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

[Paul Gevers]

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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