0s autopkgtest [16:44:49]: starting date and time: 2024-03-24 16:44:49+0000 0s autopkgtest [16:44:49]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:44:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xk9_5fl1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade atropos --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-10.secgroup --name adt-noble-arm64-atropos-20240324-164449-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 64s autopkgtest [16:45:53]: testbed dpkg architecture: arm64 65s autopkgtest [16:45:54]: testbed apt version: 2.7.12 65s autopkgtest [16:45:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 65s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 65s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 65s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 66s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 66s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 66s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 66s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 66s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 66s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 66s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 66s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 66s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 68s Fetched 9847 kB in 2s (5104 kB/s) 68s Reading package lists... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s Calculating upgrade... 73s The following packages will be REMOVED: 73s libssl3 73s The following NEW packages will be installed: 73s libssl3t64 73s The following packages have been kept back: 73s curl 73s The following packages will be upgraded: 73s openssl 74s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 74s Need to get 2777 kB of archives. 74s After this operation, 139 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 74s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 76s Fetched 2777 kB in 2s (1710 kB/s) 76s (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 ... 74819 files and directories currently installed.) 76s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 76s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 76s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 76s wget depends on libssl3 (>= 3.0.0). 76s u-boot-tools depends on libssl3 (>= 3.0.0). 76s tnftp depends on libssl3 (>= 3.0.0). 76s tcpdump depends on libssl3 (>= 3.0.0). 76s systemd-resolved depends on libssl3 (>= 3.0.0). 76s systemd depends on libssl3 (>= 3.0.0). 76s sudo depends on libssl3 (>= 3.0.0). 76s sbsigntool depends on libssl3 (>= 3.0.0). 76s rsync depends on libssl3 (>= 3.0.0). 76s python3-cryptography depends on libssl3 (>= 3.0.0). 76s openssh-server depends on libssl3 (>= 3.0.10). 76s openssh-client depends on libssl3 (>= 3.0.10). 76s mtd-utils depends on libssl3 (>= 3.0.0). 76s mokutil depends on libssl3 (>= 3.0.0). 76s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 76s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 76s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 76s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 76s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 76s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 76s libnvme1 depends on libssl3 (>= 3.0.0). 76s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 76s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 76s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 76s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 76s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 76s kmod depends on libssl3 (>= 3.0.0). 76s dhcpcd-base depends on libssl3 (>= 3.0.0). 76s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 76s 76s (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 ... 74819 files and directories currently installed.) 76s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 76s Selecting previously unselected package libssl3t64:arm64. 76s (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 ... 