Error plugin com.vernalis.knime.chem.mmp

Community Extensions
1

Hi,
i’ve istalled the vernalis plugin but it seems not compare in Node Repository.
On the start knime 4.3.0, I receive this error message:

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!

In log file, i see this:

com.vernalis.knime.chem.core (1.28.0.v202012181313) “Vernalis Chemistry Core Plugin for the KNIME Workbench” [Active]
com.vernalis.knime.chem.mmp (1.28.0.v202012181313) “Vernalis Chemistry Matched-Molecular Pairs extension for KNIME Workbench” [Resolved]

Can anyone help me?
thanks

2

Thanks @romarra,

A few questions to help see if we can pin this down:

  1. Do you have the RDKit nodes installed?
  2. Is there anything else in the log file or console (if you don’t have it set, could you set the log and console levels to INFO or DEBUG?) relating to any of those ERROR messages above?
  3. Do you see any Vernalis nodes in the node repository?

Thanks

Steve

1 Like
3

Hi Steve,
Here new information!

Thans!!

log.txt (457,6 KB)

1

3

4

Thank you. Unfortunately there is nothing at all obvious in there, and it does look like you get the rest of the nodes. I have just made a minor bug fix for another issue in the MMP nodes, where I also changed a specific feature of the interaction with RDKit. Would you be able to update to the new version (v1.28.1) and try again?

thanks

Steve

1 Like
5

Thanks Steve, could you give me a zip file new version ?

6

You should be able to update from within KNIME, from the File menu select Update KNIME...

Steve

7

Hi,

I’m also getting the same error messages. Stating the corresponding plugin bundle could not be activated.

8

Could you provide some more information please, as follows:

  • Which version of KNIME are you using?
  • Which version of the Vernalis nodes are you using?
  • Which version of the RDKit nodes do you have installed?
  • Is there any further information in the log files associated with the error message?

Thanks

Steve

2 Likes
9

I have the same issue after some recent-ish updates on my Mac.
KNIME 4.5.2
Vermalis nodes: 1.33.0.v202205191100, the current one as for May 22, 2022.

However, after I installed the RDKit, the errors are gone. It seems Vermalis does not have the dependency specified during the install. Thanks!

Henry

3 Likes
10

@henryhmo thanks for letting us know. This is a strange one, as as far as I can tell, the RDKit dependency is declared in the relevant Vernalis plugins. I’m going to tag @greglandrum and @manuelschwarze in case there is anything else from the RDKit that we need to explicitly add as a dependency?

Steve

1 Like
11

Thank you @henryhmo . I encountered the RDKit errors too everytime I open Knime. I followed your note to install the RDKit, my errors now are gone. But it’s a bit annoying that I have to install an extension I don’t use just to get rid of the errors. I’m using the latest Knime and Vernalis extension by the way. And this happened only recently.

12

Ironically, I saw this behaviour for the first time myself recently.

If you don’t need any of our cheminformatics nodes (MMP analysis, Ertl Scaffold Keys, PMI nodes) then you can safely ignore the errors, irritating as they may be. Otherwise, you need to install the RDKit nodes.

What I do not understand is why that doesn’t happen anyway automatically - the RDKit code is declared in several of our plugins as a dependency, and so my understanding is that the Eclipse framework ‘should just install it’ - going to ask if @gab1one can throw any light on that?

Steve

1 Like
13

Hi @Vernalis,

The problem is that you only have a dependency to the rdkit plugin itself, but not to the platform specific binaries that are required to make it work. You’d need to set a feature dependency to the rdkit feature. Which will install the full rdkit extension together with the vernalis one.

best,
Gabriel

2 Likes
14

Thanks @gab1one - I will look to doing that in a forthcoming patch release. Now on our bug tracker at Errors in console when RDKit nodes not manually installed · Issue #17 · vernalis/vernalis-knime-nodes · GitHub

Steve

15

This should now be fixed in the Nightly/trunk build. It will propagate to the stable build channels for KNIME 4.6 / 4.7 in the coming days. See

For any further details

Steve

1 Like
16

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