0s autopkgtest [19:39:47]: starting date: 2024-03-09 0s autopkgtest [19:39:47]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [19:39:47]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ptku7mk_/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 iva --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@bos03-arm64-14.secgroup --name adt-noble-arm64-iva-20240309-193947-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 88s autopkgtest [19:41:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 89s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 89s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 89s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2628 kB] 89s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [429 kB] 89s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 89s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [579 kB] 89s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 89s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 89s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 89s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3023 kB] 89s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 89s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 89s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 91s Fetched 6888 kB in 1s (4734 kB/s) 91s Reading package lists... 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 94s The following packages were automatically installed and are no longer required: 94s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 94s ubuntu-advantage-tools 94s Use 'sudo apt autoremove' to remove them. 94s The following packages will be REMOVED: 94s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 94s The following NEW packages will be installed: 94s libgdbm-compat4t64 libgdbm6t64 libnuma1 libsensors-config libsensors5 94s numactl sysstat 94s The following packages have been kept back: 94s libperl5.38 94s The following packages will be upgraded: 94s efibootmgr perl-base perl-modules-5.38 python3-attr ubuntu-minimal 94s ubuntu-standard 94s 6 upgraded, 7 newly installed, 5 to remove and 1 not upgraded. 94s Need to get 5605 kB of archives. 94s After this operation, 1944 kB disk space will be freed. 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] 95s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] 95s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 95s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.535 [10.5 kB] 95s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libnuma1 arm64 2.0.18-1 [23.5 kB] 95s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.535 [10.5 kB] 95s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 efibootmgr arm64 18-1build1 [31.5 kB] 95s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors-config all 1:3.6.0-9 [5458 B] 95s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libsensors5 arm64 1:3.6.0-9 [26.9 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 numactl arm64 2.0.18-1 [39.5 kB] 95s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 python3-attr all 23.2.0-2 [48.6 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 sysstat arm64 12.6.1-1ubuntu1 [480 kB] 95s Preconfiguring packages ... 96s Fetched 5605 kB in 1s (6748 kB/s) 96s (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 ... 74662 files and directories currently installed.) 96s Removing dpkg-dev (1.22.4ubuntu5) ... 96s Removing libdpkg-perl (1.22.4ubuntu5) ... 96s Removing perl (5.38.2-3) ... 96s (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 ... 74081 files and directories currently installed.) 96s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ... 96s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 96s Setting up perl-base (5.38.2-3.2) ... 96s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 96s python3-gdbm:arm64 depends on libgdbm6 (>= 1.16). 96s man-db depends on libgdbm6 (>= 1.16). 96s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 96s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 96s 96s (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 ... 74081 files and directories currently installed.) 96s Removing libgdbm6:arm64 (1.23-5) ... 96s Selecting previously unselected package libgdbm6t64:arm64. 96s (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 ... 74076 files and directories currently installed.) 96s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 96s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 96s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested: 96s libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3). 96s 96s (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 ... 74082 files and directories currently installed.) 96s Removing libgdbm-compat4:arm64 (1.23-5) ... 96s Selecting previously unselected package libgdbm-compat4t64:arm64. 96s (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 ... 74077 files and directories currently installed.) 96s Preparing to unpack .../00-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 96s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 96s Preparing to unpack .../01-perl-modules-5.38_5.38.2-3.2_all.deb ... 96s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 97s Preparing to unpack .../02-ubuntu-minimal_1.535_arm64.deb ... 97s Unpacking ubuntu-minimal (1.535) over (1.534) ... 97s Selecting previously unselected package libnuma1:arm64. 97s Preparing to unpack .../03-libnuma1_2.0.18-1_arm64.deb ... 97s Unpacking libnuma1:arm64 (2.0.18-1) ... 97s Preparing to unpack .../04-ubuntu-standard_1.535_arm64.deb ... 97s Unpacking ubuntu-standard (1.535) over (1.534) ... 97s Preparing to unpack .../05-efibootmgr_18-1build1_arm64.deb ... 97s Unpacking efibootmgr (18-1build1) over (18-1) ... 97s Selecting previously unselected package libsensors-config. 97s Preparing to unpack .../06-libsensors-config_1%3a3.6.0-9_all.deb ... 97s Unpacking libsensors-config (1:3.6.0-9) ... 97s Selecting previously unselected package libsensors5:arm64. 97s Preparing to unpack .../07-libsensors5_1%3a3.6.0-9_arm64.deb ... 97s Unpacking libsensors5:arm64 (1:3.6.0-9) ... 97s Selecting previously unselected package numactl. 97s Preparing to unpack .../08-numactl_2.0.18-1_arm64.deb ... 97s Unpacking numactl (2.0.18-1) ... 97s Preparing to unpack .../09-python3-attr_23.2.0-2_all.deb ... 97s Unpacking python3-attr (23.2.0-2) over (23.2.0-1) ... 97s Selecting previously unselected package sysstat. 97s Preparing to unpack .../10-sysstat_12.6.1-1ubuntu1_arm64.deb ... 97s Unpacking sysstat (12.6.1-1ubuntu1) ... 97s Setting up python3-attr (23.2.0-2) ... 97s Setting up efibootmgr (18-1build1) ... 97s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 97s Setting up ubuntu-minimal (1.535) ... 97s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 97s Setting up libsensors-config (1:3.6.0-9) ... 97s Setting up ubuntu-standard (1.535) ... 97s Setting up perl-modules-5.38 (5.38.2-3.2) ... 97s Setting up libsensors5:arm64 (1:3.6.0-9) ... 97s Setting up libnuma1:arm64 (2.0.18-1) ... 97s Setting up sysstat (12.6.1-1ubuntu1) ... 