The GSVA package calls functions from the GNU Scientific Library and this README file discusses several steps to be taken to make sure that this library is available to GSVA when installing it. Unix/Mac users ============== In order to successfully install and run GSVA in Unix/Mac systems you need to install first the GNU Scientific Library (GSL) which you can find in the following URL: http://www.gnu.org/software/gsl Follow the link to the FTP site and download the lastest tar ball or, in any case, one with version >= 1.12, for instance, to your 'Desktop' directory. Then go to the shell (in a Mac computer you need to open the Terminal window program under the Applications/Utilities folder) and type the following instruccions for a system-wide installation (assuming the tar ball has name 'gsl-1.15.tar.gz': $ cd Desktop $ gzip -cd gsl-1.15.tar.gz | tar xvf - $ cd gsl-1.15 $ ./configure $ make $ sudo make install The latter instruction will ask you for the system administration password which may very well be the your own user password. If you do not have system administration privileges, you can either ask your sysadmin to make this system-wide installation of GSL or install GSL yourself on another location of the filesystem where you have writing permissions. This can be done by replacing the call to 'configure' by: $ ./configure --prefix=/home/myusername/gsl Then make sure that your PATH environment variable allows you to execute the script 'gsl-config' located in the 'bin' subdirectory of the GSL installation. This can be verified by writting n the shell: $ which gsl-config without obtaining an error. If you get an error, locate the path where the 'gsl-config' script is and add it to the PATH environment variable. Alternatively, you can set the environment variable GSL_CONFIG to this path, thus avoiding to modify the PATH environment variable. After this, you can install GSVA in the usual way as with any other Bioconductor package by writting the following instructions in the R shell: source("http://www.bioconductor.org/biocLite.R") biocLite("GSVA") Windows users ============= If you install the binary GSVA package for Windows that is available through the Bioconductor website, then nothing needs to be done next to a standard installation as a Bioconductor package, i.e.: source("http://www.bioconductor.org/biocLite.R") biocLite("GSVA") since the binary GSVA package at Bioconductor already contains the necessary GNU Scientific Library functions statically linked in the package. If you want to install the package from source (not recommended for standard users), then you need to install first the GNU Scientific Library (GSL) which, in the case of windows, can be done in two ways, from the GNUWIN32 site and from the CYGWIN site. Each option requires slightly different configuration steps. Either is equally good for having GSVA running under windows and the choice is more a matter of whether incidentally you already have one of the two installed in your windows machine. If not, just take any of them. ** GNUWIN32 You should download the GNUWIN32 GSL from: http://gnuwin32.sourceforge.net/packages/gsl.htm It is recommended that you download the file under the 'Setup' link described as "Complete package, except sources'. You should execute the downloaded file and perform the installation either system-wide, for which you'll need system administration privileges, or in some path where you have writting permissions. By default, this package installs GSL at 'C:\Program Files\GnuWin32' and assume this is the case now. Go to the folder C:\Program Files\GnuWin32\bin and copy the file 'libgsl.dll' into 'libgsl-0.dll'. Then add the path where these files are located to your PATH environment variable by right-clicking on the "My PC" icon, select "Properties", go to the "Advanced" tab, click on "Environment variables", select "Path" on the "Environment variables" box, click on "Modify", and add to the end of the current string: ;C:/PROGRA~1/GNUWIN32/bin then press 'Ok' through out all previously opened dialog boxes and you should be able to install GSVA in the usual way as with any other Bioconductor package by writting the following instructions in the R shell: source("http://www.bioconductor.org/biocLite.R") biocLite("GSVA") ** CYGWIN You should have first Cygwin installed from: http://cygwin.com and follow the instructions to further install the GSL CYGWIN package. Write down where the root of the GSL installation is in your hard disk. Let's assume this path is C:\GSL. You should add an environment variable called LIB_GSL that points to the root of this GSL installation, thus setting in this example the value C:/GSL. Note that this path should be set with slashes '/' instead of backslashes '\'. Then add the path C:/GSL/i383/bin to your PATH environment variable if your windows installation is 32bit and add C:/GSL/x64/bin instead to your PATH environment variable if your windows installation is 64bit. You can add and modify environment variables by right-clicking on the "My PC" icon, select "Properties", go to the "Advanced" tab and click on "Environment variables" where you'll be able to add and/or modify these variables. Remember to separate paths of the filesystem with a semicolon ';'. Once the environment variables are set you should press 'Ok' through all previously opened dialog boxes and you should be able to install GSVA in the usual way as with any other Bioconductor package by writting the following instructions in the R shell: source("http://www.bioconductor.org/biocLite.R") biocLite("GSVA")