Hi all,

There seems to be a whole lot of discussion on this topic...and after
reading the previous post, I can see that this is something that is pretty
non-trivial.

So here is my not being able to install Rgraphviz problem:

I have installed graphviz 2.8 from the dmg available at
http://r.research.att.com/ as well as glib/gtk 1.2.10 yesterday, and have
just build R-2.5 from source...so I am pretty sure that I have all the up to
date versions of things. biocLite("Rgraphviz", type="source") is able to
download and install the package, but I cannot seem to use the package:

> library(Rgraphviz)
Loading required package: graph
Loading required package: geneplotter
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library '/Users/tonychiang/arch/i386/R
-devel/library/Rgraphviz/libs/Rgraphviz.so':


dlopen(/Users/tonychiang/arch/i386/R-devel/library/Rgraphviz/libs/Rgraphviz.so,
6): Library not loaded: /usr/local/lib/graphviz/libgcc_s.1.0.dylib
  Referenced from: /usr/local/lib/graphviz/libgvc.2.dylib
  Reason: image not found
Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
Error: package/namespace load failed for 'Rgraphviz'
*
*
It is looking for the file (dir) libgcc_s.1.0.dylib, and but it is not
there. I went to that particular directory and verified that it is actually
not there (i.e. it is not that R is not able to locate something that is
really there as was posted in a previous post).

So my question is has there been changes to either Rgraphviz or graphviz
recently? I have read in alot of posts that many people have been able to
reconcile Rgraphviz with graphviz 2-8.

Previously when I had this problem, I went into Seth's office and he just
gave me a graphviz he knew to work (from his home directory), but seeing as
I am not in Settle anymore, this just does not seem to be the best solution
these days!

> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-07 r40669)
i386-apple-darwin8.8.2

locale:
C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
geneplotter     lattice    annotate     Biobase       graph
   "1.13.7"   "0.14-16"    "1.13.6"   " 1.13.36"    "1.13.5"

Many Thanks,
--Tony

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