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

[Terry Casstevens]

Hi Spencer,

Thank you for your reply.  biojava3-core is on the CLASSPATH.  See
attached log at top shows CLASSPATH.  Also see Exception toward the
bottom.  One thing to note, is that this works under Java 7.  It's
only when running under Java 8 that this Exception occurs.

Thank you,

Terry


On Wed, May 7, 2014 at 2:29 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> 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
>> >
>> >
>> >
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: DiscoverySNPClallerPlugin.log
Type: application/octet-stream
Size: 24900 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-dev/attachments/20140507/f9142052/attachment-0002.obj>