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

Khalil El Mazouari khalil.elmazouari at gmail.com
Sat Nov 8 17:30:23 UTC 2014


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
>> 
>> ?.
>> _______________________________________________
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>> 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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