0s autopkgtest [16:49:39]: starting date and time: 2025-03-15 16:49:39+0000
  0s autopkgtest [16:49:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [16:49:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.etdz0oax/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade primer3 --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-15.secgroup --name adt-plucky-s390x-primer3-20250315-164939-juju-7f2275-prod-proposed-migration-environment-2-0cdee886-5471-418d-bf3e-af109aa6fe5c --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/
150s autopkgtest [16:52:09]: testbed dpkg architecture: s390x
150s autopkgtest [16:52:09]: testbed apt version: 2.9.33
150s autopkgtest [16:52:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup
151s autopkgtest [16:52:10]: testbed release detected to be: None
151s autopkgtest [16:52:10]: updating testbed package index (apt update)
152s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
152s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
152s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
152s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
152s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
153s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
153s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
153s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB]
153s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B]
153s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
153s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB]
153s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB]
153s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B]
153s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B]
154s Fetched 1073 kB in 2s (595 kB/s)
154s Reading package lists...
155s Reading package lists...
155s Building dependency tree...
155s Reading state information...
155s Calculating upgrade...
155s Calculating upgrade...
155s The following packages were automatically installed and are no longer required:
155s   libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
155s   linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
155s   linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
155s   linux-tools-6.11.0-8-generic
155s Use 'sudo apt autoremove' to remove them.
155s The following packages will be upgraded:
155s   pinentry-curses python3-jinja2 strace
155s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
155s Need to get 652 kB of archives.
155s After this operation, 27.6 kB of additional disk space will be used.
155s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
156s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB]
156s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
156s Fetched 652 kB in 1s (597 kB/s)
157s (Reading database ... 
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(Reading database ... 81428 files and directories currently installed.)
157s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
157s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
157s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ...
157s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
157s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
157s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
157s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
157s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
157s Setting up strace (6.13+ds-1ubuntu1) ...
157s Processing triggers for man-db (2.13.0-1) ...
157s Reading package lists...
158s Building dependency tree...
158s Reading state information...
158s Solving dependencies...
158s The following packages will be REMOVED:
158s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
158s   linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
158s   linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
158s   linux-tools-6.11.0-8-generic*
158s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
158s After this operation, 167 MB disk space will be freed.
158s (Reading database ... 
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(Reading database ... 81428 files and directories currently installed.)
158s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
158s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
158s Removing libpython3.12t64:s390x (3.12.9-1) ...
158s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
158s Removing libnsl2:s390x (1.3.0-3build3) ...
158s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
158s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
158s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
159s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
159s Processing triggers for libc-bin (2.41-1ubuntu1) ...
159s (Reading database ... 
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(Reading database ... 56328 files and directories currently installed.)
159s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
159s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
159s autopkgtest [16:52:18]: upgrading testbed (apt dist-upgrade and autopurge)
160s Reading package lists...
160s Building dependency tree...
160s Reading state information...
160s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
160s Starting 2 pkgProblemResolver with broken count: 0
160s Done
160s Entering ResolveByKeep
160s 
160s Calculating upgrade...
160s The following packages will be upgraded:
160s   libc-bin libc-dev-bin libc6 libc6-dev locales
161s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
161s Need to get 9512 kB of archives.
161s After this operation, 8192 B of additional disk space will be used.
161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
163s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
163s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
166s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
167s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
171s Preconfiguring packages ...
171s Fetched 9512 kB in 11s (885 kB/s)
171s (Reading database ... 
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(Reading database ... 56326 files and directories currently installed.)
171s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
171s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
172s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
172s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Setting up libc6:s390x (2.41-1ubuntu2) ...
172s (Reading database ... 
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(Reading database ... 56326 files and directories currently installed.)
172s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
172s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Setting up libc-bin (2.41-1ubuntu2) ...
172s (Reading database ... 
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(Reading database ... 56326 files and directories currently installed.)
172s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
172s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Setting up locales (2.41-1ubuntu2) ...
172s Generating locales (this might take a while)...
173s   en_US.UTF-8... done
173s Generation complete.
173s Setting up libc-dev-bin (2.41-1ubuntu2) ...
