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Error: object 'knime.in' not found

Member for

3 years 9 months harishpk

I am being driven crazy by this error. The data I am trying to manipulate in the R script is taking a while to load (circa 20-25 seconds) and hence the execution of the code is failing.

I built a 25 seconds delay in the code anticipating the data to load into R snippet from the previous node.

The error on the Console is ERROR R Snippet            0:12       Execute failed: R evaluation failed.

When I open the node and evaluate the script then error is Error: object 'knime.in' not found. If i wait for 15 seconds, knime.in gets loaded and then the script works fine

Can someone please help?

Comments
Wed, 02/15/2017 - 04:17

Member for

7 years 7 months

jonathan.hale

Hi harishpk,

sorry for the late reply!

When I open the node and evaluate the script

You will have to wait for the data to be loaded (knime.in show up in the workspace list on the right hand side), if you have large amounts of data this will take a while. (How many rows/columns is your input data?)

But the node should definitely not fail. I am currently working on improvements which should allow the R Snippet node to handle larger amounts of data. In Preferences > KNIME > R, you will find an option to increase the buffer size for Rserve, which may already help to prevent the

 Execute failed: R evaluation failed.

error.

If you believe this doesn't have anything to do with the data size, it would be amazing if you could send me the workflow via email: jonathan.hale@knime.com. Please also include which operating system you are running.

Please tell me if anything helped!

Regards, Jonathan.

Mon, 05/01/2017 - 10:31

Member for

5 years 8 months

jpfeuffer

Lately we are experiencing this kind of problems more and more, too.

Often associated with error 127. Sometimes data shows up in the scripting dialog only after the node was executed.

This happens with only a few rows with the random Cluster Data Generator.

Tue, 05/02/2017 - 01:09

Member for

5 years 1 month

son

I am experiencing the same kind of problem.

My workflow containing table to R nodes used to work until couple of days ago, but now it fails with the error in the KNIME console :"Execute failed: ("NullPointerException"): null".

If I open the node and evaluate the script I get "Error: object 'knime.in' not found". Moreover, I noticed that the table (1368 rows, 127 columns) doesn't appear in the workspace, no matter how long i wait for  it.

 

 

Wed, 05/03/2017 - 12:01

Member for

5 years 2 months

joshuahoran

I also get the "Error: object 'knime.in' not found" on a routine basis with the most recent version on KNIME. Even when you allow sufficient time for the data to load and wait for the knime.in object to become listed in the Workspace list -- I still get the error. Usually hitting "Reset Workspace" will fix it. If not, then closing the config window and re-opening will fix it. I've noticed that the frequency of this error is correlated with another error:

"The dialog pane for node 'R View (Table) 3:796' has thrown a 'IndexOutOfBoundsException'. That is most likely an implementation error."

I get this error about 50% of the time when I try to open the config window for an R node.

Thu, 09/21/2017 - 05:40

Member for

3 years 1 month

Judit

Replacing 'knime.in' with 'kIn' and 'knime.out' with 'rOut' solved the issue for me.

Wed, 01/03/2018 - 07:43

Member for

2 years 9 months

Ryon

Hello, 

I am having the same error: Object 'knime.in' not found when using R snippet nodes.  I tried using the aforementioned workarounds but it is still not working. I am running KNIME version 3.5.1 for Mac. The data is not particularly big: less than 20 columns and less than 500 rows.

Are there additional workarounds or things I can do?  

Much thanks in advance! 

Ryon

 

 

Thu, 02/08/2018 - 05:13

Member for

2 years 10 months

pogacsa

Hi All, I'm having the same issue too. 

I have KNIME 3.5.1, have already set the R buffer size to unlimited.

At first, if I evaluate the script (which works perfectly in RStudio), all goes well, up until the point, where I try using the nmf from the NMF package. Then I get the error message from above, which is:

ERROR: R evaluation failed.: "knime.tmp.ret<-NULL;printError<-function(e) message(paste('Error:',conditionMessage(e)));for(exp in tryCatch(parse(text=knime.tmp.script),error=printError)){tryCatch(knime.tmp.ret<-withVisible(eval(exp)),error=printError)
if(!is.null(knime.tmp.ret)) {if(knime.tmp.ret$visible) print(knime.tmp.ret$value)}};rm(knime.tmp.script,exp,printError);knime.tmp.ret$value"ERROR: R evaluation failed.: "knime.tmp.ret<-NULL;printError<-function(e) message(paste('Error:',conditionMessage(e)));for(exp in tryCatch(parse(text=knime.tmp.script),error=printError)){tryCatch(knime.tmp.ret<-withVisible(eval(exp)),error=printError)
if(!is.null(knime.tmp.ret)) {if(knime.tmp.ret$visible) print(knime.tmp.ret$value)}};rm(knime.tmp.script,exp,printError);knime.tmp.ret$value"ERROR: eval failedERROR: Could not capture output of command.ERROR: R evaluation failed.: "sink();sink(type='message')
close(knime.stdout.con);close(knime.stderr.con)
knime.output.ret<-c(paste(knime.stdout,collapse='\n'), paste(knime.stderr,collapse='\n'))
knime.output.ret"ERROR: R evaluation failed.: "sink();sink(type='message')
close(knime.stdout.con);close(knime.stderr.con)
knime.output.ret<-c(paste(knime.stdout,collapse='\n'), paste(knime.stderr,collapse='\n'))
knime.output.ret"ERROR: eval failed, request status: error code: 127ERROR: Could not execute internal command.ERROR: R evaluation failed.: "dev.off()"ERROR: R evaluation failed.: "dev.off()"ERROR: eval failed, request status: error code: 127

After which all objects are forgotton, knime.in not found, functions not found, everything not found, even though the objects are still listed on the right.

Any ideas? (I'm happy to send the wf, if you'd like to take a look.)

Mon, 02/12/2018 - 02:20

Member for

7 years 7 months

jonathan.hale

Hi all!



The data is not particularly big: less than 20 columns and less than 500 rows.

The size of the data should not be an issue with newer KNIME AP versions (e.g. 3.4 or 3.5).

 

Any ideas? (I'm happy to send the wf, if you'd like to take a look.)

Please make sure that the nmf package is properly installed. Also: Which OS are you using? In case you're on Windows, please also check that KNIME is using your own (not the bundled) R installation.
If that doesn't help, it would be indeed great if you could send me the workflow.

Cheers, Jonathan.