0s autopkgtest [05:06:27]: starting date: 2024-03-13 0s autopkgtest [05:06:27]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [05:06:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7tipjbvp/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 bali-phy --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@bos02-s390x-9.secgroup --name adt-noble-s390x-bali-phy-20240313-050627-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 104s autopkgtest [05:08:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2750 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [447 kB] 105s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [40.4 kB] 105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [586 kB] 105s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 105s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 105s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 105s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3019 kB] 105s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 105s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [24.8 kB] 105s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 107s Fetched 7000 kB in 2s (3437 kB/s) 107s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Calculating upgrade... 112s The following packages were automatically installed and are no longer required: 112s fuse3 libfuse3-3 libgdbm-compat4t64 libperl5.38 lto-disabled-list make 112s perl-modules-5.38 s390-tools-data s390-tools-signed 112s Use 'sudo apt autoremove' to remove them. 112s The following packages will be REMOVED: 112s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl s390-tools 112s sysconfig-hardware 112s The following NEW packages will be installed: 112s libgdbm-compat4t64 libgdbm6t64 112s The following packages have been kept back: 112s libperl5.38 112s The following packages will be upgraded: 112s cloud-init gdisk perl-base perl-modules-5.38 113s 4 upgraded, 2 newly installed, 7 to remove and 1 not upgraded. 113s Need to get 5973 kB of archives. 113s After this operation, 15.6 MB disk space will be freed. 113s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-base s390x 5.38.2-3.2 [1961 kB] 113s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm6t64 s390x 1.23-5.1 [36.4 kB] 113s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm-compat4t64 s390x 1.23-5.1 [6880 B] 113s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 113s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.1-0ubuntu1 [597 kB] 113s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x gdisk s390x 1.0.10-1 [262 kB] 114s Preconfiguring packages ... 114s Fetched 5973 kB in 1s (6784 kB/s) 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52188 files and directories currently installed.) 114s Removing dpkg-dev (1.22.4ubuntu5) ... 114s Removing libdpkg-perl (1.22.4ubuntu5) ... 114s Removing sysconfig-hardware (0.0.14ubuntu2) ... 114s Removing s390-tools (2.31.0-0ubuntu1) ... 114s Removing perl (5.38.2-3) ... 114s (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 ... 51349 files and directories currently installed.) 114s Preparing to unpack .../perl-base_5.38.2-3.2_s390x.deb ... 114s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 114s Setting up perl-base (5.38.2-3.2) ... 114s dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: 114s python3-gdbm:s390x depends on libgdbm6 (>= 1.16). 114s man-db depends on libgdbm6 (>= 1.16). 114s libperl5.38:s390x depends on libgdbm6 (>= 1.21). 114s libgdbm-compat4:s390x depends on libgdbm6 (>= 1.16). 114s 114s (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 ... 51349 files and directories currently installed.) 114s Removing libgdbm6:s390x (1.23-5) ... 114s Selecting previously unselected package libgdbm6t64:s390x. 115s (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 ... 51344 files and directories currently installed.) 115s Preparing to unpack .../libgdbm6t64_1.23-5.1_s390x.deb ... 115s Unpacking libgdbm6t64:s390x (1.23-5.1) ... 115s dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested: 115s libperl5.38:s390x depends on libgdbm-compat4 (>= 1.18-3). 115s 115s (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 ... 51350 files and directories currently installed.) 115s Removing libgdbm-compat4:s390x (1.23-5) ... 115s Selecting previously unselected package libgdbm-compat4t64:s390x. 115s (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 ... 51345 files and directories currently installed.) 115s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_s390x.deb ... 115s Unpacking libgdbm-compat4t64:s390x (1.23-5.1) ... 