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

[L.C. Karssen]

Hi Yurii,

I took a quick look at the tutorial at the URL you gave below. Looks
good!
Looking at the HTML code I wondered: I see a lot of <p></p> lines. IIRC
the idea of the <p> code is to create a paragraph. I guess <p></p> gives
you a separation between paragraphs as well, but I think it was meant to
be used like this:
<p>
A lot of text in a paragraph
</p>
Keep in mind though that my HTML skills are pre-2000 :-), so check
somewhere else as well. 

Furthermore, I think that drupal knows the tage <code></code> so you
might want to consider enclosing lines like R_HOME= etc. in these tags
for nice source code formatting. 



Lennart.

On Mon, 2011-02-28 at 18:29 +0100, Yurii Aulchenko wrote:
> 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>
> _______________________________________________
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> genabel-devel at lists.r-forge.r-project.org
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-- 
-----------------------------------------------
L.C. Karssen
Erasmus MC
Department of Epidemiology
Room 2224

Postbus 2040
3000 CA Rotterdam
The Netherlands

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