98s 98s Creating config file /etc/default/sysstat with new version 98s update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode 98s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-collect.timer → /usr/lib/systemd/system/sysstat-collect.timer. 98s Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-summary.timer → /usr/lib/systemd/system/sysstat-summary.timer. 98s Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /usr/lib/systemd/system/sysstat.service. 100s Setting up numactl (2.0.18-1) ... 100s Processing triggers for man-db (2.12.0-3) ... 101s Processing triggers for libc-bin (2.39-0ubuntu2) ... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s The following packages will be REMOVED: 102s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 102s ubuntu-advantage-tools* 102s 0 upgraded, 0 newly installed, 6 to remove and 0 not upgraded. 102s After this operation, 52.0 MB disk space will be freed. 102s (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 ... 74176 files and directories currently installed.) 102s Removing libperl5.38:arm64 (5.38.2-3) ... 102s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ... 102s Removing lto-disabled-list (47) ... 102s Removing make (4.3-4.1build1) ... 102s Removing perl-modules-5.38 (5.38.2-3.2) ... 102s Removing ubuntu-advantage-tools (31.1) ... 102s Processing triggers for man-db (2.12.0-3) ... 103s Processing triggers for libc-bin (2.39-0ubuntu2) ... 103s (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 ... 72199 files and directories currently installed.) 103s Purging configuration files for ubuntu-advantage-tools (31.1) ... 104s sh: Attempting to set up Debian/Ubuntu apt sources automatically 104s sh: Distribution appears to be Ubuntu 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s eatmydata is already the newest version (131-1). 105s dbus is already the newest version (1.14.10-4ubuntu1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s rng-tools-debian is already the newest version (2.4). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s haveged is already the newest version (1.9.14-1ubuntu1). 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s The following additional packages will be installed: 108s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 108s make perl perl-modules-5.38 108s Suggested packages: 108s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 108s libterm-readline-gnu-perl | libterm-readline-perl-perl 108s libtap-harness-archive-perl 108s Recommended packages: 108s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 108s libfile-fcntllock-perl 108s The following packages will be REMOVED: 108s libdb5.3 108s The following NEW packages will be installed: 108s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 108s lto-disabled-list make perl perl-modules-5.38 108s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 108s Need to get 7257 kB/10.4 MB of archives. 108s After this operation, 56.1 MB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] 109s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] 109s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] 109s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 109s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB] 109s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] 109s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 109s Fetched 7257 kB in 1s (9768 kB/s) 109s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: 109s libsasl2-modules-db:arm64 depends on libdb5.3. 109s libpython3.12-stdlib:arm64 depends on libdb5.3. 109s libpam-modules:arm64 depends on libdb5.3. 109s iproute2 depends on libdb5.3. 109s apt-utils depends on libdb5.3. 109s 109s (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 ... 72198 files and directories currently installed.) 109s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ... 109s Selecting previously unselected package libdb5.3t64:arm64. 109s (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 ... 72192 files and directories currently installed.) 109s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ... 109s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 109s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 109s Selecting previously unselected package perl-modules-5.38. 109s (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 ... 72198 files and directories currently installed.) 109s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 109s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 110s Selecting previously unselected package libgdbm-compat4t64:arm64. 110s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 110s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 110s Selecting previously unselected package libperl5.38t64:arm64. 110s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ... 110s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ... 110s Selecting previously unselected package perl. 110s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ... 110s Unpacking perl (5.38.2-3.2) ... 110s Selecting previously unselected package libdpkg-perl. 110s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 110s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 110s Selecting previously unselected package make. 110s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ... 110s Unpacking make (4.3-4.1build1) ... 110s Selecting previously unselected package lto-disabled-list. 110s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 110s Unpacking lto-disabled-list (47) ... 110s Selecting previously unselected package dpkg-dev. 110s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 110s Unpacking dpkg-dev (1.22.4ubuntu5) ... 110s Setting up lto-disabled-list (47) ... 110s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 110s Setting up make (4.3-4.1build1) ... 110s Setting up perl-modules-5.38 (5.38.2-3.2) ... 110s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ... 110s Setting up perl (5.38.2-3.2) ... 111s Setting up libdpkg-perl (1.22.4ubuntu5) ... 111s Setting up dpkg-dev (1.22.4ubuntu5) ... 111s Processing triggers for man-db (2.12.0-3) ... 111s Processing triggers for libc-bin (2.39-0ubuntu2) ... 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s The following packages will be REMOVED: 112s cloud-init* python3-configobj* python3-debconf* 112s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 112s After this operation, 3248 kB disk space will be freed. 113s (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 ... 74750 files and directories currently installed.) 113s Removing cloud-init (24.1-0ubuntu1) ... 113s Removing python3-configobj (5.0.8-3) ... 113s Removing python3-debconf (1.5.86) ... 113s Processing triggers for man-db (2.12.0-3) ... 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 ... 74361 files and directories currently installed.) 114s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 114s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 114s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s linux-generic is already the newest version (6.8.0-11.11+1). 