173s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
173s Processing triggers for man-db (2.13.0-1) ...
174s Processing triggers for systemd (257.3-1ubuntu3) ...
175s Reading package lists...
175s Building dependency tree...
175s Reading state information...
175s Starting pkgProblemResolver with broken count: 0
175s Starting 2 pkgProblemResolver with broken count: 0
175s Done
175s Solving dependencies...
175s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
175s autopkgtest [16:52:34]: rebooting testbed after setup commands that affected boot
195s autopkgtest [16:52:54]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025
197s autopkgtest [16:52:56]: @@@@@@@@@@@@@@@@@@@@ apt-source primer3
235s Get:1 http://ftpmaster.internal/ubuntu plucky/universe primer3 2.6.1-5 (dsc) [2101 B]
235s Get:2 http://ftpmaster.internal/ubuntu plucky/universe primer3 2.6.1-5 (tar) [32.9 MB]
235s Get:3 http://ftpmaster.internal/ubuntu plucky/universe primer3 2.6.1-5 (diff) [14.0 kB]
235s gpgv: Signature made Sun Dec  1 12:08:12 2024 UTC
235s gpgv:                using RSA key 52D5BD0E7D4DB084E34B5865D4A41CFADDB20DB5
235s gpgv: Can't check signature: No public key
235s dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: no acceptable signature found
235s autopkgtest [16:53:34]: testing package primer3 version 2.6.1-5
236s autopkgtest [16:53:35]: build not needed
242s autopkgtest [16:53:41]: test run-unit-test: preparing testbed
242s Reading package lists...
242s Building dependency tree...
242s Reading state information...
242s Starting pkgProblemResolver with broken count: 0
242s Starting 2 pkgProblemResolver with broken count: 0
242s Done
242s The following NEW packages will be installed:
242s   libc6-dbg primer3 primer3-examples valgrind
243s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
243s Need to get 49.6 MB of archives.
243s After this operation, 104 MB of additional disk space will be used.
243s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x primer3 s390x 2.6.1-5 [235 kB]
243s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x primer3-examples all 2.6.1-5 [31.8 MB]
278s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dbg s390x 2.41-1ubuntu2 [7966 kB]
295s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x valgrind s390x 1:3.24.0-0ubuntu1 [9636 kB]
317s Fetched 49.6 MB in 1min 15s (666 kB/s)
317s Selecting previously unselected package primer3.
317s (Reading database ... 
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(Reading database ... 56326 files and directories currently installed.)
317s Preparing to unpack .../primer3_2.6.1-5_s390x.deb ...
317s Unpacking primer3 (2.6.1-5) ...
317s Selecting previously unselected package primer3-examples.
317s Preparing to unpack .../primer3-examples_2.6.1-5_all.deb ...
317s Unpacking primer3-examples (2.6.1-5) ...
318s Selecting previously unselected package libc6-dbg:s390x.
318s Preparing to unpack .../libc6-dbg_2.41-1ubuntu2_s390x.deb ...
318s Unpacking libc6-dbg:s390x (2.41-1ubuntu2) ...
318s Selecting previously unselected package valgrind.
318s Preparing to unpack .../valgrind_1%3a3.24.0-0ubuntu1_s390x.deb ...
318s Unpacking valgrind (1:3.24.0-0ubuntu1) ...
318s Setting up primer3-examples (2.6.1-5) ...
318s Setting up libc6-dbg:s390x (2.41-1ubuntu2) ...
318s Setting up primer3 (2.6.1-5) ...
318s Setting up valgrind (1:3.24.0-0ubuntu1) ...
318s Processing triggers for man-db (2.13.0-1) ...
319s autopkgtest [16:54:58]: test run-unit-test: [-----------------------
320s example
320s kmer_lists
320s settings_files
320s src
320s test
320s testcmdline:
320s 
320s 
320s TESTING command line arguments
320s 
320s Test 1... [OK]
320s Test 2... [OK]
320s Test 3... [OK]
320s Test 4... [OK]
320s Test 5... [OK]
320s Passed all tests - [OK]
320s 
320s 
320s testcore:
320s 
320s 
320s TESTING primer3_core
320s 
320s p3test.pl for primer3_core version 2.6.1
320s 
320s 
320s p3test.pl: testing ../src/primer3_core
320s 
320s START, Sat Mar 15 16:54:59 2025
320s 
320s testing fatal errors...
