Hi Thorsten and Greg,
Many thanks for your replies.
On 16 November 2010 20:16, Thorsten Meinl <[email protected]>wrote:
> Hi George,
>
> > I installed the RDKit nodes for KNIME (by copying the plugins folder
> > manually, as I too had problems with the 'update from file' feature).
> > Inspired by the source code that was bundled with the nodes,
> Did you have the same problems as Paul, i.e. KNIME complaining about
> some osbi.bundles not being found?
This is the error I get when I use the local update site:
Cannot complete the request. See the details.
Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
0.9.0.0027626] requiredCapability:
org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.macosx.x86_64/[0.9.0.0027589,0.9.0.0027589]
Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
0.9.0.0027626] requiredCapability:
org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.linux.x86/[0.9.0.0027561,0.9.0.0027561]
Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
0.9.0.0027626] requiredCapability:
org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.linux.x86_64/[1.0.0.0027615,1.0.0.0027615]
> > However, this script throws the following runtime error:
> > Exception in thread "main" java.lang.UnsatisfiedLinkError:
> > org.RDKit.RDKFuncsJNI.MolFromSmiles(Ljava/lang/String;)J
> > at org.RDKit.RDKFuncsJNI.MolFromSmiles(Native Method)
> > at org.RDKit.RDKFuncs.MolFromSmiles(RDKFuncs.java:65)
> >
> > In the Eclipse lib folder, I included all the .jar files and the
> RDKFuncs.dll.
> > Any ideas???
> In order to use code from native libaries Java needs to be told where to
> look for them. This is usually done by defining -Djava.library.path
> appropriately. If the application consists of Eclipse plugins (i.e. not
> just a bunch of jars), then there is some magic that loads the native
> libraries w/o needing to specify the explicitly. This is what happens
> wiht the KNIME plugins. So you either need to set the Java property or
> put your code in a plugin, which depends on org.rdkit.knime.types, and
> run an Eclipse application.
>
> Thanks to your tip and my colleague Nico Fechner, it is working now.
For those with the same problem, you need this line at the beginning of your
code: System.load("Path//to//the//dll//RDKFuncs.dll");
Alternatively, as you suggested, you need to set the VM arguments
appropriately in Eclipse, i.e. -Djava.library.path=Path//to///the/dll// and
then add this line in the code: System.loadLibrary("RDKFuncs");
Thanks again,
George
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