Cannot load indigo plugin

bjwiley23 · January 14, 2023, 4:38pm

I just install KNIME Analytics Platform v.4.7.0 for MacOS and after installing Indigo extension I am seeing these errors when starting KNIME.

Probably all stemming from Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoMolCellFactory.

ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoMolCellFactory' for 'com.epam.indigo.knime.cell.IndigoMolCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoMolCellFactory.
ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoReactionCellFactory' for 'com.epam.indigo.knime.cell.IndigoReactionCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoReactionCellFactory.
ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoQueryMolCellFactory' for 'com.epam.indigo.knime.cell.IndigoQueryMolCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoQueryMolCellFactory.
ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoQueryReactionCellFactory' for 'com.epam.indigo.knime.cell.IndigoQueryReactionCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoQueryReactionCellFactory.
ERROR RepositoryManager               Node 'com.epam.indigo.knime.compjoin.IndigoComponentCombinerNodeFactory' from plugin 'com.epam.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.epam.indigo.knime.compsep.IndigoComponentSeparatorNodeFactory' from plugin 'com.epam.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.epam.indigo.knime.murcko.IndigoMurckoScaffoldNodeFactory' from plugin 'com.epam.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.epam.indigo.knime.rgdecomp.IndigoRGroupDecomposerNodeFactory' from plugin 'com.epam.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager ...

bjwiley23 · January 14, 2023, 4:50pm

I do see this when trying to install from drag and drop of URI

And this in the error logs:

Caused by: org.osgi.framework.BundleException: Error starting module. osgi.identity; osgi.identity="com.epam.indigo.knime.plugin"; type="osgi.bundle"; version:Version="2.0.0.qualifier"; singlet
on:="true" [id=570]
...
Caused by: java.lang.Error: Indigo cannot find native libraries for Mac OS X 10.6

bjwiley23 · January 15, 2023, 1:45am

Ok it seems like basic KNIME Analytics Platform is not installing correctly to where it can validate that osgi.bundle and org.knime.workbench.core are actually installed as this is the error message I see when installing from the “Source” pages. However I have both as seen in image. Indigo should be updated for version 4 of KNIME correct? I mean we are already on v4.7 of KNIME.

 Missing requirement: Indigo extensions for KNIME Workbench 2.0.0.v201603210922 (com.epam.indigo.knime.plugin 2.0.0.v201603210922) requires 'osgi.bundle; org.knime.workbench.core [3.3.0,4.0.0)' but it could not be found

aliasghar_marvi · January 19, 2023, 6:01am

Hi @bjwiley23,

We are trying to understand this issue. Can you please share which update site are you using to extract this extension?

Thanks

Best
Ali

bjwiley23 · February 9, 2023, 9:48pm

Just coming back to this. I didn’t add an update site for Indigo. I used the drag and drop (KNIME 4.71 from Indigo KNIME integration – KNIME Community Hub. It installs fine but when restarting KNIME you get these errors in the console:

ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoMolCellFactory' for 'com.epam.indigo.knime.cell.IndigoMolCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoMolCellFactory.
ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoReactionCellFactory' for 'com.epam.indigo.knime.cell.IndigoReactionCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoReactionCellFactory.
ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoQueryMolCellFactory' for 'com.epam.indigo.knime.cell.IndigoQueryMolCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoQueryMolCellFactory.
ERROR DataTypeRegistry                Could not create data cell factory 'com.epam.indigo.knime.cell.IndigoQueryReactionCellFactory' for 'com.epam.indigo.knime.cell.IndigoQueryReactionCell' from plug-in 'com.epam.indigo.knime.plugin': Plug-in com.epam.indigo.knime.plugin was unable to load class com.epam.indigo.knime.cell.IndigoQueryReactionCellFactory.
ERROR RepositoryManager               Node 'com.epam.indigo.knime.compjoin.IndigoComponentCombinerNodeFactory' from plugin 'com.epam.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!
ERROR RepositoryManager               Node 'com.epam.indigo.knime.compsep.IndigoComponentSeparatorNodeFactory' from plugin 'com.epam.indigo.knime.plugin' could not be created. The corresponding plugin bundle could not be activated!

knime.log (2.1 MB)

aliasghar_marvi · February 13, 2023, 11:06am

Hi @bjwiley23,

Apologies for looking into this a bit late. I believe this issue concerns the community developer @EPAM-LSOP . By looking at the log file it appears to be an issue on MacOS.

Thanks

bjwiley23 · February 15, 2023, 8:37am

Yes I saw that in the log as well, although searching the internet for similar problem was not fruitful for me to try to solve. How do I get in contact with @EPAM-LSOP?

bjwiley23 · February 15, 2023, 9:05am

FYI it seems to work on 4.5.0 for Mac OS and >4.6 for Ubuntu but not >4.6 for Mac OS. See Update of Indigo Knime nodes · Issue #762 · epam/Indigo · GitHub

aliasghar_marvi · February 15, 2023, 1:12pm

It appears that they are not much active on KNIME Forum. However, I am pasting this link, it mentions contact information in order to report such issues:

https://lifescience.opensource.epam.com/contact.html#feedback-on-open-source-software

Hope it helps

system · May 16, 2023, 1:12pm

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.