0s autopkgtest [17:03:10]: starting date and time: 2025-03-15 17:03:10+0000 0s autopkgtest [17:03:10]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:03:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ibt6rns3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade pyfastx --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-5.secgroup --name adt-plucky-s390x-pyfastx-20250315-170309-juju-7f2275-prod-proposed-migration-environment-2-e44f9827-1dca-4bf6-9841-3bc984e51c26 --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 [17:05:26]: testbed dpkg architecture: s390x 136s autopkgtest [17:05:26]: testbed apt version: 2.9.33 136s autopkgtest [17:05:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 136s autopkgtest [17:05:26]: testbed release detected to be: None 137s autopkgtest [17:05:27]: updating testbed package index (apt update) 137s 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/multiverse Sources [15.8 kB] 138s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 138s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 138s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 138s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 138s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 138s 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 (627 kB/s) 140s Reading package lists... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 140s 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 (531 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* 144s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 144s After this operation, 167 MB disk space will be freed. 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 ... 81428 files and directories currently installed.) 144s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 144s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 144s 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 [17:05:35]: 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] 151s 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 (920 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 ... 157s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Setting up libc6:s390x (2.41-1ubuntu2) ... 157s (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.) 157s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 157s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s Setting up libc-bin (2.41-1ubuntu2) ... 157s (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.) 157s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 157s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 157s 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) ... 159s Processing triggers for systemd (257.3-1ubuntu3) ... 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 Solving dependencies... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [17:05:51]: rebooting testbed after setup commands that affected boot 179s autopkgtest [17:06:09]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 182s autopkgtest [17:06:12]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 184s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (dsc) [2171 B] 184s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (tar) [231 kB] 184s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.2.0-1build1 (diff) [7896 B] 185s gpgv: Signature made Tue Mar 4 15:58:37 2025 UTC 185s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 185s gpgv: Can't check signature: No public key 185s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.2.0-1build1.dsc: no acceptable signature found 185s autopkgtest [17:06:15]: testing package pyfastx version 2.2.0-1build1 185s autopkgtest [17:06:15]: build not needed 186s autopkgtest [17:06:16]: test run-unit-test: preparing testbed 186s 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 187s The following NEW packages will be installed: 187s pyfastx python3-all python3-importlib-metadata python3-packaging 187s python3-pyfaidx python3-pyfastx 187s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 187s Need to get 284 kB of archives. 187s After this operation, 835 kB of additional disk space will be used. 187s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.6.1-1 [20.7 kB] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 187s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfastx s390x 2.2.0-1build1 [59.1 kB] 187s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x pyfastx s390x 2.2.0-1build1 [122 kB] 187s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.13.2-2 [886 B] 187s Fetched 284 kB in 1s (462 kB/s) 187s Selecting previously unselected package python3-importlib-metadata. 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 ... 56326 files and directories currently installed.) 187s Preparing to unpack .../0-python3-importlib-metadata_8.6.1-1_all.deb ... 187s Unpacking python3-importlib-metadata (8.6.1-1) ... 188s Selecting previously unselected package python3-packaging. 188s Preparing to unpack .../1-python3-packaging_24.2-1_all.deb ... 188s Unpacking python3-packaging (24.2-1) ... 