KNIME (eclipse-java) process disappears after uninstalling "org.knime.features.rengine.r2"

[Scott_Snyder]

I am running KNIME 2.9 and trying to learn about R integration.

I have R 3.0.1 installed on a MacBook Pro running OS X 10.9

From some of the more recent comments on this forum apparently the new R(Interactive) nodes are the best place to get started.

After trying to execute a "Table to R" node I got the following error message:

ERROR     Table to R                         Execute failed: Only R in version 2.x is supported. The R installation defined in the preferences is of version 3.x.

You can fix the problem by pointing to a valid R v2 installation or by

 - uninstalling the feature "org.knime.features.rengine.r2"

 - modifying your R installation and adding the package "rJava" (available from CRAN)

 - add a line to knime.ini: -Djava.library.path=<R-install-folder>/library/rJava/jri/x64

   (path printed to console while running install.packages("rJava") in R)

and restarting KNIME.

As I have version 3.0.1 installed this is not unreasonable. So I followed the instructions and removed the above feature, added rJava to my installation, and modified the knime.ini to the appropriate directory (incidentally the executable jars are not in the "/library/rJava/jri/x64" directory but in "/library/rJava/jri" on the Mac.)

Now I do not get any error messages but as soon as I try and configure the "Table to R" node KNIME dies and the entire processes disappears.

Since the crash leaves no error in the knime.log file it must be a system error and not a Java one. This is not unreasonable since rJava is a Java to native R bridge. Clearly there is an incompatabiity somewhere that hopefully can be resolved through configuration.

Reinstalling  the feature "org.knime.features.rengine.r2" gets me back to where I was with the above error.

If anyone is familiar with this failure can they please tell me the appropriate configuration changes or version changes that are necessary.

 

Thanks,

Scott 

[Scott_Snyder]

I have done more investigation on this problem and I think that it is related to having multiple versions of Java on the same Mac.

To continue to make progress I installed the latest v2 of R on the same laptop and used RSwitch to toggle between the two. I validated that, infact, the default R was changed to 2.15.3 but when I tried to configure one of the interactive nodes KNIME disappeared, just like when I had v3 of R and removed the "org.knime.features.rengine.r2" feature.

Since the crash only happens when KNIME actually tries to initialize R I have to assume that there is a problem with my Mac environment independent of the version of KNIME or R.

Is there a way to obtain a log from R that shows what it is attempting to do when the R initialization occurs (and fails) ?

KNIME runs under Java "1.6.0_65" although my system default is Java 7 .

java -version at a command line returns "1.7.0_45"

It is hard for me to believe that I am the only person that is seeing this problem.

 

-- Scott