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, [email protected] wrote: > Send Biojava-l mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > 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 <[email protected]> > To: [email protected] > Subject: [Biojava-l] java 8 - Biojava3 > java.util.concurrent.ExecutionException: > java.lang.ExceptionInInitializerError > Message-ID: <[email protected]> > 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 <[email protected]> > To: [email protected] > Subject: Re: [Biojava-l] java 8 - Biojava3 > java.util.concurrent.ExecutionException: > java.lang.ExceptionInInitializerError > Message-ID: <[email protected]> > 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 - [email protected] >> http://mailman.open-bio.org/mailman/listinfo/biojava-l > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-l > > End of Biojava-l Digest, Vol 141, Issue 8 > ***************************************** _______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l
