0s autopkgtest [14:29:27]: starting date and time: 2025-03-15 14:29:27+0000
  0s autopkgtest [14:29:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [14:29:27]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2zb8c8j2/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-2.secgroup --name adt-plucky-arm64-primer3-20250315-142926-juju-7f2275-prod-proposed-migration-environment-15-6a306cd8-b085-4956-a85c-495f9f4123b2 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -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/
175s autopkgtest [14:32:22]: testbed dpkg architecture: arm64
175s autopkgtest [14:32:22]: testbed apt version: 2.9.33
176s autopkgtest [14:32:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup
176s autopkgtest [14:32:23]: testbed release detected to be: None
177s autopkgtest [14:32:24]: updating testbed package index (apt update)
177s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
178s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
178s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
178s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
178s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB]
178s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
178s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
178s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB]
179s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B]
179s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
179s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB]
179s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB]
179s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
179s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B]
179s Fetched 1094 kB in 2s (589 kB/s)
181s Reading package lists...
182s + lsb_release --codename --short
182s + RELEASE=plucky
182s + cat
182s + [ plucky != trusty ]
182s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
182s Reading package lists...
182s Building dependency tree...
182s Reading state information...
183s Calculating upgrade...
183s Calculating upgrade...
183s The following packages will be upgraded:
183s   python3-jinja2 strace
184s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
184s Need to get 608 kB of archives.
184s After this operation, 11.3 kB of additional disk space will be used.
184s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
184s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
185s Fetched 608 kB in 1s (598 kB/s)
185s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
185s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
185s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
186s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
186s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
186s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
186s Setting up strace (6.13+ds-1ubuntu1) ...
186s Processing triggers for man-db (2.13.0-1) ...
187s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
187s + /usr/lib/apt/apt-helper analyze-pattern ?true
187s + uname -r
187s + sed s/\./\\./g
187s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.*
187s + + tail -n+2
187s apt list ?obsolete
187s + cut -d/ -f1
187s + grep -v ^linux-.*6\.14\.0-10-generic.*
188s + obsolete_pkgs=linux-headers-6.11.0-8-generic
188s linux-headers-6.11.0-8
188s linux-image-6.11.0-8-generic
188s linux-modules-6.11.0-8-generic
188s linux-tools-6.11.0-8-generic
188s linux-tools-6.11.0-8
188s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8
188s Reading package lists...
188s Building dependency tree...
188s Reading state information...
188s Solving dependencies...
189s The following packages will be REMOVED:
189s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
189s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
189s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
189s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
189s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
189s After this operation, 267 MB disk space will be freed.
189s (Reading database ... 
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(Reading database ... 117701 files and directories currently installed.)
189s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
189s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
190s Removing libpython3.12t64:arm64 (3.12.9-1) ...
190s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
190s Removing libnsl2:arm64 (1.3.0-3build3) ...
190s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
190s Removing libunwind8:arm64 (1.6.2-3.1) ...
190s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
190s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
192s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
192s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
192s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
192s /etc/kernel/postrm.d/initramfs-tools:
192s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
192s /etc/kernel/postrm.d/zz-flash-kernel:
192s flash-kernel: Kernel 6.11.0-8-generic has been removed.
192s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
193s /etc/kernel/postrm.d/zz-update-grub:
193s Sourcing file `/etc/default/grub'
193s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
193s Generating grub configuration file ...
193s Found linux image: /boot/vmlinuz-6.14.0-10-generic
193s Found initrd image: /boot/initrd.img-6.14.0-10-generic
194s Warning: os-prober will not be executed to detect other bootable partitions.
194s Systems on them will not be added to the GRUB boot configuration.
194s Check GRUB_DISABLE_OS_PROBER documentation entry.
194s Adding boot menu entry for UEFI Firmware Settings ...
194s done
194s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
194s Processing triggers for libc-bin (2.41-1ubuntu1) ...
194s (Reading database ... 
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(Reading database ... 81650 files and directories currently installed.)
194s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
194s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
194s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
194s + grep -q trusty /etc/lsb-release
194s + [ ! -d /usr/share/doc/unattended-upgrades ]
194s + [ ! -d /usr/share/doc/lxd ]
194s + [ ! -d /usr/share/doc/lxd-client ]
194s + [ ! -d /usr/share/doc/snapd ]
194s + type iptables
194s + cat
194s + chmod 755 /etc/rc.local
194s + . /etc/rc.local
194s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
194s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
194s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
194s + uname -m
194s + [ aarch64 = ppc64le ]
194s + [ -d /run/systemd/system ]
194s + systemd-detect-virt --quiet --vm
194s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
194s + cat
194s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
194s + echo COMPRESS=lz4
194s autopkgtest [14:32:41]: upgrading testbed (apt dist-upgrade and autopurge)
195s Reading package lists...
