0s autopkgtest [17:17:11]: starting date and time: 2025-03-15 17:17:11+0000 1s autopkgtest [17:17:12]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [17:17:12]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h8hu_rjk/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade vcftools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-17.secgroup --name adt-plucky-arm64-vcftools-20250315-171711-juju-7f2275-prod-proposed-migration-environment-2-d0c4276a-3ef1-409a-ac6f-bb89ce1c9d72 --image adt/ubuntu-plucky-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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 157s autopkgtest [17:19:48]: testbed dpkg architecture: arm64 157s autopkgtest [17:19:48]: testbed apt version: 2.9.33 157s autopkgtest [17:19:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 158s autopkgtest [17:19:49]: testbed release detected to be: None 159s autopkgtest [17:19:50]: updating testbed package index (apt update) 159s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 159s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 159s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 159s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 160s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 160s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 160s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 160s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 160s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 160s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 160s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 160s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 160s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 160s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 161s Fetched 1078 kB in 1s (731 kB/s) 162s Reading package lists... 162s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Calculating upgrade... 163s Calculating upgrade... 164s The following packages will be upgraded: 164s pinentry-curses python3-jinja2 strace 164s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 647 kB of archives. 164s After this operation, 11.3 kB of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 165s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 165s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 166s Fetched 647 kB in 2s (417 kB/s) 166s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 166s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 166s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 166s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 166s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 166s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 166s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 166s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 167s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 167s Setting up strace (6.13+ds-1ubuntu1) ... 167s Processing triggers for man-db (2.13.0-1) ... 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s Solving dependencies... 169s The following packages will be REMOVED: 169s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 169s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 169s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 169s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 169s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 169s After this operation, 267 MB disk space will be freed. 169s (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 ... 117701 files and directories currently installed.) 169s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 169s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 169s Removing libpython3.12t64:arm64 (3.12.9-1) ... 169s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 169s Removing libnsl2:arm64 (1.3.0-3build3) ... 169s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 169s Removing libunwind8:arm64 (1.6.2-3.1) ... 170s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 170s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 172s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 172s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 172s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 172s /etc/kernel/postrm.d/initramfs-tools: 172s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 172s /etc/kernel/postrm.d/zz-flash-kernel: 172s flash-kernel: Kernel 6.11.0-8-generic has been removed. 172s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 173s /etc/kernel/postrm.d/zz-update-grub: 173s Sourcing file `/etc/default/grub' 173s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 173s Generating grub configuration file ... 173s Found linux image: /boot/vmlinuz-6.14.0-10-generic 173s Found initrd image: /boot/initrd.img-6.14.0-10-generic 173s Warning: os-prober will not be executed to detect other bootable partitions. 173s Systems on them will not be added to the GRUB boot configuration. 173s Check GRUB_DISABLE_OS_PROBER documentation entry. 173s Adding boot menu entry for UEFI Firmware Settings ... 