R libraries in non-standard locations

I prefer to use Knime on a linux machine that is located in a data center that has direct access to large data sets that I work with. Some of the software libraries I use on this linux machine is installed in non-standard path locations. Adding these non-standard library locations to a user’s environment variables is normally handled by using the Environment Modules (http://modules.sourceforge.net). For example when I use R from the command line (R_Root/bin/R) it has access to necessary libraries like X11 and png that are added using the ‘modules load’ function.

When using R with Knime I set the R path in the Knime preferences to the R_Root/lib64/R/ directory, but the necessary library environment variables do not seem to be inherited by Knime and running an R script results in a failure.

My question: Is there a way to configure Knime to use the libraries necessary for R when they are stored in non-standard locations?

Can you provide an example of the error you are receiving when running the R nodes from within KNIME AP?

The Modules program is not something we have come across in other support cases, so there may be a solution involving that project, TBD.

One option that has been used for other customer when R needs to find external libraries is setting the LD_LIBRARY_PATH variable, and assigning it the values of the directories where theses libraries exist. For example /usr/local/lib sometimes isn’t included, so specifying this location via LD_LIBRARY_PATH allows R to load it when launched by KNIME.

1 Like

Thanks for your response.

To simplify matters I am using a R Source (Table) node.
If I select Configure the node opens with no error.
If I attempt to load a single R package: library(ggplot2). I get the following:

ERROR: Could not execute internal command.ERROR: R evaluation failed.: "options(device='png')
png("/tmp/knime_test52084/rtmp-dialog-52087/rsnippet-plot.png",width=400.0,height=300.0)"ERROR: R evaluation failed.: "options(device='png')
png("/tmp/knime_test52084/rtmp-dialog-52087/rsnippet-plot.png",width=400.0,height=300.0)"ERROR: eval failed, request status: error code: 127> library(ggplot2)
ERROR: 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

Also, I did add some library paths to my LD_LIBRARY_PATH variable . I then used the Extract System Properties to see if these are inherited by Knime, but they don’t appear in this nodes output. I understand that this node may not be reporting all libraries that Knime has access to.

I want to close out this ticket by indicating my problem was caused by some conflicting commands setting my environment variables. Once this problem was identified and fixed, Knime has been working fine.


This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.