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 graphviz 2.12 compiled from source. 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 are talking about Rgraphviz' version. When you run it in the X11 xterm (which I assume you are talking about), it seems as if some PATH/library settings are messed up. I don't know anything about Darwinports configuration, so I am afraid I cannot help much. Getting Rgraphviz to work requires some connection between graphviz and Rgraphviz, and it is important for us to know what you installed, and especially how. I assume Darwinports compile from source? Since you have installed several different flavours of Graphviz, are you certain that you have cleaned up after you? Using the Graphviz binary provided by Simon Urbanek should work, but I find it bit puzzling which versions (and how you installed them) you are discussing below. So, try to reinstall Rgraphviz the way you describe below. Note what version of Graphviz R is linking to, both by looking at the compile statements when installing the package (which is why you need to reinstall) as well as trying 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 new version (2.12) compiled easily for me. 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/ 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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