[Debian-med-packaging] Bug#974168: Bug#974168: Bug #974168: bioperl-run: autopkgtest issue fixed, now different build time error

[Étienne Mollier]

Hi again,

I pushed a couple of changes on salsa[0] to unlock the situation
with BEDtools integration in bioperl-run.  Now the vast majority
of tests are passing.  :)

[0] https://salsa.debian.org/med-team/bioperl-run

One of the datasets in use by the bedtools related functions is
not available in the archive, so I had to change for another
dataset which seemed to do the job as well.  However, this
impeded the reference results of 7 tests (out of more 423, which
is a really good score).  For ulterior reference, the failing
tests with the alternate dataset were returning:

	#   Failed test ' - number of lines'
	#   at t/BEDTools.t line 331.
	#          got: '87'
	#     expected: '38'
	
	#   Failed test 'correct number of features for command 'intersect''
	#   at t/BEDTools.t line 361.
	#          got: '1305'
	#     expected: '72534'
	
	#   Failed test 'correct number of features for command 'closest''
	#   at t/BEDTools.t line 361.
	#          got: '2121'
	#     expected: '845'
	
	#   Failed test 'correct number of features for command 'complement''
	#   at t/BEDTools.t line 361.
	#          got: '292'
	#     expected: '291'
	
	#   Failed test 'correct number of features for command 'subtract''
	#   at t/BEDTools.t line 361.
	#          got: '1802'
	#     expected: '57959'
	
	#   Failed test 'correct number of features for command 'coverage''
	#   at t/BEDTools.t line 361.
	#          got: '828'
	#     expected: '57261'
	
	#   Failed test 'correct number of features for command 'window''
	#   at t/BEDTools.t line 361.
	#          got: '1331'
	#     expected: '74998'
	# Looks like you failed 7 tests of 423.

After a couple of changes to smoothen the execution of test
suites and autopkgtest, I think the package is in an adequate
state to move forward.

Kind Regards,
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
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