[Biojava-dev] Biojava genome test fails

[Jose Manuel Duarte]

Maybe some files left over from a broken run? Try see if cleaning (mvn 
clean) and then building again does the trick.

Jose


On 14.07.2015 18:11, Paolo Pavan wrote:
> Hi Jose,
> Interesting! I'm also working on commit 
> 154edb7f9a5e9e54f25df3e27aeb169b4fab7799 and below is the result. At a 
> first glance it does not seem a network problem, it downloads 
> maven-metadata.xml.
> What do you think?
> Paolo
>
> -------------------------------------------------------
>  T E S T S
> -------------------------------------------------------
> Running org.biojava.nbio.genome.AppTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 
> sec - in org.biojava.nbio.genome.AppTest
> Running org.biojava.nbio.genome.FeatureListTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.502 
> sec - in org.biojava.nbio.genome.FeatureListTest
> Running org.biojava.nbio.genome.GeneFeatureHelperTest
> 18:04:40 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader - 
> Reading: 
> C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader - 
> Reading: src/test/resources/amphimedon.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader - 
> Reading: 
> C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.parsers.gff.GFF3Reader - 
> Reading: 
> C:\Users\pavanpa\Documents\Programming_workspace\biojava\biojava-genome\src\test\resources\volvox.gff3
> 18:04:41 [main] INFO org.biojava.nbio.genome.GeneFeatureHelperTest - 
> Note [protein kinase]
> 18:04:41 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene 
> EDEN found at ctgA 1050 9000 POSITIVE
> 18:04:41 [main] INFO org.biojava.nbio.genome.GeneFeatureHelper - Gene 
> rna-Apple3 found at ctgA 18000 21200 POSITIVE
> Tests run: 6, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.598 
> sec <<< FAILURE! - in org.biojava.nbio.genome.GeneFeatureHelperTest
> testOutputFastaSequenceLengthGFF3(org.biojava.nbio.genome.GeneFeatureHelperTest) 
> Time elapsed: 0.199 sec  <<< FAILURE!
> junit.framework.AssertionFailedError: actual file is shorter
>     at junit.framework.Assert.fail(Assert.java:57)
>     at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:240)
>     at 
> org.biojava.nbio.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:105)
>
>
> 2015-07-14 14:44 GMT+02:00 Jose Manuel Duarte <jose.duarte at psi.ch 
> <mailto:jose.duarte at psi.ch>>:
>
>     It works for me (on commit 154edb7f9a5e9e).
>
>     Could that be some kind of network problem?
>
>     Jose
>
>
>
>     On 14.07.2015 14:32, Paolo Pavan wrote:
>>     Hello,
>>     It seems that testOutputFastaSequenceLengthGFF3 fails in
>>     biojava-genome 4.1.1 snapshot.
>>     Is this happening to someone else?
>>
>>     bye bye,
>>     Paolo
>>
>>
>>     _______________________________________________
>>     biojava-dev mailing list
>>     biojava-dev at mailman.open-bio.org  <mailto:biojava-dev at mailman.open-bio.org>
>>     http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>
>
>     _______________________________________________
>     biojava-dev mailing list
>     biojava-dev at mailman.open-bio.org
>     <mailto:biojava-dev at mailman.open-bio.org>
>     http://mailman.open-bio.org/mailman/listinfo/biojava-dev
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biojava-dev/attachments/20150714/01a86638/attachment-0001.html>