[BioC] OS X, Rgraphviz, bioconductor

[Andrew Beckerman]

Hi all  - in regards to the recent posts on both the r-mac and the  
bioconductor mail lists, I'll share a successful effort at getting the  
graph set of packages (graph, Rgraphviz, RBGL) in Bioconductor running  
on OS X.  I'd been trying for weeks with the source of graphviz, R 1.9  
and BioC 1.4, but all seems well now with R2.0, graphviz >=1.12 and  
Bioconductor 1.5.

I am running R2.0 with OSX 10.3.5 with dev tools installed and the  
latest g77 from HPC http://hpc.sourceforge.net/ (very important, i  
think)

My process was as follows

1) download graphviz 1.16 from ATT  
http://www.graphviz.org/pub/graphviz/ARCHIVE/graphviz-1.16.tar.gz
2) move it to your home if necessary, and gunzip it, then tar -xvf it,  
both from a terminal/shell window
3) cd to that folder: graphviz-1.16
4) proceed with the "standard" 3 step build process in this terminal  
session, ignoring errors
./configure
make
sudo make install
5) quit this terminal and open X11
6) now, type export LD_LIBRARY_PATH=/usr/lib/graphviz
(this makes a temporary "link" in this shell to the location of the  
graphviz libraries, so that Rgraphviz building knows what to look for,  
i think)
7) now, start R (in X11)
8) type source("http://www.bioconductor.org/getBioC.R")
9) type getBioC("graph")
10) wait for everthing to build.... it builds biocondctor basics and  
the three graphing packages; this puts the bioconductor libraries in  
the globally accessible library set, rather than in your home library
11) voila. 8-10 are as the bioconductor website suggests.  This worked  
for me, for the subset of bioconductor for graphing.  Quitting X11 and  
restarting the aqua interface or X11now both run graph and Rgraphviz

Hope this helps.... my guess is that installing the biconductor  
packages through X11, using getBioC() will make the effort smoother,  
but still allow their use in the aqua interface.

andrew

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Dr. Andrew Beckerman
Department of Animal and Plant Sciences, University of Sheffield,
Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
ph +44 (0)114 222 0026; fx +44 (0)114 222 0002
http://www.shef.ac.uk/beckslab
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