[BioC] Rgraphviz load problem : 2nd question for MAC OS users

[Jane Fridlyand]

Dear Mac users

can anyone who successfully installed appropriate version of graphviz
(v>1.12) and was able to install/load Rgraphviz on MAC OSX  share the
steps they took with me? I was previously having issues because graphviz
version was older but not I am not quite sure. do i need to compile
graphviz from source or downloading compiled dmg from pixelglow and
placing it into applications is sufficient (does not seem to be but i am
not sure how to obtain the other components). I am new to mac so things
are often unintuitive to me.

thanks and sorry

Jane


********************************************************************************
Jane Fridlyand, Assistant Professor
Department of Epidemiology and Biostatistics
Center for Bioinformatics and Molecular Biostatistics
UCSF Comprehensive Cancer Center,
Box 0128 San Francisco, CA 94143-0128
Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179
********************************************************************************

On Thu, 27 Oct 2005, Jane Fridlyand wrote:

>
> I am trying to install Rgraphviz under Mac OS X Tiger (10.4.2). I am
> using the latest R (2.2) and Rgraphviz 1.8 . I downloaded and
> successfully installed what i think is the most current graphviz dmg for
> mac (1.10.dmg). It installed in /usr/local/lib/graphviz. I added thje
> fowllowing to .bashrc:
>
> export LD_LIBRARY_PATH=/usr/local/lib/graphviz
>
> Now, i am getting the follwoing error when installing and loading from
> within R: the package seems to install but not load
>
> > getBioC("Rgraphviz")
>
> Running getBioC version 0.8  with R version  2.2.0
>
> Running biocinstall version 1.1  with R version  2.2.0
> Warning: unable to access index for repository
> http://www.bioconductor.org/packa
> ges/data/experiment/1.7/bin/macosx/powerpc/contrib/2.2
> trying URL
> 'http://www.bioconductor.org/packages/bioc/1.7/bin/macosx/powerpc/con
> trib/2.2/Rgraphviz_1.8.0.tgz'
> Content type 'application/x-gzip' length 1263932 bytes
> opened URL
> ==================================================
> downloaded 1234Kb
>
>
> The downloaded packages are in
>         /tmp/RtmpwRAbnb/downloaded_packages
> >
> > library(Rgraphviz)
> Loading required package: graph
> Loading required package: cluster
> Loading required package: Ruuid
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library
> '/Library/Frameworks/R.framework/Resources
> /library/Rgraphviz/libs/Rgraphviz.so':
>
> dlopen(/Library/Frameworks/R.framework/Resources/library/Rgraphviz/libs/
> Rgraph
> viz.so, 6): Symbol not found: _agedgeattr
>   Referenced from:
> /Library/Frameworks/R.framework/Resources/library/Rgraphviz/l
> ibs/Rgraphviz.so
>   Expected in: flat namespace
> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
> Error: package/namespace load failed for 'Rgraphviz'
> >
>
> I also tried to install from the local file using R CMD INSTALL but get
> the follwoing error which i am not sure how to remedy:
>
> sparky$ sudo R CMD INSTALL Rgraphviz
> Password:
> * Installing *source* package 'Rgraphviz' ...
> checking for graphviz... checking for dotneato-config...
> /usr/local/bin/dotneato-config
> /usr/local/bin/dotneato-config
> failed
> configure: error: please specify a valid path to 'dotneato-config'
> version >= 1.12 using --with-graphviz=DIR
> ERROR: configuration failed for package 'Rgraphviz'
> ** Removing
> '/usr/local/lib/R.framework/Versions/2.2/Resources/library/Rgraphviz'
> ** Restoring previous
> '/usr/local/lib/R.framework/Versions/2.2/Resources/library/Rgraphviz'
>
>
> I appreciate the advice. I noticed a lot of people were having issue
> with installation and I looked thru the mailing list but most of the
> solutions amounted to installing graphviz and exporting path  both of
> which I have done
>
> Thank you again
>
> Jane
>