[BioC] having a problem loading Rgraphviz with Intel Mac
sfalcon at fhcrc.org
Wed Sep 27 22:03:48 CEST 2006
[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
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
> Thanks, Jen
> 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
> 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
> 6): Symbol not found: _agfstnode
> Referenced from:
> 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:
>> + 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
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