Rgraphviz produces segmentation fault when attempting to plot Bayesian Belief Networks
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@royce-francis-4966
Last seen 7.1 years ago
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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@sean-davis-490
Last seen 7 weeks ago
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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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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