[GenABEL-dev] [Genabel-commits] r665 - pkg/webpages

[Yurii Aulchenko]

ok, here is "How to install devel-version of GenABEL suite" (plain HTML)

also available at

https://r-forge.r-project.org/scm/viewvc.php/pkg/webpages/tutHowToInstallDevelVersion.html?view=markup&root=genabel

Any further comments appreciated. Let us have few more days for anyone
to comment, and then if no issues pop up, will move this the web-site
tutorials section.

My idea was to put this on genabel.org/tutorials, as this is now
something for 'advanced user', not a developer.

Yurii

> +<h3>
> +How to install devel-version of GenABEL suite
> +</h3>
> +<p></p>
> +<i>
> +by Yurii Aulchenko, William Astle and Lennart Karssen for the GenABEL-devel team
> +</i>
> +<p></p>
> +
> +Here are instructions on how to get devel-version of GenABEL packages
> +working, assuming you use Linux or Mac OS.
> +<p></p>
> +
> +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.
> +<p></p>
> +
> +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:
> +<a href="http://subversion.apache.org/packages.html">
> +http://subversion.apache.org/packages.html
> +</a>
> +<p></p>
> +
> +2) In order to be able to compile devel-dersion, 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 :) ).
> +<p></p>
> +
> +You can check where R is installed by running 'dirname $(which R)'
> +on Bash command prompt. Assuming R is installed at '/usr/bin', add the following lines to your ~/.bashrc file
> +<p></p>
> +
> +R_HOME=/usr/bin
> +<br>
> +export R_HOME
> +<p></p>
> +
> +or, you can try
> +<p></p>
> +
> +R_HOME=$(dirname $(which R))
> +<br>
> +export R_HOME
> +<p></p>
> +
> +
> +log out and log in again, or start a new terminal/console window.
> +<p></p>
> +
> +3) Install _stable_ GenABEL et al., 'roxygen', and 'RUnit'
> +from CRAN; for that on R command line type
> +<p></p>
> +
> +install.packages("GenABEL",dependencies=c("Depends","Suggests"))
> +<br>
> +install.packages("roxygen")
> +<br>
> +install.packages("RUnit")
> +<p></p>
> +
> +3) Change to a place, where you want the source code
> +to go. Get to the latest code by
> +<p></p>
> +
> +svn export svn://svn.r-forge.r-project.org/svnroot/genabel/pkg
> +<p></p>
> +
> +This should create directory called 'pkg' with all packages
> +in it.
> +<p></p>
> +
> +4) Compile and install latest code by
> +<p></p>
> +
> +cd pkg
> +<br>
> +R CMD INSTALL DatABEL
> +<br>
> +R CMD INSTALL GenABEL
> +<br>
> +... etc.
> +<p></p>
> +
> +Note some packages (e.g. ProbABEL) are not R packages; to
> +compile these use specific Makefile's, e.g.
> +<p></p>
> +cd ProbABEL
> +<br>
> +make
> +<p></p>
> +
> +FINITO! Enjoy :)
> +<p></p>