74808 files and directories currently installed.) 76s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 76s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 76s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 76s Setting up openssl (3.0.13-0ubuntu2) ... 76s Processing triggers for man-db (2.12.0-3) ... 77s Processing triggers for libc-bin (2.39-0ubuntu6) ... 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 80s sh: Attempting to set up Debian/Ubuntu apt sources automatically 80s sh: Distribution appears to be Ubuntu 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s eatmydata is already the newest version (131-1). 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s dbus is already the newest version (1.14.10-4ubuntu1). 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s rng-tools-debian is already the newest version (2.4). 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s The following packages will be REMOVED: 85s cloud-init* python3-configobj* python3-debconf* 87s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 87s After this operation, 3256 kB disk space will be freed. 87s (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 ... 74821 files and directories currently installed.) 87s Removing cloud-init (24.1.2-0ubuntu1) ... 87s Removing python3-configobj (5.0.8-3) ... 87s Removing python3-debconf (1.5.86) ... 87s Processing triggers for man-db (2.12.0-3) ... 87s (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 ... 74432 files and directories currently installed.) 87s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 88s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 88s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 88s invoke-rc.d: policy-rc.d denied execution of try-restart. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s linux-generic is already the newest version (6.8.0-11.11+1). 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 90s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 90s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 92s Reading package lists... 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Calculating upgrade... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s autopkgtest [16:46:23]: rebooting testbed after setup commands that affected boot 121s autopkgtest [16:46:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 124s autopkgtest [16:46:53]: @@@@@@@@@@@@@@@@@@@@ apt-source atropos 128s Get:1 http://ftpmaster.internal/ubuntu noble/universe atropos 1.1.32+dfsg-1 (dsc) [2266 B] 128s Get:2 http://ftpmaster.internal/ubuntu noble/universe atropos 1.1.32+dfsg-1 (tar) [3117 kB] 128s Get:3 http://ftpmaster.internal/ubuntu noble/universe atropos 1.1.32+dfsg-1 (diff) [6496 B] 128s gpgv: Signature made Mon Dec 11 14:17:36 2023 UTC 128s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 128s gpgv: issuer "tille@debian.org" 128s gpgv: Can't check signature: No public key 128s dpkg-source: warning: cannot verify inline signature for ./atropos_1.1.32+dfsg-1.dsc: no acceptable signature found 128s autopkgtest [16:46:57]: testing package atropos version 1.1.32+dfsg-1 129s autopkgtest [16:46:58]: build not needed 129s autopkgtest [16:46:58]: test run-unit-test: preparing testbed 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 142s Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 143s The following additional packages will be installed: 143s atropos libdeflate0 libhts3 libhtscodecs2 python3-all python3-distutils 143s python3-iniconfig python3-lib2to3 python3-packaging python3-pluggy 143s python3-pysam python3-pytest 143s The following NEW packages will be installed: 143s atropos autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 python3-all 143s python3-distutils python3-iniconfig python3-lib2to3 python3-packaging 143s python3-pluggy python3-pysam python3-pytest 143s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 5796 kB/5797 kB of archives. 