[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

[Paul Gevers]

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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