[Biojava-l] Biojava-l Digest, Vol 141, Issue 8

Mon Nov 10 07:47:12 UTC 2014

I think the current goal is to release 4.0.0 later this month, or by the
end of the year at the latest.

On Sat, Nov 8, 2014 at 6:30 PM, Khalil El Mazouari <
khalil.elmazouari at gmail.com> wrote:

> Hi,
>
> I agree ;) It's fixed on 4.0.0-SNAPSHOT.
>
> Any idea when biojava 4 will be released?
>
> Thanks
>
> kem
>
> On 08 Nov 2014, at 13:00, biojava-l-request at mailman.open-bio.org wrote:
>
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> > Today's Topics:
> >
> >   1. java 8 - Biojava3        java.util.concurrent.ExecutionException:
> >      java.lang.ExceptionInInitializerError (Khalil El Mazouari)
> >   2. Re: java 8 - Biojava3
> >      java.util.concurrent.ExecutionException:
> >      java.lang.ExceptionInInitializerError (Jose Manuel Duarte)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 7 Nov 2014 21:56:18 +0100
> > From: Khalil El Mazouari <khalil.elmazouari at gmail.com>
> > To: biojava-l at mailman.open-bio.org
> > Subject: [Biojava-l] java 8 - Biojava3
> >       java.util.concurrent.ExecutionException:
> >       java.lang.ExceptionInInitializerError
> > Message-ID: <BC1B67CE-A3EE-4734-870F-826BFEBBE93E at gmail.com>
> > Content-Type: text/plain; charset=windows-1252
> >
> > Hi
> >
> > I am porting my code from java 7 to java 8.
> >
> > Biojava3.alignment is not working on java 8! While it was OK on java 7
> >
> > All jars are in the classpath.
> >
> > Thanks
> >
> > Khalil
> >
> > java.util.concurrent.ExecutionException:
> java.lang.ExceptionInInitializerError
> >       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:289)
> >       at
> org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:612)
> >       at
> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:180)
> > ...
> > Caused by: java.lang.ExceptionInInitializerError
> >       at
> org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)
> >       at
> org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)
> >       at
> org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)
> >       at
> org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)
> >       at
> org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)
> >       at
> org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)
> >       at
> org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)
> >       at
> org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)
> >       at
> org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)
> >       at
> org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105)
> >       at
> org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)
> >       at
> org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)
> >       at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> >       at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> >       at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> >       at java.lang.Thread.run(Thread.java:745)
> > Caused by: java.lang.NullPointerException
> >       at
> java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)
> >       at
> java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)
> >       at java.util.Collections.unmodifiableList(Collections.java:1287)
> >       at
> org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)
> >       at
> org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)
> >       at
> org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)
> >       at
> org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)
> >       at
> org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)
> >       ... 16 more
> > java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError:
> Could not initialize class
> org.biojava3.core.sequence.location.SimpleLocation
> >
> > ?.
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 07 Nov 2014 23:22:06 +0100
> > From: Jose Manuel Duarte <jose.duarte at psi.ch>
> > To: biojava-l at mailman.open-bio.org
> > Subject: Re: [Biojava-l] java 8 - Biojava3
> >       java.util.concurrent.ExecutionException:
> >       java.lang.ExceptionInInitializerError
> > Message-ID: <545D460E.1040508 at psi.ch>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > Are you using Biojava 3.1? This indeed seems to be a problem in 3.1 and
> > before.
> >
> > However I've tried with the current 4.0.0-SNAPSHOT and it seems to work
> > fine.
> >
> > Jose
> >
> >
> >
> > On 07.11.2014 21:56, Khalil El Mazouari wrote:
> >> Hi
> >>
> >> I am porting my code from java 7 to java 8.
> >>
> >> Biojava3.alignment is not working on java 8! While it was OK on java 7
> >>
> >> All jars are in the classpath.
> >>
> >> Thanks
> >>
> >> Khalil
> >>
> >> java.util.concurrent.ExecutionException:
> java.lang.ExceptionInInitializerError
> >>      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:289)
> >>      at
> org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:612)
> >>      at
> org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:180)
> >> ...
> >> Caused by: java.lang.ExceptionInInitializerError
> >>      at
> org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)
> >>      at
> org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)
> >>      at
> org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)
> >>      at
> org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)
> >>      at
> org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)
> >>      at
> org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)
> >>      at
> org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)
> >>      at
> org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)
> >>      at
> org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)
> >>      at
> org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105)
> >>      at
> org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)
> >>      at
> org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)
> >>      at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> >>      at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> >>      at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> >>      at java.lang.Thread.run(Thread.java:745)
> >> Caused by: java.lang.NullPointerException
> >>      at
> java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)
> >>      at
> java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)
> >>      at java.util.Collections.unmodifiableList(Collections.java:1287)
> >>      at
> org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)
> >>      at
> org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)
> >>      at
> org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)
> >>      at
> org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)
> >>      at
> org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)
> >>      ... 16 more
> >> java.util.concurrent.ExecutionException:
> java.lang.NoClassDefFoundError: Could not initialize class
> org.biojava3.core.sequence.location.SimpleLocation
> >>
> >> ?.
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biojava-l
> >
> >
> >
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> >
> > End of Biojava-l Digest, Vol 141, Issue 8
> > *****************************************
>
>
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