Problem with Feature Remover

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1

Hi,

I have a workflow that is deployed via KNIME webort which relies on the Feature Remover node to salt strip.  Recently, the workflow has stopped working, and the error appears to be due to this node.  The node is set with only the Minor Components option checked.  If I run on KNIME Desktop I can also reproduce the error (but only with this option checked - if I select all of the other options excluding this one then the node executes fine!

The error I see is pasted below.  Any help greatly appreciated.

Kind regards

James

PS  I am using the nightly builds

 

 

2012-11-01 09:22:14,861 ERROR KNIME-Worker-45 Feature Remover : Execute failed: CMF saver: Internal error: index is invald: -1
2012-11-01 09:22:14,861 DEBUG KNIME-Worker-45 Feature Remover : Execute failed: CMF saver: Internal error: index is invald: -1
com.ggasoftware.indigo.IndigoException: CMF saver: Internal error: index is invald: -1
at com.ggasoftware.indigo.Indigo.checkResult(Indigo.java:62)
at com.ggasoftware.indigo.IndigoObject.serialize(IndigoObject.java:1057)
at com.ggasoftware.indigo.knime.cell.IndigoMolCell.<init>(IndigoMolCell.java:68)
at com.ggasoftware.indigo.knime.common.IndigoNodeModel._createNewDataCell(IndigoNodeModel.java:171)
at com.ggasoftware.indigo.knime.fremover.IndigoFeatureRemoverNodeModel.execute(IndigoFeatureRemoverNodeModel.java:263)
at org.knime.core.node.NodeModel.execute(NodeModel.java:680)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:536)
at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:995)
at org.knime.core.node.Node.execute(Node.java:889)
at org.knime.core.node.workflow.SingleNodeContainer.performExecuteNode(SingleNodeContainer.java:894)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:100)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:166)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:124)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:239)
2012-11-01 09:22:14,866 DEBUG KNIME-Worker-45 WorkflowManager : Feature Remover 2:598:32 doBeforePostExecution
2012-11-01 09:22:14,866 DEBUG KNIME-Worker-45 NodeContainer : Feature Remover 2:598:32 has new state: POSTEXECUTE
2

Hi James,

Could you share that molecule or the whole workflow with the data? 

Mikhail

 

3

Hi Mikhail,

The molecule that seems to be causing the (first) problem is the first one in my list with a salt to strip...  If I render the Indigo molecule as SMILES, this is it:

 

Cl.ClC(c1[n]cccc1)=O

On the off chance, I tried dearomatizing first but see the same result.

Kind regards

James

4

Hi James,

I was able to reproduce it, and going to fix it soon. Thank you for bug report!

Mikhail

5

 

Hi James!

We have fixed this issue. Could you try the latest nightly builds?

Mikhail

6

Hi Mikhail,

Thanks a lot (and sorry for the very slow response!)  I saw there was an update, downloaded, saw it was fixed, was happy!  Only just got around to catching-up on the forums!

Kind regards

James

7

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