173s done 174s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 174s Processing triggers for libc-bin (2.41-1ubuntu1) ... 174s (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 ... 81650 files and directories currently installed.) 174s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 174s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 174s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 174s autopkgtest [17:20:05]: upgrading testbed (apt dist-upgrade and autopurge) 174s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 176s Entering ResolveByKeep 176s 177s Calculating upgrade... 177s The following packages will be upgraded: 177s libc-bin libc-dev-bin libc6 libc6-dev locales 177s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Need to get 9530 kB of archives. 177s After this operation, 0 B of additional disk space will be used. 177s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 179s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 179s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 182s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 182s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 186s Preconfiguring packages ... 186s Fetched 9530 kB in 8s (1164 kB/s) 186s (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 ... 81647 files and directories currently installed.) 186s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 186s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 186s Setting up libc6:arm64 (2.41-1ubuntu2) ... 187s (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 ... 81647 files and directories currently installed.) 187s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 187s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up libc-bin (2.41-1ubuntu2) ... 187s (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 ... 81647 files and directories currently installed.) 187s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 187s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 187s Setting up locales (2.41-1ubuntu2) ... 188s Generating locales (this might take a while)... 190s en_US.UTF-8... done 190s Generation complete. 190s Setting up libc-dev-bin (2.41-1ubuntu2) ... 190s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 190s Processing triggers for man-db (2.13.0-1) ... 191s Processing triggers for systemd (257.3-1ubuntu3) ... 192s Reading package lists... 192s Building dependency tree... 192s Reading state information... 192s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 193s Solving dependencies... 193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 194s autopkgtest [17:20:25]: rebooting testbed after setup commands that affected boot 217s autopkgtest [17:20:48]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 220s autopkgtest [17:20:51]: @@@@@@@@@@@@@@@@@@@@ apt-source vcftools 223s Get:1 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (dsc) [2071 B] 223s Get:2 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (tar) [245 kB] 223s Get:3 http://ftpmaster.internal/ubuntu plucky/universe vcftools 0.1.16-3 (diff) [14.0 kB] 223s gpgv: Signature made Thu Oct 7 06:07:18 2021 UTC 223s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 223s gpgv: issuer "tille@debian.org" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found 223s autopkgtest [17:20:54]: testing package vcftools version 0.1.16-3 223s autopkgtest [17:20:54]: build not needed 224s autopkgtest [17:20:55]: test run-unit-test: preparing testbed 224s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 226s The following NEW packages will be installed: 226s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 226s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 226s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 226s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 226s tabix vcftools 226s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 1300 kB of archives. 226s After this operation, 5069 kB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libalgorithm-diff-perl all 1.201-1 [41.8 kB] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libcapture-tiny-perl all 0.50-1 [20.7 kB] 226s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libclass-data-inheritable-perl all 0.10-1 [8038 B] 226s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 226s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 226s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libexception-class-perl all 1.45-1 [28.6 kB] 226s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 226s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsub-uplevel-perl all 0.2800-3 [11.6 kB] 226s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtest-deep-perl all 1.204-1 [47.1 kB] 226s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtext-diff-perl all 1.45-2 [25.6 kB] 227s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtest-differences-perl all 0.71-1 [15.8 kB] 227s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtest-exception-perl all 0.43-3 [13.4 kB] 227s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtest-warn-perl all 0.37-2 [12.6 kB] 227s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 libtest-most-perl all 0.38-1 [21.5 kB] 227s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 tabix arm64 1.21+ds-1 [527 kB] 227s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 vcftools arm64 0.1.16-3 [375 kB] 228s Fetched 1300 kB in 1s (930 kB/s) 228s Selecting previously unselected package libalgorithm-diff-perl. 228s (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 ... 