Hey, KNIME Team members and KNIME community colleagues.
I know that this is not an entirely new topic with the same error, but I think this is worth notifying with a separate one as previous threads don’t seem to offer a straight step-by-step solution and seem to be stuck at some dead ends. I suggest not merging it again. My analysis showed this might be a global issue for this KNIME extension. Below is the error message I am constantly getting while trying to install this additional software. I tried to troubleshoot it with these steps:
- Tried to install the software on a separate non-corporate machine.
- Tried to use different KNIME Analytics platform versions 4.7.7 (newest) and 4.7.3 (as recommended in release notes)
- Asked another pear to install this extension on a separate operating system.
- Tried to install it with a manually downloaded zip install file.
- Tried to read a troubleshooting error thread and even went down into a deep rabbit hole of “Mamba doesn’t work behind a corporate proxy (conda does): download error”, but I wasn’t able to find obvious answers.
I see this extension is getting constant updates, so maybe this might have some impact.
I am not a new KNIME user, but maybe I still had overlooked something, so my apologies to the community if so.
Error message:
An error occurred while installing the items
session context was:(profile=KNIMEProfile, phase=org.eclipse.equinox.internal.p2.engine.phases.Install, operand=null → [R]sdl.harvard.geospatial.channel.bin.win32.x86_64 1.1.1.202306211527, action=org.knime.product.p2.actions.ShellExec).
ShellExec command exited non-zero exit value:
Logs:
2023-09-02 13:24:40,912 : ERROR : Worker-2: Node Repository Loader : : RepositoryManager : : : Node ‘com.vernalis.knime.mmp.nodes.transform.rdkit.RWMolApplyTransformNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created. The corresponding plugin bundle could not be activated!
org.knime.core.node.extension.InvalidNodeFactoryExtensionException: Node ‘com.vernalis.knime.mmp.nodes.transform.rdkit.RWMolApplyTransformNodeFactory’ from plugin ‘com.vernalis.knime.chem.mmp’ could not be created. The corresponding plugin bundle could not be activated!
at org.knime.core.node.extension.NodeFactoryExtension.createFactory(NodeFactoryExtension.java:204)
at org.knime.core.node.extension.NodeFactoryExtension.getFactory(NodeFactoryExtension.java:169)
at org.knime.workbench.repository.RepositoryFactory.createNode(RepositoryFactory.java:117)
at org.knime.workbench.repository.RepositoryManager.readNodes(RepositoryManager.java:369)
at org.knime.workbench.repository.RepositoryManager.readRepository(RepositoryManager.java:168)
at org.knime.workbench.repository.RepositoryManager.getRoot(RepositoryManager.java:574)
at org.knime.workbench.repository.view.AbstractRepositoryView.readRepository(AbstractRepositoryView.java:413)
at org.knime.workbench.repository.view.AbstractRepositoryView$4.run(AbstractRepositoryView.java:331)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
Caused by: org.eclipse.core.runtime.CoreException: Plug-in com.vernalis.knime.chem.mmp was unable to load class com.vernalis.knime.mmp.nodes.transform.rdkit.RWMolApplyTransformNodeFactory.
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:212)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:198)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:920)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:246)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:63)
at org.knime.core.node.extension.NodeFactoryExtension.createFactory(NodeFactoryExtension.java:184)
… 8 more
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle com.vernalis.knime.chem.mmp (123).
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:126)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:572)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:346)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:401)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:480)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:171)
at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:617)
at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:196)
at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:920)
at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:246)
at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:63)
at org.knime.core.node.extension.NodeFactoryExtension.createFactory(NodeFactoryExtension.java:184)
at org.knime.core.node.extension.NodeFactoryExtension.getFactory(NodeFactoryExtension.java:169)
at org.knime.core.node.extension.NodeFactoryExtension.isDeprecated(NodeFactoryExtension.java:126)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
at java.base/java.util.Iterator.forEachRemaining(Unknown Source)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ReduceOps$5.evaluateSequential(Unknown Source)
at java.base/java.util.stream.ReduceOps$5.evaluateSequential(Unknown Source)
at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
at java.base/java.util.stream.ReferencePipeline.count(Unknown Source)
at org.knime.core.node.extension.NodeFactoryExtensionManager.getInstance(NodeFactoryExtensionManager.java:126)
at org.knime.workbench.repository.RepositoryManager.readNodes(RepositoryManager.java:355)
… 5 more
Caused by: org.osgi.framework.BundleException: Exception in com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start() of bundle com.vernalis.knime.chem.mmp.
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:835)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:763)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1012)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:366)
at org.eclipse.osgi.container.Module.doStart(Module.java:605)
at org.eclipse.osgi.container.Module.start(Module.java:468)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:506)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
… 31 more
Caused by: java.lang.UnsatisfiedLinkError: ‘long org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(java.lang.String)’
at org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(Native Method)
at org.RDKit.RWMol.MolFromSmarts(RWMol.java:453)
at com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start(MatchedPairsMultipleCutsNodePlugin.java:91)
at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:814)
at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:806)
… 38 more