[Biojava-dev] maven progress

[Andreas Prlic]

Can you start using the biojava-live/biojava/sequencing module for the
fastq stuff? that way we can already be in sync. I will do svn updates
every time before I start working on something and commits when I
stop....

Andreas

On Mon, Aug 31, 2009 at 9:12 PM, Michael Heuer<heuermh at acm.org> wrote:
> Andreas Prlic wrote:
>
>> >> The new SVN location is emerging here:
>> >>
>> >> http://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/biojava
>> >
>> > That seems like an odd place for it, at the same level as branches, tags,
>> > and trunk?
>> >
>> > If you've branched for 1.7 and called for the freeze on trunk, I don't see
>> > any reason not to do this work on trunk.
>>
>> ok. makes sense.  It is easy to flip locations around in svn..  I can
>> move the old trunk  e.g. to a tag folder for archive purposes and make
>> what is called biojava right now the future trunk. (in svn this moves
>> or copy operations are cheap)  For the moment things are not
>> stabilized yet and I will do this once things are there...
>
> That's cool.  I wanted to check in some preliminary fastq stuff and wasn't
> sure where it should go.  I'm in the biojava3 branch for now, and will
> move to the right place once things settle.
>
>
>> At the moment I am chasing an "interesting" problem. When I run the
>> junit tests on the new core module in eclipse, they run fine.   When I
>> do the same via a mvn test I get several issues like the one below.
>> Anybody got an idea?
>>
>> -------------------------------------------------------------------------------
>> Test set: org.biojava.bio.seq.project.ProjectedFeatureHolderTest
>> -------------------------------------------------------------------------------
>> Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.036
>> sec <<< FAILURE!
>> testFeatureChangeEvent(org.biojava.bio.seq.project.ProjectedFeatureHolderTest)
>>  Time elapsed: 0.011 sec  <<< ERROR!
>> java.lang.AssertionError: firePreChangeEvent must be called in a
>> synchronized block locking the ChangeSupport
>>       at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:281)
>>       at org.biojava.bio.seq.projection.ReparentContext$PFChangeForwarder.preChange(ReparentContext.java:299)
>>       at org.biojava.utils.ChangeSupport.firePreChangeEvent(ChangeSupport.java:297)
>>       at org.biojava.bio.seq.impl.SimpleFeature.setLocation(SimpleFeature.java:173)
>>       at org.biojava.bio.seq.project.ProjectedFeatureHolderTest.testFeatureChangeEvent(ProjectedFeatureHolderTest.java:297)
>
> I've always disliked the change stuff, how about get rid of it all and
> make everything immutable?  ;)
>
>   michael
>
>