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 116s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 116s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 116s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 117s Reading package lists... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [19:41:47]: rebooting testbed after setup commands that affected boot 302s autopkgtest [19:44:49]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 303s autopkgtest [19:44:50]: testbed dpkg architecture: arm64 304s autopkgtest [19:44:51]: @@@@@@@@@@@@@@@@@@@@ apt-source iva 307s Get:1 http://ftpmaster.internal/ubuntu noble/universe iva 1.0.11+ds-5 (dsc) [2289 B] 307s Get:2 http://ftpmaster.internal/ubuntu noble/universe iva 1.0.11+ds-5 (tar) [8681 kB] 307s Get:3 http://ftpmaster.internal/ubuntu noble/universe iva 1.0.11+ds-5 (diff) [5992 B] 307s gpgv: Signature made Thu Feb 1 12:52:13 2024 UTC 307s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 307s gpgv: issuer "tille@debian.org" 307s gpgv: Can't check signature: No public key 307s dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found 307s autopkgtest [19:44:54]: testing package iva version 1.0.11+ds-5 307s autopkgtest [19:44:54]: build not needed 308s autopkgtest [19:44:55]: test test-example: preparing testbed 314s Reading package lists... 314s Building dependency tree... 314s Reading state information... 315s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 315s Starting 2 pkgProblemResolver with broken count: 0 315s Done 315s Done 315s Starting pkgProblemResolver with broken count: 0 315s Starting 2 pkgProblemResolver with broken count: 0 315s Done 316s The following additional packages will be installed: 316s adwaita-icon-theme at-spi2-common ca-certificates-java default-jre 316s default-jre-headless fastaq fontconfig fontconfig-config fonts-dejavu-core 316s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme 316s humanity-icon-theme iva java-common kmc libasound2 libasound2-data 316s libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 316s libbambamc0 libblas3 libcairo2 libcups2 libdatrie1 libdeflate0 316s libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libfontconfig1 316s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 316s libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 316s libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libjbig0 316s libjbzip2-java libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 316s libllvm17 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 316s libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib libsharpyuv0 316s libthai-data libthai0 libtiff6 libvulkan1 libwebp7 libx11-xcb1 libxcb-dri2-0 316s libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 316s libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 316s libxdamage1 libxfixes3 libxi6 libxinerama1 libxrandr2 libxrender1 316s libxshmfence1 libxtst6 libxxf86vm1 mummer openjdk-21-jre 316s openjdk-21-jre-headless python3-networkx python3-numpy python3-packaging 316s python3-pysam python3.11 python3.11-minimal samtools smalt trimmomatic 316s ubuntu-mono x11-common 316s Suggested packages: 316s libasound2-plugins alsa-utils cups-common gvfs liblcms2-utils pcscd 316s libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 316s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic python-networkx-doc 316s python3-gdal python3-matplotlib python3-pydot python3-pygraphviz 316s python3-scipy gcc gfortran python3-dev python3-pytest python3.11-venv 316s python3.11-doc binfmt-support cwltool 316s Recommended packages: 316s librsvg2-common r-base-core bioperl alsa-ucm-conf alsa-topology-conf 316s libgdk-pixbuf2.0-bin libgl1-amber-dri libgail-common libgtk2.0-bin 316s mesa-vulkan-drivers | vulkan-icd libatk-wrapper-java-jni fonts-dejavu-extra 316s The following NEW packages will be installed: 316s adwaita-icon-theme at-spi2-common ca-certificates-java default-jre 316s default-jre-headless fastaq fontconfig fontconfig-config fonts-dejavu-core 316s fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme 316s humanity-icon-theme iva java-common kmc libasound2 libasound2-data 316s libatk1.0-0 libavahi-client3 libavahi-common-data libavahi-common3 316s libbambamc0 libblas3 libcairo2 libcups2 libdatrie1 libdeflate0 316s libdrm-amdgpu1 libdrm-nouveau2 libdrm-radeon1 libfontconfig1 316s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgif7 libgl1 316s libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgraphite2-3 316s libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhts3 libhtscodecs2 libjbig0 316s libjbzip2-java libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 316s libllvm17 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 316s libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib libsharpyuv0 316s libthai-data libthai0 libtiff6 libvulkan1 libwebp7 libx11-xcb1 libxcb-dri2-0 316s libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 316s libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcomposite1 libxcursor1 316s libxdamage1 libxfixes3 libxi6 libxinerama1 libxrandr2 libxrender1 316s libxshmfence1 libxtst6 libxxf86vm1 mummer openjdk-21-jre 316s openjdk-21-jre-headless python3-networkx python3-numpy python3-packaging 316s python3-pysam python3.11 python3.11-minimal samtools smalt trimmomatic 316s ubuntu-mono x11-common 316s 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. 316s 1 not fully installed or removed. 316s Need to get 121 MB of archives. 316s After this operation, 552 MB of additional disk space will be used. 316s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 316s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 316s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 316s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 317s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 fastaq all 3.17.0-6 [47.9 kB] 317s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 317s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 317s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 317s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 kmc arm64 3.2.4+dfsg-1 [951 kB] 317s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 317s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libbambamc0 arm64 0.0.50-6 [37.2 kB] 317s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 smalt arm64 0.7.6-13 [95.2 kB] 317s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 317s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 317s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 317s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 317s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 317s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 317s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 317s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 317s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates-java all 20240118 [11.6 kB] 317s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 java-common all 0.75+exp1 [6798 B] 