从Java调用R-不同的R版本

Question

On the computers (running fedora) at my work R-2.15 is installed by default. I downloaded R-3.0.2 because I need several packages which are only available for R 3.

When i try to call an Rscript from java using Runtime.getRuntime().exec(command); with command being the String Array {"/path/to/Rscript/3-0" "name/of/script" "...args..."} I get the error WARNING: ignoring environment value of R_HOME and it says that it couldn't load the needed packages. When i run the very same command in a terminal it works well.

What is the difference between the call via java and the call on the console. And how can I fix it?

EDIT 1: when i run my locally installed R-3 version, libPaths returns

> .libPaths()
[1] "/home/<homedir>/.bin/R-3.0.2/library"

But when i call an Rscript from Java, libPaths returns

[1] "/home/<homedir>/R/x86_64-redhat-linux-gnu-library/2.15"
[2] "/usr/lib64/R/library"                                          
[3] "/usr/share/R/library"                                          
[4] "/home/<homedir>/.bin/R-3.0.2/library" 

The problem seems to be that Java adds any environment variables that tell R to load packages from the 2.15 installation. How can i prevent this?

EDIT 2: When i list all environment variables using the System.getenv(); method nothing R -related is shown, the same is the case when i list the environment variables using printenv in the terminal. But when i call Sys.getenv in R the variables R_HOME, R_LIBS, ... are defined. How are these defined?

Answer 1

You can choose the library to look in when you load the package. For example, when calling the script via Rscript, you could use

library(rJava, lib.loc = .libPaths()[4])