Nodes cannot be created!

armingrudd · August 19, 2020, 12:23pm

Hi,

I have installed Vernalis extension but when I start KNIME these error messages appear in console:

ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.pairgen.frag2pair.ReferenceFrag2Pair3NodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderMatchingBondsNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderCuttableBondsNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR 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!

Other nodes from Vernalis are working properly.
I’m using KNIME 4.2 on Windows Server 2016.

s.roughley · August 19, 2020, 2:00pm

Hi Armin,

Thanks for this. Could I ask you to check which version of the nodes you have installed? I’m in the process of updating them and I guess it’s just possible something strange happened mid-update.

Steve

armingrudd · August 19, 2020, 7:33pm

Hey Steve,

I have the latest version (1.27.0) but it was the same when I first installed the extension on this server (the previous version of the extension).
I have no issue on my desktop which is Windows 10.

s.roughley · August 20, 2020, 6:37am

Could you try updating - there were a couple of 1.27.0 builds that might have got through (the latest timestamp is 1.27.0.v202008181525 for the nightly) with a few minor tweaks made.

The other thing to check is that you the latest RDKit installed on the server?

Steve

armingrudd · August 20, 2020, 7:12am

I updated KNIME extensions on the server yesterday just before posting the topic.

No, I don’t have installed it on my desktop too, but there is no error on my desktop.

s.roughley · August 24, 2020, 6:42am

OK - that’s very strange. It looks like KNIME is trying to create a few nodes which have dependencies on the RDKit plugin. If you dont need them and that plugin then you can probably ignore the errors (assuming whichever Vernalis nodes you do need work OK), or instal RDKit and see if that fixes the problem?

Steve

armingrudd · August 26, 2020, 3:12pm

Hey Steve,

I installed RDKit extension and still I’m getting the errors. I was expecting this since I don’t have RDKit on my desktop and everything is fine there.

s.roughley · August 26, 2020, 9:13pm

Hi Armin,

Hmm, I feared you were going to come back and say something like that

Are you able to use the nodes that you do use from Vernalis on the server?

I’m going to ask Bernd @wiswedel whether he can think of any reason this might happen, because I’m a bit stuck for ideas on this one?

Steve

swebb · August 27, 2020, 10:20am

I’ve been trying to debug similar looking issues recently and have found that sometimes I get some useful info from the osgi console.

Steps to run on the affected machine:

$ knime.exe -console

This will open a new window, let KNIME load and then run:
(you may need to hit enter to get the osgi bit back if some error has been printed)

$ osgi> ss

what you need to do now is scroll through the list and find the ID for the Vernalis plugins. They will have a status other than ACTIVE

now run:

$ osgi > start {id}

where {id} is the ID of the vernalis feature/plugin you want to start

You will now likely see some error messages, these may give an indication of the cause of the plugin failing to load.

If you don’t get any error run the ‘ss’ command again and see if the plugin is now ACTIVE.

Disclaimer: it hasn’t always helped.

Cheers

Sam

wiswedel · August 27, 2020, 8:29pm

(Since my name was mentioned further up … I would have suggested the same thing. The OSGi console is usually helpful in those cases. Sometimes it’s also sufficient to just look into the “.log” file.)

s.roughley · August 28, 2020, 7:12am

Thanks Bernd.

@armingrudd - is there anything useful in the log file first?

Steve

armingrudd · September 3, 2020, 4:41am

Hi @swebb, @s.roughley and @wiswedel,

Here is the console messages when I get the list and try to start the plugin:

