[R-SIG-Mac] graphviz

Julin Maloof jnmaloof at ucdavis.edu
Sun Mar 19 21:59:27 CET 2006

Hi Michael,

Looks like you have two installations of graphviz; the one in sw/ is from fink.  I am not sure why it would interfere, but perhaps you should use fink to remove the one in sw.

I assume you saw my post to the group last night...Seth's recommendation to you worked for me once I used gcc_select 3.3 (the original suggestion to me to either export the LD_PATH or specify the graphviz location directly to R did not work).

that is,

#check to see that usr/local/lib/graphviz and usr/local/lib/pkginfo exist (created from the graphviz installation)

#make sure gcc3.3 is set up correctly:
sudo gcc_select 3.3

#export the location.  Note that the expot command doesn't work in csh or tcsh, so you should use bash
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig

#then compile and install Rgaphviz
R CMD INSTALL Rgraphviz_1.8.0.tar.gz 

hope that helps...


Michael Kubovy wrote:
> Hi Byron,
> On Mar 19, 2006, at 3:03 AM, Byron Ellis wrote:
>> Did you type 'sudo make install'? If not, graphviz may not have 
>> actually installed itself (making sure /usr/local/bin/dot exists is a 
>> way to check this)
>> I recently did an Rgraphviz build for myself using graphviz-2.9 
>> (though 2.8 should also work fine) and Rgraphviz 1.9.6 (the SVN 
>> version) and pkg-config (which I get from 
>> http://pkgconfig.freedesktop.org/releases/).
>> I should note that I don't use Fink or Darwinports and that Glen Low 
>> (author of Graphviz.app) seems to have wandered off to other things so 
>> the GUI version of Graphviz is pretty massively out of date these days.
> Thanks for the reply.
> I did type sudo make install.
> % which dot
> /sw/bin/dot
> % ls /usr/local/bin/dot
> /usr/local/bin/dot
> Both are executable and seem to run:
> % dot unix.dot
> and
> % /usr/local/bin/dot unix.dot
> output a file that is different from the input.
> So graphviz is installed. My guess is that Rgraphviz doesn't know it.
> _____________________________
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Julin Maloof
Assistant Professor
Section of Plant Biology
University of California, Davis
1 Shields Ave
Davis, CA, 95616

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