0s autopkgtest [04:09:33]: starting date: 2024-03-11 0s autopkgtest [04:09:33]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [04:09:33]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0065i6nt/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 vcftools --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-3@bos03-arm64-1.secgroup --name adt-noble-arm64-vcftools-20240311-040933-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 99s autopkgtest [04:11:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 99s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 100s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2623 kB] 100s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB] 100s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB] 100s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 100s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 100s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 100s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 100s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2967 kB] 100s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 100s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB] 100s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 102s Fetched 6834 kB in 1s (4853 kB/s) 102s Reading package lists... 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s The following packages were automatically installed and are no longer required: 107s libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38 107s Use 'sudo apt autoremove' to remove them. 107s The following packages will be REMOVED: 107s dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl 107s The following NEW packages will be installed: 107s libgdbm-compat4t64 libgdbm6t64 107s The following packages have been kept back: 107s libperl5.38 107s The following packages will be upgraded: 107s perl-base perl-modules-5.38 108s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded. 108s Need to get 4928 kB of archives. 108s After this operation, 4158 kB disk space will be freed. 108s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB] 108s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB] 108s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B] 108s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] 109s Fetched 4928 kB in 1s (5981 kB/s) 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 ... 74748 files and directories currently installed.) 109s Removing dpkg-dev (1.22.4ubuntu5) ... 109s Removing libdpkg-perl (1.22.4ubuntu5) ... 109s Removing perl (5.38.2-3) ... 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 ... 74167 files and directories currently installed.) 110s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ... 110s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ... 110s Setting up perl-base (5.38.2-3.2) ... 110s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested: 110s python3-gdbm:arm64 depends on libgdbm6 (>= 1.16). 110s man-db depends on libgdbm6 (>= 1.16). 110s libperl5.38:arm64 depends on libgdbm6 (>= 1.21). 110s libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16). 110s 110s (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 ... 74167 files and directories currently installed.) 110s Removing libgdbm6:arm64 (1.23-5) ... 110s Selecting previously unselected package libgdbm6t64:arm64. 110s (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 ... 74162 files and directories currently installed.) 110s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ... 110s Unpacking libgdbm6t64:arm64 (1.23-5.1) ... 110s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested: 110s libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3). 110s 110s (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 ... 74168 files and directories currently installed.) 110s Removing libgdbm-compat4:arm64 (1.23-5) ... 110s Selecting previously unselected package libgdbm-compat4t64:arm64. 111s (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 ... 74163 files and directories currently installed.) 111s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ... 111s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 111s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ... 111s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ... 111s Setting up libgdbm6t64:arm64 (1.23-5.1) ... 111s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 111s Setting up perl-modules-5.38 (5.38.2-3.2) ... 111s Processing triggers for man-db (2.12.0-3) ... 112s Processing triggers for libc-bin (2.39-0ubuntu2) ... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s The following packages will be REMOVED: 114s libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38* 115s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded. 115s After this operation, 52.0 MB disk space will be freed. 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 ... 