188s Selecting previously unselected package python3-pyfaidx. 188s Preparing to unpack .../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 188s Unpacking python3-pyfaidx (0.8.1.3-1) ... 188s Selecting previously unselected package python3-pyfastx. 188s Preparing to unpack .../3-python3-pyfastx_2.2.0-1build1_s390x.deb ... 188s Unpacking python3-pyfastx (2.2.0-1build1) ... 188s Selecting previously unselected package pyfastx. 188s Preparing to unpack .../4-pyfastx_2.2.0-1build1_s390x.deb ... 188s Unpacking pyfastx (2.2.0-1build1) ... 188s Selecting previously unselected package python3-all. 188s Preparing to unpack .../5-python3-all_3.13.2-2_s390x.deb ... 188s Unpacking python3-all (3.13.2-2) ... 188s Setting up python3-importlib-metadata (8.6.1-1) ... 188s Setting up python3-all (3.13.2-2) ... 188s Setting up python3-packaging (24.2-1) ... 188s Setting up python3-pyfaidx (0.8.1.3-1) ... 188s Setting up python3-pyfastx (2.2.0-1build1) ... 188s Setting up pyfastx (2.2.0-1build1) ... 188s Processing triggers for man-db (2.13.0-1) ... 189s autopkgtest [17:06:19]: test run-unit-test: [----------------------- 190s test_id_exception (tests.test_fakeys.IdentifierTest.test_id_exception) ... ok 190s test_key_identifier (tests.test_fakeys.IdentifierTest.test_key_identifier) ... ok 190s test_key_repr (tests.test_fakeys.IdentifierTest.test_key_repr) ... ok 190s test_key_slice (tests.test_fakeys.IdentifierTest.test_key_slice) ... ok 190s test_keys_filter (tests.test_fakeys.IdentifierTest.test_keys_filter) ... ok 190s test_keys_sort (tests.test_fakeys.IdentifierTest.test_keys_sort) ... ok 190s test_build (tests.test_fasta.FastaTest.test_build) ... ok 190s test_exception (tests.test_fasta.FastaTest.test_exception) ... ok 190s test_fasta (tests.test_fasta.FastaTest.test_fasta) ... ok 190s test_iter_full_name (tests.test_fasta.FastaTest.test_iter_full_name) ... ok 190s test_iter_object (tests.test_fasta.FastaTest.test_iter_object) ... ok 190s test_iter_tuple (tests.test_fasta.FastaTest.test_iter_tuple) ... ok 190s test_iter_upper (tests.test_fasta.FastaTest.test_iter_upper) ... ok 190s test_iter_upper_full_name (tests.test_fasta.FastaTest.test_iter_upper_full_name) ... ok 190s test_key_func (tests.test_fasta.FastaTest.test_key_func) ... ok 190s test_module (tests.test_fasta.FastaTest.test_module) ... ok 190s test_no_upper (tests.test_fasta.FastaTest.test_no_upper) ... ok 190s test_repr (tests.test_fasta.FastaTest.test_repr) ... ok 190s test_seq_fetch (tests.test_fasta.FastaTest.test_seq_fetch) ... ok 190s test_seq_flank (tests.test_fasta.FastaTest.test_seq_flank) ... ok 190s test_seq_type (tests.test_fasta.FastaTest.test_seq_type) ... ok 190s test_statistics (tests.test_fasta.FastaTest.test_statistics) ... ok 190s test_build (tests.test_fastq.FastqTest.test_build) ... ok 190s test_exception (tests.test_fastq.FastqTest.test_exception) ... ok 190s test_fastq (tests.test_fastq.FastqTest.test_fastq) ... ok 191s test_full_name (tests.test_fastq.FastqTest.test_full_name) ... ok 191s test_iter_object (tests.test_fastq.FastqTest.test_iter_object) ... ok 191s test_iter_tuple (tests.test_fastq.FastqTest.test_iter_tuple) ... ok 191s test_negative (tests.test_fastq.FastqTest.test_negative) ... ok 191s test_platform (tests.test_fastq.FastqTest.test_platform) ... ok 191s test_read_len (tests.test_fastq.FastqTest.test_read_len) ... ok 191s test_repr (tests.test_fastq.FastqTest.test_repr) ... ok 191s test_exception (tests.test_fastx.FastxTest.test_exception) ... ok 191s test_fasta_iter (tests.test_fastx.FastxTest.test_fasta_iter) ... ok 191s test_fasta_upper (tests.test_fastx.FastxTest.test_fasta_upper) ... ok 191s test_fastq_iter (tests.test_fastx.FastxTest.test_fastq_iter) ... ok 191s test_fastx_repr (tests.test_fastx.FastxTest.test_fastx_repr) ... ok 191s test_exception (tests.test_fqkeys.FastxTest.test_exception) ... ok 191s test_fastq_key (tests.test_fqkeys.FastxTest.test_fastq_key) ... ok 191s test_read (tests.test_read.ReadTest.test_read) ... ok 191s test_read_description (tests.test_read.ReadTest.test_read_description) ... ok 191s test_read_raw (tests.test_read.ReadTest.test_read_raw) ... ok 191s test_read_seq (tests.test_read.ReadTest.test_read_seq) ... ok 191s test_repr (tests.test_read.ReadTest.test_repr) ... ok 191s test_full_compo (tests.test_sequence.SequenceTest.test_full_compo) ... ok 191s test_seq_by_index (tests.test_sequence.SequenceTest.test_seq_by_index) ... ok 191s test_seq_by_key (tests.test_sequence.SequenceTest.test_seq_by_key) ... ok 191s test_seq_content (tests.test_sequence.SequenceTest.test_seq_content) ... ok 191s test_seq_exception (tests.test_sequence.SequenceTest.test_seq_exception) ... ok 191s test_seq_iter (tests.test_sequence.SequenceTest.test_seq_iter) ... ok 191s test_seq_raw (tests.test_sequence.SequenceTest.test_seq_raw) ... ok 191s test_seq_repr (tests.test_sequence.SequenceTest.test_seq_repr) ... ok 191s test_seq_reverse_complement (tests.test_sequence.SequenceTest.test_seq_reverse_complement) ... ok 191s test_seq_slice (tests.test_sequence.SequenceTest.test_seq_slice) ... ok 191s test_seq_by_index (tests.test_sequence_error.SequenceErrorTest.test_seq_by_index) ... ok 191s test_seq_by_key (tests.test_sequence_error.SequenceErrorTest.test_seq_by_key) ... ok 191s 191s ---------------------------------------------------------------------- 191s Ran 56 tests in 1.471s 191s 191s OK 192s autopkgtest [17:06:22]: test run-unit-test: -----------------------] 192s run-unit-test PASS 192s autopkgtest [17:06:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 192s autopkgtest [17:06:22]: test test-cli: preparing testbed 350s autopkgtest [17:09:00]: testbed dpkg architecture: s390x 351s autopkgtest [17:09:01]: testbed apt version: 2.9.33 351s autopkgtest [17:09:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 351s autopkgtest [17:09:01]: testbed release detected to be: plucky 352s autopkgtest [17:09:02]: updating testbed package index (apt update) 353s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 353s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 353s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 353s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 353s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 354s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 354s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 354s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 354s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 354s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 354s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 354s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 354s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 354s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 354s Fetched 1073 kB in 2s (622 kB/s) 355s Reading package lists... 356s Reading package lists... 356s Building dependency tree... 356s Reading state information... 356s Calculating upgrade... 356s Calculating upgrade... 356s The following packages were automatically installed and are no longer required: 356s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 356s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 356s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 356s linux-tools-6.11.0-8-generic 356s Use 'sudo apt autoremove' to remove them. 356s The following packages will be upgraded: 356s pinentry-curses python3-jinja2 strace 356s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 356s Need to get 652 kB of archives. 356s After this operation, 27.6 kB of additional disk space will be used. 356s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 357s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 357s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 357s Fetched 652 kB in 1s (666 kB/s) 358s (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.) 358s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 358s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 358s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 358s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 358s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 358s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 358s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 358s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 358s Setting up strace (6.13+ds-1ubuntu1) ... 358s Processing triggers for man-db (2.13.0-1) ... 358s Reading package lists... 358s Building dependency tree... 358s Reading state information... 359s Solving dependencies... 359s The following packages will be REMOVED: 359s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 359s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 359s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 359s linux-tools-6.11.0-8-generic* 359s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 359s After this operation, 167 MB disk space will be freed. 359s (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.) 359s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 359s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 359s Removing libpython3.12t64:s390x (3.12.9-1) ... 359s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 359s Removing libnsl2:s390x (1.3.0-3build3) ... 359s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 359s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 359s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 360s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 360s Processing triggers for libc-bin (2.41-1ubuntu1) ... 360s (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.) 360s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 360s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 360s autopkgtest [17:09:10]: upgrading testbed (apt dist-upgrade and autopurge) 360s Reading package lists... 360s Building dependency tree... 360s Reading state information... 361s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 361s Starting 2 pkgProblemResolver with broken count: 0 361s Done 361s Entering ResolveByKeep 361s 361s Calculating upgrade... 