115s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 115s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 115s Preparing to unpack .../cloud-init_24.1.1-0ubuntu1_all.deb ... 115s Unpacking cloud-init (24.1.1-0ubuntu1) over (24.1-0ubuntu1) ... 115s Preparing to unpack .../gdisk_1.0.10-1_s390x.deb ... 115s Unpacking gdisk (1.0.10-1) over (1.0.9-2.1) ... 115s Setting up cloud-init (24.1.1-0ubuntu1) ... 116s Setting up libgdbm6t64:s390x (1.23-5.1) ... 116s Setting up libgdbm-compat4t64:s390x (1.23-5.1) ... 116s Setting up gdisk (1.0.10-1) ... 116s Setting up perl-modules-5.38 (5.38.2-3.2) ... 116s Processing triggers for libc-bin (2.39-0ubuntu2) ... 116s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 117s Processing triggers for man-db (2.12.0-3) ... 117s Processing triggers for initramfs-tools (0.142ubuntu20) ... 117s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 117s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 121s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 121s 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 121s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 121s 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 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s The following packages will be REMOVED: 121s fuse3* libfuse3-3* libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* 121s perl-modules-5.38* s390-tools-data* s390-tools-signed* 121s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 121s After this operation, 50.6 MB disk space will be freed. 121s (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 ... 51351 files and directories currently installed.) 121s Removing fuse3 (3.14.0-5) ... 121s update-initramfs: deferring update (trigger activated) 121s Removing libfuse3-3:s390x (3.14.0-5) ... 121s Removing libperl5.38:s390x (5.38.2-3) ... 121s Removing libgdbm-compat4t64:s390x (1.23-5.1) ... 121s Removing lto-disabled-list (47) ... 121s Removing make (4.3-4.1build1) ... 121s Removing perl-modules-5.38 (5.38.2-3.2) ... 121s Removing s390-tools-data (2.31.0-0ubuntu1) ... 121s Removing s390-tools-signed (2.31.0-0ubuntu1) ... 121s Processing triggers for libc-bin (2.39-0ubuntu2) ... 121s Processing triggers for man-db (2.12.0-3) ... 122s Processing triggers for initramfs-tools (0.142ubuntu20) ... 122s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 122s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 125s (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 ... 49354 files and directories currently installed.) 125s Purging configuration files for fuse3 (3.14.0-5) ... 125s Unknown architecture, assuming PC-style ttyS0 125s sh: Attempting to set up Debian/Ubuntu apt sources automatically 125s sh: Distribution appears to be Ubuntu 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s eatmydata is already the newest version (131-1). 126s dbus is already the newest version (1.14.10-4ubuntu1). 126s dbus set to manually installed. 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s rng-tools-debian is already the newest version (2.4). 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s haveged is already the newest version (1.9.14-1ubuntu1). 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s The following additional packages will be installed: 127s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 127s make perl perl-modules-5.38 127s Suggested packages: 127s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 127s libterm-readline-gnu-perl | libterm-readline-perl-perl 127s libtap-harness-archive-perl 127s Recommended packages: 127s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 127s libfile-fcntllock-perl 127s The following packages will be REMOVED: 127s libdb5.3 127s The following NEW packages will be installed: 127s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 127s lto-disabled-list make perl perl-modules-5.38 127s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 127s Need to get 7542 kB/10.7 MB of archives. 127s After this operation, 54.4 MB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-5build1 [763 kB] 128s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libperl5.38t64 s390x 5.38.2-3.2 [5007 kB] 128s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl s390x 5.38.2-3.2 [231 kB] 128s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libdpkg-perl all 1.22.4ubuntu5 [268 kB] 128s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x make s390x 4.3-4.1build1 [182 kB] 128s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] 128s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x dpkg-dev all 1.22.4ubuntu5 [1078 kB] 128s Fetched 7542 kB in 1s (7815 kB/s) 128s dpkg: libdb5.3:s390x: dependency problems, but removing anyway as you requested: 128s libsasl2-modules-db:s390x depends on libdb5.3. 