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 < [email protected]> 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, [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 >
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