361s The following packages will be upgraded: 361s libc-bin libc-dev-bin libc6 libc6-dev locales 361s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 361s Need to get 9512 kB of archives. 361s After this operation, 8192 B of additional disk space will be used. 361s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 363s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 363s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 366s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 367s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 371s Preconfiguring packages ... 371s Fetched 9512 kB in 9s (1018 kB/s) 371s (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.) 371s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 371s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 371s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 371s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 371s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 371s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 371s Setting up libc6:s390x (2.41-1ubuntu2) ... 371s (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.) 371s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 371s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 371s Setting up libc-bin (2.41-1ubuntu2) ... 371s (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.) 371s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 371s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 371s Setting up locales (2.41-1ubuntu2) ... 371s Generating locales (this might take a while)... 372s en_US.UTF-8... done 372s Generation complete. 372s Setting up libc-dev-bin (2.41-1ubuntu2) ... 372s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 373s Processing triggers for man-db (2.13.0-1) ... 373s Processing triggers for systemd (257.3-1ubuntu3) ... 374s Reading package lists... 374s Building dependency tree... 374s Reading state information... 374s Starting pkgProblemResolver with broken count: 0 374s Starting 2 pkgProblemResolver with broken count: 0 374s Done 374s Solving dependencies... 374s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 375s autopkgtest [17:09:25]: rebooting testbed after setup commands that affected boot 399s Reading package lists... 399s Building dependency tree... 399s Reading state information... 399s Starting pkgProblemResolver with broken count: 0 399s Starting 2 pkgProblemResolver with broken count: 0 399s Done 399s The following NEW packages will be installed: 399s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 399s python3-pyfastx 400s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 400s Need to get 283 kB of archives. 400s After this operation, 828 kB of additional disk space will be used. 400s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.6.1-1 [20.7 kB] 400s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 400s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 400s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfastx s390x 2.2.0-1build1 [59.1 kB] 400s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x pyfastx s390x 2.2.0-1build1 [122 kB] 400s Fetched 283 kB in 1s (433 kB/s) 400s Selecting previously unselected package python3-importlib-metadata. 400s (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.) 400s Preparing to unpack .../python3-importlib-metadata_8.6.1-1_all.deb ... 400s Unpacking python3-importlib-metadata (8.6.1-1) ... 400s Selecting previously unselected package python3-packaging. 400s Preparing to unpack .../python3-packaging_24.2-1_all.deb ... 400s Unpacking python3-packaging (24.2-1) ... 400s Selecting previously unselected package python3-pyfaidx. 400s Preparing to unpack .../python3-pyfaidx_0.8.1.3-1_all.deb ... 400s Unpacking python3-pyfaidx (0.8.1.3-1) ... 400s Selecting previously unselected package python3-pyfastx. 400s Preparing to unpack .../python3-pyfastx_2.2.0-1build1_s390x.deb ... 400s Unpacking python3-pyfastx (2.2.0-1build1) ... 400s Selecting previously unselected package pyfastx. 400s Preparing to unpack .../pyfastx_2.2.0-1build1_s390x.deb ... 400s Unpacking pyfastx (2.2.0-1build1) ... 400s Setting up python3-importlib-metadata (8.6.1-1) ... 401s Setting up python3-packaging (24.2-1) ... 401s Setting up python3-pyfaidx (0.8.1.3-1) ... 401s Setting up python3-pyfastx (2.2.0-1build1) ... 401s Setting up pyfastx (2.2.0-1build1) ... 401s Processing triggers for man-db (2.13.0-1) ... 404s autopkgtest [17:09:54]: test test-cli: [----------------------- 404s $ pyfastx --help 404s usage: pyfastx COMMAND [OPTIONS] 404s 404s A command line tool for FASTA/Q file manipulation 404s 404s options: 404s -h, --help show this help message and exit 404s -v, --version show program's version number and exit 404s 404s Commands: 404s 404s index build index for fasta/q file 404s stat show detailed statistics information of fasta/q file 404s split split fasta/q file into multiple files 404s fq2fa convert fastq file to fasta file 404s subseq get subsequences from fasta file by region 404s sample randomly sample sequences from fasta or fastq file 404s extract extract full sequences or reads from fasta/q file 404s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 404s $ pyfastx index --help 404s usage: pyfastx index [-h] [-f] fastx [fastx ...] 