[BioC] Rgraphviz produces segmentation fault when attempting to plot Bayesian Belief Networks

[Sean Davis]

sessionInfo()?

On Thu, Nov 17, 2011 at 12:16 PM, Royce Francis <royceworld at gmail.com> wrote:
> Hello all,
>
> I have been studying the use of Bayesian Belief Networks, and have found Marco Scutari's package, "bnlearn," very helpful.  While I was learning his package, I had been using graphviz to plot the networks that were learned.
>
> Recently, I have not been able to plot any networks using graphviz because each time I call the function, graphviz.plot, I receive a message indicating that a segmentation fault has occurred.  I originally thought this was caused by updating R to 2.14.0, but when I reverted to 2.13.0, the segmentation faults persisted.
>
> Here is a snippet of code using an example in Scutari's JSS paper that will produce the error in my setup (and the corresponding output):
>
>> library("bnlearn")
>> library(Rgraphviz)
>> data(learning.test)
>> bn.hc <- hc(learning.test,score="aic")
>> graphviz.plot(bn.hc)
>
>  *** caught segfault ***
> address 0x10, cause 'memory not mapped'
>
> Traceback:
>  1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE = "Rgraphviz")
>  2: graphLayout(g)
>  3: agopen(x, name = name, layoutType = layoutType, recipEdges = recipEdges,     nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, attrs = attrs,     ...)
>  4: layoutFun(x, ...)
>  5: layoutGraph(graph.obj, attrs = attrs, nodeAttrs = node.attrs,     layoutType = layout)
>  6: graphviz.backend(nodes = nodes, arcs = arcs, highlight = highlight,     layout = layout, shape = shape, main = main, sub = sub)
>  7: graphviz.plot(bn.hc)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> I would greatly appreciate any help resolving this error, or any suggestions for alternative plotting methods.  I find the "plot" function completely inadequate and would much rather use graphviz to report my findings.
>
> Thank you in advance,
> Royce
>
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