317s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common-data arm64 0.8-13ubuntu2 [29.5 kB] 317s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-common3 arm64 0.8-13ubuntu2 [23.2 kB] 317s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libavahi-client3 arm64 0.8-13ubuntu2 [27.3 kB] 317s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libcups2 arm64 2.4.6-0ubuntu3 [270 kB] 317s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 317s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 317s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 317s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 317s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 317s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 317s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 317s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] 317s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] 317s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 317s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 317s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpcsclite1 arm64 2.0.0-1 [21.2 kB] 317s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre-headless arm64 21.0.2+13-2 [45.8 MB] 318s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.21-75+exp1 [3096 B] 318s Get:41 http://ftpmaster.internal/ubuntu noble/universe arm64 iva arm64 1.0.11+ds-5 [8582 kB] 319s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 libjbzip2-java all 0.9.1-8 [42.4 kB] 319s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-common all 2.24.33-2ubuntu2 [125 kB] 319s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 at-spi2-common all 2.50.0-1 [7864 B] 319s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libatk1.0-0 arm64 2.50.0-1 [53.8 kB] 319s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 319s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 319s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 319s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 319s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 319s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [7624 B] 319s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 319s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 319s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 319s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 319s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 319s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3 [144 kB] 319s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB] 319s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB] 319s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB] 319s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB] 319s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB] 319s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB] 319s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB] 319s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libxcomposite1 arm64 1:0.4.5-1build2 [7080 B] 319s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libxfixes3 arm64 1:6.0.0-2 [11.0 kB] 319s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libxcursor1 arm64 1:1.2.1-1 [21.3 kB] 319s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libxdamage1 arm64 1:1.1.6-1 [6032 B] 319s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxi6 arm64 2:1.8.1-1 [31.9 kB] 319s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libxinerama1 arm64 2:1.1.4-3 [7056 B] 319s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libxrandr2 arm64 2:1.5.2-2 [19.6 kB] 319s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 gtk-update-icon-cache arm64 3.24.40-2ubuntu1 [50.5 kB] 319s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 hicolor-icon-theme all 0.17-2 [9976 B] 319s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 humanity-icon-theme all 0.6.16 [1282 kB] 319s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 319s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 adwaita-icon-theme all 46~rc-1 [723 kB] 319s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libgtk2.0-0 arm64 2.24.33-2ubuntu2 [1981 kB] 319s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libglvnd0 arm64 1.7.0-1 [60.0 kB] 319s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libglapi-mesa arm64 24.0.1-1ubuntu1 [57.8 kB] 319s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libx11-xcb1 arm64 2:1.8.7-1 [7836 B] 319s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri2-0 arm64 1.15-1 [7244 B] 319s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-dri3-0 arm64 1.15-1 [7108 B] 319s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-glx0 arm64 1.15-1 [25.2 kB] 319s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-present0 arm64 1.15-1 [5732 B] 319s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-randr0 arm64 1.15-1 [18.2 kB] 319s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-sync1 arm64 1.15-1 [9412 B] 319s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-xfixes0 arm64 1.15-1 [10.3 kB] 319s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libxshmfence1 arm64 1.3-1build4 [5444 B] 319s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libxxf86vm1 arm64 1:1.1.4-1build3 [10.3 kB] 319s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libvulkan1 arm64 1.3.275.0-1 [150 kB] 319s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [20.4 kB] 319s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [17.8 kB] 319s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libdrm-radeon1 arm64 2.4.120-2 [20.9 kB] 319s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libllvm17 arm64 1:17.0.6-5build1 [25.0 MB] 320s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1-mesa-dri arm64 24.0.1-1ubuntu1 [8226 kB] 320s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libglx-mesa0 arm64 24.0.1-1ubuntu1 [166 kB] 320s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libglx0 arm64 1.7.0-1 [32.4 kB] 320s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libgl1 arm64 1.7.0-1 [107 kB] 320s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libgif7 arm64 5.2.1-2.5 [34.2 kB] 320s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 320s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libxtst6 arm64 2:1.2.3-1.1 [13.7 kB] 320s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-21-jre arm64 21.0.2+13-2 [226 kB] 320s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre arm64 2:1.21-75+exp1 [922 B] 320s Get:104 http://ftpmaster.internal/ubuntu noble/universe arm64 trimmomatic all 0.39+dfsg-2 [758 kB] 321s Fetched 121 MB in 5s (25.9 MB/s) 321s Selecting previously unselected package libdeflate0:arm64. 321s (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 ... 74306 files and directories currently installed.) 321s Preparing to unpack .../000-libdeflate0_1.19-1_arm64.deb ... 321s Unpacking libdeflate0:arm64 (1.19-1) ... 321s Selecting previously unselected package libhtscodecs2:arm64. 321s Preparing to unpack .../001-libhtscodecs2_1.6.0-1_arm64.deb ... 321s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 321s Selecting previously unselected package libhts3:arm64. 