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

[Royce Francis]

My apologies.

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] Rgraphviz_1.32.0 bnlearn_2.7      lattice_0.20-0   graph_1.32.0    

loaded via a namespace (and not attached):
[1] tools_2.14.0

On Nov 17, 2011, at 12:22 PM, Sean Davis wrote:

> 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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