[BioC] Rgraphviz load problem

Fridlyand, Jane jfridlyand at cc.ucsf.edu
Thu Oct 27 20:43:00 CEST 2005


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/Rgra
ph
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



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