321s Preparing to unpack .../002-libhts3_1.18+ds-1_arm64.deb ... 321s Unpacking libhts3:arm64 (1.18+ds-1) ... 322s Selecting previously unselected package samtools. 322s Preparing to unpack .../003-samtools_1.19.2-1_arm64.deb ... 322s Unpacking samtools (1.19.2-1) ... 322s Selecting previously unselected package fastaq. 322s Preparing to unpack .../004-fastaq_3.17.0-6_all.deb ... 322s Unpacking fastaq (3.17.0-6) ... 322s Selecting previously unselected package python3-networkx. 322s Preparing to unpack .../005-python3-networkx_2.8.8-1ubuntu1_all.deb ... 322s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 322s Selecting previously unselected package python3-packaging. 322s Preparing to unpack .../006-python3-packaging_23.2-1_all.deb ... 322s Unpacking python3-packaging (23.2-1) ... 322s Selecting previously unselected package python3-pysam. 322s Preparing to unpack .../007-python3-pysam_0.22.0+ds-1_arm64.deb ... 322s Unpacking python3-pysam (0.22.0+ds-1) ... 322s Selecting previously unselected package kmc. 322s Preparing to unpack .../008-kmc_3.2.4+dfsg-1_arm64.deb ... 322s Unpacking kmc (3.2.4+dfsg-1) ... 322s Selecting previously unselected package mummer. 322s Preparing to unpack .../009-mummer_3.23+dfsg-8_arm64.deb ... 322s Unpacking mummer (3.23+dfsg-8) ... 322s Selecting previously unselected package libbambamc0:arm64. 322s Preparing to unpack .../010-libbambamc0_0.0.50-6_arm64.deb ... 322s Unpacking libbambamc0:arm64 (0.0.50-6) ... 322s Selecting previously unselected package smalt. 322s Preparing to unpack .../011-smalt_0.7.6-13_arm64.deb ... 322s Unpacking smalt (0.7.6-13) ... 322s Selecting previously unselected package libpython3.11-minimal:arm64. 322s Preparing to unpack .../012-libpython3.11-minimal_3.11.8-1_arm64.deb ... 322s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 322s Selecting previously unselected package python3.11-minimal. 322s Preparing to unpack .../013-python3.11-minimal_3.11.8-1_arm64.deb ... 322s Unpacking python3.11-minimal (3.11.8-1) ... 323s Selecting previously unselected package libpython3.11-stdlib:arm64. 323s Preparing to unpack .../014-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 323s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 323s Selecting previously unselected package python3.11. 323s Preparing to unpack .../015-python3.11_3.11.8-1_arm64.deb ... 323s Unpacking python3.11 (3.11.8-1) ... 323s Selecting previously unselected package libblas3:arm64. 323s Preparing to unpack .../016-libblas3_3.12.0-3_arm64.deb ... 323s Unpacking libblas3:arm64 (3.12.0-3) ... 323s Selecting previously unselected package libgfortran5:arm64. 323s Preparing to unpack .../017-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 323s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 323s Selecting previously unselected package liblapack3:arm64. 323s Preparing to unpack .../018-liblapack3_3.12.0-3_arm64.deb ... 323s Unpacking liblapack3:arm64 (3.12.0-3) ... 323s Selecting previously unselected package python3-numpy. 323s Preparing to unpack .../019-python3-numpy_1%3a1.24.2-2_arm64.deb ... 323s Unpacking python3-numpy (1:1.24.2-2) ... 323s Selecting previously unselected package ca-certificates-java. 323s Preparing to unpack .../020-ca-certificates-java_20240118_all.deb ... 323s Unpacking ca-certificates-java (20240118) ... 323s Selecting previously unselected package java-common. 323s Preparing to unpack .../021-java-common_0.75+exp1_all.deb ... 323s Unpacking java-common (0.75+exp1) ... 323s Selecting previously unselected package libavahi-common-data:arm64. 323s Preparing to unpack .../022-libavahi-common-data_0.8-13ubuntu2_arm64.deb ... 323s Unpacking libavahi-common-data:arm64 (0.8-13ubuntu2) ... 323s Selecting previously unselected package libavahi-common3:arm64. 323s Preparing to unpack .../023-libavahi-common3_0.8-13ubuntu2_arm64.deb ... 323s Unpacking libavahi-common3:arm64 (0.8-13ubuntu2) ... 323s Selecting previously unselected package libavahi-client3:arm64. 323s Preparing to unpack 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fonts-dejavu-mono (2.37-8) ... 324s Selecting previously unselected package fonts-dejavu-core. 324s Preparing to unpack .../030-fonts-dejavu-core_2.37-8_all.deb ... 324s Unpacking fonts-dejavu-core (2.37-8) ... 324s Selecting previously unselected package fontconfig-config. 324s Preparing to unpack .../031-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 324s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 324s Selecting previously unselected package libfontconfig1:arm64. 324s Preparing to unpack .../032-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 324s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 324s Selecting previously unselected package libasound2-data. 324s Preparing to unpack .../033-libasound2-data_1.2.10-3build1_all.deb ... 324s Unpacking libasound2-data (1.2.10-3build1) ... 324s Selecting previously unselected package libasound2:arm64. 324s Preparing to unpack .../034-libasound2_1.2.10-3build1_arm64.deb ... 324s Unpacking libasound2:arm64 (1.2.10-3build1) ... 324s Selecting previously unselected package libgraphite2-3:arm64. 324s Preparing to unpack .../035-libgraphite2-3_1.3.14-2_arm64.deb ... 324s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 324s Selecting previously unselected package libharfbuzz0b:arm64. 324s Preparing to unpack .../036-libharfbuzz0b_8.3.0-2_arm64.deb ... 324s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 324s Selecting previously unselected package libpcsclite1:arm64. 324s Preparing to unpack .../037-libpcsclite1_2.0.0-1_arm64.deb ... 324s Unpacking libpcsclite1:arm64 (2.0.0-1) ... 324s Selecting previously unselected package openjdk-21-jre-headless:arm64. 324s Preparing to unpack .../038-openjdk-21-jre-headless_21.0.2+13-2_arm64.deb ... 324s Unpacking openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 325s Selecting previously unselected package default-jre-headless. 325s Preparing to unpack .../039-default-jre-headless_2%3a1.21-75+exp1_arm64.deb ... 325s Unpacking default-jre-headless (2:1.21-75+exp1) ... 325s Selecting previously unselected package iva. 325s Preparing to unpack .../040-iva_1.0.11+ds-5_arm64.deb ... 325s Unpacking iva (1.0.11+ds-5) ... 325s Selecting previously unselected package libjbzip2-java. 325s Preparing to unpack .../041-libjbzip2-java_0.9.1-8_all.deb ... 325s Unpacking libjbzip2-java (0.9.1-8) ... 325s Selecting previously unselected package libgtk2.0-common. 325s Preparing to unpack .../042-libgtk2.0-common_2.24.33-2ubuntu2_all.deb ... 325s Unpacking libgtk2.0-common (2.24.33-2ubuntu2) ... 325s Selecting previously unselected package at-spi2-common. 325s Preparing to unpack .../043-at-spi2-common_2.50.0-1_all.deb ... 325s Unpacking at-spi2-common (2.50.0-1) ... 325s Selecting previously unselected package libatk1.0-0:arm64. 325s Preparing to unpack .../044-libatk1.0-0_2.50.0-1_arm64.deb ... 325s Unpacking libatk1.0-0:arm64 (2.50.0-1) ... 325s Selecting previously unselected package libpixman-1-0:arm64. 