Your message dated Fri, 16 Apr 2021 21:49:03 +0000 with message-id <e1lxwkl-000frq...@fasolo.debian.org> and subject line Bug#986592: fixed in kaptive 0.7.3-3 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: 0.7.3-3 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, 16 Apr 2021 17:33:52 -0400 Source: kaptive Architecture: source Version: 0.7.3-3 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 (0.7.3-3) unstable; urgency=high . * Team upload. * d/p/extend_bad_versions: Account for crashes with error output too. If a relevant tblastn version failed with error text starting with "terminate called ", prepend the usual "tblastn crashed!" message. (Closes: #986592.) Checksums-Sha1: 57cd3bd34a32be2d365c84eb4c3ef79e56e431a9 2125 kaptive_0.7.3-3.dsc c42b98af14a8e0ac1851d2e25ffae76f151388e1 6528 kaptive_0.7.3-3.debian.tar.xz 6de4d4ee92af13088e18f654680738facc533307 11346 kaptive_0.7.3-3_source.buildinfo Checksums-Sha256: 47294e7c4d7b894763c8b7b29670f5c4febd84c1d91d7eb8932c7d9f3f3a5ee7 2125 kaptive_0.7.3-3.dsc b7cd9a952ea5a577a6e7411a4e41d93c0a8020543052ad7ae08c697f77d99577 6528 kaptive_0.7.3-3.debian.tar.xz 17ce3b7e4f09c569b514fad858df086114b7458d952fead043003721060fa974 11346 kaptive_0.7.3-3_source.buildinfo Files: 7ab278f447d56c8e5747ddcea57b0b9c 2125 science optional kaptive_0.7.3-3.dsc a6ea69c2c76208313adf9f290210cede 6528 science optional kaptive_0.7.3-3.debian.tar.xz 84f1145bfad8da773c9df880ab4b1224 11346 science optional kaptive_0.7.3-3_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmB6A4QACgkQHnCRsfFK ZKIXag/8C7eEiH1SQ4460L1edOKUBVyuZpQo5+LvbQffE6IaIV58MlXW6f6Oi1qn a+IcDsYfypaziHaizhicQ7gREd67afDxDm7e1yDs8e8CLdOzo68G6+dE+lINa0d7 EE97iXW7ONCj7kCgaXB4s4FwXu/DfZT5QDOIDMlFMHBoP9rNiDBVqEk2PPUZhoce lwehT0nMsO16GXLqH2/T3tXfFrZSYNhqTgh86Dr/0Fb0MF0gEDPotWivO44tblrd RM+O4Bvn13VlpHO30UCIfh33RevR0txJMhdDGhsXSJLbZGS7Ic/E/h+P+CuNKoCM PPU7+NJdgxpd/U+72NCt82uJ1ZsIVXTt2xP4lSUnrzF+rYn7ETuVDgPABeC9yRJb DfUwIzmZMUBpTg9c+req4U0oq4408rSgP9ywp4VZysNbb/j/9gCu1+R07JUXDHeB 60hdb++g8LKwPVdLvoJe8eJXpWgL1Dl8JTMeID5RFMLDxlVonsrovEHstPqcIh4w JbTqZihDy33mZEe3FHhv19VTEUjWPt6bFYcFqMy+C+VXAMiL9Lk27a+tIw9h1rrO rKBeW4cDhUUmJaanV2OgtnsJ//vaxav3xaM4Mg/bFblYru7mETqc/xCiPGZAzdtq Awd/uGlS//ZN0DvcAcJ8qwhOsvx/wE0JLjqAFO9Ib/87G2VeQmw= =0e+r -----END PGP SIGNATURE-----
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