Your message dated Fri, 09 Apr 2021 22:18:25 +0000 with message-id <e1luzsl-000eoa...@fasolo.debian.org> and subject line Bug#986592: fixed in kaptive 0.7.3-2 has caused the Debian Bug report #986592, regarding kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 986592: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=986592 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: kleborate Version: 2.0.1-1 Severity: serious Tags: sid bullseye X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: flaky Dear maintainer(s), Your package has an autopkgtest, great. However, I looked into the history of your autopkgtest [1] and I noticed the it fails regularly on ppc64el, while a rerun passes. I copied some of the output at the bottom of this report. It's not always the same place where the issue acures. Because the unstable-to-testing migration software now blocks on regressions in testing, flaky tests, i.e. tests that flip between passing and failing without changes to the list of installed packages, are causing people unrelated to your package to spend time on these tests. Paul PS: if you fix this for bullseye, our migration tooling will not correctly detect it can migrate according to the freeze rules due to it scheduling tests on i386 and armhf where no arch specific package is built. Ping me and if otherwise OK, I'll hint it through. [1] https://ci.debian.net/packages/k/kleborate/testing/arm64/ https://ci.debian.net/data/autopkgtest/testing/arm64/k/kleborate/11152715/log.gz autopkgtest [09:23:49]: test run-unit-test: [----------------------- strain species ST virulence_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus Klebs_HS11286 Klebsiella pneumoniae ST11 1 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 Klebs_Kp1084 Klebsiella pneumoniae ST23 2 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 MGH78578 Klebsiella pneumoniae ST38 0 - 0 - 0 - 0 - 0 - 0 - wzi50 KL15 (KL17,KL51,KL52) NTUH-K2044 Klebsiella pneumoniae ST23 4 ybt 2; ICEKp1 326 - 0 iuc 1 1 iro 1,iro 3 19,18 rmp 3; ICEKp1,rmp 1; KpVP-1 30-1LV,26 rmpA2_3-47% wzi1 KL1 strain species ST virulence_score resistance_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus AGly_acquired Col_acquired Fcyn_acquired Flq_acquired Gly_acquired MLS_acquired Phe_acquired Rif_acquired Sul_acquired Tet_acquired Tgc_acquired Tmt_acquired Bla_acquired Bla_inhR_acquired Bla_ESBL_acquired Bla_ESBL_inhR_acquired Bla_Carb_acquired Bla_chr SHV_mutations Omp_mutations Col_mutations Flq_mutations truncated_resistance_hits spurious_resistance_hits Klebs_HS11286 Klebsiella pneumoniae ST11 1 3 ybt 9; ICEKp3 15 - 0 - 0 - 0 - 0 - wzi74 KL103 aadA2^;rmtB;strA.v1^;strB.v1 - - - - - - - sul2 tet(G).v1 - dfrA12* TEM-1;TEM-1;TEM-1 - CTX-M-14;CTX-M-14 - KPC-2 SHV-11.v1 35Q OmpK35-40% PmrB-10% GyrA-83I;ParC-80I aac(3)-IId*?-0% floR.v2*?;sul1?-63% Klebs_Kp1084 Klebsiella pneumoniae ST23 2 0 ybt 1; ICEKp10 47 clb 2 37 - 0 - 0 - 0 - wzi172 KL1 - - - - - - - - - - - - - - - - - SHV-11.v1^ 35Q - - - - - MGH78578 Klebsiella pneumoniae ST38 0 1 - 0 - 0 - 0 - 0 - 0 - wzi50 KL15 (KL17,KL51,KL52) aac(6')-Ib'.v1;aadA*;ant(2'')-Ia;aph(3')-Ia;strA.v1;strB.v1 - - - - - catA1*;cmlA5 - sul1;sul2 tet(D) - - TEM-1D.v1^;TEM-1D.v1^ - SHV-12 - - SHV-11.v1^ 238S;240K;35Q;35Q OmpK35-86% - GyrA-83Y OXA-9.v1*-42% - NTUH-K2044 Klebsiella pneumoniae ST23 4 0 ybt 2; ICEKp1 326 - 0 iuc 1 1 iro 1,iro 3 19,18 rmp 3; ICEKp1,rmp 1; KpVP-1 30-1LV,26 rmpA2_3-47% wzi1 KL1 - - - - - - - - - - - - - - - - - SHV-11.v1^ 35Q - - - - - strain species ST virulence_score resistance_score Yersiniabactin YbST Colibactin CbST Aerobactin AbST Salmochelin SmST RmpADC RmST rmpA2 wzi K_locus K_locus_confidence O_locus O_locus_confidence