0s autopkgtest [11:06:52]: starting date and time: 2025-03-15 11:06:52+0000 0s autopkgtest [11:06:52]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [11:06:52]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.owu065l9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade readseq --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-18.secgroup --name adt-plucky-s390x-readseq-20250315-110652-juju-7f2275-prod-proposed-migration-environment-20-0aaff33f-65ea-4d20-b426-2e66d99416fb --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/ 124s autopkgtest [11:08:56]: testbed dpkg architecture: s390x 124s autopkgtest [11:08:56]: testbed apt version: 2.9.33 124s autopkgtest [11:08:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 124s autopkgtest [11:08:56]: testbed release detected to be: None 125s autopkgtest [11:08:57]: updating testbed package index (apt update) 125s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 125s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 126s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB] 126s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB] 126s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [80.7 kB] 126s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1852 B] 126s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 126s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [335 kB] 127s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [14.4 kB] 127s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 127s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [328 B] 127s Fetched 1034 kB in 2s (651 kB/s) 127s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Calculating upgrade... 128s Calculating upgrade... 128s The following packages were automatically installed and are no longer required: 128s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 128s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 128s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 128s linux-tools-6.11.0-8-generic 128s Use 'sudo apt autoremove' to remove them. 128s The following packages will be upgraded: 128s python3-jinja2 strace 128s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Need to get 609 kB of archives. 128s After this operation, 27.6 kB of additional disk space will be used. 128s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 129s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 129s Fetched 609 kB in 1s (625 kB/s) 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 ... 81428 files and directories currently installed.) 130s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 130s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 130s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 130s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 130s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 130s Setting up strace (6.13+ds-1ubuntu1) ... 130s Processing triggers for man-db (2.13.0-1) ... 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 131s Solving dependencies... 131s The following packages will be REMOVED: 131s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 131s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 131s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 131s linux-tools-6.11.0-8-generic* 131s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 131s After this operation, 167 MB disk space will be freed. 131s (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.) 131s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 131s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 131s Removing libpython3.12t64:s390x (3.12.9-1) ... 131s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 131s Removing libnsl2:s390x (1.3.0-3build3) ... 131s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 131s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 131s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 132s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 132s Processing triggers for libc-bin (2.41-1ubuntu1) ... 132s (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.) 132s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 132s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 132s autopkgtest [11:09:04]: upgrading testbed (apt dist-upgrade and autopurge) 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 133s Starting 2 pkgProblemResolver with broken count: 0 133s Done 133s Entering ResolveByKeep 133s 133s Calculating upgrade... 133s The following packages will be upgraded: 133s libc-bin libc-dev-bin libc6 libc6-dev locales 133s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 9512 kB of archives. 133s After this operation, 8192 B of additional disk space will be used. 133s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 135s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 138s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 139s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 144s Preconfiguring packages ... 144s Fetched 9512 kB in 10s (923 kB/s) 144s (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.) 144s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 144s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 144s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 144s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 144s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 144s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 144s Setting up libc6:s390x (2.41-1ubuntu2) ... 144s (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.) 144s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 144s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 144s Setting up libc-bin (2.41-1ubuntu2) ... 144s (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.) 144s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 144s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 144s Setting up locales (2.41-1ubuntu2) ... 144s Generating locales (this might take a while)... 145s en_US.UTF-8... done 145s Generation complete. 145s Setting up libc-dev-bin (2.41-1ubuntu2) ... 145s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 145s Processing triggers for man-db (2.13.0-1) ... 146s Processing triggers for systemd (257.3-1ubuntu3) ... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Starting pkgProblemResolver with broken count: 0 147s Starting 2 pkgProblemResolver with broken count: 0 147s Done 147s Solving dependencies... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s autopkgtest [11:09:19]: rebooting testbed after setup commands that affected boot 164s autopkgtest [11:09:36]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 166s autopkgtest [11:09:38]: @@@@@@@@@@@@@@@@@@@@ apt-source readseq 168s Get:1 http://ftpmaster.internal/ubuntu plucky/universe readseq 1-15 (dsc) [2069 B] 168s Get:2 http://ftpmaster.internal/ubuntu plucky/universe readseq 1-15 (tar) [54.6 kB] 168s Get:3 http://ftpmaster.internal/ubuntu plucky/universe readseq 1-15 (diff) [18.1 kB] 168s gpgv: Signature made Thu Mar 14 21:24:13 2024 UTC 168s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 168s gpgv: issuer "emollier@debian.org" 168s gpgv: Can't check signature: No public key 168s dpkg-source: warning: cannot verify inline signature for ./readseq_1-15.dsc: no acceptable signature found 168s autopkgtest [11:09:40]: testing package readseq version 1-15 168s autopkgtest [11:09:40]: build not needed 169s autopkgtest [11:09:41]: test Makefile: preparing testbed 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 169s Starting pkgProblemResolver with broken count: 0 169s Starting 2 pkgProblemResolver with broken count: 0 169s Done 169s The following NEW packages will be installed: 169s libncbi6t64 ncbi-data readseq 169s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 169s Need to get 8588 kB of archives. 169s After this operation, 40.1 MB of additional disk space will be used. 169s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libncbi6t64 s390x 6.1.20170106+dfsg2-5 [4563 kB] 179s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x readseq s390x 1-15 [59.1 kB] 179s Fetched 8588 kB in 10s (887 kB/s) 179s Selecting previously unselected package ncbi-data. 179s (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.) 179s Preparing to unpack .../ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 179s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 179s Selecting previously unselected package libncbi6t64:s390x. 179s Preparing to unpack .../libncbi6t64_6.1.20170106+dfsg2-5_s390x.deb ... 179s Unpacking libncbi6t64:s390x (6.1.20170106+dfsg2-5) ... 179s Selecting previously unselected package readseq. 179s Preparing to unpack .../readseq_1-15_s390x.deb ... 179s Unpacking readseq (1-15) ... 179s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 179s Setting up libncbi6t64:s390x (6.1.20170106+dfsg2-5) ... 179s Setting up readseq (1-15) ... 179s Processing triggers for man-db (2.13.0-1) ... 180s Processing triggers for libc-bin (2.41-1ubuntu2) ... 181s autopkgtest [11:09:53]: test Makefile: [----------------------- 181s 181s Test for general read/write of all chars: 181s /usr/bin/readseq -p alphabet.std -otest.alpha 181s diff test.alpha alphabet.std 181s 181s Test for valid format conversions: 181s /usr/bin/readseq -v -p -f=ig nucleic.std -otest.ig 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test 181s /usr/bin/readseq -v -p -f=gb test.ig -otest.gb 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino 181s /usr/bin/readseq -v -p -f=nbrf test.gb -otest.nbrf 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp 181s /usr/bin/readseq -v -p -f=embl test.nbrf -otest.embl 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino 181s /usr/bin/readseq -v -p -f=gcg test.embl -otest.gcg 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino 181s /usr/bin/readseq -v -p -f=strider test.gcg -otest.strider 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino 181s /usr/bin/readseq -v -p -f=fitch test.strider -otest.fitch 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. 181s /usr/bin/readseq -v -p -f=fasta test.fitch -otest.fasta 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. 181s /usr/bin/readseq -v -p -f=pir test.fasta -otest.pir 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. 181s /usr/bin/readseq -v -p -f=ig test.pir -otest.ig-b 181s Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, 181s diff test.ig test.ig-b 181s 1,2c1,2 181s < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. 181s < nucleic/amino 181s --- 181s > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. 181s > nucleic/amino, 181s 181s Test for multiple-sequence format conversions: 181s /usr/bin/readseq -p -f=ig multi.std -otest.m-ig 181s /usr/bin/readseq -p -f=gb test.m-ig -otest.m-gb 181s /usr/bin/readseq -p -f=nbrf test.m-gb -otest.m-nbrf 181s /usr/bin/readseq -p -f=embl test.m-nbrf -otest.m-embl 181s /usr/bin/readseq -p -f=fasta test.m-embl -otest.m-fasta 181s /usr/bin/readseq -p -f=pir test.m-fasta -otest.m-pir 181s /usr/bin/readseq -p -f=msf test.m-pir -otest.m-msf 181s /usr/bin/readseq -p -f=paup test.m-msf -otest.m-paup 181s /usr/bin/readseq -p -f=ig test.m-paup -otest.m-ig-b 181s diff test.m-ig test.m-ig-b 181s 1,2c1,2 181s < ;acarr58sst , 183 bases, 64754A4D checksum. 181s < acarr58sst 181s --- 181s > ;acarr58ss, 183 bases, 64754A4D checksum. 181s > acarr58ss 181s 7c7 181s < ;amgrrbst , 183 bases, C886D2FB checksum. 181s --- 181s > ;amgrrbst, 183 bases, C886D2FB checksum. 181s 13c13 181s < ;bmorrbst , 183 bases, 3E9C23D6 checksum. 181s --- 181s > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 181s 19c19 181s < ;crerrbst , 183 bases, AC88A337 checksum. 181s --- 181s > ;crerrbst, 183 bases, AC88A337 checksum. 181s 25,26c25,26 181s < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. 181s < ddirr58sst 181s --- 181s > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. 181s > ddirr58ss 181s 181s Expect differences in the header lines due to 181s different format headers. If any sequence lines 181s differ, or if the checksums differ, there is a problem. 181s ---------------------- 181s 181s To clean up test files, command me: 181s make clean 181s make: [/tmp/autopkgtest.Atcnd7/build.HZB/src/debian/tests/Makefile:26: test] Error 1 (ignored) 181s make: [/tmp/autopkgtest.Atcnd7/build.HZB/src/debian/tests/Makefile:38: test] Error 1 (ignored) 181s autopkgtest [11:09:53]: test Makefile: -----------------------] 182s autopkgtest [11:09:54]: test Makefile: - - - - - - - - - - results - - - - - - - - - - 182s Makefile PASS 182s autopkgtest [11:09:54]: @@@@@@@@@@@@@@@@@@@@ summary 182s Makefile PASS 199s nova [W] Using flock in prodstack6-s390x 199s Creating nova instance adt-plucky-s390x-readseq-20250315-110652-juju-7f2275-prod-proposed-migration-environment-20-0aaff33f-65ea-4d20-b426-2e66d99416fb from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 199s nova [W] Timed out waiting for 832167e0-6231-41f0-bf49-52ec010f3c57 to get deleted.