteinortho.tsv >test_synteny.proteinortho.tsv.xml 601s 601s All finished. 601s ***************************************************************** 601s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 601s ***************************************************************** 601s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 601s Checking input files. 601s Checking test/C_clean.faa... ok 601s Checking test/C2.faa... ok 601s Checking test/E.faa... ok 601s Checking test/L.faa... ok 601s Checking test/M.faa... ok 601s 601s **Step 1** 601s Generating indices anyway (forced). 601s Building database for 'test/L.faa' (40 sequences) 601s Generating indices anyway (forced). 601s Building database for 'test/E.faa' (72 sequences) 601s Generating indices anyway (forced). 601s Building database for 'test/C2.faa' (2 sequences) 601s Generating indices anyway (forced). 601s Building database for 'test/M.faa' (40 sequences) 601s Generating indices anyway (forced). 601s Building database for 'test/C_clean.faa' (109 sequences) 602s 602s **Step 2** using diamond 606s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 606s [OUTPUT] -> written to test_diamond.blast-graph 606s 606s **Step 3** 606s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 606s Reading test_diamond.blast-graph 606s 5 species 606s 112 paired proteins 606s 145 bidirectional edges 607s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 607s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.tsv 607s You can extract the fasta files of each orthology group with 607s proteinortho_grab_proteins.pl -tofiles test_diamond.proteinortho.tsv 'test/L.faa' 'test/E.faa' 'test/C2.faa' 'test/M.faa' 'test/C_clean.faa' 607s (Careful: This will generate a file foreach line in the file test_diamond.proteinortho.tsv). 607s [OUTPUT] -> Orthologous pairs are written to test_diamond.proteinortho-graph 607s # test_diamond.proteinortho.tsv statistics: 607s # number of groups that contains at least p% species: 607s # p species groups genes in groups 607s 0% 0 32 (100%) 111 (100%) 607s 20% 1 32 (100%) 111 (100%) 607s 40% 2 32 (100%) 111 (100%) 607s 60% 3 17 (53.12%) 75 (67.56%) 607s 80% 4 11 (34.37%) 52 (46.84%) 607s 100% 5 1 (3.12%) 5 (4.5%) 607s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 607s # number of groups for each input species: 607s L.faa 32 100% 607s M.faa 32 100% 607s E.faa 15 46.87% 607s C_clean.faa 13 40.62% 607s C2.faa 1 3.12% 607s 607s [OUTPUT] -> Summary is written to test_diamond.proteinortho-graph.summary 607s 607s [OUTPUT] -> Orthologous groups are written to test_diamond.proteinortho.html 607s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 607s proteinortho2xml.pl test_diamond.proteinortho.tsv >test_diamond.proteinortho.tsv.xml 607s 607s All finished. 607s ***************************************************************** 607s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 607s ***************************************************************** 607s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'diamond' version 2.1.9 607s Checking input files. 607s Checking test/C_clean.faa... ok 607s Checking test/C2.faa... ok 607s Checking test/E.faa... ok 607s Checking test/L.faa... ok 607s Checking test/M.faa... ok 607s 607s **Step 1** 607s Generating indices anyway (forced). 607s Building database for 'test/E.faa' (72 sequences) 607s Generating indices anyway (forced). 607s Building database for 'test/L.faa' (40 sequences) 607s Generating indices anyway (forced). 607s Building database for 'test/M.faa' (40 sequences) 607s Generating indices anyway (forced). 607s Building database for 'test/C2.faa' (2 sequences) 607s Generating indices anyway (forced). 