[Biojava-dev] [JIRA] (TAS-344) biojava with Java 8

[Spencer Bliven]

Terry–

It looks like your program isn't including biojava3-core in the classpath.
This is a bit surprising since it clearly is including biojava3-alignment.
Can you post more details about how you are running the pipeline (shell
script, eclipse project, maven, etc)? I can confirm that SimpleLocation is
present in 3.0.8, so it is most likely a problem with your configuration.

-Spencer


On Mon, May 5, 2014 at 5:49 PM, Terry Casstevens <tmc46 at cornell.edu> wrote:

> Dear Biojava Developers,
>
> We are using the biojava libraries below with Java 8, and we are getting
> the following exception.   Do you what is our problem?
>
> biojava3-alignment-3.0.8.jar
> biojava3-core-3.0.8.jar
> biojava3-phylo-3.0.8.jar
> forester_1030.jar
>
>
> java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError:
> Could not initialize class
> org.biojava3.core.sequence.location.SimpleLocation
> at java.util.concurrent.FutureTask.report(FutureTask.java:122)
> at java.util.concurrent.FutureTask.get(FutureTask.java:192)
> at
> org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> at
> org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> at
>
> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
> at net.maizegenetics.dna.map.TagLocus.getVariableSites(TagLocus.java:501)
> at net.maizegenetics.dna.map.TagLocus.getSNPCallsQuant(TagLocus.java:297)
>
>
> Thank you,
>
> Terry
>
>
>
> On Mon, May 5, 2014 at 11:28 AM, Terry Casstevens <tmc46 at cornell.edu>
> wrote:
>
> > I downloaded these libraries to try with the GBS Pipeline...
> >
> > biojava3-alignment-3.0.8.jar
> > biojava3-core-3.0.8.jar
> > biojava3-phylo-3.0.8.jar
> > forester_1030.jar
> >
> >
> > Under Java 7, GBS Pipeline runs but yields different results than
> previous
> > libraries. Didn't check to see how different.
> >
> > Under Java 8, Same problem as before
> > "java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError:
> > Could not initialize class
> > org.biojava3.core.sequence.location.SimpleLocation"
> >
> > Also, the new forester library still exits Tassel when you close it.
> >
> >
> > Best,
> >
> > Terry
> >
> >
> >
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