KNIME 2.10.1 Full Extensions Installer faulty for MAC

KNIME Analytics Platform
1

Hi,

I have just installed KNIME 2.10.1 Full extensions installer for the MAC (Operating System 10.9.4), and am having issues from the off.

As soon as KNIME loads, it complains about issues with RDKit and recommends uninstalling and reinstalling but this doesnt fix the issue. Also when I go and install the Indigo extensions these are full of errors too. Ideas? Below is a sample set of errors;

ERROR     RDKitTypesPluginActivator          Could not load native RDKit library: no GraphMolWrap in java.library.path

ERROR     RDKitTypesPluginActivator          Loading of library libGraphMolWrap.dylib failed: no GraphMolWrap in java.library.path

ERROR     RDKitTypesPluginActivator          The library libGraphMolWrap.dylib is missing.

ERROR     RDKitTypesPluginActivator          Suggestion for fix: Please uninstall and reinstall the RDKit Nodes.

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoMoleculeLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoMoleculeLoaderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryMoleculeLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoQueryMoleculeLoaderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoMoleculeSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoMoleculeSaverNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryMoleculeSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.molecule.IndigoQueryMoleculeSaverNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoReactionLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoReactionLoaderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryReactionLoaderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoQueryReactionLoaderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoReactionSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoReactionSaverNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoQueryReactionSaverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.convert.reaction.IndigoQueryReactionSaverNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.compjoin.IndigoComponentCombinerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.compjoin.IndigoComponentCombinerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.compsep.IndigoComponentSeparatorNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.compsep.IndigoComponentSeparatorNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.murcko.IndigoMurckoScaffoldNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.murcko.IndigoMurckoScaffoldNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoRGroupDecomposerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.rgdecomp.IndigoRGroupDecomposerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoScaffoldFinderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.scaffold.IndigoScaffoldFinderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoSubstructureMatchCounterNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.submatchcounter.IndigoSubstructureMatchCounterNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoSubstructureMatcherNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.submatcher.IndigoSubstructureMatcherNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.transform.IndigoMoleculeTransformNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.transform.IndigoMoleculeTransformNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.rautomapper.ReactionAutomapperNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.rautomapper.IndigoReactionAutomapperNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoSubstructureMatcherNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.submatcher.IndigoSubstructureMatcherNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.rbuilder.IndigoReactionBuilderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.rbuilder.IndigoReactionBuilderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.rsplitter.IndigoReactionSplitterNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.rsplitter.IndigoReactionSplitterNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoAromatizerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.arom.IndigoAromatizerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoDearomatizerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.dearom.IndigoDearomatizerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.areplacer.IndigoAtomReplacerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.areplacer.IndigoAtomReplacerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.bondreplacer.IndigoBondReplacerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.bondreplacer.IndigoBondReplacerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.fremover.IndigoFeatureRemoverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.fremover.IndigoFeatureRemoverNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoHydrogenAdderNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.hadder.IndigoHydrogenAdderNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoHydrogenRemoverNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.hremover.IndigoHydrogenRemoverNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.layout.IndigoLayout2DNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.layout.IndigoLayout2DNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoMoleculePropertiesNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.molprop.IndigoMoleculePropertiesNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoValenceCheckerNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.valence.IndigoValenceCheckerNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoFingerprintSimilarityNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.fpsim.IndigoFingerprintSimilarityNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.IndigoMoleculeFingerprinterNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.molfp.IndigoMoleculeFingerprinterNodeFactory The corresponding plugin bundle could not be activated!

ERROR     RepositoryManager                  Node com.ggasoftware.indigo.knime.combchem.IndigoReactionGeneratorNodeFactory' from plugin 'com.ggasoftware.indigo.knime.plugin' could not be created: Can't load factory class for node: com.ggasoftware.indigo.knime.combchem.IndigoReactionGeneratorNodeFactory The corresponding plugin bundle could not be activated!

2

Ironically, this seems to be a problem with the "trusted" build of RDKit.  Updating to nightly resolves the problem for me (also for Indigo).  I will see if I can initiate an update of the plugins in their respective trusted/stable builds.  

3

I have the same case on Windows 10, however Knime works fine. At date, i don´t have fixed it.

4

Is there a reason you don’t upgrade KNIME to a more recent version?

5

I´m working on 4.0.0 version.
The warning began after install aditional extensions.

6

Please start a new post since this one refers to KNIME 2.10.

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