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
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
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