How to make a patch to GenABEL
by Nicola Pirastu
OK, so you want to fix something that's not working in one of the
GenABEL suite packages and don't know where to start. Actually it's easier
than you think.
The first thing you need to do is to download the last version 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) option 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
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 the GenABEL package)
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:
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.
From the root directory of the 'pkg' directory run
svn diff ./pkg > patch_file_name
This is your patch file.
Now to check that it works fine, you could copy back the original
version of the function (for example from an svn checkout in a
temporary directory) and try if the patch works from the directory
where you have created it with
patch -p0 -i patch_file_name
Rerun the 'R CMD' commands and re-check everything and you are ready to
submit the patch file to the community. Don't forget to describe what
you fixed (if possible including a bug number from the bug tracker)
and maybe give an example of the new/improved functionality.