Dear Karim,
I suggest that you run the workbench using one of the zip files available here :
Ok, I had downloaded the plain "biocep.jar". I have now replaced it by "RWorkbench_NO_R.zip" (as I already have R 2.8.1 on my system).
if you would like to enforce biocep to use the packages (rJava ... ) you have installed yourself, you have to use :
java -Duse.default.libs=true -jar {some_directory}/biocep.jar
This made the trick and no longer it tries to install the packages. BTW, I think the packages could not be installed because an internet connection is only available on my system using the command-line parameter --internet2 when invoking R. Is there a way to parametrize the way a local R server is launched? In the same vein, is there a way to load an .Rprofile file on startup? But then, a java exception was thrown with a message telling that it could not locate the native JRI library. Adding the path to it on the command line didn't solve it: java -Djava.library.path=C:\Progra~1\R\R-2.8.1\library\rJava\jri -Duse.default.libs=true -jar biocep.jar In case someone is in the same situation, I've solved both problems by manually installing from within R the required packages (rJava, JavaGD, TypeInfo, Cairo and iplots) on directory "<RBenchmarkPath>\library\R-version-2.8.1". Now everything works! Many thanks for your answer and help. Best, Enrique