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

[Michael Heuer]

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