Hi Thomas,

On Wed, Nov 24, 2010 at 8:25 AM, Thomas Strunz <beginn...@hotmail.de> wrote:
> I'm doing a small project for school using cdk and started with version
> 1.2.7. I now switched to 1.3.7 and all logging from my project is now
> disabled.

How are you running your code?

Both version should have logging disabled by default, which you can
enable by running the CDK-based code with:

java -Dcdk.debugging=true -Dcdk.debug.stdout=true your.cdk.using.Class

> It worked with 1.2.7 and I can easily reproduce the issue by
> switching back.
> I use slf4j-1.6.1 and logback 0.9.26 and I use the cdk-jar with all
> dependencies for simplicity.

Were you using the logging to file functionality, using log4j? If so,
that could interfere with these two libraries...

In CDK 1.3 you can write a custom ILoggingTool implementation that
makes use of your favorite logging utility. The output to STDOUT uses
this API too:

https://github.com/cdk/cdk/blob/master/src/main/org/openscience/cdk/tools/SystemOutLoggingTool.java

Bioclipse also has a custom implementation:

https://github.com/bioclipse/bioclipse.cheminformatics/blob/master/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/logging/BioclipseLoggingTool.java

It is important to set your custom ILoggingTool before you run any CDK
code, which you can do with
LoggingToolFactory.setLoggingToolClass(..):

https://github.com/cdk/cdk/blob/master/src/main/org/openscience/cdk/tools/LoggingToolFactory.java

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Research Associate
University of Cambridge
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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