128s libpython3.12-stdlib:s390x depends on libdb5.3. 128s libpython3.11-stdlib:s390x depends on libdb5.3. 128s libpam-modules:s390x depends on libdb5.3. 128s iproute2 depends on libdb5.3. 128s apt-utils depends on libdb5.3. 128s 128s (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 ... 49353 files and directories currently installed.) 128s Removing libdb5.3:s390x (5.3.28+dfsg2-4) ... 128s Selecting previously unselected package libdb5.3t64:s390x. 129s (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 ... 49347 files and directories currently installed.) 129s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_s390x.deb ... 129s Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-5build1) ... 129s Setting up libdb5.3t64:s390x (5.3.28+dfsg2-5build1) ... 129s Selecting previously unselected package perl-modules-5.38. 129s (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 ... 49353 files and directories currently installed.) 129s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 129s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 129s Selecting previously unselected package libgdbm-compat4t64:s390x. 129s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_s390x.deb ... 129s Unpacking libgdbm-compat4t64:s390x (1.23-5.1) ... 129s Selecting previously unselected package libperl5.38t64:s390x. 129s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_s390x.deb ... 129s Unpacking libperl5.38t64:s390x (5.38.2-3.2) ... 129s Selecting previously unselected package perl. 129s Preparing to unpack .../3-perl_5.38.2-3.2_s390x.deb ... 129s Unpacking perl (5.38.2-3.2) ... 129s Selecting previously unselected package libdpkg-perl. 129s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 129s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 129s Selecting previously unselected package make. 129s Preparing to unpack .../5-make_4.3-4.1build1_s390x.deb ... 129s Unpacking make (4.3-4.1build1) ... 129s Selecting previously unselected package lto-disabled-list. 129s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 129s Unpacking lto-disabled-list (47) ... 129s Selecting previously unselected package dpkg-dev. 129s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 129s Unpacking dpkg-dev (1.22.4ubuntu5) ... 129s Setting up lto-disabled-list (47) ... 129s Setting up libgdbm-compat4t64:s390x (1.23-5.1) ... 129s Setting up make (4.3-4.1build1) ... 129s Setting up perl-modules-5.38 (5.38.2-3.2) ... 129s Setting up libperl5.38t64:s390x (5.38.2-3.2) ... 129s Setting up perl (5.38.2-3.2) ... 129s Setting up libdpkg-perl (1.22.4ubuntu5) ... 129s Setting up dpkg-dev (1.22.4ubuntu5) ... 129s Processing triggers for man-db (2.12.0-3) ... 130s Processing triggers for libc-bin (2.39-0ubuntu2) ... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s The following packages will be REMOVED: 133s cloud-init* python3-configobj* python3-debconf* 134s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 134s After this operation, 3252 kB disk space will be freed. 134s (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 ... 51898 files and directories currently installed.) 134s Removing cloud-init (24.1.1-0ubuntu1) ... 134s Removing python3-configobj (5.0.8-3) ... 134s Removing python3-debconf (1.5.86) ... 134s Processing triggers for man-db (2.12.0-3) ... 134s (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 ... 51509 files and directories currently installed.) 134s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 135s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 135s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s linux-generic is already the newest version (6.8.0-11.11+1). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 136s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 137s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 137s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 137s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 140s Reading package lists... 