AGly_acquired Col_acquired Fcyn_acquired Flq_acquired Gly_acquired MLS_acquired Phe_acquired Rif_acquired Sul_acquired Tet_acquired Tgc_acquired Tmt_acquired Bla_acquired Bla_inhR_acquired Bla_ESBL_acquired Bla_ESBL_inhR_acquired Bla_Carb_acquired Bla_chr SHV_mutations Omp_mutations Col_mutations Flq_mutations truncated_resistance_hits spurious_resistance_hits Error: Kaptive failed to run with the following error: /usr/lib/python3/dist-packages/Bio/GenBank/__init__.py:1288: BiopythonParserWarning: The NCBI states double-quote characters like " should be escaped as "" (two double - quotes), but here it was not: 'undecaprenyl-phosphate galactose phosphotransferase" glucose-1-phosphate transferase' warnings.warn( Error: tblastn encountered an error: terminate called after throwing an instance of 'ncbi::CMutexException' what(): NCBI C++ Exception: T0 "c++/include/corelib/ncbidiag.hpp", line 417: Error: (CMutexException::eOwner) ncbi::ncbi_namespace_mutex_mt::SSystemMutex::ThrowNotOwned() - Mutex is not owned by current thread autopkgtest [09:29:05]: test run-unit-test: -----------------------]
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--- Begin Message ---Source: kaptive Source-Version: 0.7.3-2 Done: Aaron M. Ucko <u...@debian.org> We believe that the bug you reported is fixed in the latest version of kaptive, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 986...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <u...@debian.org> (supplier of updated kaptive package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 09 Apr 2021 18:08:16 -0400 Source: kaptive Architecture: source Version: 0.7.3-2 Distribution: unstable Urgency: high Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <u...@debian.org> Closes: 986592 Changes: kaptive (0.7.3-2) unstable; urgency=high . * Team upload. * debian/patches/extend_bad_versions: Extend the range of tblastn versions that might not be entirely stable with multiple threads through 2.11.x, switching to a regular expression along the way. (Closes: #986592.) Checksums-Sha1: 375ad26423a2814b71a691b6e2e06b88b1db97df 2125 kaptive_0.7.3-2.dsc d4deb46ee83c3c2115cd0ed742c926e2bcb6d20a 6120 kaptive_0.7.3-2.debian.tar.xz 8f20085d29bed2312dc70acefa93096bf2f1b394 11376 kaptive_0.7.3-2_source.buildinfo Checksums-Sha256: 86b98c209275ca31469cde3ae737fd34c388a016b110f9d03938fa7457218ea3 2125 kaptive_0.7.3-2.dsc 013a2aad97db5f5022631bd20167f3cecba8f11eeebaddef98c6ed62d099ade3 6120 kaptive_0.7.3-2.debian.tar.xz 2d920da375289177379d4b079f4be87654855dffc4091c0c0725f444d66774d9 11376 kaptive_0.7.3-2_source.buildinfo Files: bd7a11f332303893f205aa73d7360951 2125 science optional kaptive_0.7.3-2.dsc 022a5064cd6229bb078aee2c7a854fc3 6120 science optional kaptive_0.7.3-2.debian.tar.xz 9aad9308ae0544de3bd3089a1a2d78fe 11376 science optional kaptive_0.7.3-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmBw0MYACgkQHnCRsfFK ZKLEOhAAl9Xr8xMI+o8221I2gDAY3AIqvOyUFAu5ig2zxdwCxQOSHrwW8aCmiZ23 kGzbrp7EZ10yVIzlzL0UlkBG68nXahllaFa9jtHB44PygYh6hQN94R1CyCo8/cUw CL2tCZTuo4dBTck8uAolOvGHIg2bawVdSg6GdbQb4kAx6IgubhdXmFB2QKgp9MsO hKL+VyEpayTDLtWCIpGRPQNrg7jHmTQgsekB7XvRpppWQKn2sjJZ3DEK07aB+VrD 5XBpqCg+NDOQCXsRE3IunbvWhjG9Vt6JwwgaWJoTFsDuuUKK097ay99nRWTDm4ay DWES67Az1NqjlMXlmWuKgOlKx9tq/k9fqsLchHq1CvpakOIgR4b0mlMFqnC9QiAK AROXL5w9pavuwrM3daoW7PiUzZhQoAvksakCYyL5Is/4r3tmISaqgnuoWCpz7DKj l6GStyBFxbA0A/JR2s1MirDNJ4i4ZSXwHmgFWWgZTQluJIuoIJd07grc79OINDXj 3htoqsJZZjhJFzdadhvhXuQ9uU7z7ETtr2mjYjYh89pN+MP1yDMOTEpRAVg1DuLB RXyfIXXJdBtcBqII3ysbiIF+9Jkn4cmpJcvpZxEJhKfU+rprc9WzJZm0qXMUVX6B SClfFsRnsSx7nLlu19cqD8Rw9qV8BJb8o5P+PPiJzV6eyi5cMqs= =H+Pm -----END PGP SIGNATURE-----
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