R, GenePattern and KNIME


I am trying to run GenePattern with R from KNIME.  Outside of KNIME, I am running the following code with no problems in several different ways.  In KNIME, I get the following error:

> library("GenePattern")
Loading required package: rJava
> username <- "brian.muchmore@genyo.es"
> password <- NULL
> servername <- "http://localhost:8888"
> gp.client <- gp.login(servername, username, password)
Error in gp.login(servername, username, password) :
  java.lang.NoClassDefFoundError: org/genepattern/client/GPClient

Can anyone help me?  Thanks.

-Brian Muchmore

Just as an update, I found a kind of rediculous work-around that nonetheless works:  I use the Bash node to call a RapidMiner-with-R-extension workflow.  This, however, is obviously way less than optimal.  Any help would still be appreciated (I assume it is a rather easy fix, whatever is going on).



Hi Brian, 

It could be that the version of R running inside of KNIME using a different JVM than the gene pattern server.  You could check this (and potentially fix it) by adding a line to your script in KNIME.  For example, you can use Sys.getenv("JAVA_HOME") to find out which JVM R is using in both KNIME and your alternate R enviroment to make sure they  are using the same path. More details in the link below. Give it a try and let us know how it goes.



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