[Debian-med-packaging] Bug#942404: discosnp: flaky autopkgtest: discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa: No such file or directory

[Olivier Sallou]

Just did a test on sid up-to-date, and tests were fine.

Will be difficult to forward upstream with bug occuring "sometimes" and
not really reproducible.

On 10/15/19 9:35 PM, Paul Gevers wrote:
> Source: discosnp
> Version: 2.3.0-2
> 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),
>
> With a recent upload of python-defaults to unstable, the autopkgtest of
> discosnp failed in testing when that autopkgtest was run with the binary
> packages of python-defaults from unstable. However, as we check for
> regression, the reference was retried and failed as well, without
> further changes. I looked into the history of your autopkgtest and it
> fails very often.
>
> 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. Please either fix the test to be more robust, or or use the
> "flaky" restriction for the offending test until a solution has been found.
>
> I copied the output at the bottom of this report. All the failing tests
> that I inspected look like it.
>
> I'll have the migration software ignore the results of your autopkgtest
> until this bug is fixed.
>
> Paul
>
> https://ci.debian.net/data/autopkgtest/unstable/amd64/d/discosnp/3153055/log.gz
>
> autopkgtest [08:02:13]: test run-unit-test: [-----------------------
> use read set: fof.txt
> 	Running discoSnp++ 2.3.X, in directory /usr with following parameters:
> 		 read_sets=fof.txt
> 		 prefix=discoRes_k_31_c_auto
> 		 c=auto
> 		 C=2147483647
> 		 k=31
> 		 b=0
> 		 d=1
> 		 D=100
> 	 starting date=Mon Oct 14 08:02:14 UTC 2019
>
> 	############################################################
> 	#################### GRAPH CREATION  #######################
> 	############################################################
> /usr/bin/dbgh5 -in
> fof.txt_discoRes_k_31_c_auto_D_100_P_1_b_0_removemeplease -out
> discoRes_k_31_c_auto -kmer-size 31 -abundance-min auto -abundance-max
> 2147483647 -solidity-kind one -verbose 1 -skip-bcalm -skip-bglue -no-mphf
>
> [DSK: counting kmers                     ]  0    %   elapsed:   0 min 0
>  sec   remaining:   0 min 0  sec   cpu:  -1.0 %   mem: [  14,   14,
> 36] MB
> [DSK: Pass 1/1, Step 1: partitioning     ]  0    %   elapsed:   0 min 0
>  sec   remaining:   0 min 0  sec   cpu:  -1.0 %   mem: [  46,   46,
> 46] MB
> EXCEPTION: Pool allocation failed for 128 bytes (kmers alloc),
> mainbuffer is null?. Current usage is 144 and capacity is 5242881056
> Pool allocation failed for 1288 bytes (kmers alloc), mainbuffer is
> null?. Current usage is 1448 and capacity is 5242881056
>
> there was a problem with graph construction
> diff: discoRes_k_31_c_auto_D_100_P_1_b_0_coherent.fa: No such file or
> directory
> *** Test: FAILURE on diff .fa
> autopkgtest [08:02:15]: test run-unit-test: -----------------------]
>
>
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-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

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