[BioC] Problem with Rgraphviz on OSX with libgvc

[Kasper Daniel Hansen]

Jarrett:

You can do two things:

The easy way:
Install the binary version of Graphviz 2.8 which Seth has linked to.  
Using that version of Graphviz you can install binaries from  
Bioconductor.

The (slightly) harder way:
If you want to use Graphviz 2.12 for other purposes, install it from  
source as you have already done. Now, you need to use the development  
version of Rgraphviz and you need to compile Rgraphviz from source,  
you cannot use the binary version as that is compiled against  
Graphviz 2.8. It does not matter if you install the dependencies from  
source or binary. I would assume you have already install the  
dependencies in your earlier attempt. The easy way is to download the  
tar ball of Rgraphviz from Bioconductor (you need to do this since  
you are running R-2.4.1 and not R-2.5.0 devel), use the link
   http://www.bioconductor.org/packages/2.0/bioc/src/contrib/ 
Rgraphviz_1.13.8.tar.gz
The in the command prompt you do
# R CMD INSTALL Rgraphviz
and it should work

Kasper


On Jan 9, 2007, at 9:48 PM, Seth Falcon wrote:

> Jarrett Byrnes <jebyrnes at ucdavis.edu> writes:
>
>> Nope, this was installed from source.
>         ^^^^
>
> Sometimes email is a frustrating medium. :-\
>
>> I'm running R 2.4.1.  The error message I gave was after installing
>> graphviz 2.12 from source.
>
> Ok.  If you want to use that version of graphviz, you need to install
> _Rgraphviz_ from source.  And that will require having the right tools
> and setup for building source packages with R.
>
>
>>  I have since tried installing graphviz
>> 1.16 from source, as was listed in one of the past messages on this
>> listserv, but it did not install any libgvc that I can tell.  Is
>> there a particular version of graphviz that I should install to make
>> this work?
>
> Yes, install the binary version of graphviz 2.8 that I linked to in my
> previous message.  That is the _only_ graphviz that is expected to
> work with the Rgraphviz binary.
>
>> Also, I installed Rgraphviz from the bioconductor binary using the R
>> package manager, including all dependencies.
>
> Better to use biocLite for installing Bioconductor packages in the
> future.
>
> + seth
>
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