[Biojava-dev] Biojava with Java 8

[Terry Casstevens]

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
>> >
>> >
>> >
>> >
>
>
>
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