0s autopkgtest [16:41:22]: starting date and time: 2025-03-15 16:41:22+0000
  0s autopkgtest [16:41:22]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [16:41:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bpekus3j/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade phybin --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-2@bos03-s390x-3.secgroup --name adt-plucky-s390x-phybin-20250315-164121-juju-7f2275-prod-proposed-migration-environment-2-2cdf01de-9388-4ca6-8001-083a72219844 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/
136s autopkgtest [16:43:38]: testbed dpkg architecture: s390x
136s autopkgtest [16:43:38]: testbed apt version: 2.9.33
136s autopkgtest [16:43:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup
137s autopkgtest [16:43:39]: testbed release detected to be: None
137s autopkgtest [16:43:39]: updating testbed package index (apt update)
138s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
138s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
138s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
138s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
138s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
138s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
138s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
139s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB]
139s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B]
139s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
139s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB]
139s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB]
139s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B]
139s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B]
139s Fetched 1073 kB in 2s (695 kB/s)
140s Reading package lists...
140s Reading package lists...
140s Building dependency tree...
140s Reading state information...
141s Calculating upgrade...
141s Calculating upgrade...
141s The following packages were automatically installed and are no longer required:
141s   libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
141s   linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
141s   linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
141s   linux-tools-6.11.0-8-generic
141s Use 'sudo apt autoremove' to remove them.
141s The following packages will be upgraded:
141s   pinentry-curses python3-jinja2 strace
141s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
141s Need to get 652 kB of archives.
141s After this operation, 27.6 kB of additional disk space will be used.
141s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
142s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB]
142s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
142s Fetched 652 kB in 1s (630 kB/s)
142s (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.)
142s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
142s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
142s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ...
142s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
142s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
142s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
142s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
142s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
142s Setting up strace (6.13+ds-1ubuntu1) ...
142s Processing triggers for man-db (2.13.0-1) ...
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
143s Solving dependencies...
143s The following packages will be REMOVED:
143s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
143s   linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
143s   linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
143s   linux-tools-6.11.0-8-generic*
143s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
143s After this operation, 167 MB disk space will be freed.
143s (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.)
143s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
143s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
143s Removing libpython3.12t64:s390x (3.12.9-1) ...
144s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
144s Removing libnsl2:s390x (1.3.0-3build3) ...
144s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
144s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
144s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
144s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
145s Processing triggers for libc-bin (2.41-1ubuntu1) ...
145s (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.)
145s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
145s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
145s autopkgtest [16:43:47]: upgrading testbed (apt dist-upgrade and autopurge)
145s Reading package lists...
145s Building dependency tree...
145s Reading state information...
145s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
145s Starting 2 pkgProblemResolver with broken count: 0
145s Done
145s Entering ResolveByKeep
146s 
146s Calculating upgrade...
146s The following packages will be upgraded:
146s   libc-bin libc-dev-bin libc6 libc6-dev locales
146s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
146s Need to get 9512 kB of archives.
146s After this operation, 8192 B of additional disk space will be used.
146s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
148s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
148s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
151s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
152s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
156s Preconfiguring packages ...
156s Fetched 9512 kB in 10s (959 kB/s)
156s (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.)
156s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
156s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
156s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
156s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
156s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
156s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
156s Setting up libc6:s390x (2.41-1ubuntu2) ...
156s (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.)
156s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
156s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
156s Setting up libc-bin (2.41-1ubuntu2) ...
156s (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.)
156s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
156s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
156s Setting up locales (2.41-1ubuntu2) ...
157s Generating locales (this might take a while)...
158s   en_US.UTF-8... done
158s Generation complete.
158s Setting up libc-dev-bin (2.41-1ubuntu2) ...
158s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
158s Processing triggers for man-db (2.13.0-1) ...
158s Processing triggers for systemd (257.3-1ubuntu3) ...
159s 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 Solving dependencies...
