[BioC] topGO dependency: Rgrapphviz

Thompson, Kevin kthom110 at uncc.edu
Wed May 30 19:17:19 CEST 2012


   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; (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


  Ask further questions on the Bioconductor mailing list


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)

[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


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