Hi,

I am trying to run KEGGgraph and run into this problem.  Can somebody help me with this? It happens only if I run the program on IMAC (10.6.8 or 10.6.6)


> library(Rgraphviz)
> nodeInfo <- getKEGGnodeData(toyGraph)
> nodeType <- sapply(nodeInfo, getType)
> makeNodeRenderAttrs <- function(g, label=nodes(g),
+ shape="ellipse", fill="#e0e0e0",...) {
+ rv <- list(label=label, shape=shape, fill=fill, ...)
+ nA <- nodeRenderInfo(g)
+ for(i in seq(along=rv)) {
+ if (length(rv[[i]]) == 1) {
+ rv[[i]] <- rep(rv[[i]], numNodes(g))
+ } else {
+ if (length(rv[[i]]) != numNodes(g))
+ stop("Attribute vector must have as many elements as 'g' has nodes.")
+ }
+ names(rv[[i]]) <- nodes(g)
+ nA[[ names(rv)[[i]] ]] <- rv[[i]]
+ }
+ nodeRenderInfo(g) <- nA
+ return(g)
+ }
> toyDrawn <- plotKEGGgraph(toyGraph)

*** 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)
 6: plotKEGGgraph(toyGraph)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Many Thanks

Jing Huang

Oregon Health & Sciences University
Radiation Oncology


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