[Biojava-dev] build errors

[George Waldon]

Hi,

I just started playing with git and I am getting the following build  
errors, possibly an end-of-line issue somewhere but not really sure.  
Could someone help me setting git possibly?

org.biojava.bio.seq.db.EmblCDROMIndexStoreTest
org.biojava.bio.BioException: Couldn't grab region of file
         at  
org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:134)
         at  
org.biojava.bio.seq.db.IndexedSequenceDB.getSequence(IndexedSequenceDB.java:267)
         at  
org.biojava.bio.seq.db.EmblCDROMIndexStoreTest.testFetch(EmblCDROMIndexStoreTest.java:130)

This one likely an URL not working:
org.biojava.dasobert.TestExternalSource
java.io.FileNotFoundException: http://vega.sanger.ac.uk/das/sources
	at  
sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1624)
	at  
org.biojava.dasobert.TestExternalSource.testExternalSource(TestExternalSource.java:51)

org.biojava3.genome.GeneFeatureHelperTest
junit.framework.AssertionFailedError: actual file is longer
         at junit.framework.Assert.fail(Assert.java:57)
         at junitx.framework.FileAssert.assertBinaryEquals(FileAssert.java:237)
         at  
org.biojava3.genome.GeneFeatureHelperTest.testOutputFastaSequenceLengthGFF3(GeneFeatureHelperTest.java:82)

org.biojava3.ronn.JronnTest
java.lang.ExceptionInInitializerError: null
         at java.util.Scanner.throwFor(Scanner.java:840)
         at java.util.Scanner.next(Scanner.java:1461)
         at java.util.Scanner.nextInt(Scanner.java:2091)
         at java.util.Scanner.nextInt(Scanner.java:2050)
         at org.biojava3.ronn.ModelLoader.loadModels(ModelLoader.java:170)
         at org.biojava3.ronn.Jronn.<clinit>(Jronn.java:58)
         at org.biojava3.ronn.JronnTest.verifyRanges(JronnTest.java:15)

org.biojava3.ronn.NonstandardProteinCompoundTest
java.lang.ExceptionInInitializerError: null
         at java.util.Scanner.throwFor(Scanner.java:840)
         at java.util.Scanner.next(Scanner.java:1461)
         at java.util.Scanner.nextInt(Scanner.java:2091)
         at java.util.Scanner.nextInt(Scanner.java:2050)
         at org.biojava3.ronn.ModelLoader.loadModels(ModelLoader.java:170)
         at org.biojava3.ronn.Jronn.<clinit>(Jronn.java:58)
         at  
org.biojava3.ronn.NonstandardProteinCompoundTest.testUniprot(NonstandardProteinCompoundTest.java:56)
         at  
org.biojava3.ronn.NonstandardProteinCompoundTest.test(NonstandardProteinCompoundTest.java:32)

Thanks,
George

--------------------------------
George Waldon