160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
160s autopkgtest [16:44:02]: rebooting testbed after setup commands that affected boot
179s autopkgtest [16:44:21]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025
182s autopkgtest [16:44:24]: @@@@@@@@@@@@@@@@@@@@ apt-source phybin
183s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (dsc) [1607 B]
183s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (tar) [112 kB]
183s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (diff) [7276 B]
183s gpgv: Signature made Fri Dec 30 05:57:25 2022 UTC
183s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
183s gpgv: Can't check signature: No public key
183s dpkg-source: warning: cannot verify inline signature for ./phybin_0.3-6.dsc: no acceptable signature found
183s autopkgtest [16:44:25]: testing package phybin version 0.3-6
184s autopkgtest [16:44:26]: build not needed
185s autopkgtest [16:44:27]: test run-unit-test: preparing testbed
185s Reading package lists...
186s Building dependency tree...
186s Reading state information...
186s Starting pkgProblemResolver with broken count: 0
186s Starting 2 pkgProblemResolver with broken count: 0
186s Done
186s The following NEW packages will be installed:
186s   phybin
186s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
186s Need to get 9675 kB of archives.
186s After this operation, 54.9 MB of additional disk space will be used.
186s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x phybin s390x 0.3-6 [9675 kB]
196s Fetched 9675 kB in 10s (963 kB/s)
196s Selecting previously unselected package phybin.
196s (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.)
196s Preparing to unpack .../phybin_0.3-6_s390x.deb ...
196s Unpacking phybin (0.3-6) ...
197s Setting up phybin (0.3-6) ...
197s Processing triggers for man-db (2.13.0-1) ...
198s autopkgtest [16:44:40]: test run-unit-test: [-----------------------
198s Test 1 - Testing phybin on 112.tr
198s Tree "112"
198s ((6_134_D-alanine--D-alanine_ligase_wRi_WRi_001550,
198s   7_88_D-alanine--D-alanine_ligase_wMel_WD0095),
198s  ((1_177_D-alanine--D-alanine_ligase_family_protein_wUni-gwu_gwu_177,
198s    2_1056_D-alanine--D-alanine_ligase_family_protein_wVitA-gwv_gwv_1056),
198s   ((3_584_D-alanine--D-alanine_ligase_wBm_Wbm0570,
198s     14_97_D-alanine--D-alanine_ligase_wOo_wOo_01490),
198s    (13_1000_D-alanine--D-alanine_ligase_wAlbB_WALBB_840007,
198s     (19_986_D-alanine--D-alanine_ligase_wNo_wNo_10410,
198s      5_356_D-alanine--D-alanine_ligase_wPip-Pel_WPa_0403)))),
198s  18_124_D-alanine--D-alanine_ligase_wHa_wHa_01330);
198s =================================
198s PASS
198s Test 2 - Testing phybin on t30_mismatched
198s Input is a directory, reading all regular files contained (1 regular files found):  "t30_mismatched"
198s Cleaning away previous phybin outputs...
198s Parsing 1 Newick tree files.
198s 
198s Total unique taxa (10):
198s   1_ 7_ 6_ 18 13 5_ 19 3_ 14 2_
198s Note: defaulting to expecting ALL 10 to be present..
198s 
198s Number of input tree files: 1
198s Number of bad/unreadable input tree files: 1
198s Number of VALID trees (correct # of leaves/taxa): 2
198s Total tree nodes contained in valid trees: 20
198s Average branch len over valid trees: 0.0
198s Max/Min branch lengths: (0.0,0.0)
198s Creating equivalence classes (bins)...
198s  Outcome: 2 clusters found, 0 non-singleton, top bin sizes: [1,1]
198s   Up to first 30 bin sizes, excluding singletons:
198s  [finished] Wrote contents of each bin to cluster<N>_<binsize>.txt
198s             Wrote representative trees to cluster<N>_<binsize>_avg.tr
198s Waiting for 1 asynchronous tasks to finish...
198s Phybin completed.
198s ==================================
198s PASS
198s autopkgtest [16:44:40]: test run-unit-test: -----------------------]
199s run-unit-test        PASS
199s autopkgtest [16:44:41]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
199s autopkgtest [16:44:41]: @@@@@@@@@@@@@@@@@@@@ summary
199s run-unit-test        PASS
217s nova [W] Using flock in prodstack6-s390x
217s Creating nova instance adt-plucky-s390x-phybin-20250315-164121-juju-7f2275-prod-proposed-migration-environment-2-2cdf01de-9388-4ca6-8001-083a72219844 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
217s nova [W] Timed out waiting for 179e4873-2e09-4da6-b915-e8592dea843d to get deleted.