74169 files and directories currently installed.) 115s Removing libperl5.38:arm64 (5.38.2-3) ... 115s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ... 115s Removing lto-disabled-list (47) ... 115s Removing make (4.3-4.1build1) ... 115s Removing perl-modules-5.38 (5.38.2-3.2) ... 115s Processing triggers for man-db (2.12.0-3) ... 115s Processing triggers for libc-bin (2.39-0ubuntu2) ... 116s sh: Attempting to set up Debian/Ubuntu apt sources automatically 116s sh: Distribution appears to be Ubuntu 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s eatmydata is already the newest version (131-1). 117s dbus is already the newest version (1.14.10-4ubuntu1). 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s rng-tools-debian is already the newest version (2.4). 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s haveged is already the newest version (1.9.14-1ubuntu1). 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 The following additional packages will be installed: 120s libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list 120s make perl perl-modules-5.38 120s Suggested packages: 120s debian-keyring gcc | c-compiler git bzr make-doc perl-doc 120s libterm-readline-gnu-perl | libterm-readline-perl-perl 120s libtap-harness-archive-perl 120s Recommended packages: 120s build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl 120s libfile-fcntllock-perl 120s The following packages will be REMOVED: 120s libdb5.3 120s The following NEW packages will be installed: 120s dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 120s lto-disabled-list make perl perl-modules-5.38 120s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded. 120s Need to get 7257 kB/10.4 MB of archives. 120s After this operation, 56.1 MB of additional disk space will be used. 120s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB] 120s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB] 121s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB] 121s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB] 121s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB] 121s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] 121s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB] 121s Fetched 7257 kB in 1s (8372 kB/s) 121s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: 121s libsasl2-modules-db:arm64 depends on libdb5.3. 121s libpython3.12-stdlib:arm64 depends on libdb5.3. 121s libpam-modules:arm64 depends on libdb5.3. 121s iproute2 depends on libdb5.3. 121s apt-utils depends on libdb5.3. 121s 122s (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.) 122s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ... 122s Selecting previously unselected package libdb5.3t64:arm64. 122s (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.) 122s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ... 122s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 122s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ... 122s Selecting previously unselected package perl-modules-5.38. 122s (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.) 122s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... 122s Unpacking perl-modules-5.38 (5.38.2-3.2) ... 122s Selecting previously unselected package libgdbm-compat4t64:arm64. 122s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ... 122s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ... 122s Selecting previously unselected package libperl5.38t64:arm64. 123s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ... 123s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ... 123s Selecting previously unselected package perl. 123s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ... 123s Unpacking perl (5.38.2-3.2) ... 123s Selecting previously unselected package libdpkg-perl. 123s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ... 123s Unpacking libdpkg-perl (1.22.4ubuntu5) ... 123s Selecting previously unselected package make. 123s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ... 123s Unpacking make (4.3-4.1build1) ... 124s Selecting previously unselected package lto-disabled-list. 124s Preparing to unpack .../6-lto-disabled-list_47_all.deb ... 124s Unpacking lto-disabled-list (47) ... 124s Selecting previously unselected package dpkg-dev. 124s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ... 124s Unpacking dpkg-dev (1.22.4ubuntu5) ... 124s Setting up lto-disabled-list (47) ... 124s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ... 124s Setting up make (4.3-4.1build1) ... 124s Setting up perl-modules-5.38 (5.38.2-3.2) ... 124s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ... 124s Setting up perl (5.38.2-3.2) ... 124s Setting up libdpkg-perl (1.22.4ubuntu5) ... 124s Setting up dpkg-dev (1.22.4ubuntu5) ... 124s Processing triggers for man-db (2.12.0-3) ... 