143s After this operation, 45.9 MB of additional disk space will be used. 143s Get:1 /tmp/autopkgtest.ZRaCp5/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 143s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 143s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 143s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 144s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 145s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 atropos arm64 1.1.32+dfsg-1 [271 kB] 145s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 145s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 145s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 145s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 145s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 145s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 145s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 146s Fetched 5796 kB in 2s (2833 kB/s) 146s Selecting previously unselected package libdeflate0:arm64. 146s (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 ... 74377 files and directories currently installed.) 146s Preparing to unpack .../00-libdeflate0_1.19-1_arm64.deb ... 146s Unpacking libdeflate0:arm64 (1.19-1) ... 146s Selecting previously unselected package libhtscodecs2:arm64. 146s Preparing to unpack .../01-libhtscodecs2_1.6.0-1_arm64.deb ... 146s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 146s Selecting previously unselected package libhts3:arm64. 146s Preparing to unpack .../02-libhts3_1.18+ds-1_arm64.deb ... 146s Unpacking libhts3:arm64 (1.18+ds-1) ... 146s Selecting previously unselected package python3-pysam. 146s Preparing to unpack .../03-python3-pysam_0.22.0+ds-1_arm64.deb ... 146s Unpacking python3-pysam (0.22.0+ds-1) ... 147s Selecting previously unselected package atropos. 147s Preparing to unpack .../04-atropos_1.1.32+dfsg-1_arm64.deb ... 147s Unpacking atropos (1.1.32+dfsg-1) ... 147s Selecting previously unselected package python3-lib2to3. 147s Preparing to unpack .../05-python3-lib2to3_3.11.5-1_all.deb ... 147s Unpacking python3-lib2to3 (3.11.5-1) ... 147s Selecting previously unselected package python3-distutils. 147s Preparing to unpack .../06-python3-distutils_3.11.5-1_all.deb ... 147s Unpacking python3-distutils (3.11.5-1) ... 147s Selecting previously unselected package python3-all. 147s Preparing to unpack .../07-python3-all_3.12.1-0ubuntu2_arm64.deb ... 147s Unpacking python3-all (3.12.1-0ubuntu2) ... 147s Selecting previously unselected package python3-iniconfig. 147s Preparing to unpack .../08-python3-iniconfig_1.1.1-2_all.deb ... 147s Unpacking python3-iniconfig (1.1.1-2) ... 147s Selecting previously unselected package python3-packaging. 147s Preparing to unpack .../09-python3-packaging_23.2-1_all.deb ... 147s Unpacking python3-packaging (23.2-1) ... 147s Selecting previously unselected package python3-pluggy. 147s Preparing to unpack .../10-python3-pluggy_1.4.0-1_all.deb ... 147s Unpacking python3-pluggy (1.4.0-1) ... 147s Selecting previously unselected package python3-pytest. 147s Preparing to unpack .../11-python3-pytest_7.4.4-1_all.deb ... 147s Unpacking python3-pytest (7.4.4-1) ... 147s Selecting previously unselected package autopkgtest-satdep. 147s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 147s Unpacking autopkgtest-satdep (0) ... 147s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 147s Setting up python3-iniconfig (1.1.1-2) ... 147s Setting up libdeflate0:arm64 (1.19-1) ... 147s Setting up python3-packaging (23.2-1) ... 147s Setting up python3-pluggy (1.4.0-1) ... 148s Setting up python3-lib2to3 (3.11.5-1) ... 148s Setting up python3-distutils (3.11.5-1) ... 148s python3.12: can't get files for byte-compilation 148s Setting up libhts3:arm64 (1.18+ds-1) ... 148s Setting up python3-pysam (0.22.0+ds-1) ... 148s Setting up python3-pytest (7.4.4-1) ... 148s Setting up atropos (1.1.32+dfsg-1) ... 148s Setting up python3-all (3.12.1-0ubuntu2) ... 148s Setting up autopkgtest-satdep (0) ... 148s Processing triggers for man-db (2.12.0-3) ... 149s Processing triggers for libc-bin (2.39-0ubuntu6) ... 152s (Reading database ... 