Re: [Joelib-devel] Pb with CDK UpDate

[Joerg K. W. <we...@in...>]

Hi Nicolas,

sorry :-)

1. CDK has implemented it's own logging implementation (not 
standard-log4j), so this can not cause the problem, i think.

2. ant is part of JOELib: simply try:
   joelib> sh build.sh compile or
   joelib> sh build.sh dist

   eventually you must set the base directory with
   setenv JOELIBDIR yourBase/joelib
   or
   export JOELIBDIR=yourBase/joelib
   if you're a bash user

3. the java-property-files
     joelib.properties
     log4j.properties
    should be in the base classpath or in the .jar file
    Have you copied them also to your CLASS_PATH directory?
    Example in log4j.properties:
    log4j.category.joelib.data.JOEAromaticTyper=ERROR
    So only error are printed:
    Try:
    log4j.category.joelib.data.JOEAromaticTyper=DEBUG
    and also DEBUG messages wil be shown.
    Much more screen-filling are things like:
    log4j.category.joelib.smarts.JOESmartsPattern=DEBUG
    log4j.category.joelib.smarts.JOESSMatch=DEBUG
    log4j.category.joelib.smarts.ParseSmart=DEBUG
    or
    log4j.category.joelib.molecule.JOEMol=DEBUG

I know that dependencies are not easy, but on the other side there is a 
huge benefit from using default open-source-packages, so be patient and 
try it from different directions ...

Kind regards, Joerg

> 	I've tried to update all my classes this morning (log4j and JOELib),
> but the result is the same. I haven't any ANT installation so I can't build
> anything for the moment. If I've really need this new CDK update, I'll
> install ANT correctly. However, what I don't understand is the first time I
> would launch CDK and JOELib Classes, I 've just make a copy of all JOELib
> Classes and put them in my CLASS_PATH directory. I have also put the log4j
> classes in org/apache/ dir. And all ran correctly. Now, I have just put a
> new version of CDK, and I have these errors messages. Moreover, I'm not an
> expert in logging methods, so it's difficult for me to set params like you
> said (switch on/off info/warn/error etc...).
> 
> 	I'll see following my needs what I can realy do with that pb.
> 
> Thanks,
> Nico
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
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