140s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 140s 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 140s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 140s 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 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s autopkgtest [05:08:48]: rebooting testbed after setup commands that affected boot 154s autopkgtest [05:09:01]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 155s autopkgtest [05:09:02]: testbed dpkg architecture: s390x 156s autopkgtest [05:09:03]: @@@@@@@@@@@@@@@@@@@@ apt-source bali-phy 157s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 157s 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 157s W: Target Packages (main/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target CNF (main/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target Packages (universe/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target CNF (universe/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target Packages (restricted/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target CNF (restricted/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target Packages (multiverse/binary-s390x/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 157s W: Target CNF (multiverse/cnf/Commands-s390x) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 157s 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 158s Get:1 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (dsc) [2216 B] 158s Get:2 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (tar) [1124 kB] 158s Get:3 http://ftpmaster.internal/ubuntu noble/universe bali-phy 3.6.1+dfsg-2build1 (diff) [5408 B] 158s gpgv: Signature made Tue Dec 19 15:00:40 2023 UTC 158s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 158s gpgv: Can't check signature: No public key 158s dpkg-source: warning: cannot verify inline signature for ./bali-phy_3.6.1+dfsg-2build1.dsc: no acceptable signature found 158s autopkgtest [05:09:05]: testing package bali-phy version 3.6.1+dfsg-2build1 158s autopkgtest [05:09:05]: build not needed 159s autopkgtest [05:09:06]: test run-unit-test: preparing testbed 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 164s Done 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 165s The following additional packages will be installed: 165s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 165s libboost-chrono1.83.0 libboost-filesystem1.83.0 165s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 165s libfontconfig1 libfreetype6 libpixman-1-0 libxcb-render0 libxcb-shm0 165s libxrender1 165s Suggested packages: 165s figtree seaview 165s Recommended packages: 165s r-base gnuplot 165s The following NEW packages will be installed: 165s bali-phy fontconfig-config fonts-dejavu-core fonts-dejavu-mono 165s libboost-chrono1.83.0 libboost-filesystem1.83.0 165s libboost-program-options1.83.0 libboost-random1.83.0 libcairo2 165s libfontconfig1 libfreetype6 libpixman-1-0 libxcb-render0 libxcb-shm0 165s libxrender1 165s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded. 165s 1 not fully installed or removed. 165s Need to get 9090 kB of archives. 165s After this operation, 37.1 MB of additional disk space will be used. 165s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libboost-chrono1.83.0 s390x 1.83.0-2ubuntu1 [323 kB] 165s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libboost-filesystem1.83.0 s390x 1.83.0-2ubuntu1 [372 kB] 165s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libboost-program-options1.83.0 s390x 1.83.0-2ubuntu1 [418 kB] 165s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libboost-random1.83.0 s390x 1.83.0-2ubuntu1 [320 kB] 165s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 165s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 165s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 165s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 165s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 165s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 165s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 165s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 165s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 165s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 165s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x bali-phy s390x 3.6.1+dfsg-2build1 [4908 kB] 166s Fetched 9090 kB in 1s (9587 kB/s) 166s Selecting previously unselected package libboost-chrono1.83.0:s390x. 166s (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 ... 51454 files and directories currently installed.) 166s Preparing to unpack .../00-libboost-chrono1.83.0_1.83.0-2ubuntu1_s390x.deb ... 166s Unpacking libboost-chrono1.83.0:s390x (1.83.0-2ubuntu1) ... 166s Selecting previously unselected package libboost-filesystem1.83.0:s390x. 166s Preparing to unpack .../01-libboost-filesystem1.83.0_1.83.0-2ubuntu1_s390x.deb ... 166s Unpacking libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 166s Selecting previously unselected package libboost-program-options1.83.0:s390x. 166s Preparing to unpack .../02-libboost-program-options1.83.0_1.83.0-2ubuntu1_s390x.deb ... 