[Biojava-dev] Biojava with Java 8

[Andreas Prlic]

Hi Terry,

The NoClassDefFoundError sounds a bit more like a configuration error, than
a BioJava specific issue. Are you using the latest version of the source
from github? One of our students here submitted a few patches recently that
make the current trunk code work on Java 1.8 without problems (as well as
on windows). Might be easiest to get a checkout from there.

https://github.com/biojava/biojava

Having said that, there was a lot of change in the code since the last
release and we should probably think about preparing another release soon.

Andreas



On Tue, Jul 29, 2014 at 11:01 AM, Terry Casstevens <tmc46 at cornell.edu>
wrote:

> Dear Spencer,
>
> I would very much appreciate your help with this.  I think it will
> effect your other users also.
>
> I am the software lead of the Buckler Lab at Cornell University, and
> we use the biojava library in our software.
>
> I'm hoping to move to your latest released jars, but I don't think
> this is specific to that version.
> biojava3-alignment-3.0.8.jar
> biojava3-phylo-3.0.8.jar
> biojava3-core-3.0.8.jar
>
> We have everything working when compiling and running our code with Java 7.
>
> But when running with Java 8 (compiling with Java 7 or Java 8), we are
> getting NoClassDefFoundError.
>
>
> This will show you the problem.  Compile this with Java 7, and run it
> under Java 7 and Java 8.  You will see that it works in Java 7 and not
> in Java 8.
>
> public static void main(String[] args) {
>         SimpleLocation location = new SimpleLocation(1, 7);
> }
>
>
> I believe your problem is in
> org.biojava3.core.sequence.location.template.Location.  This line is
> causing the problem in Java 8.
>
> public static final Location EMPTY =
>             new SimpleLocation(Integer.MIN_VALUE, Integer.MAX_VALUE,
> Strand.UNDEFINED);
>
>
>
> Best,
>
> Terry
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>
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