125s Processing triggers for libc-bin (2.39-0ubuntu2) ... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s The following packages will be REMOVED: 127s cloud-init* python3-configobj* python3-debconf* 129s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 129s After this operation, 3248 kB disk space will be freed. 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 ... 74750 files and directories currently installed.) 129s Removing cloud-init (24.1-0ubuntu1) ... 130s Removing python3-configobj (5.0.8-3) ... 130s Removing python3-debconf (1.5.86) ... 130s Processing triggers for man-db (2.12.0-3) ... 130s (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.) 130s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 131s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 131s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s linux-generic is already the newest version (6.8.0-11.11+1). 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [04:11:49]: rebooting testbed after setup commands that affected boot 371s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 377s autopkgtest [04:15:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 377s autopkgtest [04:15:50]: testbed dpkg architecture: arm64 378s autopkgtest [04:15:51]: @@@@@@@@@@@@@@@@@@@@ apt-source vcftools 381s Get:1 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (dsc) [2071 B] 381s Get:2 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (tar) [245 kB] 381s Get:3 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (diff) [14.0 kB] 381s gpgv: Signature made Thu Oct 7 06:07:18 2021 UTC 381s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 381s gpgv: issuer "tille@debian.org" 381s gpgv: Can't check signature: No public key 381s dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found 381s autopkgtest [04:15:54]: testing package vcftools version 0.1.16-3 381s autopkgtest [04:15:54]: build not needed 382s autopkgtest [04:15:55]: test run-unit-test: preparing testbed 384s Reading package lists... 384s Building dependency tree... 384s Reading state information... 384s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 384s Starting 2 pkgProblemResolver with broken count: 0 384s Done 385s Done 385s Starting pkgProblemResolver with broken count: 0 385s Starting 2 pkgProblemResolver with broken count: 0 385s Done 386s The following additional packages will be installed: 386s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 386s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 386s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 386s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 386s tabix vcftools 386s Recommended packages: 386s libalgorithm-diff-xs-perl 386s The following NEW packages will be installed: 386s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 386s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 386s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 386s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 386s tabix vcftools 386s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 386s 1 not fully installed or removed. 386s Need to get 1270 kB of archives. 386s After this operation, 4733 kB of additional disk space will be used. 386s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 386s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 386s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 tabix arm64 1.18+ds-1 [505 kB] 386s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libclass-data-inheritable-perl all 0.08-3 [8084 B] 386s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 386s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libexception-class-perl all 1.45-1 [28.6 kB] 386s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-deep-perl all 1.204-1 [47.1 kB] 386s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libcapture-tiny-perl all 0.48-2 [20.2 kB] 386s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libalgorithm-diff-perl all 1.201-1 [41.8 kB] 386s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libtext-diff-perl all 1.45-2 [25.6 kB] 386s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-differences-perl all 0.71-1 [15.8 kB] 386s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libsub-uplevel-perl all 0.2800-3 [11.6 kB] 386s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-exception-perl all 0.43-3 [13.4 kB] 386s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-warn-perl all 0.37-2 [12.6 kB] 387s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libtest-most-perl all 0.38-1 [21.5 kB] 387s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 vcftools arm64 0.1.16-3 [375 kB] 387s Fetched 1270 kB in 1s (1717 kB/s) 387s Selecting previously unselected package libdeflate0:arm64. 387s (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.) 387s Preparing to unpack .../00-libdeflate0_1.19-1_arm64.deb ... 