How to make a patch.

OK, so you want to fix something that's not working in one of the
*ABEL packages and don't know where to start. Actually it's easier
than you think.

The first thing you need to do is to dowload the last vesion of the
GenABEL suite source code with the command:

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

it is important to use co (checkout) and not export because otherwise
the command diff needed to make the patch will not work.

You will now notice that a new directory has been created called ./pkg
Inside you will find a directory for each package.

You can find the source for each function in the corresponding package directory in the R directory so for example the source for polygenic will be in ./pkg/GenABEL/R/polygenic.R.

Now open the file you intend to fix and make all the changes you intend to make.
Once you are done go to the pkg directory and recompile the package you have fixed using the command (assuming you made changes to GenABEL)

R CMD INSTALL GenABEL

Open R and check that you actually fixed the problem.
If this is the case also run

R CMD check GenABEL

to verify that everything is working fine.
If everything goes well you are ready to make the patch that can be
sent to the maintainers.

At this point it is important to update your version of the source
code by going to the pkg directory and running:

svn update

This is important since it probably took you some time to make the patch and probably other changes have been made which could complicate the creation of the patch.

Now it is time for the actual creation of the patch.