607s Building database for 'test/C_clean.faa' (109 sequences) 607s 607s **Step 2** using diamond 611s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 611s [OUTPUT] -> written to test_diamondmoresensitive.blast-graph 611s 611s **Step 3** 611s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 611s Reading test_diamondmoresensitive.blast-graph 611s 5 species 611s 112 paired proteins 611s 145 bidirectional edges 612s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 612s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.tsv 612s You can extract the fasta files of each orthology group with 612s proteinortho_grab_proteins.pl -tofiles test_diamondmoresensitive.proteinortho.tsv 'test/E.faa' 'test/L.faa' 'test/M.faa' 'test/C2.faa' 'test/C_clean.faa' 612s (Careful: This will generate a file foreach line in the file test_diamondmoresensitive.proteinortho.tsv). 612s [OUTPUT] -> Orthologous pairs are written to test_diamondmoresensitive.proteinortho-graph 612s # test_diamondmoresensitive.proteinortho.tsv statistics: 612s # number of groups that contains at least p% species: 612s # p species groups genes in groups 612s 0% 0 32 (100%) 111 (100%) 612s 20% 1 32 (100%) 111 (100%) 612s 40% 2 32 (100%) 111 (100%) 612s 60% 3 17 (53.12%) 75 (67.56%) 612s 80% 4 11 (34.37%) 52 (46.84%) 612s 100% 5 1 (3.12%) 5 (4.5%) 612s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 612s # number of groups for each input species: 612s L.faa 32 100% 612s M.faa 32 100% 612s E.faa 15 46.87% 612s C_clean.faa 13 40.62% 612s C2.faa 1 3.12% 612s 612s [OUTPUT] -> Summary is written to test_diamondmoresensitive.proteinortho-graph.summary 612s 612s [OUTPUT] -> Orthologous groups are written to test_diamondmoresensitive.proteinortho.html 612s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 612s proteinortho2xml.pl test_diamondmoresensitive.proteinortho.tsv >test_diamondmoresensitive.proteinortho.tsv.xml 612s 612s All finished. 613s ***************************************************************** 613s Proteinortho with PoFF version 6.3.1 - An orthology detection tool 613s ***************************************************************** 613s Detected 2 CPU threads (1 threads per processes each with 2 threads) adjust this with -cpus, Detected 'blastp+' version 2.12.0+ 613s Checking input files. 613s Checking test/C_clean.faa... ok 613s Checking test/C2.faa... ok 613s Checking test/E.faa... ok 613s Checking test/L.faa... ok 613s Checking test/M.faa... ok 613s 613s **Step 1** 613s Generating indices anyway (forced). 613s Building database for 'test/L.faa' (40 sequences) 613s Generating indices anyway (forced). 613s Building database for 'test/E.faa' (72 sequences) 613s Generating indices anyway (forced). 613s Building database for 'test/C2.faa' (2 sequences) 613s Generating indices anyway (forced). 613s Building database for 'test/M.faa' (40 sequences) 613s Generating indices anyway (forced). 613s Building database for 'test/C_clean.faa' (109 sequences) 613s 613s **Step 2** using blastp+ 618s Running blast analysis: 0% (0/10) Running blast analysis: 10% (1/10) Running blast analysis: 20% (2/10) Running blast analysis: 30% (3/10) Running blast analysis: 40% (4/10) Running blast analysis: 50% (5/10) Running blast analysis: 60% (6/10) Running blast analysis: 70% (7/10) Running blast analysis: 80% (8/10) Running blast analysis: 100% (10/10) Running blast analysis: 90% (9/10) Running blast analysis: 100% (10/10) 618s [OUTPUT] -> written to test_blastall.blast-graph 618s 618s **Step 3** 618s Clustering by similarity (Proteinortho mode) using 2 cpu core(s). Please wait... 618s Reading test_blastall.blast-graph 618s 5 species 618s 112 paired proteins 618s 149 bidirectional edges 619s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components 619s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.tsv 619s You can extract the fasta files of each orthology group with 619s proteinortho_grab_proteins.pl -tofiles test_blastall.proteinortho.tsv 'test/L.faa' 'test/E.faa' 'test/C2.faa' 'test/M.faa' 'test/C_clean.faa' 619s (Careful: This will generate a file foreach line in the file test_blastall.proteinortho.tsv). 