195s Building dependency tree...
195s Reading state information...
196s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
196s Starting 2 pkgProblemResolver with broken count: 0
196s Done
197s Entering ResolveByKeep
197s 
197s Calculating upgrade...
198s The following packages will be upgraded:
198s   libc-bin libc-dev-bin libc6 libc6-dev locales
198s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
198s Need to get 9530 kB of archives.
198s After this operation, 0 B of additional disk space will be used.
198s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
200s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
200s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
203s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
203s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
207s Preconfiguring packages ...
208s Fetched 9530 kB in 9s (1004 kB/s)
208s (Reading database ... 
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208s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
208s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
208s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
208s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
208s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
208s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
208s Setting up libc6:arm64 (2.41-1ubuntu2) ...
208s (Reading database ... 
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208s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
208s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
208s Setting up libc-bin (2.41-1ubuntu2) ...
209s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
209s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
209s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
209s Setting up locales (2.41-1ubuntu2) ...
209s Generating locales (this might take a while)...
211s   en_US.UTF-8... done
211s Generation complete.
211s Setting up libc-dev-bin (2.41-1ubuntu2) ...
211s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
211s Processing triggers for man-db (2.13.0-1) ...
212s Processing triggers for systemd (257.3-1ubuntu3) ...
213s Reading package lists...
214s Building dependency tree...
214s Reading state information...
214s Starting pkgProblemResolver with broken count: 0
214s Starting 2 pkgProblemResolver with broken count: 0
214s Done
215s Solving dependencies...
215s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
215s autopkgtest [14:33:02]: rebooting testbed after setup commands that affected boot
239s autopkgtest [14:33:26]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025
242s autopkgtest [14:33:29]: @@@@@@@@@@@@@@@@@@@@ apt-source primer3
273s Get:1 http://ftpmaster.internal/ubuntu plucky/universe primer3 2.6.1-5 (dsc) [2101 B]
273s Get:2 http://ftpmaster.internal/ubuntu plucky/universe primer3 2.6.1-5 (tar) [32.9 MB]
273s Get:3 http://ftpmaster.internal/ubuntu plucky/universe primer3 2.6.1-5 (diff) [14.0 kB]
273s gpgv: Signature made Sun Dec  1 12:08:12 2024 UTC
273s gpgv:                using RSA key 52D5BD0E7D4DB084E34B5865D4A41CFADDB20DB5
273s gpgv: Can't check signature: No public key
273s dpkg-source: warning: cannot verify inline signature for ./primer3_2.6.1-5.dsc: no acceptable signature found
274s autopkgtest [14:34:01]: testing package primer3 version 2.6.1-5
275s autopkgtest [14:34:02]: build not needed
281s autopkgtest [14:34:08]: test run-unit-test: preparing testbed
281s Reading package lists...
281s Building dependency tree...
281s Reading state information...
282s Starting pkgProblemResolver with broken count: 0
282s Starting 2 pkgProblemResolver with broken count: 0
282s Done
283s The following NEW packages will be installed:
283s   libc6-dbg primer3 primer3-examples valgrind
283s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
283s Need to get 47.6 MB of archives.
283s After this operation, 99.0 MB of additional disk space will be used.
283s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 primer3 arm64 2.6.1-5 [211 kB]
283s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 primer3-examples all 2.6.1-5 [31.8 MB]
314s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dbg arm64 2.41-1ubuntu2 [6666 kB]
320s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 valgrind arm64 1:3.24.0-0ubuntu1 [8935 kB]
330s Fetched 47.6 MB in 47s (1014 kB/s)
330s Selecting previously unselected package primer3.
330s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
330s Preparing to unpack .../primer3_2.6.1-5_arm64.deb ...
330s Unpacking primer3 (2.6.1-5) ...
330s Selecting previously unselected package primer3-examples.
330s Preparing to unpack .../primer3-examples_2.6.1-5_all.deb ...
330s Unpacking primer3-examples (2.6.1-5) ...
331s Selecting previously unselected package libc6-dbg:arm64.
331s Preparing to unpack .../libc6-dbg_2.41-1ubuntu2_arm64.deb ...
331s Unpacking libc6-dbg:arm64 (2.41-1ubuntu2) ...
