<div dir="ltr">.. and to add something I just noticed. Since we are in the process of switching our project hosting to OSS Sonatype and Maven Central, our current trunk builds are available from here at the moment:<div><br>
</div><div><a href="https://oss.sonatype.org/content/repositories/snapshots/org/biojava/">https://oss.sonatype.org/content/repositories/snapshots/org/biojava/</a></div><div><br></div><div>A<br><div class="gmail_extra"><br>
<br><div class="gmail_quote">On Wed, Jul 30, 2014 at 2:21 PM, Andreas Prlic <span dir="ltr"><<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">next version will be 4.0.0. There was some refactoring in the protein structure modules which require some minor API changes, hence the version increase<span class=""><font color="#888888"><div><br></div></font></span><div>
<span class=""><font color="#888888">A</font></span><div><div class="h5"><br><div><br></div><div><br></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jul 30, 2014 at 2:15 PM, Terry Casstevens <span dir="ltr"><<a href="mailto:tmc46@cornell.edu" target="_blank">tmc46@cornell.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hi Andreas,<br>
<br>
Thank you very much!<br>
<br>
Which version 3.1.0 or 4.0.0 will be the next public release? We are<br>
hoping to update our biojava and forester libraries. Which level do<br>
you recommend we use?<br>
<br>
Thank you,<br>
<br>
Terry<br>
<div><div><br>
<br>
On Wed, Jul 30, 2014 at 11:20 AM, Andreas Prlic <<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>> wrote:<br>
> Hi Terry,<br>
><br>
> Agreed, the fix is not windows specific. We have not set a release date yet.<br>
> However you don't need to wait for it. If you use maven you can switch to<br>
> our latest SNAPSHOT builds. Just add this to your project pom.xml<br>
><br>
> <dependencies><br>
> ...<br>
> <dependency><br>
> <groupId>org.biojava</groupId><br>
> <artifactId>biojava3-core</artifactId><br>
> <version>4.0.0-SNAPSHOT</version><br>
> </dependency><br>
> <!-- other biojava jars as needed --><br>
> </dependencies><br>
> <repositories><br>
> ...<br>
> <repository><br>
> <id>biojava-maven-repo</id><br>
> <name>BioJava repository</name><br>
> <url><a href="http://www.biojava.org/download/maven/" target="_blank">http://www.biojava.org/download/maven/</a></url><br>
> </repository><br>
> </repositories><br>
><br>
> alternatively you could manually download the jar files from the repository<br>
> as well...<br>
><br>
> Andreas<br>
><br>
><br>
> On Wed, Jul 30, 2014 at 8:07 AM, Terry Casstevens <<a href="mailto:tmc46@cornell.edu" target="_blank">tmc46@cornell.edu</a>> wrote:<br>
>><br>
>> Hi Andreas,<br>
>><br>
>> Thank you for your reply. Looking at the github repository, it does<br>
>> look like the last change to SimpleLocation will fix our problem.<br>
>> Although, I don't think it's specific to Windows. I think it's a<br>
>> change in Java 8 (maybe with default methods on Interfaces).<br>
>><br>
>> Your Location Interface creates an static instance of SimpleLocation<br>
>> which ends up calling a SimpleLocation constructor that uses<br>
>> EMPTY_LOCS. And EMPTY_LOCS, a static variable in SimpleLocation,<br>
>> doesn't seem to be initialized at that time. The change to use new<br>
>> ArrayList<Location>() instead of EMPTY_LOCS gets around that.<br>
>><br>
>> Do you know when another release would be available?<br>
>><br>
>> Thank you,<br>
>><br>
>> Terry<br>
>><br>
>><br>
>> On Tue, Jul 29, 2014 at 5:03 PM, Andreas Prlic <<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>> wrote:<br>
>> > Hi Terry,<br>
>> ><br>
>> > The NoClassDefFoundError sounds a bit more like a configuration error,<br>
>> > than<br>
>> > a BioJava specific issue. Are you using the latest version of the source<br>
>> > from github? One of our students here submitted a few patches recently<br>
>> > that<br>
>> > make the current trunk code work on Java 1.8 without problems (as well<br>
>> > as on<br>
>> > windows). Might be easiest to get a checkout from there.<br>
>> ><br>
>> > <a href="https://github.com/biojava/biojava" target="_blank">https://github.com/biojava/biojava</a><br>
>> ><br>
>> > Having said that, there was a lot of change in the code since the last<br>
>> > release and we should probably think about preparing another release<br>
>> > soon.<br>
>> ><br>
>> > Andreas<br>
>> ><br>
>> ><br>
>> ><br>
>> > On Tue, Jul 29, 2014 at 11:01 AM, Terry Casstevens <<a href="mailto:tmc46@cornell.edu" target="_blank">tmc46@cornell.edu</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Dear Spencer,<br>
>> >><br>
>> >> I would very much appreciate your help with this. I think it will<br>
>> >> effect your other users also.<br>
>> >><br>
>> >> I am the software lead of the Buckler Lab at Cornell University, and<br>
>> >> we use the biojava library in our software.<br>
>> >><br>
>> >> I'm hoping to move to your latest released jars, but I don't think<br>
>> >> this is specific to that version.<br>
>> >> biojava3-alignment-3.0.8.jar<br>
>> >> biojava3-phylo-3.0.8.jar<br>
>> >> biojava3-core-3.0.8.jar<br>
>> >><br>
>> >> We have everything working when compiling and running our code with<br>
>> >> Java<br>
>> >> 7.<br>
>> >><br>
>> >> But when running with Java 8 (compiling with Java 7 or Java 8), we are<br>
>> >> getting NoClassDefFoundError.<br>
>> >><br>
>> >><br>
>> >> This will show you the problem. Compile this with Java 7, and run it<br>
>> >> under Java 7 and Java 8. You will see that it works in Java 7 and not<br>
>> >> in Java 8.<br>
>> >><br>
>> >> public static void main(String[] args) {<br>
>> >> SimpleLocation location = new SimpleLocation(1, 7);<br>
>> >> }<br>
>> >><br>
>> >><br>
>> >> I believe your problem is in<br>
>> >> org.biojava3.core.sequence.location.template.Location. This line is<br>
>> >> causing the problem in Java 8.<br>
>> >><br>
>> >> public static final Location EMPTY =<br>
>> >> new SimpleLocation(Integer.MIN_VALUE, Integer.MAX_VALUE,<br>
>> >> Strand.UNDEFINED);<br>
>> >><br>
>> >><br>
>> >><br>
>> >> Best,<br>
>> >><br>
>> >> Terry<br>
>> >> _______________________________________________<br>
>> >> biojava-dev mailing list<br>
>> >> <a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
>> >> <a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
><br>
><br>
><br>
><br>
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