‍‍‍‍osgi> start 79 
org.osgi.framework.BundleException: Error loading bundle activator.
        at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:786)
        at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1015)
        at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:365)
        at org.eclipse.osgi.container.Module.doStart(Module.java:603)
        at org.eclipse.osgi.container.Module.start(Module.java:467)
        at org.eclipse.osgi.internal.framework.EquinoxBundle.start(EquinoxBundle.java:439)
        at org.apache.felix.gogo.command.Basic.start(Basic.java:739)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.felix.gogo.runtime.Reflective.invoke(Reflective.java:139)
        at org.apache.felix.gogo.runtime.CommandProxy.execute(CommandProxy.java:91)
        at org.apache.felix.gogo.runtime.Closure.executeCmd(Closure.java:599)
        at org.apache.felix.gogo.runtime.Closure.executeStatement(Closure.java:526)
        at org.apache.felix.gogo.runtime.Closure.execute(Closure.java:415)
        at org.apache.felix.gogo.runtime.Pipe.doCall(Pipe.java:416)
        at org.apache.felix.gogo.runtime.Pipe.call(Pipe.java:229)
        at org.apache.felix.gogo.runtime.Pipe.call(Pipe.java:59)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassNotFoundException: An error occurred while automatically activating bundle com.vernalis.knime.chem.mmp (79).
        at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:126)
        at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:571)
        at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:346)
        at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:398)
        at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:477)
        at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:171)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
        at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:620)
        at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:196)
        at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:923)
        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:162)
        at org.knime.core.node.extension.NodeFactoryExtension.isDeprecated(NodeFactoryExtension.java:121)
        at org.knime.core.node.extension.NodeFactoryExtensionManager.lambda$0(NodeFactoryExtensionManager.java:130)
        at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:174)
        at java.util.Iterator.forEachRemaining(Iterator.java:116)
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
        at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.LongPipeline.reduce(LongPipeline.java:461)
        at java.util.stream.LongPipeline.sum(LongPipeline.java:419)
        at java.util.stream.ReferencePipeline.count(ReferencePipeline.java:593)
        at org.knime.core.node.extension.NodeFactoryExtensionManager.getInstance(NodeFactoryExtensionManager.java:130)
        at org.knime.workbench.repository.RepositoryManager.readNodes(RepositoryManager.java:355)
        at org.knime.workbench.repository.RepositoryManager.readRepository(RepositoryManager.java:168)
        at org.knime.workbench.repository.RepositoryManager.getRoot(RepositoryManager.java:573)
        at org.knime.workbench.repository.view.AbstractRepositoryView.readRepository(AbstractRepositoryView.java:413)
        at org.knime.workbench.repository.view.AbstractRepositoryView$4.run(AbstractRepositoryView.java:331)
        at org.eclipse.core.internal.jobs.Worker.run(Worker.java:63)
Caused by: org.osgi.framework.BundleException: Exception in com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start() of bundle com.vernalis.knime.chem.mmp.
        at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:863)
        at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:791)
        at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1015)
        at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:365)
        at org.eclipse.osgi.container.Module.doStart(Module.java:603)
        at org.eclipse.osgi.container.Module.start(Module.java:467)
        at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:493)
        at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
        ... 31 more
Caused by: java.lang.UnsatisfiedLinkError: org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(Ljava/lang/String;)J
        at org.RDKit.RDKFuncsJNI.RWMol_MolFromSmarts__SWIG_3(Native Method)
        at org.RDKit.RWMol.MolFromSmarts(RWMol.java:436)
        at com.vernalis.knime.mmp.MatchedPairsMultipleCutsNodePlugin.start(MatchedPairsMultipleCutsNodePlugin.java:91)
        at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:842)
        at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:834)
        ... 38 more
java.lang.ClassNotFoundException: An error occurred while automatically activating bundle com.vernalis.knime.chem.mmp (79).

armingrudd · September 4, 2020, 4:03am

And here is the log:

log.txt (32.5 KB)

The dll file at C:\KNIME\plugins\org.rdkit.knime.bin.win32.x86_64_4.0.1.v202002120849\os\win32\x86_64\GraphMolWrap.dll does exist but I don’t know why it cannot be loaded.

After running OSGi console, the number of errors increased. Now I see these when I start KNIME:

ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.loop.CutTypeLoopStartNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.uniquifyids.UniquifyIdsNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.maxcuts.rdkit.RDKitMMPMaxCutsNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.filter.rdkit.RDKitMMPFilterNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.filter.rdkit.RDKitMMPSplitterNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.fragment.rdkit.RDKitMMPFragmentNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.fragment.rdkit.RDKitMulticutMMPFragmentNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.pairgen.frag2pair.Frag2Pair3NodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.pairgen.frag2pair.ReferenceFrag2Pair3NodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderMatchingBondsNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.vernalis.knime.mmp.nodes.fragutil.render.rdkit.RDKitMMPRenderCuttableBondsNodeFactory' from plugin 'com.vernalis.knime.chem.mmp' could not be created. The corresponding plugin bundle could not be activated!
ERROR 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!

s.roughley · September 4, 2020, 7:58am

Thanks Armin. That looks like some sort of problem with the RDKit types plugin not being able to load properly (even if you don’t have the RDKit nodes, you need the RDKit types to be able to create out MMP nodes plugin). I’m going to tag @greglandrum here to see if he can think what the problem there might be with the GraphMolWrap.dll

Steve

swebb · September 5, 2020, 11:51am

If you want to take a look for potential reasons before Greg responds it may be worth running Dependency Walker against that dll

https://www.dependencywalker.com/

It may show what’s missing and preventing the dll being loaded.

armingrudd · September 5, 2020, 4:02pm

Thank you @swebb. Here is the dwi file (you have to change the file extension to .dwi). I cannot understand it.

GraphMolWrap.txt (1.1 MB)

The error appears both on the server (where I have the issue) and on my desktop (where I don’t have any issues).

s.roughley · September 8, 2020, 7:23am

Thanks Armin - I hope Sam @swebb can make something of that output?!

Steve

swebb · September 8, 2020, 6:10pm

@s.roughley Unfortunately it’s not a clear as issues I’ve investigated in the past.

@armingrudd

Does it look like they when loaded for you? I’m not sure if it updates after loading based on the new machine.

I imported the dll from my KNIME install and it seems to give the same output as yours but the plugin is loading fine in my KNIME. I thought that maybe we’d see a dependency missing that we needed to install.

armingrudd · September 8, 2020, 7:15pm

Yes, this is what I see when I load the file. This is the same for my desktop and the server. But I have no issues using the extension on my desktop as well. On the other hand, errors appear in console when KNIME starts on the server.

mwiegand · December 21, 2021, 9:13am

Just FYI – Installing the RDKit Nodes resolved it for me. Thanks for the hint @s.roughley!