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Gavai, Anand
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@gavai-anand-2004
Last seen 10.0 years ago
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/l
ibs/i386/Rgraphviz.so, 6): Symbol not found: _agfstnode
Referenced from: /Library/Frameworks/R.framework/Resources/library/R
graphviz/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