The GenePattern modules available in the Broad Institute repository (Modules & Pipelines>Install from repository) all work with R 2.5. However, some GenePattern modules require different versions of R; for example, ExpressionFileCreator v.10 requires R 2.8. Unfortunately, R is not backward compatible. If you simply install and run the latest version of R, modules may fail or (worse) may produce invalid results even though they do not fail.
In GenePattern, each module definition includes a command line that runs the analysis program. For an R module, the R version is defined by a command line substitution parameter. For example, the <R> parameter is substituted with the full path to the R 2.0.1 executable. The <R2.5> parameter is substituted with the full path to the R 2.5 executable. Similar parameters are used for other versions of R.
GenePattern version 3.1 and later installs R 2.5 and sets the <R2.5> parameter. If you upgraded from GenePattern 3.0, your GenePattern installation also includes R 2.0.1 and sets the <R> parameter.
To add a different version of R to your GenePattern installation (for example R 2.8 on Mac OS X, for ExpressionFileCreator v. 10):
/Library/Frameworks/R.framework/Resourceswith the actual path to the correct installed version of R as described by this posting from the R-SIG-Mac mailing list. The file r_mac_osx_binary_patches.tar contains patches for modifying some versions of R. For other versions, here are the important scripts to modify (not all present in every version):
/Library/Frameworks/R.framework/Versions/<your R version>/Resources/bin/R
/Library/Frameworks/R.framework/Versions/<your R version>/Resources/bin/R32
/Library/Frameworks/R.framework/Versions/<your R version>/Resources/bin/R64
/Library/Frameworks/R.framework/Versions/<your R version>/Resources/etc/i386/Makeconf
/Library/Frameworks/R.framework/Versions/<your R version>/Resources/etc/x86_64/Makeconf
There are some GenePattern modules which rely on R version 2.0.1:
To use these modules on your server you need to add R version 2.0.1.
To add R2.0.1 to your GenePattern installation:
GenePattern can now run modules written for R2.0.1.