How to install devel-version of GenABEL suite

by Yurii Aulchenko, William Astle and Lennart Karssen for the GenABEL-devel team

Here are instructions on how to get devel-version of GenABEL packages working, assuming you use Linux or Mac OS.

To get GenABEL & Co. running in devel-setting, you need to do a number of things. Plan to spend about 30 minutes on that. You will need good Inet connection and you also will need to have Subversion (svn) installed.

1) Check if Subversion is installed. For that, try 'svn help'. If you do get help, everyting must be all right. If Subversion is not there, here is the link, which may help: http://subversion.apache.org/packages.html

2) In order to be able to compile devel-version, you need to set an environmental variable R_HOME to point the location, where R is installed. We assume that you use Bash (most people do); if not, try to figure out how you can set environmental variables for your particular environment (and let us know so we can add it here :) ).

You can check where R is installed by running 'dirname $(which R)' on Bash command prompt. Assuming R is installed at '/usr/bin', add the following lines to your ~/.bashrc file (with Mac OS X, use ~/.bash_profile). 

R_HOME=/usr/bin
export R_HOME

or, you can try 

R_HOME=$(dirname $(which R))
export R_HOME

log out and log in again, or start a new terminal/console window.

3) Install _stable_ GenABEL et al., 'roxygen', and 'RUnit' from CRAN; for that on R command line type 

install.packages("GenABEL",dependencies=c("Depends","Suggests"))
install.packages("roxygen")
install.packages("RUnit")

4) Change to a place, where you want the source code to go. Get to the latest code by 

svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg

This should create directory called 'pkg' with all packages in it.

5) Compile and install latest code by 

cd pkg
R CMD INSTALL DatABEL
R CMD INSTALL GenABEL
... etc.

Note some packages (e.g. ProbABEL) are not R packages; to compile these use specific Makefile's, e.g. 

cd ProbABEL
autoreconf -i
./configure
make

FINITO! Enjoy :)