320s   ./primer_global_err/annealing_temp_salt
320s Testing --output and --error flags on
320s ../src/primer3_core --strict_tags ./primer_global_err/annealing_temp_salt.in --output ./primer_global_err/annealing_temp_salt.tmp --error ./primer_global_err/annealing_temp_salt.tmp2
320s   ./primer_global_err/bad_divalent_dntp_conc_1
320s   ./primer_global_err/bad_divalent_dntp_conc_2
320s   ./primer_global_err/bad_divalent_dntp_conc_3
320s   ./primer_global_err/bad_divalent_dntp_conc_4
320s   ./primer_global_err/bad_dna_conc
320s   ./primer_global_err/bad_first_base_index
320s   ./primer_global_err/bad_float_1
320s   ./primer_global_err/bad_float_2
320s   ./primer_global_err/bad_float_3
320s   ./primer_global_err/bad_float_4
320s   ./primer_global_err/bad_gc_1
320s   ./primer_global_err/bad_gc_2
320s   ./primer_global_err/bad_gc_3
320s   ./primer_global_err/bad_gc_int_1
320s   ./primer_global_err/bad_gc_int_2
320s   ./primer_global_err/bad_gc_int_3
320s   ./primer_global_err/bad_min_three_prime_distance
320s   ./primer_global_err/bad_num_ns
320s   ./primer_global_err/bad_num_ns_int
320s   ./primer_global_err/bad_product_sizes_1
320s   ./primer_global_err/bad_product_sizes_2
320s   ./primer_global_err/bad_product_sizes_3
320s   ./primer_global_err/bad_product_sizes_4
320s   ./primer_global_err/bad_salt_conc
320s   ./primer_global_err/bad_self_any
320s   ./primer_global_err/bad_self_any_int
320s   ./primer_global_err/bad_self_end
320s   ./primer_global_err/bad_self_end_int
320s   ./primer_global_err/bad_settings0
320s   ./primer_global_err/bad_settings1
320s   ./primer_global_err/bad_settings2
320s   ./primer_global_err/bad_settings3
320s   ./primer_global_err/bad_settings4
320s   ./primer_global_err/bad_settings5
320s   ./primer_global_err/bad_settings6
320s   ./primer_global_err/empty_1
320s   ./primer_global_err/empty_product_size
320s   ./primer_global_err/gc_clamp_min_size
320s   ./primer_global_err/incorrect_task
320s   ./primer_global_err/io_gc_content_obj_fn
320s   ./primer_global_err/io_obj_fn
320s   ./primer_global_err/junction_overlap_max_size
320s   ./primer_global_err/junction_overlap_min_size
320s   ./primer_global_err/max_annealing_temp
320s   ./primer_global_err/max_min_bound
320s   ./primer_global_err/max_min_bound_int
320s   ./primer_global_err/max_min_tm
320s   ./primer_global_err/max_min_tm_int
320s   ./primer_global_err/max_opt_bound
320s   ./primer_global_err/max_opt_bound_int
320s   ./primer_global_err/max_opt_tm
320s   ./primer_global_err/max_opt_tm_int
320s   ./primer_global_err/MAX_PRIMER_LENGTH
320s   ./primer_global_err/max_size_limit_int
320s   ./primer_global_err/max_size_limit_with_overhang
320s   ./primer_global_err/max_size_min_product
320s   ./primer_global_err/max_size_min_product_int
320s   ./primer_global_err/min_opt_tm
320s   ./primer_global_err/min_opt_tm_int
320s   ./primer_global_err/mishyb_obj_fn
320s   ./primer_global_err/mispr_obj_fn
320s   ./primer_global_err/must_match_length_0
320s   ./primer_global_err/must_match_length_1
320s   ./primer_global_err/must_match_length_10
320s   ./primer_global_err/must_match_length_2
320s   ./primer_global_err/must_match_length_3
320s   ./primer_global_err/must_match_length_4
320s   ./primer_global_err/must_match_length_5
320s   ./primer_global_err/must_match_length_6
320s   ./primer_global_err/must_match_length_7
