<div dir="ltr">I think the current goal is to release 4.0.0 later this month, or by the end of the year at the latest.<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Nov 8, 2014 at 6:30 PM, Khalil El Mazouari <span dir="ltr"><<a href="mailto:khalil.elmazouari@gmail.com" target="_blank">khalil.elmazouari@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I agree ;) It's fixed on 4.0.0-SNAPSHOT.<br>
<br>
Any idea when biojava 4 will be released?<br>
<br>
Thanks<br>
<br>
kem<br>
<br>
On 08 Nov 2014, at 13:00, <a href="mailto:biojava-l-request@mailman.open-bio.org">biojava-l-request@mailman.open-bio.org</a> wrote:<br>
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> 1. java 8 - Biojava3 java.util.concurrent.ExecutionException:<br>
> java.lang.ExceptionInInitializerError (Khalil El Mazouari)<br>
> 2. Re: java 8 - Biojava3<br>
> java.util.concurrent.ExecutionException:<br>
> java.lang.ExceptionInInitializerError (Jose Manuel Duarte)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Fri, 7 Nov 2014 21:56:18 +0100<br>
> From: Khalil El Mazouari <<a href="mailto:khalil.elmazouari@gmail.com">khalil.elmazouari@gmail.com</a>><br>
> To: <a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a><br>
> Subject: [Biojava-l] java 8 - Biojava3<br>
> java.util.concurrent.ExecutionException:<br>
> java.lang.ExceptionInInitializerError<br>
> Message-ID: <<a href="mailto:BC1B67CE-A3EE-4734-870F-826BFEBBE93E@gmail.com">BC1B67CE-A3EE-4734-870F-826BFEBBE93E@gmail.com</a>><br>
> Content-Type: text/plain; charset=windows-1252<br>
><br>
> Hi<br>
><br>
> I am porting my code from java 7 to java 8.<br>
><br>
> Biojava3.alignment is not working on java 8! While it was OK on java 7<br>
><br>
> All jars are in the classpath.<br>
><br>
> Thanks<br>
><br>
> Khalil<br>
><br>
> java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError<br>
> at java.util.concurrent.FutureTask.report(FutureTask.java:122)<br>
> at java.util.concurrent.FutureTask.get(FutureTask.java:192)<br>
> at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:289)<br>
> at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:612)<br>
> at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:180)<br>
> ...<br>
> Caused by: java.lang.ExceptionInInitializerError<br>
> at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)<br>
> at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)<br>
> at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)<br>
> at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)<br>
> at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)<br>
> at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)<br>
> at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)<br>
> at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)<br>
> at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)<br>
> at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105)<br>
> at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)<br>
> at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)<br>
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)<br>
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)<br>
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)<br>
> at java.lang.Thread.run(Thread.java:745)<br>
> Caused by: java.lang.NullPointerException<br>
> at java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)<br>
> at java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)<br>
> at java.util.Collections.unmodifiableList(Collections.java:1287)<br>
> at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)<br>
> at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)<br>
> at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)<br>
> at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)<br>
> at org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)<br>
> ... 16 more<br>
> java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation<br>
><br>
> ?.<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Fri, 07 Nov 2014 23:22:06 +0100<br>
> From: Jose Manuel Duarte <<a href="mailto:jose.duarte@psi.ch">jose.duarte@psi.ch</a>><br>
> To: <a href="mailto:biojava-l@mailman.open-bio.org">biojava-l@mailman.open-bio.org</a><br>
> Subject: Re: [Biojava-l] java 8 - Biojava3<br>
> java.util.concurrent.ExecutionException:<br>
> java.lang.ExceptionInInitializerError<br>
> Message-ID: <<a href="mailto:545D460E.1040508@psi.ch">545D460E.1040508@psi.ch</a>><br>
> Content-Type: text/plain; charset=windows-1252; format=flowed<br>
><br>
> Are you using Biojava 3.1? This indeed seems to be a problem in 3.1 and<br>
> before.<br>
><br>
> However I've tried with the current 4.0.0-SNAPSHOT and it seems to work<br>
> fine.<br>
><br>
> Jose<br>
><br>
><br>
><br>
> On 07.11.2014 21:56, Khalil El Mazouari wrote:<br>
>> Hi<br>
>><br>
>> I am porting my code from java 7 to java 8.<br>
>><br>
>> Biojava3.alignment is not working on java 8! While it was OK on java 7<br>
>><br>
>> All jars are in the classpath.<br>
>><br>
>> Thanks<br>
>><br>
>> Khalil<br>
>><br>
>> java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError<br>
>> at java.util.concurrent.FutureTask.report(FutureTask.java:122)<br>
>> at java.util.concurrent.FutureTask.get(FutureTask.java:192)<br>
>> at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:289)<br>
>> at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:612)<br>
>> at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:180)<br>
>> ...<br>
>> Caused by: java.lang.ExceptionInInitializerError<br>
>> at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)<br>
>> at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)<br>
>> at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)<br>
>> at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)<br>
>> at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)<br>
>> at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)<br>
>> at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)<br>
>> at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)<br>
>> at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)<br>
>> at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105)<br>
>> at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)<br>
>> at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)<br>
>> at java.util.concurrent.FutureTask.run(FutureTask.java:266)<br>
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)<br>
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)<br>
>> at java.lang.Thread.run(Thread.java:745)<br>
>> Caused by: java.lang.NullPointerException<br>
>> at java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)<br>
>> at java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)<br>
>> at java.util.Collections.unmodifiableList(Collections.java:1287)<br>
>> at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)<br>
>> at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)<br>
>> at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)<br>
>> at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)<br>
>> at org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)<br>
>> ... 16 more<br>
>> java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation<br>
>><br>
>> ?.<br>
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</blockquote></div><br></div>