KEGGgraph
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Jing Huang ▴ 380
@jing-huang-4737
Last seen 8.1 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 [[alternative HTML version deleted]]
graph KEGGgraph graph KEGGgraph • 905 views
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@jitao-david-zhang-3188
Last seen 5.7 years ago
Hi dear Jian, This is due to the old dependency of KEGGgraph on the Rgraphviz package. It is solved in the devel version. Please try to re-install the Rgraphviz package, or update to the devel version of KEGGgraph. Best wishes, David Am schrieb Jing Huang <huangji@ohsu.edu>: > 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 > > nodeType > > makeNodeRenderAttrs > + shape="ellipse", fill="#e0e0e0",...) { > + rv > + nA > + for(i in seq(along=rv)) { > + if (length(rv[[i]]) == 1) { > + rv[[i]] > + } else { > + if (length(rv[[i]]) != numNodes(g)) > + stop("Attribute vector must have as many elements as 'g' has nodes.") > + } > + names(rv[[i]]) > + nA[[ names(rv)[[i]] ]] > + } > + nodeRenderInfo(g) > + return(g) > + } > > toyDrawn > *** 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 > [[alternative HTML version deleted]] > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Thank you so much David. I have re-installed the R and all the packages. It did not solved the problem. What else can I do? Many thanks Jing From: "DavidvonPKU@gmail.com<mailto:davidvonpku@gmail.com>" <davidvonpku@gmail.com<mailto:davidvonpku@gmail.com>> Date: Tue, 12 Jul 2011 10:54:44 -0700 To: Jing Huang <huangji@ohsu.edu<mailto:huangji@ohsu.edu>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] KEGGgraph Hi dear Jian, This is due to the old dependency of KEGGgraph on the Rgraphviz package. It is solved in the devel version. Please try to re-install the Rgraphviz package, or update to the devel version of KEGGgraph. Best wishes, David Am schrieb Jing Huang <huangji@ohsu.edu<mailto:huangji@ohsu.edu>>: > 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 > > nodeType > > makeNodeRenderAttrs > + shape="ellipse", fill="#e0e0e0",...) { > > + rv > + nA > + for(i in seq(along=rv)) { > > + if (length(rv[[i]]) == 1) { > > + rv[[i]] > + } else { > > + if (length(rv[[i]]) != numNodes(g)) > > + stop("Attribute vector must have as many elements as 'g' has nodes.") > > + } > > + names(rv[[i]]) > + nA[[ names(rv)[[i]] ]] > + } > > + nodeRenderInfo(g) > + return(g) > > + } > > > toyDrawn > > > *** 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 > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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