[GenABEL-dev] how to get devel-version of GenABEL packages working on Linux or Mac OS, and how to commit changes

[L.C. Karssen]

Hi Yurii, 

Following William's example, here are some more suggestions.

On Wed, 2011-02-23 at 15:18 +0100, Yurii Aulchenko wrote:
> 0) In order to commit the code, you need to be registered at the
> project dev-site. If you did not so yet, register @R-forge

Maybe emphasize a bit more that this is only necessary when one wants to
commit? 

> 1) in order to be able to compile dev-dersion, make some changes to .profile
> 
> assuming that R s installed at /usr/loca/bin, add to ~/.profile:

Mind the typo in /usr/local/bin

> 
> R_HOME=/usr/local
> export R_HOME
> 

As William pointed out, R is not always in /usr/local/. You could try
the following:
R_HOME=$(dirname $(which R))
which gives /usr/bin/ on my Ubuntu machine. 
Minor note: I've set an alias for R in my .bashrc file. On Ubuntu
machines this doesn't give a problem, but on a CentOS 5.4 machine the
above doesn't work because 'which' returns two lines, my alias and the
real file:
$ which R
 alias R='/usr/bin/R --no-save'
	/usr/bin/R


> log out and log in again, or start a new terminal/console window
> 
> 2) install GenABEL et al., 'roxygen', and 'RUnit'; for that from
> within R use command
> 
> install.packages("GenABEL",dependencies=c("Depends","Suggests"))
> install.packages("roxygen")
> install.packages("RUnit")
> 
> 3) Get to the latest code by (you need to be registered
> @RForge::GenABEL in order to do next parts)
> 
> svn checkout svn+ssh://yourRforgeUserName@svn.r-forge.r-project.org/svnroot/genabel
> 

I think you should say here that the user should create a separate
directory before doing the checkout or move to their directory of choice
(this also makes sure they have left R after the previous step). 

Do you want to mention here that if you didn't do step 0 (register with
r-forge) because you want read-only access, the following will do an
anonymous checkout?
svn checkout svn://svn.r-forge.r-project.org/svnroot/genabel


> 4) compile and install latest code by
> 
> cd genabel/pkg
> 
> if you wish to be in sync with latest versions of *ABELs, which are
> used by MixABEL (as indicated by MixABEL/DESCRIPTION), do
> 
> R CMD INSTALL DatABEL
> R CMD INSTALL GenABEL
> 
> then install MixABEL with
> 
> R CMD INSTALL MixABEL
> 
> 
> ... now you can start R and run example code I have sent in previous e-mail.
> 
> 5) you can commit modified MixABEL code by
> 
> # get to the point
> cd /path_to_where_genabel_is_locally/genabel/pkg/MixABEL
> # clean-up
> sh ./cleanup
> cd ..
> # commit
> svn commit MixABEL -m "What are the changes about"
> 
> That should be it. FINITO!
> 
> Hopefully will work ok, and let us know if there is any problem with
> this description (or if it worked just fine), also any suggestions on
> how to improve this description are most welcome. When this procedure
> is approved/modified/extended by you, we will add these instructions
> to the dev part of our web-site.
> 
> best wishes,
> Yurii
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel



Lennart.

-- 
-----------------------------------------------
L.C. Karssen
Erasmus MC
Department of Epidemiology
Room Ee2224

Postbus 2040
3000 CA Rotterdam
The Netherlands

phone: +31-10-7044217
fax: +31-10-7044657
email: l.karssen at erasmusmc.nl
GPG key ID: 0E1D39E3
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