325s Preparing to unpack .../045-libpixman-1-0_0.42.2-1_arm64.deb ... 325s 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previously unselected package libjbig0:arm64. 326s Preparing to unpack .../051-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 326s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 326s Selecting previously unselected package liblerc4:arm64. 326s Preparing to unpack .../052-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 326s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 326s Selecting previously unselected package libsharpyuv0:arm64. 326s Preparing to unpack .../053-libsharpyuv0_1.3.2-0.4_arm64.deb ... 326s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 326s Selecting previously unselected package libwebp7:arm64. 326s Preparing to unpack .../054-libwebp7_1.3.2-0.4_arm64.deb ... 326s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 326s Selecting previously unselected package libtiff6:arm64. 326s Preparing to unpack .../055-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 326s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 326s Selecting previously unselected package libgdk-pixbuf-2.0-0:arm64. 326s 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libpango-1.0-0:arm64 (1.51.0+ds-4) ... 326s Selecting previously unselected package libpangoft2-1.0-0:arm64. 326s Preparing to unpack .../062-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ... 326s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 326s Selecting previously unselected package libpangocairo-1.0-0:arm64. 326s Preparing to unpack .../063-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ... 326s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 326s Selecting previously unselected package libxcomposite1:arm64. 326s Preparing to unpack .../064-libxcomposite1_1%3a0.4.5-1build2_arm64.deb ... 326s Unpacking libxcomposite1:arm64 (1:0.4.5-1build2) ... 326s Selecting previously unselected package libxfixes3:arm64. 326s Preparing to unpack .../065-libxfixes3_1%3a6.0.0-2_arm64.deb ... 326s Unpacking libxfixes3:arm64 (1:6.0.0-2) ... 326s Selecting previously unselected package libxcursor1:arm64. 326s Preparing to unpack .../066-libxcursor1_1%3a1.2.1-1_arm64.deb ... 326s Unpacking libxcursor1:arm64 (1:1.2.1-1) ... 326s Selecting previously unselected package libxdamage1:arm64. 326s Preparing to unpack .../067-libxdamage1_1%3a1.1.6-1_arm64.deb ... 326s Unpacking libxdamage1:arm64 (1:1.1.6-1) ... 326s Selecting previously unselected package libxi6:arm64. 326s Preparing to unpack .../068-libxi6_2%3a1.8.1-1_arm64.deb ... 326s Unpacking libxi6:arm64 (2:1.8.1-1) ... 326s Selecting previously unselected package libxinerama1:arm64. 326s Preparing to unpack .../069-libxinerama1_2%3a1.1.4-3_arm64.deb ... 326s Unpacking libxinerama1:arm64 (2:1.1.4-3) ... 326s Selecting previously unselected package libxrandr2:arm64. 327s Preparing to unpack .../070-libxrandr2_2%3a1.5.2-2_arm64.deb ... 327s Unpacking libxrandr2:arm64 (2:1.5.2-2) ... 327s Selecting previously unselected package gtk-update-icon-cache. 327s Preparing to unpack .../071-gtk-update-icon-cache_3.24.40-2ubuntu1_arm64.deb ... 327s Unpacking gtk-update-icon-cache (3.24.40-2ubuntu1) ... 327s Selecting previously unselected package hicolor-icon-theme. 327s Preparing to unpack .../072-hicolor-icon-theme_0.17-2_all.deb ... 327s Unpacking hicolor-icon-theme (0.17-2) ... 327s Selecting previously unselected package humanity-icon-theme. 327s Preparing to unpack .../073-humanity-icon-theme_0.6.16_all.deb ... 327s Unpacking humanity-icon-theme (0.6.16) ... 327s Selecting previously unselected package ubuntu-mono. 327s Preparing to unpack .../074-ubuntu-mono_24.04-0ubuntu1_all.deb ... 327s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 327s Selecting previously unselected package adwaita-icon-theme. 327s Preparing to unpack .../075-adwaita-icon-theme_46~rc-1_all.deb ... 327s Unpacking adwaita-icon-theme (46~rc-1) ... 328s Selecting previously unselected package libgtk2.0-0:arm64. 328s Preparing to unpack .../076-libgtk2.0-0_2.24.33-2ubuntu2_arm64.deb ... 328s Unpacking libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 328s Selecting previously unselected package libglvnd0:arm64. 328s Preparing to unpack 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(5.2.1-2.5) ... 330s Selecting previously unselected package x11-common. 330s Preparing to unpack .../099-x11-common_1%3a7.7+23ubuntu2_all.deb ... 330s Unpacking x11-common (1:7.7+23ubuntu2) ... 330s Selecting previously unselected package libxtst6:arm64. 330s Preparing to unpack .../100-libxtst6_2%3a1.2.3-1.1_arm64.deb ... 330s Unpacking libxtst6:arm64 (2:1.2.3-1.1) ... 330s Selecting previously unselected package openjdk-21-jre:arm64. 330s Preparing to unpack .../101-openjdk-21-jre_21.0.2+13-2_arm64.deb ... 330s Unpacking openjdk-21-jre:arm64 (21.0.2+13-2) ... 330s Selecting previously unselected package default-jre. 330s Preparing to unpack .../102-default-jre_2%3a1.21-75+exp1_arm64.deb ... 330s Unpacking default-jre (2:1.21-75+exp1) ... 330s Selecting previously unselected package trimmomatic. 330s Preparing to unpack .../103-trimmomatic_0.39+dfsg-2_all.deb ... 330s Unpacking trimmomatic (0.39+dfsg-2) ... 330s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 330s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 330s Setting up libxcb-dri3-0:arm64 (1.15-1) ... 330s Setting up liblcms2-2:arm64 (2.14-2) ... 330s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 330s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 330s Setting up libx11-xcb1:arm64 (2:1.8.7-1) ... 330s Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... 330s Setting up libxdamage1:arm64 (1:1.1.6-1) ... 330s Setting up libxcb-xfixes0:arm64 (1.15-1) ... 330s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 330s Setting up hicolor-icon-theme (0.17-2) ... 330s Setting up libxi6:arm64 (2:1.8.1-1) ... 330s Setting up java-common (0.75+exp1) ... 330s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 330s Setting up libdatrie1:arm64 (0.2.13-3) ... 330s Setting up libxcb-render0:arm64 (1.15-1) ... 330s Setting up libdrm-radeon1:arm64 (2.4.120-2) ... 330s Setting up libglvnd0:arm64 (1.7.0-1) ... 330s Setting up libxcb-glx0:arm64 (1.15-1) ... 330s Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... 330s Setting up x11-common (1:7.7+23ubuntu2) ... 330s Setting up libdeflate0:arm64 (1.19-1) ... 330s Setting up libxcb-shm0:arm64 (1.15-1) ... 330s Setting up python3-networkx (2.8.8-1ubuntu1) ... 331s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 331s "graph [edge [ source u'u\4200' target u'u\4200' ] " 331s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 331s + "node [ id u'u\4200' label b ] ]" 331s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 331s Setting up libxxf86vm1:arm64 (1:1.1.4-1build3) ... 331s Setting up libxcb-present0:arm64 (1.15-1) ... 331s Setting up libasound2-data (1.2.10-3build1) ... 331s Setting up libblas3:arm64 (3.12.0-3) ... 331s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 331s Setting up python3-packaging (23.2-1) ... 