387s Unpacking libdeflate0:arm64 (1.19-1) ... 387s Selecting previously unselected package libhtscodecs2:arm64. 387s Preparing to unpack .../01-libhtscodecs2_1.6.0-1_arm64.deb ... 387s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 387s Selecting previously unselected package tabix. 387s Preparing to unpack .../02-tabix_1.18+ds-1_arm64.deb ... 387s Unpacking tabix (1.18+ds-1) ... 387s Selecting previously unselected package libclass-data-inheritable-perl. 387s Preparing to unpack .../03-libclass-data-inheritable-perl_0.08-3_all.deb ... 387s Unpacking libclass-data-inheritable-perl (0.08-3) ... 387s Selecting previously unselected package libdevel-stacktrace-perl. 387s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 387s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 387s Selecting previously unselected package libexception-class-perl. 387s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 387s Unpacking libexception-class-perl (1.45-1) ... 387s Selecting previously unselected package libtest-deep-perl. 387s Preparing to unpack .../06-libtest-deep-perl_1.204-1_all.deb ... 387s Unpacking libtest-deep-perl (1.204-1) ... 387s Selecting previously unselected package libcapture-tiny-perl. 388s Preparing to unpack .../07-libcapture-tiny-perl_0.48-2_all.deb ... 388s Unpacking libcapture-tiny-perl (0.48-2) ... 388s Selecting previously unselected package libalgorithm-diff-perl. 388s Preparing to unpack .../08-libalgorithm-diff-perl_1.201-1_all.deb ... 388s Unpacking libalgorithm-diff-perl (1.201-1) ... 388s Selecting previously unselected package libtext-diff-perl. 388s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 388s Unpacking libtext-diff-perl (1.45-2) ... 388s Selecting previously unselected package libtest-differences-perl. 388s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 388s Unpacking libtest-differences-perl (0.71-1) ... 388s Selecting previously unselected package libsub-uplevel-perl. 388s Preparing to unpack .../11-libsub-uplevel-perl_0.2800-3_all.deb ... 388s Unpacking libsub-uplevel-perl (0.2800-3) ... 388s Selecting previously unselected package libtest-exception-perl. 388s Preparing to unpack .../12-libtest-exception-perl_0.43-3_all.deb ... 388s Unpacking libtest-exception-perl (0.43-3) ... 388s Selecting previously unselected package libtest-warn-perl. 388s Preparing to unpack .../13-libtest-warn-perl_0.37-2_all.deb ... 388s Unpacking libtest-warn-perl (0.37-2) ... 388s Selecting previously unselected package libtest-most-perl. 388s Preparing to unpack .../14-libtest-most-perl_0.38-1_all.deb ... 388s Unpacking libtest-most-perl (0.38-1) ... 388s Selecting previously unselected package vcftools. 388s Preparing to unpack .../15-vcftools_0.1.16-3_arm64.deb ... 388s Unpacking vcftools (0.1.16-3) ... 388s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 388s Setting up vcftools (0.1.16-3) ... 388s Setting up libtest-deep-perl (1.204-1) ... 388s Setting up libalgorithm-diff-perl (1.201-1) ... 388s Setting up libdeflate0:arm64 (1.19-1) ... 388s Setting up libclass-data-inheritable-perl (0.08-3) ... 388s Setting up libtext-diff-perl (1.45-2) ... 388s Setting up libcapture-tiny-perl (0.48-2) ... 388s Setting up libsub-uplevel-perl (0.2800-3) ... 388s Setting up libdevel-stacktrace-perl (2.0500-1) ... 388s Setting up tabix (1.18+ds-1) ... 388s Setting up libtest-warn-perl (0.37-2) ... 388s Setting up libtest-differences-perl (0.71-1) ... 388s Setting up libexception-class-perl (1.45-1) ... 388s Setting up libtest-exception-perl (0.43-3) ... 388s Setting up libtest-most-perl (0.38-1) ... 388s Setting up autopkgtest-satdep (0) ... 388s Processing triggers for man-db (2.12.0-3) ... 388s Processing triggers for libc-bin (2.39-0ubuntu2) ... 392s (Reading database ... 74586 files and directories currently installed.) 392s Removing autopkgtest-satdep (0) ... 393s autopkgtest [04:16:06]: test run-unit-test: [----------------------- 393s FaSlice.pm 393s Vcf.pm 393s VcfStats.pm 393s fill-aa 393s fill-an-ac 393s fill-fs 393s fill-ref-md5 393s test.t 393s vcf-annotate 393s vcf-compare 393s vcf-concat 393s vcf-consensus 393s vcf-contrast 393s vcf-convert 393s vcf-fix-newlines 393s vcf-fix-ploidy 393s vcf-indel-stats 393s vcf-isec 393s vcf-merge 393s vcf-phased-join 393s vcf-query 393s vcf-shuffle-cols 393s vcf-sort 393s vcf-stats 393s vcf-subset 393s vcf-to-tab 393s vcf-tstv 393s vcf-validator 393s vcftools 393s 1..68 393s ok 1 - Is bgzip OK? .. cat /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf | bgzip -c > /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 393s ok 2 - Is tabix OK? .. tabix /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 393s ok 3 - Testing validator .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/valid-3.3.vcf 393s ok 4 - Testing validator .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/valid-4.0.vcf 393s ok 5 - Testing validator .