<div dir="ltr">Hi Terry,<div><br></div><div>Agreed, the fix is not windows specific. We have not set a release date yet. However you don't need to wait for it. If you use maven you can switch to our latest SNAPSHOT builds. Just add this to your project pom.xml</div>
<div><br></div><div><pre style="font-family:monospace,'Courier New';padding:1em;border:1px dashed rgb(47,111,171);color:rgb(0,0,0);line-height:1.3em;font-size:12.800000190734863px;background-color:rgb(249,249,249)">
<dependencies>
...
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>4.0.0-SNAPSHOT</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies>
<repositories>
...
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url><a href="http://www.biojava.org/download/maven/">http://www.biojava.org/download/maven/</a></url>
</repository>
</repositories></pre></div><div class="gmail_extra">alternatively you could manually download the jar files from the repository as well...</div><div class="gmail_extra"><br>Andreas</div><div class="gmail_extra"><br>
</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 30, 2014 at 8:07 AM, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
<div class="HOEnZb"><div class="h5"><br>
<br>
On Tue, Jul 29, 2014 at 5:03 PM, Andreas Prlic <<a href="mailto:andreas@sdsc.edu">andreas@sdsc.edu</a>> wrote:<br>
> Hi Terry,<br>
><br>
> The NoClassDefFoundError sounds a bit more like a configuration error, 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 that<br>
> make the current trunk code work on Java 1.8 without problems (as well 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 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">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 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">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>
</div></div></blockquote></div><br><br clear="all"><div><br></div>
</div></div>