=============== Installing GSVA =============== In order to successfully install and run GSVA you need to install first the GNU Scientific Library (GSL) which you can find in the following URL: http://www.gnu.org/software/gsl Once you have installed the GSL, if you have done it "system-wide" then you can install GSVA in the usual way as with any other Bioconductor package: biocLite("GSVA") However, if you have installed the GSL in a non system-wide location of you hard disk, you should provide this location to biocLite() as follows: biocLite("GSVA", configure.args="--with-gsl-lib=\"/where/gsl/lib/is\" --with-gsl-include=\"/where/gsl/include/is\"") If, alternatively, you have downloaded yourself the source tarball of GSVA and want to install it from the shell, then you should use: R CMD INSTALL --configure-args="--with-gsl-lib=`R RHOME`/lib --with-gsl-include=`R RHOME`/include" GSVA_X.Y.Z.tar.gz where X.Y.Z is the corresponding version of GSVA that you have actually downloaded.