0s autopkgtest [16:40:23]: starting date and time: 2025-03-15 16:40:23+0000 0s autopkgtest [16:40:23]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:40:23]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s5vvvf3h/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade phast --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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-15.secgroup --name adt-plucky-s390x-phast-20250315-164023-juju-7f2275-prod-proposed-migration-environment-20-dba6d31d-dfd0-4c43-a591-6e9aa0b40bad --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 107s autopkgtest [16:42:10]: testbed dpkg architecture: s390x 108s autopkgtest [16:42:11]: testbed apt version: 2.9.33 108s autopkgtest [16:42:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 108s autopkgtest [16:42:11]: testbed release detected to be: None 109s autopkgtest [16:42:12]: updating testbed package index (apt update) 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 109s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 110s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 110s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 110s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 110s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 110s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 111s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 111s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 111s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 111s Fetched 1073 kB in 2s (610 kB/s) 111s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Calculating upgrade... 112s Calculating upgrade... 112s The following packages were automatically installed and are no longer required: 112s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 112s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 112s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 112s linux-tools-6.11.0-8-generic 112s Use 'sudo apt autoremove' to remove them. 112s The following packages will be upgraded: 112s pinentry-curses python3-jinja2 strace 113s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 652 kB of archives. 113s After this operation, 27.6 kB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 114s Fetched 652 kB in 1s (609 kB/s) 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81428 files and directories currently installed.) 114s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 114s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 114s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 114s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 114s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 114s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 114s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 114s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 114s Setting up strace (6.13+ds-1ubuntu1) ... 114s Processing triggers for man-db (2.13.0-1) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Solving dependencies... 115s The following packages will be REMOVED: 115s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 115s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 115s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 115s linux-tools-6.11.0-8-generic* 115s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 115s After this operation, 167 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 ... 81428 files and directories currently installed.) 115s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 115s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 115s Removing libpython3.12t64:s390x (3.12.9-1) ... 115s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 115s Removing libnsl2:s390x (1.3.0-3build3) ... 115s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 115s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 115s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 116s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 116s Processing triggers for libc-bin (2.41-1ubuntu1) ... 116s (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 ... 56328 files and directories currently installed.) 116s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 116s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 116s autopkgtest [16:42:19]: upgrading testbed (apt dist-upgrade and autopurge) 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s Entering ResolveByKeep 117s 117s Calculating upgrade... 117s The following packages will be upgraded: 117s libc-bin libc-dev-bin libc6 libc6-dev locales 117s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Need to get 9512 kB of archives. 117s After this operation, 8192 B of additional disk space will be used. 117s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 119s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 119s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 122s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 123s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 127s Preconfiguring packages ... 127s Fetched 9512 kB in 10s (976 kB/s) 127s (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 ... 56326 files and directories currently installed.) 127s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 127s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 127s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 127s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 127s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 128s Setting up libc6:s390x (2.41-1ubuntu2) ... 128s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 128s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 128s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 128s Setting up libc-bin (2.41-1ubuntu2) ... 128s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56326 files and directories currently installed.) 128s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 128s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 128s Setting up locales (2.41-1ubuntu2) ... 128s Generating locales (this might take a while)... 129s en_US.UTF-8... done 129s Generation complete. 129s Setting up libc-dev-bin (2.41-1ubuntu2) ... 129s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 129s Processing triggers for man-db (2.13.0-1) ... 130s Processing triggers for systemd (257.3-1ubuntu3) ... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Starting pkgProblemResolver with broken count: 0 131s Starting 2 pkgProblemResolver with broken count: 0 131s Done 131s Solving dependencies... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [16:42:34]: rebooting testbed after setup commands that affected boot 152s autopkgtest [16:42:55]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 155s autopkgtest [16:42:58]: @@@@@@@@@@@@@@@@@@@@ apt-source phast 158s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phast 1.7+dfsg-2 (dsc) [2218 B] 158s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phast 1.7+dfsg-2 (tar) [1810 kB] 158s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phast 1.7+dfsg-2 (diff) [58.7 kB] 158s gpgv: Signature made Sun Jan 5 20:19:26 2025 UTC 158s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 158s gpgv: issuer "emollier@debian.org" 158s gpgv: Can't check signature: No public key 158s dpkg-source: warning: cannot verify inline signature for ./phast_1.7+dfsg-2.dsc: no acceptable signature found 158s autopkgtest [16:43:01]: testing package phast version 1.7+dfsg-2 159s autopkgtest [16:43:02]: build not needed 160s autopkgtest [16:43:03]: test run-unit-test: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s The following NEW packages will be installed: 160s libblas3 libgfortran5 liblapack3 phast 161s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 6988 kB of archives. 161s After this operation, 21.8 MB of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 161s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 164s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x phast s390x 1.7+dfsg-2 [3145 kB] 167s Fetched 6988 kB in 6s (1086 kB/s) 167s Selecting previously unselected package libblas3:s390x. 167s (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 ... 56326 files and directories currently installed.) 167s Preparing to unpack .../libblas3_3.12.1-2_s390x.deb ... 167s Unpacking libblas3:s390x (3.12.1-2) ... 167s Selecting previously unselected package libgfortran5:s390x. 167s Preparing to unpack .../libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 167s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 167s Selecting previously unselected package liblapack3:s390x. 167s Preparing to unpack .../liblapack3_3.12.1-2_s390x.deb ... 167s Unpacking liblapack3:s390x (3.12.1-2) ... 167s Selecting previously unselected package phast. 167s Preparing to unpack .../phast_1.7+dfsg-2_s390x.deb ... 167s Unpacking phast (1.7+dfsg-2) ... 167s Setting up libblas3:s390x (3.12.1-2) ... 167s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 167s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 167s Setting up liblapack3:s390x (3.12.1-2) ... 167s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 167s Setting up phast (1.7+dfsg-2) ... 167s Processing triggers for man-db (2.13.0-1) ... 168s Processing triggers for libc-bin (2.41-1ubuntu2) ... 169s autopkgtest [16:43:12]: test run-unit-test: [----------------------- 169s *** Testing msa_view *** 169s msa_view hmrc.ss -i SS --end 10000 > hmrc.fa 169s if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.fa -o PHYLIP > hmrc.ph 169s msa_view hmrc.ph -i PHYLIP > hmrc.fa 169s if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm 169s msa_view hmrc.mpm --in-format MPM > hmrc.fa 169s if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.fa -o SS > hmrc_short_a.ss 169s msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss 169s if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi 169s msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa 169s msa_view --seqs human,cow hmrc.fa > hm_b.fa 169s if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa 169s msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa 169s if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa 169s msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa 169s if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa 169s msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa 169s if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 169s msa_view hmrc.ss --summary -i SS > hmrc_summary 169s if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi 169s -e Passed all tests. 169s 170s autopkgtest [16:43:13]: test run-unit-test: -----------------------] 170s run-unit-test PASS 170s autopkgtest [16:43:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 171s autopkgtest [16:43:14]: @@@@@@@@@@@@@@@@@@@@ summary 171s run-unit-test PASS 176s nova [W] Using flock in prodstack6-s390x 176s Creating nova instance adt-plucky-s390x-phast-20250315-164023-juju-7f2275-prod-proposed-migration-environment-20-dba6d31d-dfd0-4c43-a591-6e9aa0b40bad from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 176s nova [W] Timed out waiting for 1a9d92a9-921a-4b23-b136-3deaa6f876fa to get deleted.