Re: [Debian-med-packaging] Bug#974168: Bug #974168: bioperl-run: autopkgtest issue fixed, now different build time error
Hi Étienne,
thanks a lot - I've uploaded on behalf of you and granted DM upload
permissions in case you want to become involved next time. I think
it would be great if you inform upstream about the missing data set.
Kind regards
Andreas.
On Sat, Dec 05, 2020 at 12:52:23AM +0100, Étienne Mollier wrote:
> 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@mailoo.org>
> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
> Sent from /dev/pts/3, please excuse my verbosity.
--
http://fam-tille.de
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