[Biojava-dev] build errors

[George Waldon]

Hi Andreas,

No, I build the two projects separately; both are giving errors. The  
builds were done using JKD1.7 (windows7/NB IDE 7.4). I do not think we  
still have automatic builds for legacy;  
org.biojava.dasobert.TestExternalSource should be easily reproducible.  
I was thinking of an end-of-line issue for the others errors since  
org.biojava3.ronn.ModelLoader.loadModels(ModelLoader.java:170) is just  
after "scan.useDelimiter("\n");" suggesting my end-of-lines might have  
changed during the checkout. No clue indeed.

Thanks,
George

Quoting Andreas Prlic <andreas at sdsc.edu>:

> 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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>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>



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