81647 files and directories currently installed.) 228s Preparing to unpack .../00-libalgorithm-diff-perl_1.201-1_all.deb ... 228s Unpacking libalgorithm-diff-perl (1.201-1) ... 228s Selecting previously unselected package libcapture-tiny-perl. 228s Preparing to unpack .../01-libcapture-tiny-perl_0.50-1_all.deb ... 228s Unpacking libcapture-tiny-perl (0.50-1) ... 228s Selecting previously unselected package libclass-data-inheritable-perl. 228s Preparing to unpack .../02-libclass-data-inheritable-perl_0.10-1_all.deb ... 228s Unpacking libclass-data-inheritable-perl (0.10-1) ... 228s Selecting previously unselected package libdeflate0:arm64. 228s Preparing to unpack .../03-libdeflate0_1.23-1_arm64.deb ... 228s Unpacking libdeflate0:arm64 (1.23-1) ... 228s Selecting previously unselected package libdevel-stacktrace-perl. 228s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 228s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 228s Selecting previously unselected package libexception-class-perl. 228s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 228s Unpacking libexception-class-perl (1.45-1) ... 228s Selecting previously unselected package libhtscodecs2:arm64. 228s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_arm64.deb ... 228s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 228s Selecting previously unselected package libsub-uplevel-perl. 228s Preparing to unpack .../07-libsub-uplevel-perl_0.2800-3_all.deb ... 228s Unpacking libsub-uplevel-perl (0.2800-3) ... 228s Selecting previously unselected package libtest-deep-perl. 228s Preparing to unpack .../08-libtest-deep-perl_1.204-1_all.deb ... 228s Unpacking libtest-deep-perl (1.204-1) ... 228s Selecting previously unselected package libtext-diff-perl. 228s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 228s Unpacking libtext-diff-perl (1.45-2) ... 228s Selecting previously unselected package libtest-differences-perl. 228s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 228s Unpacking libtest-differences-perl (0.71-1) ... 228s Selecting previously unselected package libtest-exception-perl. 228s Preparing to unpack .../11-libtest-exception-perl_0.43-3_all.deb ... 228s Unpacking libtest-exception-perl (0.43-3) ... 228s Selecting previously unselected package libtest-warn-perl. 228s Preparing to unpack .../12-libtest-warn-perl_0.37-2_all.deb ... 228s Unpacking libtest-warn-perl (0.37-2) ... 228s Selecting previously unselected package libtest-most-perl. 228s Preparing to unpack .../13-libtest-most-perl_0.38-1_all.deb ... 228s Unpacking libtest-most-perl (0.38-1) ... 228s Selecting previously unselected package tabix. 228s Preparing to unpack .../14-tabix_1.21+ds-1_arm64.deb ... 228s Unpacking tabix (1.21+ds-1) ... 229s Selecting previously unselected package vcftools. 229s Preparing to unpack .../15-vcftools_0.1.16-3_arm64.deb ... 229s Unpacking vcftools (0.1.16-3) ... 229s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 229s Setting up vcftools (0.1.16-3) ... 229s Setting up libtest-deep-perl (1.204-1) ... 229s Setting up libalgorithm-diff-perl (1.201-1) ... 229s Setting up libdeflate0:arm64 (1.23-1) ... 229s Setting up libclass-data-inheritable-perl (0.10-1) ... 229s Setting up libtext-diff-perl (1.45-2) ... 229s Setting up libcapture-tiny-perl (0.50-1) ... 229s Setting up libsub-uplevel-perl (0.2800-3) ... 229s Setting up libdevel-stacktrace-perl (2.0500-1) ... 229s Setting up tabix (1.21+ds-1) ... 229s Setting up libtest-warn-perl (0.37-2) ... 229s Setting up libtest-differences-perl (0.71-1) ... 229s Setting up libexception-class-perl (1.45-1) ... 229s Setting up libtest-exception-perl (0.43-3) ... 229s Setting up libtest-most-perl (0.38-1) ... 229s Processing triggers for man-db (2.13.0-1) ... 229s Processing triggers for libc-bin (2.41-1ubuntu2) ... 231s autopkgtest [17:21:02]: test run-unit-test: [----------------------- 231s FaSlice.pm 231s Vcf.pm 231s VcfStats.pm 231s fill-aa 231s fill-an-ac 231s fill-fs 231s fill-ref-md5 231s test.t 231s vcf-annotate 231s vcf-compare 231s vcf-concat 231s vcf-consensus 231s vcf-contrast 231s vcf-convert 231s vcf-fix-newlines 231s vcf-fix-ploidy 231s vcf-indel-stats 231s vcf-isec 231s vcf-merge 231s vcf-phased-join 231s vcf-query 231s vcf-shuffle-cols 231s vcf-sort 231s vcf-stats 231s vcf-subset 231s vcf-to-tab 231s vcf-tstv 231s vcf-validator 231s vcftools 231s 1..68 231s ok 1 - Is bgzip OK? .. cat /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf | bgzip -c > /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 231s ok 2 - Is tabix OK? .. tabix /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 231s ok 3 - Testing validator .