[Biojava-dev] Biojava with Java 8

[Andreas Prlic]

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

A




On Wed, Jul 30, 2014 at 2:15 PM, Terry Casstevens <tmc46 at cornell.edu> wrote:

> Hi Andreas,
>
> Thank you very much!
>
> Which version 3.1.0 or 4.0.0 will be the next public release?  We are
> hoping to update our biojava and forester libraries.  Which level do
> you recommend we use?
>
> Thank you,
>
> Terry
>
>
> On Wed, Jul 30, 2014 at 11:20 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> > 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
> >> >
> >> >
> >> >
> >> >
> >
> >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biojava-dev/attachments/20140730/db0d13b3/attachment-0001.html>