Source: kleborate
Version: 2.0.1-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci@lists.debian.org
User: debian-ci@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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