[Debian-med-packaging] Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

[Andreas Tille]

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-ci at lists.debian.org
> User: debian-ci at 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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