[BioC] Rgraphviz windows version incompatible with current Graphviz

[Martin Morgan]

On 05/05/2011 12:40 PM, Gregory D.Rodd wrote:
> Kasper Daniel Hansen<kasperdanielhansen at ...>  writes:
>
>>
>> On Mon, Mar 28, 2011 at 2:11 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at ...>  wrote:
>
>>> Now, I have been playing with the idea to experiment with bundling the
>>> source code of Graphviz with Rgraphviz.  If one could get it to work
>>> (which is a big if, since GRaphviz is really meant to be build by
>>> Visual Studio), it would simplify the installation process greatly
>>> (and it would also solve the 64bit R on WIndows problem that may be
>>> getting hard to ignore).  However, it is pretty non-trivial and would
>>> probably require as much as week or more of fulltime work for me
>>> (partly because of needing to use Windows) , something that I find
>>> hard to justify (especially since I am not really using Rgraphviz and
>>> certainly not Windows, myself).
>>
>> Hmm, I did look again at graphviz.org and they now provide mingw
>> building instructions, indicating that they support mingw building
>> (unlike in the past).  This suddenly makes this idea much more doable.
>>
>> Kasper
>>
>>> Of course, volunteers are always welcome.
>
> I will be glad to look into how I can help, but, is there anyone who has been
> able to get the combination of Rraphviz and the other pieces to work under
> windows?  And, what version of Visual Studio would be appropriate?  I am really
> needing back compatibility for 32 bit R 2.11, so if there is an earlier

Hi Greg --

Have you followed the instructions in the README file in Rgraphviz 
1.26.0 (this is the version for Bioconductor 2.6 / R-2.11), which say in 
part

sing 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

?? What goes wrong?

Martin

> combination that would work, great.  Also, in a 2008 post Jenny Drnevich posted
> help which suggested installing the Microsoft Visual C++ 2005 SP1
> Redistributable.  I suppose that is intended to help Graphviz function. Clues
> would be appreciated.
>
> Greg
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


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

Location: M1-B861
Telephone: 206 667-2793