619s [OUTPUT] -> Orthologous pairs are written to test_blastall.proteinortho-graph 619s # test_blastall.proteinortho.tsv statistics: 619s # number of groups that contains at least p% species: 619s # p species groups genes in groups 619s 0% 0 32 (100%) 112 (100%) 619s 20% 1 32 (100%) 112 (100%) 619s 40% 2 32 (100%) 112 (100%) 619s 60% 3 17 (53.12%) 74 (66.07%) 619s 80% 4 11 (34.37%) 51 (45.53%) 619s 100% 5 1 (3.12%) 5 (4.46%) 619s # NOTE: p=100% correspond to the core proteome and p=0% to all groups 619s # number of groups for each input species: 619s L.faa 32 100% 619s M.faa 32 100% 619s E.faa 15 46.87% 619s C_clean.faa 13 40.62% 619s C2.faa 1 3.12% 619s 619s [OUTPUT] -> Summary is written to test_blastall.proteinortho-graph.summary 619s 619s [OUTPUT] -> Orthologous groups are written to test_blastall.proteinortho.html 619s [OUTPUT] -> You can extract an OrthoXML (v0.3) version of the orthology group output using: 619s proteinortho2xml.pl test_blastall.proteinortho.tsv >test_blastall.proteinortho.tsv.xml 619s 619s All finished. 619s - test max_of_diag() : OK 619s - test generate_random_vector() : OK 619s - test get_new_x() : OK 619s - test makeOrthogonal() : OK 619s - test normalize() : OK 619s - test getY() : OK 619s - test lapack() : OK 619s - test power() : OK 619s - test smirnov-grubb() : OK 619s All test passed. 619s Reading test_blastp.blast-graph 619s 5 species 619s 112 paired proteins 619s 147 bidirectional edges 619s Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack# Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 620s * + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 0@power) connected components Clustering: working on (13@lapack* + 0@power) connected components Clustering: working on (12@lapack* + 0@power) connected components Clustering: working on (11@lapack* + 0@power) connected components Clustering: working on (10@lapack* + 0@power) connected components Clustering: working on (9@lapack* + 0@power) connected components Clustering: working on (8@lapack* + 0@power) connected components Clustering: working on (7@lapack* + 0@power) connected components Clustering: working on (6@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (5@lapack* + 0@power) connected components Clustering: working on (4@lapack* + 0@power) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 0@power) connected components Reading 5 5 1 C_10 C_10;test E_10 L_10 M_10 620s 4 4 1 * C_11 E_11 L_11 M_11 620s 4 6 0.149 * C_12,C_21 E_313,E_315 L_313 M_313 620s 4 4 1 * C_14 E_14 L_14 M_14 620s 4 4 1 * C_15 E_15 L_15 M_15 620s 4 4 1 * C_16 E_16 L_16 M_16 620s 4 4 1 * C_17 E_17 L_17 M_17 620s 4 4 1 * C_64 E_18 L_18 M_18 620s 4 5 0.2 * C_63,C_22 E_19 L_19 M_19 620s 3 3 1 * C_20 * L_20 M_20 620s 3 6 0.333 * C_2,C_164,C_166,C_167 * L_2 M_2 620s 2 2 1 * * * L_619 M_619 620s 3 3 0.33 * * E_367 L_319 M_319 620s 2 2 1 * * * L_617 M_617 620s 2 5 0.166 * * * L_641,L_643 M_642,M_640,M_649 620s 2 4 0.5 * * * L_645,L_647 M_644,M_646 620s 3 3 0.33 * * E_432 L_328 M_328 620s 2 2 1 * * * L_333 M_333 620s 2 2 1 * * * L_3 M_3 620s 2 2 1 * * * L_4 M_4 620s 2 2 1 * * * L_5 M_5 620s 2 2 1 * * * L_6 M_6 620s 2 2 1 * * * L_8 M_8 620s 2 2 1 * * * L_9 M_9 620s 2 2 1 * * * L_623 M_623 620s 4 4 1 * C_13 E_13 L_621 M_621 620s 2 4 0.146 * * * L_637,L_639 M_636,M_638 620s 3 3 0.33 * * E_437 L_317 M_317 620s 2 2 1 * * * L_331 M_331 620s 3 5 0.2 * * E_317 L_635 M_336,M_323,M_634 620s 2 3 0.33 * * * L_631,L_633 M_632 620s 4 7 0.119 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 620s test_blastp.blast-graph 620s 5 species 620s 112 paired proteins 620s 147 bidirectional edges 620s Clustering: working on (2@lapack* + 0@power) connected components # Species Genes Alg.-Conn. C2.faa C_clean.faa E.faa L.faa M.faa 621s Clustering: working on (27@lapack* + 0@power) connected components Clustering: working on (26@lapack* + 0@power) connected components Clustering: working on (25@lapack* + 0@power) connected components Clustering: working on (24@lapack* + 0@power) connected components Clustering: working on (23@lapack* + 0@power) connected components Clustering: working on (22@lapack* + 0@power) connected components Clustering: working on (21@lapack* + 0@power) connected components Clustering: working on (20@lapack* + 0@power) connected components Clustering: working on (19@lapack* + 0@power) connected components Clustering: working on (18@lapack* + 0@power) connected components Clustering: working on (17@lapack* + 0@power) connected components Clustering: working