Hello everyone,
I am having problems making Rgraphviz working with graphviz.
I installed R from Darwin ports "http://darwinports.opendarwin.org/getdp/";
by
>sudo port install r
I set my environment variables in my .bash_profile e.g export
PATH=/opt/local/bin:$PATH
I also installed other packages which are required for Rgraphviz like
"graphviz" and "pkgconfig" by
>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 bioconductor
packages by sourcing it from bioconductor website
>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 = subGList,
recipEdges = recipEdges)
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 configure
2.8 previously with no luck.
in X11
when i load this library("Rgraphviz") in X11 interface it gives following error
message
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 past with
Suse Linux we managed to solve it, and my Windows station is working fine with
Graphviz 2.8 and Rgraphviz
only my mac system (intel tiger) is a bit of a problem. I manually tried to
install graphviz and Rgraphviz using the source files and setting
LD_LIBRARY_PATH and PKG_LIBRARY_PATH but in vain the only way to install them
together without errors is through a darwinport.
Regards,
Anand
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