Control: tags -1 help
Hi Aaron,
do you have possibly any hint what might be wrong here?
Kind regards
Andreas.
On Wed, Apr 07, 2021 at 09:35:42PM +0200, Paul Gevers wrote:
> 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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