166s Unpacking libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 166s Selecting previously unselected package libboost-random1.83.0:s390x. 166s Preparing to unpack .../03-libboost-random1.83.0_1.83.0-2ubuntu1_s390x.deb ... 166s Unpacking libboost-random1.83.0:s390x (1.83.0-2ubuntu1) ... 166s Selecting previously unselected package libfreetype6:s390x. 166s Preparing to unpack .../04-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 166s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 166s Selecting previously unselected package fonts-dejavu-mono. 166s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 166s Unpacking fonts-dejavu-mono (2.37-8) ... 166s Selecting previously unselected package fonts-dejavu-core. 166s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 166s Unpacking fonts-dejavu-core (2.37-8) ... 166s Selecting previously unselected package fontconfig-config. 166s Preparing to unpack .../07-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 166s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 166s Selecting previously unselected package libfontconfig1:s390x. 166s Preparing to unpack .../08-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 166s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 166s Selecting previously unselected package libpixman-1-0:s390x. 166s Preparing to unpack .../09-libpixman-1-0_0.42.2-1_s390x.deb ... 166s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 166s Selecting previously unselected package libxcb-render0:s390x. 166s Preparing to unpack .../10-libxcb-render0_1.15-1_s390x.deb ... 166s Unpacking libxcb-render0:s390x (1.15-1) ... 166s Selecting previously unselected package libxcb-shm0:s390x. 166s Preparing to unpack .../11-libxcb-shm0_1.15-1_s390x.deb ... 166s Unpacking libxcb-shm0:s390x (1.15-1) ... 166s Selecting previously unselected package libxrender1:s390x. 166s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 166s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 166s Selecting previously unselected package libcairo2:s390x. 166s Preparing to unpack .../13-libcairo2_1.18.0-1_s390x.deb ... 166s Unpacking libcairo2:s390x (1.18.0-1) ... 166s Selecting previously unselected package bali-phy. 166s Preparing to unpack .../14-bali-phy_3.6.1+dfsg-2build1_s390x.deb ... 166s Unpacking bali-phy (3.6.1+dfsg-2build1) ... 167s Setting up libboost-program-options1.83.0:s390x (1.83.0-2ubuntu1) ... 167s Setting up libpixman-1-0:s390x (0.42.2-1) ... 167s Setting up libxrender1:s390x (1:0.9.10-1.1) ... 167s Setting up libxcb-render0:s390x (1.15-1) ... 167s Setting up libboost-random1.83.0:s390x (1.83.0-2ubuntu1) ... 167s Setting up libxcb-shm0:s390x (1.15-1) ... 167s Setting up libboost-filesystem1.83.0:s390x (1.83.0-2ubuntu1) ... 167s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 167s Setting up fonts-dejavu-mono (2.37-8) ... 167s Setting up fonts-dejavu-core (2.37-8) ... 167s Setting up libboost-chrono1.83.0:s390x (1.83.0-2ubuntu1) ... 167s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 167s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ... 167s Setting up libcairo2:s390x (1.18.0-1) ... 167s Setting up bali-phy (3.6.1+dfsg-2build1) ... 167s Setting up autopkgtest-satdep (0) ... 167s Processing triggers for man-db (2.12.0-3) ... 167s Processing triggers for libc-bin (2.39-0ubuntu2) ... 169s (Reading database ... 52185 files and directories currently installed.) 169s Removing autopkgtest-satdep (0) ... 170s autopkgtest [05:09:17]: test run-unit-test: [----------------------- 170s VERSION: 3.6.1 [3.6.1] 170s BUILD: Dec 19 2023 14:51:09 170s ARCH: linux s390x 170s COMPILER: gcc 13.2.0 s390x 171s Bayesian Inference of Alignment and Phylogeny 171s Usage: bali-phy [ ...] [OPTIONS] 171s Basic options: 171s 171s General options: 171s -h [ --help ] [=arg(=basic)] Print usage information. 171s -v [ --version ] Print version information. 171s -t [ --test ] Analyze the initial values and exit. 171s -c [ --config ] arg Command file to read. 171s 171s MCMC options: 171s -i [ --iterations ] arg The number of iterations to run. 171s -n [ --name ] arg Name for the output directory to create. 171s 171s Parameter options: 171s --align arg Sequence file & initial alignment. 171s -T [ --tree ] arg File with initial tree 171s 171s Model options: 171s -A [ --alphabet ] arg The alphabet. 171s -S [ --smodel ] arg Substitution model. 171s -I [ --imodel ] arg Insertion-deletion model. 171s -R [ --scale ] arg Prior on the scale. 171s -L [ --link ] arg Link partitions. 171s 171s Showing basic command line options. Not all options are shown! 171s * See `bali-phy help advanced` to see more options. 171s 171s See `bali-phy help option` for help on option. For example, 171s * `bali-phy help alphabet` shows help on the --alphabet command. 