75221 files and directories currently installed.) 152s Removing autopkgtest-satdep (0) ... 153s autopkgtest [16:47:22]: test run-unit-test: [----------------------- 153s ============================= test session starts ============================== 153s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.12 153s cachedir: .pytest_cache 153s rootdir: /tmp/autopkgtest.ZRaCp5/autopkgtest_tmp 162s collecting ... collected 222 items 162s 162s tests/test_adapters.py::test_issue_52 PASSED [ 0%] 162s tests/test_adapters.py::test_issue_80 PASSED [ 0%] 162s tests/test_adapters.py::test_str PASSED [ 1%] 162s tests/test_adapters.py::test_color PASSED [ 1%] 162s tests/test_adapters.py::test_parse_braces PASSED [ 2%] 162s tests/test_adapters.py::test_parse_braces_fail PASSED [ 2%] 162s tests/test_adapters.py::test_linked_adapter PASSED [ 3%] 162s tests/test_adapters.py::test_random_match_probabilities PASSED [ 3%] 162s tests/test_align.py::TestAligner::test PASSED [ 4%] 162s tests/test_align.py::TestAligner::test_100_percent_error_rate PASSED [ 4%] 162s tests/test_align.py::test_polya PASSED [ 4%] 162s tests/test_align.py::test_compare_prefixes PASSED [ 5%] 162s tests/test_align.py::test_compare_suffixes PASSED [ 5%] 162s tests/test_align.py::test_wildcards_in_adapter PASSED [ 6%] 162s tests/test_align.py::test_wildcards_in_read PASSED [ 6%] 162s tests/test_align.py::test_wildcards_in_both PASSED [ 7%] 162s tests/test_align.py::test_no_match PASSED [ 7%] 162s tests/test_align.py::test_factorial PASSED [ 8%] 162s tests/test_align.py::test_match_probability PASSED [ 8%] 162s tests/test_align.py::test_insert_align PASSED [ 9%] 162s tests/test_align.py::test_short_adapter_overlap PASSED [ 9%] 162s tests/test_align.py::test_insert_align_different_lengths PASSED [ 9%] 162s tests/test_align.py::test_multi_aligner_no_mismatches PASSED [ 10%] 162s tests/test_align.py::test_multi_aligner_with_mismatches PASSED [ 10%] 162s tests/test_atropos.py::test_example PASSED [ 11%] 162s tests/test_atropos.py::test_small PASSED [ 11%] 162s tests/test_atropos.py::test_empty PASSED [ 12%] 162s tests/test_atropos.py::test_newlines PASSED [ 12%] 162s tests/test_atropos.py::test_lowercase PASSED [ 13%] 162s tests/test_atropos.py::test_rest PASSED [ 13%] 162s tests/test_atropos.py::test_restfront PASSED [ 13%] 163s tests/test_atropos.py::test_discard PASSED [ 14%] 163s tests/test_atropos.py::test_discard_untrimmed PASSED [ 14%] 163s tests/test_atropos.py::test_plus PASSED [ 15%] 163s tests/test_atropos.py::test_extensiontxtgz PASSED [ 15%] 163s tests/test_atropos.py::test_format PASSED [ 16%] 163s tests/test_atropos.py::test_minimum_length PASSED [ 16%] 163s tests/test_atropos.py::test_too_short PASSED [ 17%] 163s tests/test_atropos.py::test_too_short_no_primer PASSED [ 17%] 163s tests/test_atropos.py::test_maximum_length PASSED [ 18%] 163s tests/test_atropos.py::test_too_long PASSED [ 18%] 163s tests/test_atropos.py::test_length_tag PASSED [ 18%] 163s tests/test_atropos.py::test_overlap_a PASSED [ 19%] 163s tests/test_atropos.py::test_overlap_b PASSED [ 19%] 163s tests/test_atropos.py::test_qualtrim PASSED [ 20%] 163s tests/test_atropos.py::test_qualbase PASSED [ 20%] 163s tests/test_atropos.py::test_quality_trim_only PASSED [ 21%] 163s tests/test_atropos.py::test_twoadapters PASSED [ 21%] 163s tests/test_atropos.py::test_polya PASSED [ 22%] 163s tests/test_atropos.py::test_polya_brace_notation PASSED [ 22%] 163s tests/test_atropos.py::test_mask_adapter PASSED [ 22%] 163s tests/test_atropos.py::test_gz_multiblock PASSED [ 23%] 163s tests/test_atropos.py::test_suffix PASSED [ 23%] 163s tests/test_atropos.py::test_read_wildcard PASSED [ 24%] 163s tests/test_atropos.py::test_adapter_wildcard PASSED [ 24%] 163s tests/test_atropos.py::test_wildcard_N PASSED [ 25%] 163s tests/test_atropos.py::test_illumina_adapter_wildcard PASSED [ 25%] 163s tests/test_atropos.py::test_adapter_front PASSED [ 26%] 163s tests/test_atropos.py::test_literal_N PASSED [ 26%] 163s tests/test_atropos.py::test_literal_N2 PASSED [ 27%] 163s