[MOBY-dev] Compiling datatypes

[Edward Kawas]

Hmm, I tried generating for both the old test registry
(bioinfo.icapture.ubc.ca) and the new one (mobytest.biordf.net) and I got
both times:

compile-datatypes:
    [javac] Compiling 586 source files to
/home/ubuntu/moby-live/Java/build/others/datatypes

jar-datatypes:
      [jar] Building jar:
/home/ubuntu/moby-live/Java/build/lib/biomoby-datatypes.jar

BUILD SUCCESSFUL

How are you generating the datatypes (from the command line or through
dashboard)? If through dashboard, delete the cache directory that dashboard
uses (usually /tmp/your_username/). 

If you are using the command line, try typing in 'ant clean' then look for a
directory called myCache and remove it. If a directory called generated also
exists, remove that too. Then try again.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kathrin Klee
Sent: Tuesday, December 01, 2009 6:08 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Compiling datatypes

Thanks for your help so far.

Now I've removed my hole cache (by hand as well as via ant-clean) and 
tried to run jar-datatypes. Copying the class files to my build folder 
worked fine but while compiling datatypes it still failed with the 
fallowing error messages.

compile-datatypes:
    [javac] Compiling 1 source file to 
/home/pcb/klee/workspace/jMoby/build/others/datatypes
    [javac] 
/home/pcb/klee/workspace/jMoby/generated/datatypes/org/biomoby/shared/dataty
pes/GCP_Contact.java:95: 
getMoby_affiliation() in org.biomoby.shared.datatypes.GCP_Contact cannot 
override getMoby_affiliation() in 
org.biomoby.shared.datatypes.GCP_Person; attempting to use incompatible 
return type
    [javac] found   : org.biomoby.shared.datatypes.GCP_Organization
    [javac] required: org.biomoby.shared.datatypes.GCP_LegalEntity[]
    [javac]     public GCP_Organization getMoby_affiliation() {
    [javac]                             ^
    [javac] 1 error

BUILD FAILED

I am working on the testing registry and I'm using Java 1.5
If you have some more suggestions I would be happy to hear them.

Thanks a lot
Kathrin


Edward Kawas wrote:
> Okay, I just removed my .m2/ folder (maven dependencies), ant clean,
> followed by ant jar-datatypes and I had no problems.
>
> So perhaps, like Martin said, you may want to clear your cache (ant clean
> should do it) and try again. If that doesn't help, and you are using java
6,
> maybe check for an upgrade to the java 6 update that you have.
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
> Sent: Sunday, November 29, 2009 1:52 PM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Compiling datatypes
>
> Hi,
>
> Which moby registry are you using? Probably the default one? Anyway, your
> local cache may have some incompatible (meaning older) datatypes. The
first
> step would be to remove the whole cache and let it fill again (from the
> Dashboard or by the command-line programs).
>
> Sorry for this vague answer, but I am now travelling and I cannot check it
> on my computer. Perhaps Eddie can be more specific (he works now with moby
> much much more than I do :-)).
>
> Cheers,
> Martin
>
>   

-- 

--------------------------------------------------
Kathrin Klee
Bioinformatician
Max Planck Institute for Plant Breeding Research
Plant Computational Biology
Carl-von-Linne Weg 10
50829 Koeln
Germany
+49 (0)221 / 5062 - 449
--------------------------------------------------


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