171s * `bali-phy help normal` shows help on the normal distribution. 171s * `bali-phy help tn93` shows help on the TN93 model. 171s * `bali-phy help log` shows help on the log function. 171s 171s To see help on one of the following topics, run `bali-phy help topic` 171s 171s alphabets/ commands/ distributions/ functions/ models/ 171s parameters/ 171s 173s T:topology ~ uniform on tree topologies 173s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 173s 173s Partition P1: 173s file = sequences/5S-rRNA/5d.fasta 173s alphabet = DNA 173s subst = tn93 (S1) 173s indel = rs07 (I1) 173s scale ~ gamma[0.5,2] (Scale1) 173s 173s Substitution model S1 priors: 173s tn93:kappaPur ~ log_normal[log[2],0.25] 173s tn93:kappaPyr ~ log_normal[log[2],0.25] 173s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 173s 173s Insertion/deletion model I1 priors: 173s rs07:log_rate ~ laplace[-4,0.707] 173s rs07:mean_length ~ shifted_exponential[10,1] 173s 173s iter = 0 prior = -33.790694740510119 likelihood = -1483.234816657316969 posterior = -1517.025511397827131 prior_A = -37.769371881270153 |A| = 126 #indels = 4 |indels| = 12 #substs = 260 P1/likelihood = -1483.234816657316969 P1/prior_A = -37.769371881270153 P1/|A| = 126 P1/#indels = 4 P1/|indels| = 12 P1/#substs = 260 Scale[1]*|T| = 0.312887353008491 |T| = 0.480024947609822 rs07:log_rate = -4.360922545264546 rs07:mean_length = 4.97131803540848 tn93:kappaPur = 2.674531993935546 tn93:kappaPyr = 1.9206197631901862 tn93:pi[A] = 0.3300618075544738 tn93:pi[C] = 0.1097957500009612 tn93:pi[G] = 0.32253993433256817 tn93:pi[T] = 0.23760250811199682 scale[1] = 0.6518147745579553 scale1 = 0.6518147745579553 173s Created directory '5d-1/' for output files. 175s T:topology ~ uniform on tree topologies 175s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 175s 175s Partition P1: 175s file = sequences/5S-rRNA/5d.fasta 175s alphabet = DNA 175s subst = tn93 (S1) 175s indel = rs07 (I1) 175s scale ~ gamma[0.5,2] (Scale1) 175s 175s Substitution model S1 priors: 175s tn93:kappaPur ~ log_normal[log[2],0.25] 175s tn93:kappaPyr ~ log_normal[log[2],0.25] 175s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 175s 175s Insertion/deletion model I1 priors: 175s rs07:log_rate ~ laplace[-4,0.707] 175s rs07:mean_length ~ shifted_exponential[10,1] 175s 175s Beginning pre-burnin: 3 iterations. 175s Start #1 prior = -33.7907 likelihood = -1483.23 |T| = 0.480025 Scale1*|T| = 0.312887 175s 175s Tree (S)ize #1 prior = -15.3853 likelihood = -918.651 |T| = 0.351153 Scale1*|T| = 13.4823 175s Tree (S)ize #2 prior = -8.67375 likelihood = -921.505 |T| = 0.557146 Scale1*|T| = 11.6476 175s Tree (S)ize #3 prior = -10.9776 likelihood = -916.148 |T| = 1.76036 Scale1*|T| = 17.2445 175s 175s (S)+Branch (L)engths #1 prior = -16.2584 likelihood = -913.26 |T| = 2.47609 Scale1*|T| = 13.0113 175s (S)+Branch (L)engths #2 prior = -16.8078 likelihood = -894.729 |T| = 3.04489 Scale1*|T| = 6.59351 175s (S)+Branch (L)engths #3 prior = -13.1975 likelihood = -886.107 |T| = 2.05444 Scale1*|T| = 5.6581 175s 175s (S)+(L)+(P)arameters #1 prior = -18.8487 likelihood = -843.212 |T| = 1.94953 Scale1*|T| = 5.31078 175s (S)+(L)+(P)arameters #2 prior = -13.6692 likelihood = -799.58 |T| = 1.45035 Scale1*|T| = 5.99899 175s (S)+(L)+(P)arameters #3 prior = -16.2199 likelihood = -794.492 |T| = 1.25891 Scale1*|T| = 6.13717 175s 175s (S)+(L)+(P)+NNI #1 prior = -14.3438 likelihood = -794.463 |T| = 0.950972 Scale1*|T| = 8.25425 175s (S)+(L)+(P)+NNI #2 prior = -13.0194 likelihood = -796.879 |T| = 0.922848 Scale1*|T| = 5.82845 175s (S)+(L)+(P)+NNI #3 prior = -20.7114 likelihood = -793.84 |T| = 2.12375 Scale1*|T| = 5.74906 175s (S)+(L)+(P)+NNI #4 prior = -17.9262 likelihood = -792.257 |T| = 1.86364 Scale1*|T| = 6.4008 175s 175s SPR #1 prior = -17.1706 likelihood = -791.452 |T| = 2.03026 Scale1*|T| = 7.65838 175s 175s (S)+(L)+(P)+NNI #1 prior = -19.9971 likelihood = -792.17 |T| = 2.12702 Scale1*|T| = 8.17853 175s (S)+(L)+(P)+NNI #2 prior = -12.6645 likelihood = -794.309 |T| = 1.28717 Scale1*|T| = 7.80855 175s (S)+(L)+(P)+NNI #3 prior = -14.7901 likelihood = -792.908 |T| = 1.42784 Scale1*|T| = 10.0019 175s 175s Finished pre-burnin in 0.06 seconds. 175s 175s 175s BAli-Phy does NOT detect how many iterations is sufficient: 175s You need to monitor convergence and kill it when done. 175s Maximum number of iterations set to 50. 175s 175s Beginning MCMC computations. 