331s Selecting previously unselected package valgrind.
331s Preparing to unpack .../valgrind_1%3a3.24.0-0ubuntu1_arm64.deb ...
331s Unpacking valgrind (1:3.24.0-0ubuntu1) ...
331s Setting up primer3-examples (2.6.1-5) ...
331s Setting up libc6-dbg:arm64 (2.41-1ubuntu2) ...
331s Setting up primer3 (2.6.1-5) ...
331s Setting up valgrind (1:3.24.0-0ubuntu1) ...
331s Processing triggers for man-db (2.13.0-1) ...
333s autopkgtest [14:35:00]: test run-unit-test: [-----------------------
335s example
335s kmer_lists
335s settings_files
335s src
335s test
335s testcmdline:
335s 
335s 
335s TESTING command line arguments
335s 
335s Test 1... [OK]
335s Test 2... [OK]
335s Test 3... [OK]
335s Test 4... [OK]
335s Test 5... [OK]
335s Passed all tests - [OK]
335s 
335s 
335s testcore:
335s 
335s 
335s TESTING primer3_core
335s 
335s p3test.pl for primer3_core version 2.6.1
335s 
335s 
335s p3test.pl: testing ../src/primer3_core
335s 
335s START, Sat Mar 15 14:35:02 2025
335s 
335s testing fatal errors...
335s   ./primer_global_err/annealing_temp_salt
335s Testing --output and --error flags on
335s ../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
335s   ./primer_global_err/bad_divalent_dntp_conc_1
335s   ./primer_global_err/bad_divalent_dntp_conc_2
335s   ./primer_global_err/bad_divalent_dntp_conc_3
335s   ./primer_global_err/bad_divalent_dntp_conc_4
335s   ./primer_global_err/bad_dna_conc
335s   ./primer_global_err/bad_first_base_index
335s   ./primer_global_err/bad_float_1
335s   ./primer_global_err/bad_float_2
335s   ./primer_global_err/bad_float_3
335s   ./primer_global_err/bad_float_4
335s   ./primer_global_err/bad_gc_1
335s   ./primer_global_err/bad_gc_2
335s   ./primer_global_err/bad_gc_3
335s   ./primer_global_err/bad_gc_int_1
335s   ./primer_global_err/bad_gc_int_2
335s   ./primer_global_err/bad_gc_int_3
335s   ./primer_global_err/bad_min_three_prime_distance
335s   ./primer_global_err/bad_num_ns
335s   ./primer_global_err/bad_num_ns_int
335s   ./primer_global_err/bad_product_sizes_1
335s   ./primer_global_err/bad_product_sizes_2
335s   ./primer_global_err/bad_product_sizes_3
335s   ./primer_global_err/bad_product_sizes_4
335s   ./primer_global_err/bad_salt_conc
335s   ./primer_global_err/bad_self_any
335s   ./primer_global_err/bad_self_any_int
335s   ./primer_global_err/bad_self_end
335s   ./primer_global_err/bad_self_end_int
335s   ./primer_global_err/bad_settings0
335s   ./primer_global_err/bad_settings1
335s   ./primer_global_err/bad_settings2
335s   ./primer_global_err/bad_settings3
335s   ./primer_global_err/bad_settings4
335s   ./primer_global_err/bad_settings5
335s   ./primer_global_err/bad_settings6
335s   ./primer_global_err/empty_1
335s   ./primer_global_err/empty_product_size
335s   ./primer_global_err/gc_clamp_min_size
335s   ./primer_global_err/incorrect_task
335s   ./primer_global_err/io_gc_content_obj_fn
335s   ./primer_global_err/io_obj_fn
335s   ./primer_global_err/junction_overlap_max_size
335s   ./primer_global_err/junction_overlap_min_size
335s   ./primer_global_err/max_annealing_temp
335s   ./primer_global_err/max_min_bound
335s   ./primer_global_err/max_min_bound_int
335s   ./primer_global_err/max_min_tm
335s   ./primer_global_err/max_min_tm_int
335s   ./primer_global_err/max_opt_bound
335s   ./primer_global_err/max_opt_bound_int
335s   ./primer_global_err/max_opt_tm
335s   ./primer_global_err/max_opt_tm_int
335s   ./primer_global_err/MAX_PRIMER_LENGTH
335s   ./primer_global_err/max_size_limit_int
335s   ./primer_global_err/max_size_limit_with_overhang
335s   ./primer_global_err/max_size_min_product
335s   ./primer_global_err/max_size_min_product_int
335s   ./primer_global_err/min_opt_tm
