Problem with nightly build 28.02.2011

Hi Greg

thanks for the amazing job you are doing with RDKit.

I just installed latest build for RDkit and wanted to use Murcko scaffolds.

I am using an Athlon based PC (3Gb RAM) with Windows XP still (SP3).

After reading in SDF files with SDF reader, wanted to change in RDKit (molecule to RDKit). Linking and saving were ok, however, when I tried to run it Knime crashed without warning.

Previous RDKit download did not show any problem in doing so. Anything sudden change in latest nightly build?


Andrea Z

Hi Andrea,
There’s nothing I’m aware of that should cause a crash (in fact, crashes shouldn’t happen at all… they make Bernd very unhappy with me). Can you please take a look in the knime log file and see if there are any useful error messages?


Hi Greg

the log did not reveal anything useful. I 'd already sent to you. Wanted just to be sure nothing has changed in your new build. So now it is on me: my knime installation may have gone somewhere corrupted.

Thanks, though.




sorry to bother. Actually I did manage to make it work reinstalling everything on 32bit version. now it seems that Molecule->RDKit works fine. However, Murcko decomposition still gives me headache with following message

ERROR     Find Murcko Scaffolds     Execute failed: org.RDKit.RDKFuncsJNI.MurckoDecompose(JLorg/RDKit/ROMol;)J

Any hint for me?

Beside this, still mol->rdkit when linked with interactive table caused the latest node to run and finish with green light but w/o visualization

ERROR     Interactive Table     View instantiation failed: org.RDKit.RDKFuncsJNI.MolToSVG__SWIG_0(JLorg/RDKit/ROMol;)Ljava/lang/String;

Another face of same coin?



Dear Andrea,

These are unfortunately tough to diagnose just from the error message. It would be most helpful to have the molecule(s) that is/are causing the problem.

Did any of the molecules run or did the murcko decompose error immediately appear?

If you construct a simple molecule, say “Cc1ccccc1”, do you see the problem there as well?


These kind of error messages often appear if some expected Java methods are not available. Andrea, could you double-check that you have the latest version of both the RDKit binaries and RDKit nodes?