320s   ./primer_global_err/must_match_length_8
320s   ./primer_global_err/must_match_length_9
320s   ./primer_global_err/no_equal
320s   ./primer_global_err/no_terminal_equal
320s   ./primer_global_err/opt_max_size
320s   ./primer_global_err/opt_max_size_int
320s   ./primer_global_err/opt_min_size
320s   ./primer_global_err/opt_min_size_int
320s   ./primer_global_err/pair_mispr
320s   ./primer_global_err/pr_gc_content_obj_fn
320s   ./primer_global_err/product_size_obj_fn
320s   ./primer_global_err/product_tm_obj_fn
320s   ./primer_global_err/repeat_lib_err
320s   ./primer_global_err/repeat_lib_err1
320s   ./primer_global_err/repeat_lib_err2
320s   ./primer_global_err/repeat_lib_err3
320s   ./primer_global_err/repeat_lib_err4
320s   ./primer_global_err/repeat_lib_err5
320s   ./primer_global_err/repeat_lib_err6
320s   ./primer_global_err/repeat_lib_int_err
320s   ./primer_global_err/repeat_lib_int_err1
320s   ./primer_global_err/repeat_lib_int_err2
320s   ./primer_global_err/repeat_lib_int_err3
320s   ./primer_global_err/repeat_lib_int_err4
320s   ./primer_global_err/repeat_lib_int_err5
320s   ./primer_global_err/repeat_lib_int_err6
320s   ./primer_global_err/seq_quality1
320s   ./primer_global_err/seq_quality2
320s   ./primer_global_err/seq_quality3
320s   ./primer_global_err/seq_quality4
320s   ./primer_global_err/too_many_product_sizes
320s   ./primer_global_err/zero_min_size
320s   ./primer_global_err/zero_num_return
320s [OK]
320s primer_must_use_th...0s [OK]
320s primer_sec_struct_dpal...0s [OK]
321s primer_task_th...1s [OK]
321s primer_thal_args...0s [OK]
322s primer_thal_max_seq_error...1s [OK]
322s primer_first_base_index...0s [OK]
322s primer_must_match...0s [OK]
322s test_compl_error...0s [OK]
322s test_left_to_right_of_right...0s [OK]
322s dv_conc_vs_dntp_conc...0s [OK]
322s primer_boundary...0s [OK]
322s primer_boundary1...0s [OK]
322s primer_boundary_formatted...0s [OK]
322s primer_boundary1_formatted...0s [OK]
322s primer3_v1_1_4_default_settings...0s [OK]
322s primer3web_v0_4_0_default_settings...0s [OK]
323s primer3web_v3_0_0_default_settings...1s [OK]
323s primer3web_v4_0_0_default_settings...0s [OK]
323s primer_internal...0s [OK]
323s primer_internal1...0s [OK]
323s primer_internal_formatted...0s [OK]
323s primer_internal1_formatted...0s [OK]
323s primer_ok_regions...0s [OK]
323s primer_ok_regions_formatted...0s [OK]
329s primer_ok_regions2...6s [OK]
329s primer_tm_lc_masking...0s [OK]
329s primer_tm_lc_masking_formatted...0s [OK]
329s primer_start_codon...0s [OK]
329s primer_task...0s [OK]
329s primer_task_formatted...0s [OK]
329s primer_renewed_tasks...0s [OK]
330s primer_dmso_formamide...1s [OK]
330s primer_new_tasks...0s [OK]
330s primer_new_tasks_formatted...0s [OK]
330s primer_internal_position...0s [OK]
330s primer_annealing_temp...0s [OK]
331s primer_windows_newlines...1s [OK]
331s primer_must_overlap_point...0s [OK]
331s primer_overlap_junction...0s [OK]
331s primer_all_settingsfiles...0s [OK]
331s primer_high_tm_load_set...0s [OK]
331s primer_high_gc_load_set...0s [OK]
331s primer_gc_end...0s [OK]
331s primer_check...0s [OK]
331s primer_must_use...0s [OK]
331s primer_must_use_formatted...0s [OK]
331s primer_syntax...0s [OK]
331s primer_end_pathology...0s [OK]
331s primer_num_best...0s [OK]
331s primer_quality_boundary...0s [OK]
332s primer...1s [OK]