335s   ./primer_global_err/min_opt_tm_int
335s   ./primer_global_err/mishyb_obj_fn
335s   ./primer_global_err/mispr_obj_fn
335s   ./primer_global_err/must_match_length_0
335s   ./primer_global_err/must_match_length_1
335s   ./primer_global_err/must_match_length_10
335s   ./primer_global_err/must_match_length_2
335s   ./primer_global_err/must_match_length_3
335s   ./primer_global_err/must_match_length_4
335s   ./primer_global_err/must_match_length_5
335s   ./primer_global_err/must_match_length_6
335s   ./primer_global_err/must_match_length_7
335s   ./primer_global_err/must_match_length_8
335s   ./primer_global_err/must_match_length_9
335s   ./primer_global_err/no_equal
335s   ./primer_global_err/no_terminal_equal
335s   ./primer_global_err/opt_max_size
335s   ./primer_global_err/opt_max_size_int
335s   ./primer_global_err/opt_min_size
335s   ./primer_global_err/opt_min_size_int
335s   ./primer_global_err/pair_mispr
335s   ./primer_global_err/pr_gc_content_obj_fn
335s   ./primer_global_err/product_size_obj_fn
335s   ./primer_global_err/product_tm_obj_fn
335s   ./primer_global_err/repeat_lib_err
335s   ./primer_global_err/repeat_lib_err1
335s   ./primer_global_err/repeat_lib_err2
335s   ./primer_global_err/repeat_lib_err3
335s   ./primer_global_err/repeat_lib_err4
335s   ./primer_global_err/repeat_lib_err5
335s   ./primer_global_err/repeat_lib_err6
335s   ./primer_global_err/repeat_lib_int_err
335s   ./primer_global_err/repeat_lib_int_err1
335s   ./primer_global_err/repeat_lib_int_err2
335s   ./primer_global_err/repeat_lib_int_err3
335s   ./primer_global_err/repeat_lib_int_err4
335s   ./primer_global_err/repeat_lib_int_err5
335s   ./primer_global_err/repeat_lib_int_err6
335s   ./primer_global_err/seq_quality1
335s   ./primer_global_err/seq_quality2
335s   ./primer_global_err/seq_quality3
335s   ./primer_global_err/seq_quality4
335s   ./primer_global_err/too_many_product_sizes
335s   ./primer_global_err/zero_min_size
335s   ./primer_global_err/zero_num_return
335s [OK]
335s primer_must_use_th...0s [OK]
335s primer_sec_struct_dpal...0s [OK]
336s primer_task_th...1s [OK]
336s primer_thal_args...0s [OK]
337s primer_thal_max_seq_error...1s [OK]
337s primer_first_base_index...0s [OK]
337s primer_must_match...0s [OK]
337s test_compl_error...0s [OK]
337s test_left_to_right_of_right...0s [OK]
337s dv_conc_vs_dntp_conc...0s [OK]
337s primer_boundary...0s [OK]
337s primer_boundary1...0s [OK]
337s primer_boundary_formatted...0s [OK]
337s primer_boundary1_formatted...0s [OK]
337s primer3_v1_1_4_default_settings...0s [OK]
337s primer3web_v0_4_0_default_settings...0s [OK]
338s primer3web_v3_0_0_default_settings...1s [OK]
338s primer3web_v4_0_0_default_settings...0s [OK]
338s primer_internal...0s [OK]
338s primer_internal1...0s [OK]
338s primer_internal_formatted...0s [OK]
338s primer_internal1_formatted...0s [OK]
338s primer_ok_regions...0s [OK]
338s primer_ok_regions_formatted...0s [OK]
344s primer_ok_regions2...6s [OK]
344s primer_tm_lc_masking...0s [OK]
344s primer_tm_lc_masking_formatted...0s [OK]
344s primer_start_codon...0s [OK]
344s primer_task...0s [OK]
344s primer_task_formatted...0s [OK]
344s primer_renewed_tasks...0s [OK]
344s primer_dmso_formamide...0s [OK]
344s primer_new_tasks...0s [OK]
345s primer_new_tasks_formatted...1s [OK]
345s primer_internal_position...0s [OK]
345s primer_annealing_temp...0s [OK]
346s primer_windows_newlines...1s [OK]
346s primer_must_overlap_point...0s [OK]
346s primer_overlap_junction...0s [OK]
346s primer_all_settingsfiles...0s [OK]
346s primer_high_tm_load_set...0s [OK]
346s primer_high_gc_load_set...0s [OK]
346s primer_gc_end...0s [OK]
346s primer_check...0s [OK]
