[BioC] having a problem loading Rgraphviz with Intel Mac

[Seth Falcon]

[cc'd the list for the archives, etc]

"Jen Buhay" <jenbuhay at gmail.com> writes:
> Hi Seth -
> I have R 1.16 (3198) which I downloaded from r-project.org.  My Mac is
> an intel.  We took off the previous downloads and installed the binary
> version you listed below.... same problem.  For some reason, R can't
> find Rgraphviz.   The error message is below.  Got any more
> suggestions?

Did you install the graphviz binary before installing Rgraphviz with
biocLite?  If so, then I'm somewhat at a lost as to how to help.  I
would recommend posting to the r-sig-mac email list.  Simon, the
volunteer who builds the BioC binary packages for the Mac might have
some suggestions...

+ seth


> Thanks, Jen
>
>> source("http://bioconductor.org/biocLite.R");
>> biocLite("Rgraphviz")
> Running getBioC version 0.1.8 with R version 2.3.1
> Running biocinstall version 1.8.5 with R version 2.3.1
> Your version of R requires version 1.8 of Bioconductor.
> trying URL 'http://bioconductor.org/packages/1.8/bioc/bin/macosx/i386/contrib/2.3/Rgraphviz_1.10.0.tgz'
> Content type 'application/x-gzip' length 568248 bytes
> opened URL
> ==================================================
> downloaded 554Kb
>
>
> The downloaded packages are in
> 	/tmp/RtmpzS94Lh/downloaded_packages
> Warning messages:
> 1: number of rows of result
> 	is not a multiple of vector length (arg 2) in: cbind(1, res0,
> Repository = repos)
> 2: cannot create HTML package index in: make.packages.html()
> Loading required package: graph
> Loading required package: Ruuid
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> 	unable to load shared library
> '/Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
>  dlopen(/Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so,
> 6): Symbol not found: _agfstnode
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/2.3/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so
>  Expected in: flat namespace
> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
> Error: package/namespace load failed for 'Rgraphviz'
>
>
> On 9/26/06, Seth Falcon <sfalcon at fhcrc.org> wrote:
>> Hi Jen,
>>
>> "Jen Buhay" <jenbuhay at gmail.com> writes:
>> > Hi All -
>> > I've downloaded Graphviz 2.8 (and graphviz 2.9 intel)
>>
>> So which version do you have?  How and where did you install it?
>>
>> > intel Macs (I have OSX 10.4.7)
>>
>> And an intel mac, yes?
>>
>> > /usr/local/lib/graphviz).  Here's the error message I get when I try
>> > to load Rgraphviz:
>>
>> How did you install Rgraphviz?  For that matter, how did you install
>> R?  It looks like you are using an R  2.3.x from the error messages,
>> but did you build from source, install the binary from CRAN, or ???
>>
>> With a few more details, we may be able to provide some guidance.
>>
>> Basically, if you are using the CRAN binary version of  R.app, then you
>> should follow these instructions:
>>
>> 1. Install the _graphviz_ binary from http://r.research.att.com/.
>>   [First, remove any other graphviz installs.]
>>
>>  2. Install the _binary_ version of the BioC Rgraphviz package:
>>
>>     source("http://bioconductor.org/biocLite.R")
>>     biocLite("Rgraphviz")
>>
>>  + seth
>>
>
>
>
> -- 
> Jennifer E. Buhay, Ph.D.
> Indiana University
> Department of Biology
> 1001 East Third Street
> Bloomington IN 47405
> jenbuhay at indiana.edu
>

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org