tests/test_atropos.py::test_literal_N_brace_notation PASSED [ 27%] 163s tests/test_atropos.py::test_literal_N2_brace_notation PASSED [ 27%] 163s tests/test_atropos.py::test_anchored_front PASSED [ 28%] 163s tests/test_atropos.py::test_anchored_front_ellipsis_notation PASSED [ 28%] 163s tests/test_atropos.py::test_anchored_back PASSED [ 29%] 163s tests/test_atropos.py::test_anchored_back_no_indels PASSED [ 29%] 163s tests/test_atropos.py::test_no_indels PASSED [ 30%] 163s tests/test_atropos.py::test_issue_46 PASSED [ 30%] 163s tests/test_atropos.py::test_strip_suffix PASSED [ 31%] 163s tests/test_atropos.py::test_info_file PASSED [ 31%] 163s tests/test_atropos.py::test_info_file_times PASSED [ 31%] 163s tests/test_atropos.py::test_info_file_fasta PASSED [ 32%] 163s tests/test_atropos.py::test_named_adapter PASSED [ 32%] 163s tests/test_atropos.py::test_adapter_with_U PASSED [ 33%] 163s tests/test_atropos.py::test_no_trim PASSED [ 33%] 163s tests/test_atropos.py::test_bzip2 PASSED [ 34%] 163s tests/test_atropos.py::test_xz PASSED [ 34%] 163s tests/test_atropos.py::test_qualfile_only PASSED [ 35%] 163s tests/test_atropos.py::test_no_args PASSED [ 35%] 163s tests/test_atropos.py::test_two_fastqs PASSED [ 36%] 163s tests/test_atropos.py::test_anchored_no_indels PASSED [ 36%] 163s tests/test_atropos.py::test_anchored_no_indels_wildcard_read PASSED [ 36%] 163s tests/test_atropos.py::test_anchored_no_indels_wildcard_adapt PASSED [ 37%] 163s tests/test_atropos.py::test_unconditional_cut_front PASSED [ 37%] 163s tests/test_atropos.py::test_unconditional_cut_back PASSED [ 38%] 163s tests/test_atropos.py::test_unconditional_cut_both PASSED [ 38%] 163s tests/test_atropos.py::test_untrimmed_output PASSED [ 39%] 163s tests/test_atropos.py::test_adapter_file PASSED [ 39%] 163s tests/test_atropos.py::test_adapter_file_5p_anchored PASSED [ 40%] 163s tests/test_atropos.py::test_adapter_file_3p_anchored PASSED [ 40%] 163s tests/test_atropos.py::test_adapter_file_5p_anchored_no_indels PASSED [ 40%] 163s tests/test_atropos.py::test_adapter_file_3p_anchored_no_indels PASSED [ 41%] 163s tests/test_atropos.py::test_demultiplex PASSED [ 41%] 163s tests/test_atropos.py::test_max_n PASSED [ 42%] 163s tests/test_atropos.py::test_quiet_is_quiet PASSED [ 42%] 163s tests/test_atropos.py::test_nextseq PASSED [ 43%] 163s tests/test_atropos.py::test_linked PASSED [ 43%] 163s tests/test_atropos.py::test_fasta PASSED [ 44%] 163s tests/test_atropos.py::test_custom_bisulfite_1 PASSED [ 44%] 163s tests/test_atropos.py::test_custom_bisulfite_2 PASSED [ 45%] 163s tests/test_atropos.py::test_custom_bisulfite_3 PASSED [ 45%] 163s tests/test_atropos.py::test_custom_bisulfite_4 PASSED [ 45%] 163s tests/test_atropos.py::test_sra SKIPPED (No internet connection or s...) [ 46%] 163s tests/test_colorspace.py::test_encode PASSED [ 46%] 163s tests/test_colorspace.py::test_decode PASSED [ 47%] 163s tests/test_colorspace.py::test_qualtrim_csfastaqual PASSED [ 47%] 163s tests/test_colorspace.py::test_E3M PASSED [ 48%] 163s tests/test_colorspace.py::test_bwa PASSED [ 48%] 163s tests/test_colorspace.py::test_bfast PASSED [ 49%] 163s tests/test_colorspace.py::test_trim_095 PASSED [ 49%] 163s tests/test_colorspace.py::test_solid PASSED [ 50%] 163s tests/test_colorspace.py::test_solid_basespace_adapter PASSED [ 50%] 163s tests/test_colorspace.py::test_solid5p PASSED [ 50%] 163s tests/test_colorspace.py::test_solid5p_prefix_notrim PASSED [ 51%] 163s tests/test_colorspace.py::test_solid5p_prefix PASSED [ 51%] 163s tests/test_colorspace.py::test_solid5p_fastq PASSED [ 52%] 163s tests/test_colorspace.py::test_solid5p_prefix_notrim_fastq PASSED [ 52%] 163s tests/test_colorspace.py::test_solid5p_prefix_fastq PASSED [ 53%] 163s tests/test_colorspace.py::test_sra_fastq PASSED [ 53%] 163s tests/test_colorspace.py::test_no_zero_cap PASSED [ 54%] 163s tests/test_commands.py::test_order_preserving_writer PASSED [ 54%] 163s tests/test_filters.py::test_ncontentfilter PASSED [ 54%] 163s tests/test_filters.py::test_ncontentfilter_paired PASSED [ 55%] 