404s 404s positional arguments: 404s fastx fasta or fastq file, gzip support 404s 404s options: 404s -h, --help show this help message and exit 404s -f, --full build full index, base composition will be calculated 404s $ pyfastx stat --help 404s usage: pyfastx stat [-h] fastx [fastx ...] 404s 404s positional arguments: 404s fastx fasta or fastq file, gzip support 404s 404s options: 404s -h, --help show this help message and exit 404s $ pyfastx split --help 404s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 404s 404s positional arguments: 404s fastx fasta or fastq file, gzip support 404s 404s options: 404s -h, --help show this help message and exit 404s -n int split a fasta/q file into N new files with even size 404s -c int split a fasta/q file into multiple files containing the 404s same sequence counts 404s -o, --out-dir str output directory, default is current folder 404s $ pyfastx fq2fa --help 404s usage: pyfastx fq2fa [-h] [-o str] fastx 404s 404s positional arguments: 404s fastx fastq file, gzip support 404s 404s options: 404s -h, --help show this help message and exit 404s -o, --out-file str output file, default: output to stdout 404s $ pyfastx subseq --help 404s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 404s 404s positional arguments: 404s fastx input fasta file, gzip support 404s region format is chr:start-end, start and end position is 404s 1-based, multiple regions were separated by space 404s 404s options: 404s -h, --help show this help message and exit 404s -r, --region-file str 404s tab-delimited file, one region per line, both start 404s and end position are 1-based 404s -b, --bed-file str tab-delimited BED file, 0-based start position and 404s 1-based end position 404s -o, --out-file str output file, default: output to stdout 404s $ pyfastx sample --help 404s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 404s [-o str] 404s fastx 404s 404s positional arguments: 404s fastx fasta or fastq file, gzip support 404s 404s options: 404s -h, --help show this help message and exit 404s -n int number of sequences to be sampled 404s -p float proportion of sequences to be sampled, 0~1 404s -s, --seed int random seed, default is the current system time 404s --sequential-read start sequential reading, particularly suitable for 404s sampling large numbers of sequences 404s -o, --out-file str output file, default: output to stdout 404s $ pyfastx extract --help 404s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 404s [-o str] [--sequential-read] 404s fastx [name ...] 404s 404s positional arguments: 404s fastx fasta or fastq file, gzip support 404s name sequence name or read name, multiple names were 404s separated by space 404s 404s options: 404s -h, --help show this help message and exit 404s -l, --list-file str a file containing sequence or read names, one name per 404s line 404s --reverse-complement output reverse complement sequence 404s --out-fasta output fasta format when extract reads from fastq, 404s default output fastq format 404s -o, --out-file str output file, default: output to stdout 404s --sequential-read start sequential reading, particularly suitable for 404s extracting large numbers of sequences 404s $ pyfastx --version 404s pyfastx version 2.2.0 404s $ pyfastx index protein.fa 404s $ pyfastx index rna.fa 404s $ pyfastx index test.fa 404s $ pyfastx index test.fq 404s $ pyfastx index test.fa.gz 404s $ pyfastx index test.fq.gz 405s $ pyfastx stat protein.fa 405s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 405s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 405s $ pyfastx split -n 2 protein.fa 405s $ pyfastx fq2fa test.fq -o test.fa 405s $ pyfastx subseq protein.fa UPI0000000011:1-4 405s >UPI0000000011:1-4 405s MVDA 405s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 405s $ pyfastx extract protein.fa UPI0000000011 405s >UPI0000000011 status=active 405s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 405s IPGTIILYATYVKSLLMKS 405s autopkgtest [17:09:55]: test test-cli: -----------------------] 406s test-cli PASS 406s autopkgtest [17:09:56]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 406s autopkgtest [17:09:56]: @@@@@@@@@@@@@@@@@@@@ summary 406s run-unit-test PASS 406s test-cli PASS 425s nova [W] Using flock in prodstack6-s390x 425s Creating nova instance adt-plucky-s390x-pyfastx-20250315-170309-juju-7f2275-prod-proposed-migration-environment-2-e44f9827-1dca-4bf6-9841-3bc984e51c26 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 425s nova [W] Timed out waiting for 532cb5bd-54cc-417f-9a9b-1650338da131 to get deleted. 425s nova [W] Using flock in prodstack6-s390x 425s flock: timeout while waiting to get lock 425s Creating nova instance adt-plucky-s390x-pyfastx-20250315-170309-juju-7f2275-prod-proposed-migration-environment-2-e44f9827-1dca-4bf6-9841-3bc984e51c26 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 425s nova [W] Timed out waiting for 221c4b9c-9019-4d5f-a8e9-1cb4ec56f6b9 to get deleted.