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:
Loading required package: rJava
> username <- "email@example.com"
> password <- NULL
> servername <- "http://localhost:8888"
> gp.client <- gp.login(servername, username, password)
Error in gp.login(servername, username, password) :
Can anyone help me? Thanks.
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).
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.