175s - Future screen output sent to '5d-1/C1.out' 175s - Future debugging output sent to '5d-1/C1.err' 175s - Sampled trees logged to '5d-1/C1.trees' 175s - Sampled alignments logged to '5d-1/C1.P.fastas' 175s - Run info written to '5d-1/C1.run.json' 175s - Sampled numerical parameters logged to '5d-1/C1.log' as TSV 175s 175s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 175s See the manual at http://www.bali-phy.org/README.xhtml for further information. 180s Created directory '5d-2/' for output files. 182s Partition #1: 126 columns -> 110 unique patterns. 182s T:topology ~ uniform on tree topologies 182s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 182s 182s Partition P1: 182s file = sequences/5S-rRNA/5d.fasta 182s alphabet = DNA 182s subst = tn93 (S1) 182s indel = none 182s scale ~ gamma[0.5,2] (Scale1) 182s 182s Substitution model S1 priors: 182s tn93:kappaPur ~ log_normal[log[2],0.25] 182s tn93:kappaPyr ~ log_normal[log[2],0.25] 182s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 182s 182s Beginning pre-burnin: 3 iterations. 182s Start #1 prior = 3.66627 likelihood = -1521.58 |T| = 0.596738 Scale1*|T| = 0.388962 182s 182s Tree (S)ize #1 prior = -20.0519 likelihood = -925.895 |T| = 0.882719 Scale1*|T| = 34.6447 182s Tree (S)ize #2 prior = -24.3393 likelihood = -921.384 |T| = 0.882719 Scale1*|T| = 42.0429 182s Tree (S)ize #3 prior = -24.233 likelihood = -921.47 |T| = 0.882719 Scale1*|T| = 41.8591 182s 182s (S)+Branch (L)engths #1 prior = -21.242 likelihood = -918.932 |T| = 2.6265 Scale1*|T| = 54.994 182s (S)+Branch (L)engths #2 prior = -20.0058 likelihood = -915.641 |T| = 2.85599 Scale1*|T| = 52.1019 182s (S)+Branch (L)engths #3 prior = -18.7336 likelihood = -915.654 |T| = 3.4078 Scale1*|T| = 36.1988 182s 182s (S)+(L)+(P)arameters #1 prior = -14.0743 likelihood = -838.854 |T| = 2.16918 Scale1*|T| = 17.0259 182s (S)+(L)+(P)arameters #2 prior = -8.3735 likelihood = -827.845 |T| = 1.26424 Scale1*|T| = 9.98903 182s (S)+(L)+(P)arameters #3 prior = -9.91045 likelihood = -825.447 |T| = 1.00143 Scale1*|T| = 10.5296 182s 182s (S)+(L)+(P)+NNI #1 prior = -15.3467 likelihood = -816.19 |T| = 2.26734 Scale1*|T| = 8.40198 182s (S)+(L)+(P)+NNI #2 prior = -8.19633 likelihood = -792.187 |T| = 1.91628 Scale1*|T| = 6.5609 182s (S)+(L)+(P)+NNI #3 prior = -10.4653 likelihood = -794.019 |T| = 2.00651 Scale1*|T| = 7.691 182s (S)+(L)+(P)+NNI #4 prior = -10.5093 likelihood = -794.981 |T| = 1.83101 Scale1*|T| = 8.14948 182s 182s SPR #1 prior = -9.71503 likelihood = -794.17 |T| = 2.01453 Scale1*|T| = 9.01076 182s 182s (S)+(L)+(P)+NNI #1 prior = -7.67389 likelihood = -790.993 |T| = 0.925182 Scale1*|T| = 6.89699 182s (S)+(L)+(P)+NNI #2 prior = -7.38032 likelihood = -793.615 |T| = 1.83607 Scale1*|T| = 6.24615 182s (S)+(L)+(P)+NNI #3 prior = -6.06074 likelihood = -791.981 |T| = 1.24881 Scale1*|T| = 7.05904 182s 182s Finished pre-burnin in 0.08 seconds. 182s 182s 182s BAli-Phy does NOT detect how many iterations is sufficient: 182s You need to monitor convergence and kill it when done. 182s Maximum number of iterations set to 200. 182s 182s Beginning MCMC computations. 182s - Future screen output sent to '5d-2/C1.out' 182s - Future debugging output sent to '5d-2/C1.err' 182s - Sampled trees logged to '5d-2/C1.trees' 182s - Sampled alignments logged to '5d-2/C1.P.fastas' 182s - Run info written to '5d-2/C1.run.json' 182s - Sampled numerical parameters logged to '5d-2/C1.log' as TSV 182s 182s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 182s See the manual at http://www.bali-phy.org/README.xhtml for further information. 184s Created directory '5d-3/' for output files. 186s T:topology ~ uniform on tree topologies 186s T:lengths ~ iid[num_branches[tree],gamma[0.5,div[2,num_branches[tree]]]] 186s 186s Partition P1: 186s file = sequences/5S-rRNA/5d.fasta 186s alphabet = DNA 186s subst = tn93 (S1) 186s indel = rs07 (I1) 186s scale ~ gamma[0.5,2] (Scale1) 186s 186s Substitution model S1 priors: 186s tn93:kappaPur ~ log_normal[log[2],0.25] 186s tn93:kappaPyr ~ log_normal[log[2],0.25] 186s tn93:pi ~ symmetric_dirichlet_on[letters[@a],1] 186s 186s Insertion/deletion model I1 priors: 186s rs07:log_rate ~ laplace[-4,0.707] 186s rs07:mean_length ~ shifted_exponential[10,1] 186s 186s Beginning pre-burnin: 3 iterations. 