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/valid-4.1.vcf 393s ok 6 - Testing validator .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite/../testdata/floats.vcf 393s ok 7 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 393s ok 8 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 394s ok 9 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.W82onh/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 394s ok 10 - Testing next_data_array 394s ok 11 - Testing next_data_array 394s ok 12 - Testing next_data_array 394s ok 13 - Testing next_data_array 394s ok 14 - Testing add_columns with genotypes full, 4.0. 394s ok 15 - Testing add_columns with genotypes brief, 4.0. 394s ok 16 - Testing add_columns brief, 4.0. 394s ok 17 - Testing add_columns no gtypes, 4.0. 394s ok 18 - Testing vcf-isec .. perl -I../. -MVcf /usr/bin/vcf-isec -f -n +2 merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz 394s ok 19 - Testing vcf-query .. perl -I../. -MVcf /usr/bin/vcf-query -f '%CHROM:%POS\tref=%REF\talt=%ALT\tqual=%QUAL\t%INFO/DP[\t%SAMPLE=%GT]\n' cmp-test-a.vcf 394s ok 20 - Testing vcf-shuffle-cols .. perl -I../. -MVcf /usr/bin/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf 394s ok 21 - Testing vcf-concat .. perl -I../. -MVcf /usr/bin/vcf-concat -s 3 concat-a.vcf.gz concat-b.vcf.gz concat-c.vcf.gz 394s ok 22 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/fill-an-ac concat-a.vcf 394s ok 23 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/vcf-indel-stats -e indel-stats.tab < indel-stats.vcf 394s Looks as fasta file snippet, the sequence 1 starts at position 1 394s Looks as fasta file snippet, the sequence 2 starts at position 1 394s ok 24 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus consensus.vcf.gz < consensus.fa 394s Looks as fasta file snippet, the sequence 1 starts at position 1 394s Looks as fasta file snippet, the sequence 2 starts at position 1 394s ok 25 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa 394s ok 26 - Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../. -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n' 394s ok 27 - Testing API event_type(A,C) .. s 1 C 394s ok 28 - Testing API event_type(A,ACGT) .. i 3 CGT 394s ok 29 - Testing API event_type(ACGT,A) .. i -3 CGT 394s ok 30 - Testing API event_type(ACGT,ACT) .. i -1 G 394s ok 31 - Testing API event_type(ACGT,AAA) .. o 3 AAA 394s ok 32 - Testing API event_type(A,.) .. r 0 A 394s ok 33 - Testing API event_type(A,) .. u 0 394s ok 34 - Testing API event_type(ACG,AGC) .. s 2 AGC 394s ok 35 - Testing API event_type(A,.A) .. b 394s ok 36 - Testing API event_type(A,A.) .. b 394s ok 37 - Testing get_tag_index(GT:GL:PL,'GT',':') 394s ok 38 - Testing get_tag_index(GT:GL:PL,'GL',':') 394s ok 39 - Testing get_tag_index(GT:GL:PL,'PL',':') 394s ok 40 - Testing get_tag_index(GT:GL:PL,0,':') 394s ok 41 - Testing get_tag_index(GT:GL:PL,1,':') 394s ok 42 - Testing get_tag_index(GT:GL:PL,2,':') 394s ok 43 - Testing get_tag_index(GT:GL:PL,'XX',0,':') 394s ok 44 - Testing get_tag_index(GT:GL:PL,'XX',1,':') 394s ok 45 - Testing get_tag_index(GT:GL:PL,'XX',2,':') 394s ok 46 - Testing get_tag_index(GT:GL:PL,'XX',4,':') 394s ok 47 - Testing decode_genotype('C',['G','T'],'0/1/2|1/0|1|2') 394s ok 48 - Testing decode_genotype('C',['G','T'],'2|1') 394s ok 49 - Testing decode_genotype('C',['G','T'],'2') 394s ok 50 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'NS') 394s ok 51 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AF') 394s ok 52 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AFA') 394s ok 53 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'HM') 394s ok 54 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DB') 394s ok 55 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DBX') 394s ok 56 - Testing get_info_field('DB','DB') 394s ok 57 - Testing get_info_field('XDB','DB') 394s ok 58 - Testing split_gt('0/1') 394s ok 59 - Testing split_gt('0') 394s ok 60 - Testing normalize_alleles(TTGGTAT,TTGGTATCTAGTGGTAT,TGGTATCTAGTGGTAT) 394s ok 61 - Testing normalize_alleles(TT,TCTAGTGGTAAT,TCT) 394s ok 62 - Testing normalize_alleles(TGGGGGG,TGGGGGGG) 394s ok 63 - Testing normalize_alleles(CAAAAAA,CAAAAA) 394s ok 64 - Testing normalize_alleles(CA,CT) 394s ok 65 - Testing normalize_alleles_pos(GAACCCACA,GA) 394s ok 66 - Testing normalize_alleles_pos(CAGTAAAA,CAGAAAA) 394s ok 67 - Testing normalize_alleles_pos(CAGTAAA,CAGAAAA) 394s ok 68 - Testing normalize_alleles_pos(GA,GACC) 394s PASS 395s autopkgtest [04:16:08]: test run-unit-test: -----------------------] 395s run-unit-test PASS 395s autopkgtest [04:16:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 395s autopkgtest [04:16:08]: @@@@@@@@@@@@@@@@@@@@ summary 395s run-unit-test PASS 413s Creating nova instance adt-noble-arm64-vcftools-20240311-040933-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...