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/valid-3.3.vcf 231s ok 4 - Testing validator .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/valid-4.0.vcf 231s ok 5 - Testing validator .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/valid-4.1.vcf 231s ok 6 - Testing validator .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite/../testdata/floats.vcf 231s ok 7 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 231s ok 8 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 231s ok 9 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.VU0ihP/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 231s ok 10 - Testing next_data_array 231s ok 11 - Testing next_data_array 231s ok 12 - Testing next_data_array 231s ok 13 - Testing next_data_array 231s ok 14 - Testing add_columns with genotypes full, 4.0. 231s ok 15 - Testing add_columns with genotypes brief, 4.0. 231s ok 16 - Testing add_columns brief, 4.0. 231s ok 17 - Testing add_columns no gtypes, 4.0. 232s 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 232s 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 232s ok 20 - Testing vcf-shuffle-cols .. perl -I../. -MVcf /usr/bin/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf 232s 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 232s ok 22 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/fill-an-ac concat-a.vcf 232s ok 23 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/vcf-indel-stats -e indel-stats.tab < indel-stats.vcf 232s Looks as fasta file snippet, the sequence 1 starts at position 1 232s Looks as fasta file snippet, the sequence 2 starts at position 1 232s ok 24 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus consensus.vcf.gz < consensus.fa 232s ok 25 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa 232s 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' 232s ok 27 - Testing API event_type(A,C) .. s 1 C 232s ok 28 - Testing API event_type(A,ACGT) .. i 3 CGT 232s ok 29 - Testing API event_type(ACGT,A) .. i -3 CGT 232s ok 30 - Testing API event_type(ACGT,ACT) .. i -1 G 232s ok 31 - Testing API event_type(ACGT,AAA) .. o 3 AAA 232s ok 32 - Testing API event_type(A,.) .. r 0 A 232s ok 33 - Testing API event_type(A,) .. u 0 232s ok 34 - Testing API event_type(ACG,AGC) .. s 2 AGC 232s ok 35 - Testing API event_type(A,.A) .. b 232s ok 36 - Testing API event_type(A,A.) .. b 232s ok 37 - Testing get_tag_index(GT:GL:PL,'GT',':') 232s ok 38 - Testing get_tag_index(GT:GL:PL,'GL',':') 232s ok 39 - Testing get_tag_index(GT:GL:PL,'PL',':') 232s ok 40 - Testing get_tag_index(GT:GL:PL,0,':') 232s ok 41 - Testing get_tag_index(GT:GL:PL,1,':') 232s ok 42 - Testing get_tag_index(GT:GL:PL,2,':') 232s ok 43 - Testing get_tag_index(GT:GL:PL,'XX',0,':') 232s ok 44 - Testing get_tag_index(GT:GL:PL,'XX',1,':') 232s ok 45 - Testing get_tag_index(GT:GL:PL,'XX',2,':') 232s ok 46 - Testing get_tag_index(GT:GL:PL,'XX',4,':') 232s ok 47 - Testing decode_genotype('C',['G','T'],'0/1/2|1/0|1|2') 232s ok 48 - Testing decode_genotype('C',['G','T'],'2|1') 232s ok 49 - Testing decode_genotype('C',['G','T'],'2') 232s ok 50 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'NS') 232s ok 51 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AF') 232s ok 52 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AFA') 232s ok 53 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'HM') 232s Looks as fasta file snippet, the sequence 1 starts at position 1 232s Looks as fasta file snippet, the sequence 2 starts at position 1 232s ok 54 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DB') 232s ok 55 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DBX') 232s ok 56 - Testing get_info_field('DB','DB') 232s ok 57 - Testing get_info_field('XDB','DB') 232s ok 58 - Testing split_gt('0/1') 232s ok 59 - Testing split_gt('0') 232s ok 60 - Testing normalize_alleles(TTGGTAT,TTGGTATCTAGTGGTAT,TGGTATCTAGTGGTAT) 232s ok 61 - Testing normalize_alleles(TT,TCTAGTGGTAAT,TCT) 232s ok 62 - Testing normalize_alleles(TGGGGGG,TGGGGGGG) 232s ok 63 - Testing normalize_alleles(CAAAAAA,CAAAAA) 232s ok 64 - Testing normalize_alleles(CA,CT) 232s ok 65 - Testing normalize_alleles_pos(GAACCCACA,GA) 232s ok 66 - Testing normalize_alleles_pos(CAGTAAAA,CAGAAAA) 232s ok 67 - Testing normalize_alleles_pos(CAGTAAA,CAGAAAA) 232s ok 68 - Testing normalize_alleles_pos(GA,GACC) 232s PASS 233s autopkgtest [17:21:04]: test run-unit-test: -----------------------] 233s run-unit-test PASS 233s autopkgtest [17:21:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 234s autopkgtest [17:21:05]: @@@@@@@@@@@@@@@@@@@@ summary 234s run-unit-test PASS 253s nova [W] Using flock in prodstack6-arm64 253s flock: timeout while waiting to get lock 253s Creating nova instance adt-plucky-arm64-vcftools-20250315-171711-juju-7f2275-prod-proposed-migration-environment-2-d0c4276a-3ef1-409a-ac6f-bb89ce1c9d72 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 253s nova [W] Timed out waiting for 7e1208dd-24a1-468a-86ff-cc5c573ea3f5 to get deleted.