[R] Rgraphviz installation

[Martin Morgan]

Hi Paul

Rgraphviz is a bioconductor package, so ask on the Bioconductor mailing 
list.

  http://bioconductor.org/docs/mailList.html

Install Bioconductor packages following the instructions here

  http://bioconductor.org/docs/install/

Rgraphviz on Windows installed from binary (as you're doing below) 
requires that your computer has the same version of graphviz as the 
computer used to build Rgraphviz. The details are in the package README 
file (inconveniently linked from here

  http://bioconductor.org/packages/2.5/bioc/html/Rgraphviz.html

at

  
http://bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz

Cutting and pasting from this file, the instructions are:

o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution from

      
http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi

   in a directory that we'll call $DIR.  We use the following as an example:

         C:\Graphviz2.20
  
   If you install it in other dir, just use your dir correspondingly.

o. Add Graphviz' bin diretory to the user PATH variable, e.g.,

     c:\Graphviz2.20\bin

o. Check the configuration by starting a new DOS window and displaying
   the PATH environment variable, e.g.,

      c:\> echo %PATH%

o.  Use biocLite('Rgraphviz') to install Rgraphviz



Paul Evans wrote:
> Hi,
>
> I wanted to install Rgraphviz. From the R GUI, I downloaded the package but when I tried to load it I got the following error message:
> "This application has failed to start because libcdt-4.dll was not
> found. Re-installing the application may fix this problem."
>
> The R commands and errors are:
>   
>> utils:::menuInstallPkgs()
>>     
> trying URL 'http://www.bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/Rgraphviz_1.24.0.zip'
> Content type 'application/zip' length 969595 bytes (946 Kb)
> opened URL
> downloaded 946 Kb
>
> package 'Rgraphviz' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>         C:\Users\pe\AppData\Local\Temp\RtmpoebdlH\downloaded_packages
>   
>> library(Rgraphviz)
>>     
> Error in inDL(x, as.logical(local), as.logical(now), ...) : 
>   unable to load shared library 'C:/Users/pe/Documents/R/win-library/2.10/Rgraphviz/libs/Rgraphviz.dll':
>   LoadLibrary failure:  The specified module could not be found.
>
>
> Error: package/namespace load failed for 'Rgraphviz'
> My sessioninfo is:
>   
>> sessionInfo()
>>     
> R version 2.10.0 (2009-10-26) 
> i386-pc-mingw32 
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
>  [1] GOstats_2.12.0       Category_2.12.0      multtest_2.2.0       R.utils_1.2.4        R.oo_1.6.5           R.methodsS3_1.0.3    genefilter_1.28.0   
>  [8] hgu133a.db_2.3.5     org.Hs.eg.db_2.3.6   GEOquery_2.8.0       RCurl_1.2-1          bitops_1.0-4.1       biomaRt_2.2.0        affy_1.24.1         
> [15] int.intact.db_1.1.1  int.geneint.db_1.1.1 PAnnBuilder_1.8.0    RpsiXML_1.6.0        hypergraph_1.18.0    XML_2.6-0            RBGL_1.20.0         
> [22] annotate_1.24.0      GO.db_2.3.5          RSQLite_0.7-3        DBI_0.2-4            AnnotationDbi_1.8.0  Biobase_2.6.0        graph_1.24.1        
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        GSEABase_1.8.0       MASS_7.3-3           org.Sc.sgd.db_2.3.5  preprocessCore_1.8.0 splines_2.10.0       survival_2.35-7     
> [8] tools_2.10.0         xtable_1.5-6        
>   
>
> What do I need to do to install and load this successfully?
>
> thanks!
>
>
>       
> 	[[alternative HTML version deleted]]
>
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>   


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793