[Biojava-dev] build errors

[Andreas Prlic]

Hi George,

looking at your errors it seems you have a mix of biojava-legacy and
biojava 3 somehow. How did you check this out? I believe the old SVN repo
is still accessible as read only, and that is the only way I can imagine
you might have gotten both.

Checking out from git should be straightforward:

git clone git at github.com:biojava/biojava.git ./biojava

You could also try using the github application.

see also: http://biojava.org/wiki/Get_source

Let us know if you have any problems with that!

Andreas


On Mon, Jan 6, 2014 at 9:22 PM, George Waldon <gwaldon at geneinfinity.org>wrote:

> 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
>
>
>
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