[BioC] Mac os x graphviz-Rgraphviz problem

Your example works fine for me on Mac OS X ppc 10.4.8 with R-2.4.1 and

You can check your graphviz version from R by doing
R> graphvizVersion()

You have an error in the Graphviz version reported below, I assume you

Getting Rgraphviz to work requires some connection between graphviz and

So, try to reinstall Rgraphviz the way you describe below. Note what

R> graphvizVersion()
and then see if something is not matching.

Btw. you are most certainly not running Graphviz 2.8 under MS
Windows, unless you have taken major pains to do so.

Personally, Graphviz used to be a pain to install on the Mac, but the

Kasper



On Feb 1, 2007, at 1:45 PM, Gavai, Anand wrote:

Hello everyone,
I am having problems making Rgraphviz working with graphviz.
I installed R from Darwin ports "http://darwinports.opendarwin.org/

by

sudo port install r

I set my environment variables in my .bash_profile e.g export PATH=/

I also installed other packages which are required for Rgraphviz like

sudo port install graphviz

sudo port install pkgconig

both these commands will also install dependencies which are
required. After this

I start up an R session being root and get the latest version of

source("http://www.bioconductor.org/biocLite.R")
biocLite()

waited for a while and then install

biocLite("Rgraphviz",depend=TRUE,type="source")

it worked fine when i opened it in a Terminal window, only the
loading part but when I run something like this

library("Rgraphviz")
a<-c(1,0)
b<-c(1,1)
d<-rbind(a,b)
graphObj = ftM2graphNEL(d)
plot(graphObj)

it gives me the following error messages

*** caught bus error ***
address 0x40, cause 'non-existent physical address'

Traceback:
 1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE =
"Rgraphviz")
 2: layoutGraph(g)
 3: agopen(x, name = name, layout = TRUE, layoutType = y, attrs =
attrs,     nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, subGList =

 4: .local(x, y, ...)
 5: plot(graphObj)
 6: plot(graphObj)

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

I cannot put here the sessionInfo() as i need to abort it, the

the Graphviz version i have is 1.310.  I also tried to install and

in  X11
when i load this library("Rgraphviz") in X11 interface it gives

Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library '/Library/Frameworks/
R.framework/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
  dlopen(/Library/Frameworks/R.framework/Resources/library/
Rgraphviz/libs/i386/Rgraphviz.so, 6): Symbol not found: _agfstnode
  Referenced from: /Library/Frameworks/R.framework/Resources/
library/Rgraphviz/libs/i386/Rgraphviz.so
  Expected in: dynamic lookup
Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
Error: package/namespace load failed for 'Rgraphviz'

the sessionInfo() here is

sessionInfo()

R version 2.4.1 (2006-12-18)
i386-apple-darwin8.8.1

locale:
C

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

other attached packages:
geneplotter    annotate     Biobase       graph
   "1.12.0"    "1.12.1"    "1.12.2"    "1.12.0"

Any help in this regard is appreciated. I had simimar problem in the

only my mac system (intel tiger) is a bit of a problem. I manually

Regards,
Anand