331s Setting up libxfixes3:arm64 (1:6.0.0-2) ... 331s Setting up libxcb-sync1:arm64 (1.15-1) ... 331s Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... 331s Setting up libxinerama1:arm64 (2:1.1.4-3) ... 331s Setting up libbambamc0:arm64 (0.0.50-6) ... 331s Setting up fonts-dejavu-mono (2.37-8) ... 331s Setting up libxrandr2:arm64 (2:1.5.2-2) ... 331s Setting up fonts-dejavu-core (2.37-8) ... 331s Setting up libjbzip2-java (0.9.1-8) ... 331s Setting up libpcsclite1:arm64 (2.0.0-1) ... 331s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 331s Setting up libglapi-mesa:arm64 (24.0.1-1ubuntu1) ... 331s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 331s Setting up libvulkan1:arm64 (1.3.275.0-1) ... 331s Setting up libwebp7:arm64 (1.3.2-0.4) ... 331s Setting up libxcb-dri2-0:arm64 (1.15-1) ... 331s Setting up libgif7:arm64 (5.2.1-2.5) ... 331s Setting up libxshmfence1:arm64 (1.3-1build4) ... 331s Setting up at-spi2-common (2.50.0-1) ... 331s Setting up libxcb-randr0:arm64 (1.15-1) ... 331s Setting up libasound2:arm64 (1.2.10-3build1) ... 331s Setting up mummer (3.23+dfsg-8) ... 331s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 331s Setting up libthai-data (0.1.29-2) ... 331s Setting up libgtk2.0-common (2.24.33-2ubuntu2) ... 331s Setting up libatk1.0-0:arm64 (2.50.0-1) ... 331s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 331s Setting up ca-certificates-java (20240118) ... 331s No JRE found. Skipping Java certificates setup. 331s Setting up libllvm17:arm64 (1:17.0.6-5build1) ... 331s Setting up kmc (3.2.4+dfsg-1) ... 331s Setting up libxcomposite1:arm64 (1:0.4.5-1build2) ... 331s Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... 331s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 331s Setting up python3.11-minimal (3.11.8-1) ... 332s Setting up smalt (0.7.6-13) ... 332s Setting up liblapack3:arm64 (3.12.0-3) ... 332s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 332s Setting up libhts3:arm64 (1.18+ds-1) ... 332s Setting up python3-pysam (0.22.0+ds-1) ... 332s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 332s Setting up libxtst6:arm64 (2:1.2.3-1.1) ... 332s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 332s Setting up libxcursor1:arm64 (1:1.2.1-1) ... 332s Setting up libgl1-mesa-dri:arm64 (24.0.1-1ubuntu1) ... 332s Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... 332s Setting up samtools (1.19.2-1) ... 333s Setting up libthai0:arm64 (0.1.29-2) ... 333s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 333s Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3) ... 333s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 333s Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... 333s Setting up gtk-update-icon-cache (3.24.40-2ubuntu1) ... 333s Setting up python3.11 (3.11.8-1) ... 334s Setting up fontconfig (2.15.0-1ubuntu1) ... 336s Regenerating fonts cache... done. 336s Setting up libglx-mesa0:arm64 (24.0.1-1ubuntu1) ... 336s Setting up libglx0:arm64 (1.7.0-1) ... 336s Setting up fastaq (3.17.0-6) ... 336s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' 336s phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') 336s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' 336s gbk_regex = re.compile('^LOCUS\s+\S') 336s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ... 336s Setting up libcairo2:arm64 (1.18.0-1) ... 336s Setting up libgl1:arm64 (1.7.0-1) ... 336s Setting up python3-numpy (1:1.24.2-2) ... 337s Setting up libcups2:arm64 (2.4.6-0ubuntu3) ... 337s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ... 337s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ... 338s Setting up openjdk-21-jre-headless:arm64 (21.0.2+13-2) ... 338s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode 338s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 338s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 338s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 338s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 338s Setting up adwaita-icon-theme (46~rc-1) ... 338s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 338s Setting up libgtk2.0-0:arm64 (2.24.33-2ubuntu2) ... 338s Setting up humanity-icon-theme (0.6.16) ... 338s Setting up ubuntu-mono (24.04-0ubuntu1) ... 338s Processing triggers for systemd (255.2-3ubuntu2) ... 338s Processing triggers for man-db (2.12.0-3) ... 339s Processing triggers for libc-bin (2.39-0ubuntu2) ... 339s Processing triggers for ca-certificates-java (20240118) ... 340s Adding debian:ACCVRAIZ1.pem 340s Adding debian:AC_RAIZ_FNMT-RCM.pem 340s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 340s Adding debian:ANF_Secure_Server_Root_CA.pem 340s Adding debian:Actalis_Authentication_Root_CA.pem 340s Adding debian:AffirmTrust_Commercial.pem 340s Adding debian:AffirmTrust_Networking.pem 340s Adding debian:AffirmTrust_Premium.pem 340s Adding debian:AffirmTrust_Premium_ECC.pem 340s Adding debian:Amazon_Root_CA_1.pem 340s Adding debian:Amazon_Root_CA_2.pem 340s Adding debian:Amazon_Root_CA_3.pem 340s Adding debian:Amazon_Root_CA_4.pem 340s Adding debian:Atos_TrustedRoot_2011.pem 340s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 340s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 340s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 340s Adding debian:BJCA_Global_Root_CA1.pem 340s Adding debian:BJCA_Global_Root_CA2.pem 340s Adding debian:Baltimore_CyberTrust_Root.pem 340s Adding debian:Buypass_Class_2_Root_CA.pem 340s Adding debian:Buypass_Class_3_Root_CA.pem 340s Adding debian:CA_Disig_Root_R2.pem 340s Adding debian:CFCA_EV_ROOT.pem 340s Adding debian:COMODO_Certification_Authority.pem 340s Adding debian:COMODO_ECC_Certification_Authority.pem 340s Adding debian:COMODO_RSA_Certification_Authority.pem 340s Adding debian:Certainly_Root_E1.pem 340s Adding debian:Certainly_Root_R1.pem 340s Adding debian:Certigna.pem 340s Adding debian:Certigna_Root_CA.pem 340s Adding debian:Certum_EC-384_CA.pem 340s Adding debian:Certum_Trusted_Network_CA.pem 340s Adding debian:Certum_Trusted_Network_CA_2.pem 340s Adding debian:Certum_Trusted_Root_CA.pem 340s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 340s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 340s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 340s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 340s Adding debian:Comodo_AAA_Services_root.pem 340s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 340s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 340s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 340s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 340s Adding debian:DigiCert_Assured_ID_Root_CA.pem 340s Adding debian:DigiCert_Assured_ID_Root_G2.pem 340s Adding debian:DigiCert_Assured_ID_Root_G3.pem 340s Adding debian:DigiCert_Global_Root_CA.pem 340s Adding debian:DigiCert_Global_Root_G2.pem 340s Adding debian:DigiCert_Global_Root_G3.pem 340s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 340s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 340s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 340s Adding debian:DigiCert_Trusted_Root_G4.pem 340s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 340s Adding debian:Entrust_Root_Certification_Authority.pem 340s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 340s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 340s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 341s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 341s Adding debian:GLOBALTRUST_2020.pem 341s Adding debian:GTS_Root_R1.pem 341s Adding debian:GTS_Root_R2.pem 341s Adding debian:GTS_Root_R3.pem 341s Adding debian:GTS_Root_R4.pem 341s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 341s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 341s Adding debian:GlobalSign_Root_CA.pem 341s Adding debian:GlobalSign_Root_CA_-_R3.pem 341s Adding debian:GlobalSign_Root_CA_-_R6.pem 341s Adding debian:GlobalSign_Root_E46.pem 341s Adding debian:GlobalSign_Root_R46.pem 341s Adding debian:Go_Daddy_Class_2_CA.pem 341s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 341s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 341s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 341s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 341s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 341s Adding debian:HiPKI_Root_CA_-_G1.pem 341s Adding debian:Hongkong_Post_Root_CA_3.pem 341s Adding debian:ISRG_Root_X1.pem 341s Adding debian:ISRG_Root_X2.pem 341s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 341s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 341s Adding debian:Izenpe.com.pem 341s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 341s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 341s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 341s Adding debian:NAVER_Global_Root_Certification_Authority.pem 341s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 341s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 341s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 341s Adding debian:QuoVadis_Root_CA_1_G3.pem 341s Adding debian:QuoVadis_Root_CA_2.pem 341s Adding debian:QuoVadis_Root_CA_2_G3.pem 341s Adding debian:QuoVadis_Root_CA_3.pem 341s Adding debian:QuoVadis_Root_CA_3_G3.pem 341s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 341s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 341s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 341s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 341s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 341s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 341s Adding debian:SZAFIR_ROOT_CA2.pem 341s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 341s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 341s Adding debian:SecureSign_RootCA11.pem 341s Adding debian:SecureTrust_CA.pem 341s Adding debian:Secure_Global_CA.pem 341s Adding debian:Security_Communication_ECC_RootCA1.pem 341s Adding debian:Security_Communication_RootCA2.pem 341s Adding debian:Security_Communication_RootCA3.pem 341s Adding debian:Security_Communication_Root_CA.pem 341s Adding debian:Starfield_Class_2_CA.pem 341s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 341s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 341s Adding debian:SwissSign_Gold_CA_-_G2.pem 341s Adding debian:SwissSign_Silver_CA_-_G2.pem 341s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 341s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 341s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 341s Adding debian:TWCA_Global_Root_CA.pem 341s Adding debian:TWCA_Root_Certification_Authority.pem 341s Adding debian:TeliaSonera_Root_CA_v1.pem 341s Adding debian:Telia_Root_CA_v2.pem 341s Adding debian:TrustAsia_Global_Root_CA_G3.pem 341s Adding debian:TrustAsia_Global_Root_CA_G4.pem 341s Adding debian:Trustwave_Global_Certification_Authority.pem 341s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 341s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 341s Adding debian:TunTrust_Root_CA.pem 341s Adding debian:UCA_Extended_Validation_Root.pem 341s Adding debian:UCA_Global_G2_Root.pem 341s Adding debian:USERTrust_ECC_Certification_Authority.pem 341s Adding debian:USERTrust_RSA_Certification_Authority.pem 341s Adding debian:XRamp_Global_CA_Root.pem 341s Adding debian:certSIGN_ROOT_CA.pem 341s Adding debian:certSIGN_Root_CA_G2.pem 341s Adding debian:e-Szigno_Root_CA_2017.pem 341s Adding debian:ePKI_Root_Certification_Authority.pem 341s Adding debian:emSign_ECC_Root_CA_-_C3.pem 341s Adding debian:emSign_ECC_Root_CA_-_G3.pem 341s Adding debian:emSign_Root_CA_-_C1.pem 341s Adding debian:emSign_Root_CA_-_G1.pem 341s Adding debian:vTrus_ECC_Root_CA.pem 341s Adding debian:vTrus_Root_CA.pem 341s done. 341s Setting up openjdk-21-jre:arm64 (21.0.2+13-2) ... 341s Setting up default-jre-headless (2:1.21-75+exp1) ... 341s Setting up iva (1.0.11+ds-5) ... 341s /usr/lib/python3/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 341s 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), 341s /usr/lib/python3/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 341s 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), 341s /usr/lib/python3/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 341s 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), 341s /usr/lib/python3/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 341s 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), 341s /usr/lib/python3/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 341s 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), 341s /usr/lib/python3/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' 341s self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') 341s /usr/lib/python3/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' 341s return re.sub('\W', '_', s).strip('_') 341s /usr/lib/python3/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' 341s s = re.sub('\^.', '', s) 341s Setting up default-jre (2:1.21-75+exp1) ... 341s Setting up trimmomatic (0.39+dfsg-2) ... 341s Setting up autopkgtest-satdep (0) ... 347s (Reading database ... 91395 files and directories currently installed.) 347s Removing autopkgtest-satdep (0) ... 350s autopkgtest [19:45:37]: test test-example: [----------------------- 959s Running iva in test mode... 959s Copied input test files into here: /tmp/tmp.BEUaNIvMO3/test 959s Current working directory: /tmp/tmp.BEUaNIvMO3/test 959s Running iva on the test data with the command: 959s /usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out 959s Finished running iva 959s Looks OK. Final output contigs file is: /tmp/tmp.BEUaNIvMO3/test/iva.out/contigs.fasta 960s autopkgtest [19:55:47]: test test-example: -----------------------] 960s autopkgtest [19:55:47]: test test-example: - - - - - - - - - - results - - - - - - - - - - 960s test-example PASS 960s autopkgtest [19:55:47]: @@@@@@@@@@@@@@@@@@@@ summary 960s test-example PASS 971s Creating nova instance adt-noble-arm64-iva-20240309-193947-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240308.img (UUID ddbc0ee7-bb97-4aa3-b5e1-9386758c2ba2)...