[BioC] Re: [R-SIG-Mac] OS X, Rgraphviz, bioconductor

[stefano iacus]

Hi Andrew,
thanks for your report.
I guess that steps from 5 to 11 will work under the aqua gui as well  
(using Sys.putenv for example and running the x11 server)
stefano

On Nov 3, 2004, at 10:09 AM, Andrew Beckerman wrote:

> 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
>
> ----------------------------------------------------------------------- 
> ----------
> 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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