[BioC] topGO dependency: Rgrapphviz

[Thompson, Kevin]

Hi,

   I do have Rgraphviz installed and working now with graphviz 2.28 (sudo port install graphviz).  
            dot -V   ->  dot - graphviz version 2.28.0 (20120530.1810)

   I was mainly trying to let the developers know that the dependency (Rgraphviz) is lot listed, nor does it initially load with the topGO library:

> library(topGO)
Loading required package: graph
Loading required package: Biobase
Loading required package: BiocGenerics
             ...
Attaching package: 'BiocGenerics'
             ...
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI


    Previously it appears that the graph library was sufficient to produce the topGO graphics (showSigOfNodes), as Rgraphviz was not required.
    
Thanks,
Kevin
 
________________________________________
From: Dan Tenenbaum [dtenenba at fhcrc.org]
Sent: Thursday, May 31, 2012 12:15 PM
To: Thompson, Kevin
Cc: bioconductor at r-project.org
Subject: Re: [BioC] topGO dependency: Rgrapphviz

Hi Kevin,

On Wed, May 30, 2012 at 10:17 AM, Thompson, Kevin <kthom110 at uncc.edu> wrote:
> Hi,
>
>   FYI, I have recently updated the topGO package and it now appears the Rgraphviz is a dependency, although not listed as so.    I do have graphviz installed (2.28) installed on OS X am working on the configuration issue.  If anyone has any suggestions I would greatly appreciate them.
>
>> library(topGO)
>> data(GOdata)
>> showSigOfNodes(GOdata)
>
> Loading required package: Rgraphviz
> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>  call: value[[3L]](cond)
>  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgraphviz/libs/x86_64/Rgraphviz.so':
>  dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgraphviz/libs/x86_64/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.5.dylib
>  Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rgraphviz/libs/x86_64/Rgraphviz.so
>  Reason: image not found
>
>  Check that (1) graphviz is installed on your system; (2) the
>  installed version of graphviz matches '2.26.3'; this is the version
>  used to build this Rgraphviz package;

This is likely the problem right here. Rgraphviz can be particular
about the version of graphviz that you use.
It works on my system with 2.26.3, which you can get here:

http://www.graphviz.org/pub/graphviz/stable/macos/snowleopard/graphviz-2.26.3.pkg

(Don't worry about the 'snowleopard' in the directory name; this
version will work on Leopard or Lion as well).




> (3) graphviz is accessible to
>  R, e.g., the path to the graphviz 'bin' directory is in the system
>  'PATH' variable.  See additional instructions in the 'README' file of
>  the Rgraphviz 'source' distribution, available at
>


You should doublecheck that graphviz is indeed in your path; maybe all
that's necessary is to add it.
Try this command in a terminal window:

which neato

If it returns something, then graphviz is in your path, otherwise it's not.

Dan

>  http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
>
>  Ask further questions on the Bioconductor mailing list
>
>  http://bioconductor.org/docs/mailList.html
>
>
> Error in showSigOfNodes(GOdata) : package Rgraphviz is required
>
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] topGO_2.8.0          SparseM_0.96         GO.db_2.7.1
> [4] RSQLite_0.11.1       DBI_0.2-5            AnnotationDbi_1.18.1
> [7] Biobase_2.16.0       BiocGenerics_0.2.0   graph_1.34.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.14.3 lattice_0.20-6 stats4_2.15.0  tools_2.15.0
>
>
> Thanks,
> Kevin
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