If you happen to have a system which does not have Java3D,
and also not the jmol.jar copied into cdk/jars/libio, then the build
This is caused by the patched being 'conflicting'... i.e. once either
one is applied, the other cannot be applied. This will be solved in
the next CDK release in about two weeks.
For now, a workaround is to download the binary Jmol distrib v7
from sf.net, and copy the jmol.jar into the /cdk/jars/libio directory.
(There are worse workarounds ;)
Sorry for the incovenience,