[R-SIG-Mac] installing Rgraphviz

Patrick Aboyoun paboyoun at fhcrc.org
Mon May 4 22:49:36 CEST 2009


Change Mac OS X 10.5 (Tiger)


Mac OS X 10.5 (Leopard)


Patrick Aboyoun wrote:
> Jarrett,
> This is a Bioconductor related question and really should be addressed 
> on the Bioconductor mailing list. The sort answer is if you are 
> running on a Mac OS X 10.4 (Tiger) box, you will need to build both 
> graphviz and Rgraphviz from source in order to use the package. If you 
> are running on a
> Mac OS X 10.5 (Tiger) box, continue reading.
> The issue is that graphviz.org distributes their latest version of 
> Graphviz for Mac OS X 10.5 (Leopard) only and we use that when we 
> build our mac.binary.leopard version of Rgraphviz. I am guessing that 
> you are using the cross Mac OS X pre-compiled version of R, which uses 
> the mac.binary build of the package from our Mac OS X 10.4 (Tiger) 
> build machine that has an old (unmaintained) version of graphviz on 
> it. I recommend that all Bioconductor users running on leopard to use 
> a leopard-only build of R available at http://r.research.att.com/, 
> since that is what we use on our build machine. These leopard only R 
> binaries download, via biocLite, mac.binary.leopard versions of the 
> packages that are produced by our Leopard machine. These leopard only 
> binaries have the added benefit of 64-bit Intel support so end-users 
> don't have to build their own packages once they leave the 32-bit world.
> Patrick
> Jarrett Byrnes wrote:
>> I know variants of this have been answered a few times, but thus far 
>> I've had no luck:
>> I'm attempting to install Rgraphviz from bioconductor.  I downloaded 
>> the stablemac version from http://www.graphviz.org/Download_macos.php 
>> and used biocite to install Rgraphviz after installing bioconductor.  
>> However, when I attempt to load Rgraphviz, I get the following error.
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared library 
>> '/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so':
>> dlopen(/Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so, 
>> 6): Library not loaded: /usr/local/lib/libgvc.3.dylib
>>   Referenced from: 
>> /Users/jbyr/Library/R/2.9/library/Rgraphviz/libs/ppc/Rgraphviz.so
>>   Reason: image not found
>> Error: package/namespace load failed for 'Rgraphviz'
>> I went to look for libgvc.3.dylib, and there in /usr/lib found 
>> libgvc.5.dylib .
>> Is the answer here to install an older version of graphviz? If so 
>> which one?  Or can Rgraphviz be made to work with my existing 
>> installation of graphviz?
>> -Jarrett
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