on (16@lapack* + 0@power) connected components Clustering: working on (15@lapack* + 0@power) connected components Clustering: working on (14@lapack* + 1@power) connected components Clustering: working on (13@lapack* + 2@power) connected components Clustering: working on (12@lapack* + 3@power) connected components Clustering: working on (11@lapack* + 4@power) connected components Clustering: working on (10@lapack* + 5@power) connected components Clustering: working on (9@lapack* + 6@power) connected components Clustering: working on (8@lapack* + 7@power) connected components Clustering: working on (7@lapack* + 8@power) connected components Clustering: working on (6@lapack* + 9@power) connected components Clustering: working on (5@lapack* + 10@power) connected components Clustering: working on (4@lapack* + 11@power) connected components Clustering: working on (3@lapack* + 12@power) connected components Clustering: working on (2@lapack* + 13@power) connected components Clustering: working on (0@lapack + 15@power*) connected components Clustering: working on (0@lapack + 14@power*) connected components Clustering: working on (0@lapack + 13@power*) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (3@lapack* + 10@power) connected components Clustering: working on (2@lapack* + 10@power) connected components Clustering: working on (0@lapack + 12@power*) connected components Clustering: working on (0@lapack + 11@power*) connected components Clustering: working on (0@lapack + 10@power*) connected components Clustering: working on (0@lapack + 9@power*) connected components Clustering: working on (0@lapack + 8@power*) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (4@lapack* + 4@power) connected components Clustering: working on (3@lapack* + 4@power) connected components Clustering: working on (2@lapack* + 5@power) connected components Clustering: working on (0@lapack + 7@power*) connected components Clustering: working on (0@lapack + 6@power*) connected components Clustering: working on (0@lapack + 5@power*) connected components Clustering: working on (0@lapack + 4@power*) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components Clustering: working on (3@lapack* + 0@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (3@lapack* + 1@power) connected components Clustering: working on (2@lapack* + 1@power) connected components Clustering: working on (0@lapack + 3@power*) connected components Clustering: working on (0@lapack + 2@power*) connected components 3 3 1 * C_20 * L_20 M_20 621s 2 2 1 * * * L_619 M_619 621s 3 3 0.33 * * E_367 L_319 M_319 621s 2 2 1 * * * L_617 M_617 621s 3 3 0.33 * * E_432 L_328 M_328 621s 2 2 1 * * * L_333 M_333 621s 2 2 1 * * * L_3 M_3 621s 2 2 1 * * * L_4 M_4 621s 2 2 1 * * * L_5 M_5 621s 2 2 1 * * * L_6 M_6 621s 2 2 1 * * * L_8 M_8 621s 2 2 1 * * * L_9 M_9 621s 5 5 0.687 C_10 C_10;test E_10 L_10 M_10 621s 4 4 0.727 * C_11 E_11 L_11 M_11 621s 4 6 0.137 * C_12,C_21 E_313,E_315 L_313 M_313 621s 2 2 1 * * * L_623 M_623 621s 4 4 0.74 * C_14 E_14 L_14 M_14 621s 4 4 0.814 * C_15 E_15 L_15 M_15 621s 4 4 0.815 * C_16 E_16 L_16 M_16 621s 4 4 0.824 * C_17 E_17 L_17 M_17 621s 4 4 0.779 * C_64 E_18 L_18 M_18 621s 4 5 0.178 * C_63,C_22 E_19 L_19 M_19 621s 3 3 0.33 * * E_437 L_317 M_317 621s 3 6 0.314 * C_2,C_164,C_166,C_167 * L_2 M_2 621s 2 5 0.16 * * * L_641,L_643 M_642,M_640,M_649 621s 2 4 0.478 * * * L_645,L_647 M_644,M_646 621s 4 4 0.717 * C_13 E_13 L_621 M_621 621s 2 4 0.145 * * * L_637,L_639 M_636,M_638 621s 2 3 0.33 * * * L_631,L_633 M_632 621s 2 2 1 * * * L_331 M_331 621s 4 7 0.108 * C_1 E_368,E_366 L_323,L_627,L_336 M_627 621s 3 5 0.181 * * E_317 L_635 M_336,M_323,M_634 621s Test okay 621s autopkgtest [04:43:16]: test run-unit-test: -----------------------] 621s autopkgtest [04:43:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 621s run-unit-test PASS 622s autopkgtest [04:43:17]: @@@@@@@@@@@@@@@@@@@@ summary 622s run-unit-test PASS 645s Creating nova instance adt-noble-amd64-proteinortho-20240312-043255-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240311.img (UUID c2a5d9e5-5339-4ecf-b21e-575e87191962)...