346s primer_must_use...0s [OK]
346s primer_must_use_formatted...0s [OK]
346s primer_syntax...0s [OK]
346s primer_end_pathology...0s [OK]
346s primer_num_best...0s [OK]
346s primer_quality_boundary...0s [OK]
347s primer...1s [OK]
347s primer_list_files...[OK]
347s primer1...0s [OK]
347s primer1_list_files...[OK]
348s primer_mispriming...1s [OK]
348s primer_mispriming_formatted...0s [OK]
348s primer_mispriming_boundary1...0s [OK]
348s primer_mispriming_boundary1_formatted...0s [OK]
348s primer_mispriming_boundary2...0s [OK]
348s primer_mispriming_boundary2_formatted...0s [OK]
348s primer_mispriming_long_lib...0s [OK]
348s primer_rat...0s [OK]
349s primer_human...1s [OK]
349s long_seq...0s [OK]
350s primer_position_penalty...1s [OK]
350s primer_position_penalty_formatted...0s [OK]
350s p3-tmpl-mispriming...0s [OK]
350s primer_poly_x...0s [OK]
350s primer_three_prime_distance...0s [OK]
353s primer_obj_fn...2s [OK]
353s p3_3_prime_n...0s [OK]
354s primer_masker...2s [OK]
356s primer_masker_formatted...2s [OK]
356s primer_overhang...0s [OK]
367s primer_overhang_th...11s [OK]
375s primer_mispriming_th...8s [OK]
387s th-w-other-tasks...12s [OK]
387s th-w-other-tasks_list_files...[OK]
403s primer_new_tasks_th...16s [OK]
416s primer_sec_struct_thal...13s [OK]
453s primer_thermod_align...37s [OK]
491s primer_thermod_align_formatted...38s [OK]
588s primer1_th...97s [OK]
588s primer1_th_list_files...[OK]
588s primer_lib_amb_codes...
588s NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more).
706s starting primer_lib_amb_codes at Sat Mar 15 14:39:15 2025...118s [OK]
706s 
706s Tests in p3test.pl ran for 371 s (6.18333333333333 min)
706s 
706s DONE Sat Mar 15 14:41:13 2025 Passed all tests - [OK]
706s 
706s 
706s testdpal:
706s 
706s 
706s TESTING ALIGNMENT CALCS
706s 
706s Error handling of too-long sequence...[OK]
707s Default implementations + alignment...[OK]
707s Default implementations + NO alignment 1...[OK]
707s Default implementations + NO alignment 2...[OK]
708s Force _dpal_generic...[OK]
708s Force _dpal_long_nopath_generic 1...[OK]
708s Force _dpal_long_nopath_generic 2...[OK]
709s Force long maxgap1 functions 1...[OK]
709s Force long maxgap1 functions 2...[OK]
709s testthal:
709s 
709s 
709s TESTING THERMODYNAMIC ALIGNMENT CALCS
709s 
709s Error handling of too-long sequence...
709s 1................................... [OK]
710s Default implementations + alignment...[OK]
711s Default implementations + NO alignment 1...[OK]
711s Default implementations + NO alignment 2...[OK]
713s Default implementations + alignment (interactive)...[OK]
714s Default implementations + NO alignment 1 (interactive)...[OK]
715s Default implementations + NO alignment 2 (interactive)...[OK]
715s Default implementations + alignment (interactive batch inputs)...[OK]
715s Default implementations + alignment + HAIRPIN (interactive batch inputs)...[OK]
715s testtm:
715s 
715s TESTING Tm CALCULATIONS
715s 
715s Tm tests nr 1-50: [OK]
715s 
715s 
715s PASS
715s autopkgtest [14:41:22]: test run-unit-test: -----------------------]
716s run-unit-test        PASS
716s autopkgtest [14:41:23]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
717s autopkgtest [14:41:24]: @@@@@@@@@@@@@@@@@@@@ summary
718s run-unit-test        PASS
736s nova [W] Using flock in prodstack6-arm64
736s flock: timeout while waiting to get lock
736s Creating nova instance adt-plucky-arm64-primer3-20250315-142926-juju-7f2275-prod-proposed-migration-environment-15-6a306cd8-b085-4956-a85c-495f9f4123b2 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
736s nova [W] Timed out waiting for 268b47cf-a9c3-43df-9cd6-a3daf9180c71 to get deleted.