[Biojava-dev] test failures on biojava/biojava git repo

[Andreas Prlic]

Hi Michael,

Works fine for me on linux and osx.  Are you doing this from command
line or an IDE? Can you verify that the src/test/resources directory
is on your project build path? -

- besides this, agreed that this should be using a tmp file rather
than creating files at that location.

Andreas

On Tue, Aug 7, 2012 at 8:15 AM, Michael Heuer <heuermh at gmail.com> wrote:
> Hello,
>
> Thought I would try working with the git mirrors today but
> unfortunately biojava/biojava git repo fails unit tests for me on OSX
>
> -------------------------------------------------------
>  T E S T S
> -------------------------------------------------------
> Running org.biojava3.genome.GeneFeatureHelperTest
> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading src/test/resources/amphimedon.gff3
> Gene EDEN found at ctgA 1050 9000 POSITIVE
> Gene rna-Apple3 found at ctgA 18000 21200 POSITIVE
> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading
> /Users/mheuer/working/biojava-git/biojava3-genome/src/test/resources/volvox.gff3
> Note [protein kinase]
> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading
> /Users/mheuer/working/biojava-git/biojava3-genome/src/test/resources/volvox.gff3
> Aug 7, 2012 10:03:18 AM org.biojava3.genome.parsers.gff.GFF3Reader read
> INFO: Gff.read(): Reading
> /Users/mheuer/working/biojava-git/biojava3-genome/src/test/resources/volvox.gff3
> Tests run: 6, Failures: 0, Errors: 3, Skipped: 0, Time elapsed: 0.649
> sec <<< FAILURE!
> Running org.biojava3.genome.AppTest
> Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
>
> Results :
>
> Tests in error:
>   testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(org.biojava3.genome.GeneFeatureHelperTest)
>   testOutputFastaSequenceLengthGFF3(org.biojava3.genome.GeneFeatureHelperTest)
>   testGetProteinSequences(org.biojava3.genome.GeneFeatureHelperTest)
>
> ...
>
> -------------------------------------------------------------------------------
> Test set: org.biojava3.genome.GeneFeatureHelperTest
> -------------------------------------------------------------------------------
> Tests run: 6, Failures: 0, Errors: 3, Skipped: 0, Time elapsed: 0.648
> sec <<< FAILURE!
> testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(org.biojava3.genome.GeneFeatureHelperTest)
>  Time elapsed: 0.156 sec  <<< ERROR!
> java.io.FileNotFoundException:
> src/test/resources/testoutput/volvox_all_genes_exon_uppercase.gff3 (No
> such file or directory)
>         at java.io.FileOutputStream.open(Native Method)
>         at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
>         at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
>         at org.biojava3.genome.GeneFeatureHelperTest.testLoadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(GeneFeatureHelperTest.java:63)
> ...
> testOutputFastaSequenceLengthGFF3(org.biojava3.genome.GeneFeatureHelperTest)
>  Time elapsed: 0.007 sec  <<< ERROR!
> java.io.FileNotFoundException:
> src/test/resources/testoutput/volvox_length.gff3 (No such file or
> directory)
>         at java.io.FileOutputStream.open(Native Method)
>         at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
>         at java.io.FileOutputStream.<init>(FileOutputStream.java:145)
>         at java.io.FileWriter.<init>(FileWriter.java:73)
>         at org.biojava3.genome.GeneFeatureHelper.outputFastaSequenceLengthGFF3(GeneFeatureHelper.java:163)
>         at org.biojava3.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:78)
> ...
> testGetProteinSequences(org.biojava3.genome.GeneFeatureHelperTest)
> Time elapsed: 0.152 sec  <<< ERROR!
> java.io.FileNotFoundException:
> src/test/resources/testoutput/volvox_all.faa (No such file or
> directory)
>         at java.io.FileOutputStream.open(Native Method)
>         at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
>         at java.io.FileOutputStream.<init>(FileOutputStream.java:145)
>         at org.biojava3.core.sequence.io.FastaWriterHelper.writeProteinSequence(FastaWriterHelper.java:57)
>         at org.biojava3.genome.GeneFeatureHelperTest.testGetProteinSequences(GeneFeatureHelperTest.java:107)
>
>
> This directory is not present
>
> src/test/resources/testoutput
>
> nor is this one
>
> biojava3-genome/src/test/resources/testoutput
>
> Files that are written out during unit tests should probably use
> File.createTempFile(...).
>
>
> svn trunk built fine for me on linux last night.  ssh is blocked at
> work so I cannot try svn trunk here.
>
>    michael
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