[R-sig-Debian] Rgraphviz and R 2.9 in ubuntu jaunty

[Michael Rutter]

Laura,

My first suggestion would be to go here:

http://cran.r-project.org/bin/linux/ubuntu/

This will give you instructions on how to make sure you are using the
most recent version of R in Ubuntu.  Once you have upgraded to 9.2
(which I think is a good thing if you are using biocondctor), then try 
to get Rgaphviz.  Updating to 2.9 may also fix the biocinstall issue.

I have not used Rgraphviz before, so I am going to make a couple of 
general suggestions.  First, make sure you run install command as "sudo 
R CMD INSTALL Rgraphviz --configure-args="--with-graphviz=/usr/share" ", 
as you will need root access.  I also do not think you need the 
--with-graphviz option, because under Ubuntu, that is where prts of it 
are installed.

If you installed graphviz from source, I would recommend the Ubuntu 
packages.  You may also need graphviz-dev and libgraphviz-dev packages 
installed in order to compile things under R.

Let us know if you have further questions,
Michael

Laura Salazar wrote:
> Dear people,
> 
> I'm new here, so this is my first try. I have ubuntu 9.04 installed
> with R 2.8 (which surprises me because I realized that the last
> version R 2.9 is available but in the Synaptic Package Manager 2.8
> appears as the last one). I have also graphviz 2.20.2. I have been
> trying to install Rgraphviz either from R running
> "biocLite("Rgraphviz")" and from the shell running "R CMD INSTALL
> Rgraphviz --configure-args="--with-graphviz=/usr/share" "
> 
> This is the error in both cases:
> 
> configure: Using Graphviz dir '/usr/share' configure: error:
> /usr/share/bin/dot not found.  Check Graphviz installation. ERROR:
> configuration failed for package 'Rgraphviz' ** Removing
> '/home/laura/R/i486-pc-linux-gnu-library/2.8/Rgraphviz' I specify the
> directory /usr/share because there is where graphviz was installed
> (or at least is located there).
> 
> I also get this warning in R: Running biocinstall version 2.3.13 with
> R version 2.8.1 Your version of R requires version 2.3 of
> Bioconductor.
> 
> But even if I download manually and try to install R 2.9, the version
> taht it runs is 2.8.
> 
> Well, two problems in one: Rgraphviz package and R update.
> 
> I appreciate any help. I'm sorry if I'm skipping something obvious,
> but I still don't get it.
> 
> Thanks!
> 
> Laura
> 
> 
> 
> 
> 
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> 
> 
> 
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-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter