[Biojava-dev] Biojava with Java 8

[Andreas Prlic]

Hi Terry,

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

  <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>http://www.biojava.org/download/maven/</url>			
		</repository>
	</repositories>

alternatively you could manually download the jar files from the repository
as well...

Andreas


On Wed, Jul 30, 2014 at 8:07 AM, Terry Casstevens <tmc46 at cornell.edu> wrote:

> Hi Andreas,
>
> Thank you for your reply.  Looking at the github repository, it does
> look like the last change to SimpleLocation will fix our problem.
> Although, I don't think it's specific to Windows.  I think it's a
> change in Java 8 (maybe with default methods on Interfaces).
>
> Your Location Interface creates an static instance of SimpleLocation
> which ends up calling a SimpleLocation constructor that uses
> EMPTY_LOCS.  And EMPTY_LOCS, a static variable in SimpleLocation,
> doesn't seem to be initialized at that time.   The change to use new
> ArrayList<Location>() instead of EMPTY_LOCS gets around that.
>
> Do you know when another release would be available?
>
> Thank you,
>
> Terry
>
>
> On Tue, Jul 29, 2014 at 5:03 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> > 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
> >> _______________________________________________
> >> biojava-dev mailing list
> >> biojava-dev at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biojava-dev
> >
> >
> >
> >
>
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