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.moll...@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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