163s tests/test_modifiers.py::test_unconditional_cutter PASSED [ 55%] 163s tests/test_modifiers.py::test_nend_trimmer PASSED [ 56%] 163s tests/test_modifiers.py::test_quality_trimmer PASSED [ 56%] 163s tests/test_modifiers.py::test_Modifiers_single PASSED [ 57%] 163s tests/test_modifiers.py::test_Modifiers_paired_legacy PASSED [ 57%] 163s tests/test_modifiers.py::test_Modifiers_paired_both PASSED [ 58%] 163s tests/test_modifiers.py::test_min_cutter_T_T PASSED [ 58%] 163s tests/test_modifiers.py::test_min_cutter_F_T PASSED [ 59%] 163s tests/test_modifiers.py::test_min_cutter_T_F PASSED [ 59%] 163s tests/test_modifiers.py::test_non_directional_bisulfite_trimmer PASSED [ 59%] 163s tests/test_modifiers.py::test_TruSeq_trimmer PASSED [ 60%] 163s tests/test_modifiers.py::test_Swift_trimmer PASSED [ 60%] 163s tests/test_modifiers.py::test_overlapping PASSED [ 61%] 163s tests/test_modifiers.py::test_overlapping_with_error_correction PASSED [ 61%] 163s tests/test_modifiers.py::test_mismatched_adapter_overlaps PASSED [ 62%] 163s tests/test_modifiers.py::test_error_correction PASSED [ 62%] 163s tests/test_modifiers.py::test_error_correction_no_insert_match_one_adapter_match PASSED [ 63%] 163s tests/test_modifiers.py::test_error_correction_no_insert_match_two_adapter_matches PASSED [ 63%] 163s tests/test_modifiers.py::test_error_correction_unequal_read_lengths PASSED [ 63%] 163s tests/test_modifiers.py::test_overwrite_read PASSED [ 64%] 163s tests/test_multicore.py::test_wait_on PASSED [ 64%] 165s tests/test_multicore.py::test_timeout PASSED [ 65%] 165s tests/test_multicore.py::test_enqueue_dequeue PASSED [ 65%] 169s tests/test_multicore.py::test_enqueue_timeout PASSED [ 66%] 173s tests/test_multicore.py::test_dequeue_timeout PASSED [ 66%] 173s tests/test_paired.py::test_paired_separate PASSED [ 67%] 173s tests/test_paired.py::test_paired_end_legacy PASSED [ 67%] 173s tests/test_paired.py::test_untrimmed_paired_output PASSED [ 68%] 173s tests/test_paired.py::test_explicit_format_with_paired PASSED [ 68%] 173s tests/test_paired.py::test_no_trimming_legacy PASSED [ 68%] 173s tests/test_paired.py::test_no_trimming PASSED [ 69%] 173s tests/test_paired.py::test_missing_file PASSED [ 69%] 173s tests/test_paired.py::test_first_too_short PASSED [ 70%] 174s tests/test_paired.py::test_second_too_short PASSED [ 70%] 174s tests/test_paired.py::test_unmatched_read_names PASSED [ 71%] 174s tests/test_paired.py::test_legacy_minlength PASSED [ 71%] 174s tests/test_paired.py::test_paired_end PASSED [ 72%] 174s tests/test_paired.py::test_paired_anchored_back_no_indels PASSED [ 72%] 174s tests/test_paired.py::test_paired_end_qualtrim PASSED [ 72%] 174s tests/test_paired.py::test_paired_end_qualtrim_swapped PASSED [ 73%] 174s tests/test_paired.py::test_paired_end_cut PASSED [ 73%] 174s tests/test_paired.py::test_paired_end_A_only PASSED [ 74%] 174s tests/test_paired.py::test_paired_end_mask_adapter PASSED [ 74%] 174s tests/test_paired.py::test_discard_untrimmed PASSED [ 75%] 174s tests/test_paired.py::test_discard_trimmed PASSED [ 75%] 174s tests/test_paired.py::test_interleaved PASSED [ 76%] 174s tests/test_paired.py::test_interleaved_no_paired_output PASSED [ 76%] 174s tests/test_paired.py::test_pair_filter PASSED [ 77%] 174s tests/test_paired.py::test_too_short_paired_output PASSED [ 77%] 174s tests/test_paired.py::test_too_long_output PASSED [ 77%] 174s tests/test_paired.py::test_too_short_output_paired_option_missing PASSED [ 78%] 174s tests/test_paired.py::test_custom_bisulfite_1 PASSED [ 78%] 174s tests/test_paired.py::test_custom_bisulfite_2 PASSED [ 79%] 174s tests/test_paired.py::test_no_insert_match PASSED [ 79%] 174s tests/test_paired.py::test_overwrite PASSED [ 80%] 184s tests/test_paired.py::test_no_writer_process PASSED [ 80%] 194s tests/test_paired.py::test_summary PASSED [ 81%] 194s tests/test_qualtrim.py::test_nextseq_trim PASSED [ 81%] 194s tests/test_seqio.py::TestAlphabet::test_alphabet PASSED [ 81%] 194s tests/test_seqio.py::TestSequence::test_too_many_qualities PASSED [ 82%] 