Entering edit mode
Jing Huang
▴
380
@jing-huang-4737
Last seen 10.3 years ago
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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