332s primer_list_files...[OK]
333s primer1...0s [OK]
333s primer1_list_files...[OK]
333s primer_mispriming...1s [OK]
333s primer_mispriming_formatted...0s [OK]
333s primer_mispriming_boundary1...0s [OK]
333s primer_mispriming_boundary1_formatted...0s [OK]
333s primer_mispriming_boundary2...0s [OK]
333s primer_mispriming_boundary2_formatted...0s [OK]
333s primer_mispriming_long_lib...0s [OK]
334s primer_rat...0s [OK]
334s primer_human...1s [OK]
334s long_seq...0s [OK]
335s primer_position_penalty...1s [OK]
335s primer_position_penalty_formatted...0s [OK]
335s p3-tmpl-mispriming...0s [OK]
335s primer_poly_x...0s [OK]
335s primer_three_prime_distance...0s [OK]
337s primer_obj_fn...2s [OK]
337s p3_3_prime_n...0s [OK]
337s primer_overhang...0s [OK]
348s primer_overhang_th...11s [OK]
356s primer_mispriming_th...8s [OK]
369s th-w-other-tasks...13s [OK]
369s th-w-other-tasks_list_files...[OK]
384s primer_new_tasks_th...15s [OK]
397s primer_sec_struct_thal...13s [OK]
432s primer_thermod_align...35s [OK]
467s primer_thermod_align_formatted...35s [OK]
568s primer1_th...101s [OK]
568s primer1_th_list_files...[OK]
568s primer_lib_amb_codes...
568s NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more).
679s starting primer_lib_amb_codes at Sat Mar 15 16:59:07 2025...111s [OK]
679s 
679s Tests in p3test.pl ran for 359 s (5.98333333333333 min)
679s 
679s DONE Sat Mar 15 17:00:58 2025 Passed all tests - [OK]
679s 
679s 
679s testdpal:
679s 
679s 
679s TESTING ALIGNMENT CALCS
679s 
679s Error handling of too-long sequence...[OK]
679s Default implementations + alignment...[OK]
680s Default implementations + NO alignment 1...[OK]
680s Default implementations + NO alignment 2...[OK]
680s Force _dpal_generic...[OK]
680s Force _dpal_long_nopath_generic 1...[OK]
680s Force _dpal_long_nopath_generic 2...[OK]
680s Force long maxgap1 functions 1...[OK]
680s Force long maxgap1 functions 2...[OK]
680s testthal:
680s 
680s 
680s TESTING THERMODYNAMIC ALIGNMENT CALCS
680s 
680s Error handling of too-long sequence...
680s 1................................... [OK]
681s Default implementations + alignment...[OK]
681s Default implementations + NO alignment 1...[OK]
681s Default implementations + NO alignment 2...[OK]
682s Default implementations + alignment (interactive)...[OK]
682s Default implementations + NO alignment 1 (interactive)...[OK]
683s Default implementations + NO alignment 2 (interactive)...[OK]
683s Default implementations + alignment (interactive batch inputs)...[OK]
683s Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK]
683s testtm:
683s 
683s TESTING Tm CALCULATIONS
683s 
683s Tm tests nr 1-50: [OK]
683s 
683s 
683s PASS
683s autopkgtest [17:01:02]: test run-unit-test: -----------------------]
684s run-unit-test        PASS
684s autopkgtest [17:01:03]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
684s autopkgtest [17:01:03]: @@@@@@@@@@@@@@@@@@@@ summary
684s run-unit-test        PASS
689s nova [W] Using flock in prodstack6-s390x
689s flock: timeout while waiting to get lock
689s Creating nova instance adt-plucky-s390x-primer3-20250315-164939-juju-7f2275-prod-proposed-migration-environment-2-0cdee886-5471-418d-bf3e-af109aa6fe5c from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
689s nova [W] Timed out waiting for 98af57a1-bf3f-4195-afa6-d1145f591dad to get deleted.