[BioC] install Rgraphviz

[Martin Morgan]

On 06/08/2010 02:34 PM, Cristobal Fresno Rodríguez wrote:
> Hi Yuan,
> What version of graphviz do you have? you can get the latest at
> http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.26.3.msi Have

This is not the recommended solution. Please instead visit

http://bioconductor.org/packages/2.6/bioc/html/Rgraphviz.html

and follow the directions (very carefully) in the README file of
Rgraphviz. These say

Using the Windows binary
------------------------

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




To this I would add that you should start R and try

  strsplit(Sys.getenv("PATH"), ";")

inspect the result of this and, when you find the component that you
think is the 'graphviz bin directory mentioned above, confirm that it
points to a valid location, e.g.,

> strsplit(Sys.getenv("PATH"), ";")$PATH[13]
[1] "C:\\Program Files\\Graphviz2.20\\bin"
> list.files(strsplit(Sys.getenv("PATH"), ";")$PATH[13])
 [1] "acyclic.exe"                    "bcomps.exe"
 [3] "ccomps.exe"                     "circo.exe"
 [5] "comdlg32.ocx"                   "config"
...


Martin




> you tried the examples (out of R)?
> Have you check if the dll exists? Do you have read/write permissions
> on 'C:/PROGRA~1/R/R-211~1.1/
> library/Rgraphviz/libs/Rgraphviz.dll'?
> 
> Kachelo
> 
> El 7 de junio de 2010 18:20, Yuan Jian <jayuan2008 at yahoo.com> escribió:
> 
>> Hi Kachelo
>>
>> yes, windows 32.
>>
>> thanks
>>
>>
>>
>> --- On *Mon, 7/6/10, Cristobal Fresno Rodríguez <cristobalfresno at gmail.com
>>> * wrote:
>>
>>
>> From: Cristobal Fresno Rodríguez <cristobalfresno at gmail.com>
>> Subject: Re: [BioC] install Rgraphviz
>> To: "Yuan Jian" <jayuan2008 at yahoo.com>
>> Cc: bioconductor at stat.math.ethz.ch
>> Received: Monday, 7 June, 2010, 5:31 PM
>>
>>
>> Hi Yuan,
>> Do you have installed graphviz for windows?
>> Kachelo
>>
>>
>> 2010/6/5 Yuan Jian <jayuan2008 at yahoo.com<http://mc/compose?to=jayuan2008@yahoo.com>
>>>
>>
>>> Hi,
>>>
>>> could you tell me what the problem in installation of "Rgraphviz" package?
>>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite("Rgraphviz")
>>>> sessionInfo()
>>> R version 2.11.1 (2010-05-31)
>>> i386-pc-mingw32
>>> locale:
>>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>>> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_Australia.1252
>>> attached base packages:
>>> [1] grid      stats     graphics  grDevices utils     datasets  methods
>>> base
>>> other attached packages:
>>> [1] limma_3.4.2  graph_1.26.0
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.11.1
>>>
>>>> library(Rgraphviz)
>>> Loading required package: graph
>>> Loading required package: grid
>>> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>>>   call: value[[3L]](cond)
>>>   error: unable to load shared library
>>> 'C:/PROGRA~1/R/R-211~1.1/library/Rgraphviz/libs/Rgraphviz.dll':
>>>   LoadLibrary failure:  The specified module could not be found.
>>>
>>>> sessionInfo()
>>> R version 2.11.1 (2010-05-31)
>>> i386-pc-mingw32
>>> locale:
>>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>>> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_Australia.1252
>>> attached base packages:
>>> [1] grid      stats     graphics  grDevices utils     datasets  methods
>>> base
>>> other attached packages:
>>> [1] limma_3.4.2  graph_1.26.0
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.11.1
>>>>
>>>
>>>
>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>>
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>>
>>
>>
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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