186s Start #1 prior = -75.3114 likelihood = -1347.23 |T| = 1.17007 Scale1*|T| = 2.77041 186s 186s Tree (S)ize #1 prior = -12.7852 likelihood = -1307.55 |T| = 1.17007 Scale1*|T| = 15.9044 186s Tree (S)ize #2 prior = -18.5966 likelihood = -1296.53 |T| = 1.4687 Scale1*|T| = 30.9812 186s Tree (S)ize #3 prior = -20.4291 likelihood = -1296.71 |T| = 2.97597 Scale1*|T| = 29.7912 186s 186s (S)+Branch (L)engths #1 prior = -14.3954 likelihood = -1295.93 |T| = 1.61309 Scale1*|T| = 18.3665 186s (S)+Branch (L)engths #2 prior = -10.1743 likelihood = -1261.98 |T| = 1.33605 Scale1*|T| = 8.17134 186s (S)+Branch (L)engths #3 prior = -11.7056 likelihood = -1258.01 |T| = 1.72992 Scale1*|T| = 5.73725 186s 186s (S)+(L)+(P)arameters #1 prior = -15.1593 likelihood = -828.807 |T| = 1.2133 Scale1*|T| = 4.43117 186s (S)+(L)+(P)arameters #2 prior = -26.2805 likelihood = -809.516 |T| = 2.36716 Scale1*|T| = 8.55976 186s (S)+(L)+(P)arameters #3 prior = -20.5287 likelihood = -795.007 |T| = 1.46928 Scale1*|T| = 5.41055 186s 186s (S)+(L)+(P)+NNI #1 prior = -20.1829 likelihood = -795.402 |T| = 1.63417 Scale1*|T| = 4.59961 186s (S)+(L)+(P)+NNI #2 prior = -20.6205 likelihood = -794.28 |T| = 1.51091 Scale1*|T| = 6.16628 186s (S)+(L)+(P)+NNI #3 prior = -21.9284 likelihood = -791.333 |T| = 1.60156 Scale1*|T| = 7.55299 186s (S)+(L)+(P)+NNI #4 prior = -21.4072 likelihood = -791.528 |T| = 2.12407 Scale1*|T| = 7.00363 186s 186s SPR #1 prior = -20.5897 likelihood = -789.66 |T| = 1.95372 Scale1*|T| = 6.88146 186s 186s (S)+(L)+(P)+NNI #1 prior = -18.9068 likelihood = -789.904 |T| = 1.48225 Scale1*|T| = 7.55182 186s (S)+(L)+(P)+NNI #2 prior = -20.9352 likelihood = -790.765 |T| = 1.7437 Scale1*|T| = 6.43352 186s (S)+(L)+(P)+NNI #3 prior = -18.2111 likelihood = -792.423 |T| = 1.11375 Scale1*|T| = 7.04299 186s 186s Finished pre-burnin in 0.07 seconds. 186s 186s 186s BAli-Phy does NOT detect how many iterations is sufficient: 186s You need to monitor convergence and kill it when done. 186s Maximum number of iterations set to 100. 186s 186s Beginning MCMC computations. 186s - Future screen output sent to '5d-3/C1.out' 186s - Future debugging output sent to '5d-3/C1.err' 186s - Sampled trees logged to '5d-3/C1.trees' 186s - Sampled alignments logged to '5d-3/C1.P.fastas' 186s - Run info written to '5d-3/C1.run.json' 186s - Sampled numerical parameters logged to '5d-3/C1.log' as TSV 186s 186s You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical). 186s See the manual at http://www.bali-phy.org/README.xhtml for further information. 196s /usr/bin/bp-analyze:452: SyntaxWarning: invalid escape sequence '\s' 196s self.version = self.find_header_attribute("VERSION").split('\s+')[0] 196s /usr/bin/bp-analyze:1118: SyntaxWarning: invalid escape sequence '\s' 196s m = re.search('([^\s]+) ~ ([^\s]+)\s+\((.+),(.+)\)',line) 196s /usr/bin/bp-analyze:1126: SyntaxWarning: invalid escape sequence '\s' 196s m = re.search('t @ (.+)\s+Ne = ([^ ]+)\s+burnin = (Not Converged!|[^ ]+)', lines[i]) 196s /usr/bin/bp-analyze:1135: SyntaxWarning: invalid escape sequence '\s' 196s m = re.search('PSRF-80%CI = ([^ ]+)\s+PSRF-RCF = ([^ ]+)',lines[i]) 196s /usr/bin/bp-analyze:1142: SyntaxWarning: invalid escape sequence '\s' 196s m = re.search('\s+(.+) = (.+)', line) 197s Program 'gnuplot' not found: Some graphs will not be generated. 197s 197s Program 'R' not found: Some mixing graphs will not be generated. 197s 197s Creating new directory Results/ for summary files. 197s Summarizing distribution of numerical parameters: done. 197s Analyzing scalar variables: /usr/bin/bp-analyze:1227: SyntaxWarning: invalid escape sequence '\(' 197s m = re.search(' const.: ([^ ]+) \(([^ ]+)\%\)', line) 197s /usr/bin/bp-analyze:1232: SyntaxWarning: invalid escape sequence '\(' 197s m = re.search('inform.: ([^ ]+) \(([^ ]+)\%\)', line) 197s /usr/bin/bp-analyze:2092: SyntaxWarning: invalid escape sequence '\[' 197s asdsf = self.get_value_from_file('Results/partitions.bs','ASDSF\[min=0.100\] =') 197s done. 197s 197s Summarizing topology distribution: done. 197s Drawing trees: c50 c66 c80 c90 c95 c99 c100 greedy MAP . done. 197s 197s Generate mixing diagnostics for topologies ... done. 197s Generate SRQ plot for partitions: done. 197s Generate SRQ plot for c50 tree: done. 197s Computing initial alignments: done. 197s 197s Computing WPD alignments: done. 197s Computing ancestral state alignment: done. 197s Drawing alignments: **** done. 197s Generating AU values for 'P1.initial'... done. 197s Generating AU values for 'P1.max'... done. 197s 197s NOTE: burnin (scalar) <= Not Converged! 197s NOTE: min_ESS (scalar) = 8.008 197s NOTE: min_ESS (partition) = 0.000 197s NOTE: ASDSF = NA 197s NOTE: MSDSF = NA 197s NOTE: PSRF-80%CI = NA 197s NOTE: PSRF-RCF = NA 197s 197s Report written to 'Results/index.html 197s autopkgtest [05:09:44]: test run-unit-test: -----------------------] 198s run-unit-test PASS 198s autopkgtest [05:09:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 198s autopkgtest [05:09:45]: @@@@@@@@@@@@@@@@@@@@ summary 198s run-unit-test PASS 231s Creating nova instance adt-noble-s390x-bali-phy-20240313-050627-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240312.img (UUID b0773a3c-d6d5-492e-ad15-d4b10dff01a1)...