[R-SIG-Mac] [BioC] Mac os x graphviz-Rgraphviz problem
Li.Long at isb-sib.ch
Li.Long at isb-sib.ch
Mon Feb 5 10:32:00 CET 2007
Just add one thing to what Kasper already said: I suspect that the issue
is that the .so from graphviz are not visible to the loader. You can fix
up the LD_LIBRARY_PATH in someway: "make install" from graphviz has some
PATH="$PATH:/sbin" ldconfig -n /home/vital-it/lilong/bin/graphviz-2.12/lib
Libraries have been installed in:
that hints how to do it. I didn't see "ldconfig" quoted in the msg...
> 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.
> 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/
>>> 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 "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
>> waited for a while and then install
>> it worked fine when i opened it in a Terminal window, only the
>> loading part but when I run something like this
>>> graphObj = ftM2graphNEL(d)
>> it gives me the following error messages
>> *** caught bus error ***
>> address 0x40, cause 'non-existent physical address'
>> 1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE =
>> 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
>> 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/
>> Rgraphviz/libs/i386/Rgraphviz.so, 6): Symbol not found: _agfstnode
>> Referenced from: /Library/Frameworks/R.framework/Resources/
>> Expected in: dynamic lookup
>> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>> Error: package/namespace load failed for 'Rgraphviz'
>> the sessionInfo() here is
>> R version 2.4.1 (2006-12-18)
>> attached base packages:
>>  "tools" "stats" "graphics" "grDevices" "utils"
>>  "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.
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