194s tests/test_seqio.py::TestSequence::test_too_many_qualities_colorspace PASSED [ 82%] 194s tests/test_seqio.py::TestSequence::test_invalid_primer PASSED [ 83%] 194s tests/test_seqio.py::TestFastaReader::test PASSED [ 83%] 194s tests/test_seqio.py::TestFastaReader::test_with_comments PASSED [ 84%] 194s tests/test_seqio.py::TestFastaReader::test_wrong_format PASSED [ 84%] 194s tests/test_seqio.py::TestFastaReader::test_fastareader_keeplinebreaks PASSED [ 85%] 194s tests/test_seqio.py::TestFastaReader::test_context_manager PASSED [ 85%] 194s tests/test_seqio.py::TestFastqReader::test_fastqreader PASSED [ 86%] 194s tests/test_seqio.py::TestFastqReader::test_fastqreader_dos PASSED [ 86%] 194s tests/test_seqio.py::TestFastqReader::test_fastq_wrongformat PASSED [ 86%] 194s tests/test_seqio.py::TestFastqReader::test_fastq_incomplete PASSED [ 87%] 194s tests/test_seqio.py::TestFastqReader::test_context_manager PASSED [ 87%] 194s tests/test_seqio.py::TestFastqReader::test_alphabet PASSED [ 88%] 194s tests/test_seqio.py::TestFastaQualReader::test_mismatching_read_names PASSED [ 88%] 194s tests/test_seqio.py::TestFastaQualReader::test_invalid_quality_value PASSED [ 89%] 194s tests/test_seqio.py::TestSeqioOpen::test_sequence_reader PASSED [ 89%] 194s tests/test_seqio.py::TestSeqioOpen::test_autodetect_fasta_format PASSED [ 90%] 194s tests/test_seqio.py::TestSeqioOpen::test_write_qualities_to_fasta PASSED [ 90%] 194s tests/test_seqio.py::TestSeqioOpen::test_autodetect_fastq_format PASSED [ 90%] 194s tests/test_seqio.py::TestSeqioOpen::test_fastq_qualities_missing PASSED [ 91%] 194s tests/test_seqio.py::TestInterleavedReader::test PASSED [ 91%] 194s tests/test_seqio.py::TestInterleavedReader::test_missing_partner PASSED [ 92%] 194s tests/test_seqio.py::TestInterleavedReader::test_incorrectly_paired PASSED [ 92%] 194s tests/test_seqio.py::TestFastaWriter::test PASSED [ 93%] 194s tests/test_seqio.py::TestFastaWriter::test_linelength PASSED [ 93%] 194s tests/test_seqio.py::TestFastaWriter::test_write_sequence_object PASSED [ 94%] 194s tests/test_seqio.py::TestFastaWriter::test_write_zero_length_sequence PASSED [ 94%] 194s tests/test_seqio.py::TestFastqWriter::test PASSED [ 95%] 194s tests/test_seqio.py::TestFastqWriter::test_twoheaders PASSED [ 95%] 194s tests/test_seqio.py::TestInterleavedWriter::test PASSED [ 95%] 194s tests/test_seqio.py::TestPairedSequenceReader::test_sequence_names_match PASSED [ 96%] 194s tests/test_seqio.py::test_truncated_gz PASSED [ 96%] 194s tests/test_seqio.py::test_truncated_gz_iter PASSED [ 97%] 194s tests/test_trim.py::test_cs_5p PASSED [ 97%] 194s tests/test_trim.py::test_statistics PASSED [ 98%] 194s tests/test_xopen.py::test_context_manager PASSED [ 98%] 194s tests/test_xopen.py::test_append PASSED [ 99%] 194s tests/test_xopen.py::test_xopen_text PASSED [ 99%] 194s tests/test_xopen.py::test_xopen_binary PASSED [100%] 194s 194s =============================== warnings summary =============================== 194s tests/test_paired.py:638 194s /tmp/autopkgtest.ZRaCp5/autopkgtest_tmp/tests/test_paired.py:638: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 194s @pytest.mark.timeout(10) 194s 194s tests/test_paired.py::test_no_writer_process 194s tests/test_paired.py::test_no_writer_process 194s tests/test_paired.py::test_summary 194s tests/test_paired.py::test_summary 194s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=1418) is multi-threaded, use of fork() may lead to deadlocks in the child. 194s self.pid = os.fork() 194s 194s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 194s ================= 221 passed, 1 skipped, 5 warnings in 41.03s ================== 195s autopkgtest [16:48:04]: test run-unit-test: -----------------------] 196s run-unit-test PASS 196s autopkgtest [16:48:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 196s autopkgtest [16:48:05]: @@@@@@@@@@@@@@@@@@@@ summary 196s run-unit-test PASS 208s Creating nova instance adt-noble-arm64-atropos-20240324-164449-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...