Rgraphviz in windows 7 - problem with GUI?
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@alessandro-magrini-4407
Last seen 10.3 years ago
Hi, I've the same problem in running Rgraphviz on Windows 7. I've follow the procedure here explained but without positive results. Please, do you have other suggestions to solve this problem?
Rgraphviz Rgraphviz • 1.5k views
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@martin-morgan-1513
Last seen 5 months ago
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On 12/18/2010 06:01 AM, Alessandro Magrini wrote: > Hi, > > I've the same problem in running Rgraphviz on Windows 7. I've follow the > procedure here explained but without positive results. > > Please, do you have other suggestions to solve this problem? Hi Alessandro -- Please provide more information, including the output of sessionInfo() and Sys.getenv("PATH") list.files("<...>") where "<...>" is the part of the return value of Sys.getenv("PATH") that points to your installation of graphviz. Please state exactly how Rgraphviz does not work. While the solution might be relatively easy, it is also possible that you will need to install Rgraphviz from 'source' as described in the README file contained in this link http://bioconductor.org/packages/2.7/bioc/src/contrib/Rgraphviz_1.28.0 .tar.gz Martin > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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@alessandro-magrini-4407
Last seen 10.3 years ago
I've followed all instructions in READ ME file of the package, like installed corrected versions of graphviz and Rgraphviz and setted correctly PATH variable...but the problem remains: Rgraphviz loads successfully BUT plot() method on a graph crushes...
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Are you able to run graphviz without a crash? i.e. go to start menu > programs > graphviz > dotty.exe It sounds like you have an incompatible version of graphviz installed. I know 64-bit Windows requires a newish version to work correctly. Cheers, Fraser -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Alessandro Magrini Sent: Thursday, December 23, 2010 5:45 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Rgraphviz in windows 7 - problem with GUI? I've followed all instructions in READ ME file of the package, like installed corrected versions of graphviz and Rgraphviz and setted correctly PATH variable...but the problem remains: Rgraphviz loads successfully BUT plot() method on a graph crushes... _______________________________________________ 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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@alessandro-magrini-4407
Last seen 10.3 years ago
mmh no...I have 32-bit Windows 7. graphviz works correctly, I have installed the version suggested (2.20.3.1)...
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Hi, I got the similar problem when I run the KEGGgraph package. Below is the detailed information. please note that I use 64-bit windows 7 I run the following codes: mapkKGML <- system.file("extdata/hsa04010.xml", package="KEGGgraph") ################################################### ### chunk number 4: parsemapk ################################################### mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE) mapkG ################################################### ### chunk number 5: parsemapk2 ################################################### mapkpathway <- parseKGML(mapkKGML) mapkpathway mapkG2 <- KEGGpathway2Graph(mapkpathway, expandGenes=TRUE) mapkG2 ################################################### ### chunk number 6: nodeandedge ################################################### mapkNodes <- nodes(mapkG) nodes(mapkG)[1:3] mapkEdges <- edges(mapkG) edges(mapkG)[1] ################################################### ### chunk number 7: keggnodedata ################################################### mapkGnodedata <- getKEGGnodeData(mapkG) mapkGnodedata[[2]] ################################################### ### chunk number 8: keggnodedataalt eval=FALSE ################################################### ## getKEGGnodeData(mapkG, 'hsa:5924') ################################################### ### chunk number 9: keggedgedata ################################################### mapkGedgedata <- getKEGGedgeData(mapkG) mapkGedgedata[[4]] ################################################### ### chunk number 10: keggedgedataalt eval=FALSE ################################################### ## getKEGGedgeData(mapkG,'hsa:627~hsa:4915') ################################################### ### chunk number 11: inout ################################################### mapkGoutdegrees <- sapply(edges(mapkG), length) mapkGindegrees <- sapply(inEdges(mapkG), length) topouts <- sort(mapkGoutdegrees, decreasing=T) topins <- sort(mapkGindegrees, decreasing=T) topouts[1:3] topins[1:3] ################################################### ### chunk number 12: subsetprepare ################################################### library(Rgraphviz) set.seed(123) randomNodes <- sample(nodes(mapkG), 25) mapkGsub <- subGraph(randomNodes, mapkG) mapkGsub ################################################### ### chunk number 13: makeattr ################################################### makeAttr <- function(graph, default, valNodeList) { tmp <- nodes(graph) x <- rep(default, length(tmp)); names(x) <- tmp if(!missing(valNodeList)) { stopifnot(is.list(valNodeList)) allnodes <- unlist(valNodeList) stopifnot(all(allnodes %in% tmp)) for(i in seq(valNodeList)) { x[valNodeList[[i]]] <- names(valNodeList)[i] } } return(x) } ################################################### ### chunk number 14: subsetplot ################################################### outs <- sapply(edges(mapkGsub), length) > 0 ins <- sapply(inEdges(mapkGsub), length) > 0 ios <- outs | ins ## translate the KEGG IDs into Gene Symbol if(require(org.Hs.eg.db)) { ioGeneID <- translateKEGGID2GeneID(names(ios)) nodesNames <- sapply(mget(ioGeneID, org.Hs.egSYMBOL, ifnotfound=NA), "[[",1) } else { nodesNames <- names(ios) } names(nodesNames) <- names(ios) nAttrs <- list(); nAttrs$fillcolor <- makeAttr(mapkGsub, "lightgrey", list(orange=names(ios)[ios])) nAttrs$label <- nodesNames Everything is fine so far, and the sessionInfo() is following: R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.3.6 RSQLite_0.8-4 DBI_0.2-5 AnnotationDbi_1.8.2 Biobase_2.6.1 [6] KEGGgraph_1.2.2 Rgraphviz_1.24.0 graph_1.26.0 XML_2.6-0 loaded via a namespace (and not attached): [1] tools_2.10.1 However when I run plot(mapkGsub, "neato", nodeAttrs=nAttrs, attrs=list(node=list(fillcolor="lightgreen", width="0.75", shape="ellipse"), edge=list(arrowsize="0.7"))) The R GUI stopped, and shows that: R for windows GUI front-end has stopped working A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available Anybody can tell me why this happens and how to solve it? Thanks, Grace On Sat, Dec 25, 2010 at 12:03 AM, Alessandro Magrini < alessandro.magrini@hotmail.it> wrote: > mmh no...I have 32-bit Windows 7. > > graphviz works correctly, I have installed the version suggested > (2.20.3.1)... > > _______________________________________________ > 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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If your problem really is the same as the thread you replied to, I do not think there is a solution yet. Martin ----- Original Message ----- > Hi, I got the similar problem when I run the KEGGgraph package. Below > is the > detailed information. please note that I use 64-bit windows 7 > > I run the following codes: > > mapkKGML <- system.file("extdata/hsa04010.xml", > package="KEGGgraph") > > > > > > ################################################### > > ### chunk number 4: parsemapk > > ################################################### > > mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE) > > mapkG > > > > > > ################################################### > > ### chunk number 5: parsemapk2 > > ################################################### > > mapkpathway <- parseKGML(mapkKGML) > > mapkpathway > > mapkG2 <- KEGGpathway2Graph(mapkpathway, expandGenes=TRUE) > > mapkG2 > > > > > > ################################################### > > ### chunk number 6: nodeandedge > > ################################################### > > mapkNodes <- nodes(mapkG) > > nodes(mapkG)[1:3] > > mapkEdges <- edges(mapkG) > > edges(mapkG)[1] > > > > > > ################################################### > > ### chunk number 7: keggnodedata > > ################################################### > > mapkGnodedata <- getKEGGnodeData(mapkG) > > mapkGnodedata[[2]] > > > > > > ################################################### > > ### chunk number 8: keggnodedataalt eval=FALSE > > ################################################### > > ## getKEGGnodeData(mapkG, 'hsa:5924') > > > > > > ################################################### > > ### chunk number 9: keggedgedata > > ################################################### > > mapkGedgedata <- getKEGGedgeData(mapkG) > > mapkGedgedata[[4]] > > > > > > ################################################### > > ### chunk number 10: keggedgedataalt eval=FALSE > > ################################################### > > ## getKEGGedgeData(mapkG,'hsa:627~hsa:4915') > > > > > > ################################################### > > ### chunk number 11: inout > > ################################################### > > mapkGoutdegrees <- sapply(edges(mapkG), length) > > mapkGindegrees <- sapply(inEdges(mapkG), length) > > topouts <- sort(mapkGoutdegrees, decreasing=T) > > topins <- sort(mapkGindegrees, decreasing=T) > > topouts[1:3] > > topins[1:3] > > > > > > ################################################### > > ### chunk number 12: subsetprepare > > ################################################### > > library(Rgraphviz) > > set.seed(123) > > randomNodes <- sample(nodes(mapkG), 25) > > mapkGsub <- subGraph(randomNodes, mapkG) > > mapkGsub > > > > > > ################################################### > > ### chunk number 13: makeattr > > ################################################### > > makeAttr <- function(graph, default, valNodeList) { > > tmp <- nodes(graph) > > x <- rep(default, length(tmp)); names(x) <- tmp > > > > if(!missing(valNodeList)) { > > stopifnot(is.list(valNodeList)) > > allnodes <- unlist(valNodeList) > > stopifnot(all(allnodes %in% tmp)) > > for(i in seq(valNodeList)) { > > x[valNodeList[[i]]] <- names(valNodeList)[i] > > } > > } > > return(x) > > } > > > > > > ################################################### > > ### chunk number 14: subsetplot > > ################################################### > > outs <- sapply(edges(mapkGsub), length) > 0 > > ins <- sapply(inEdges(mapkGsub), length) > 0 > > ios <- outs | ins > > > > ## translate the KEGG IDs into Gene Symbol > > if(require(org.Hs.eg.db)) { > > ioGeneID <- translateKEGGID2GeneID(names(ios)) > > nodesNames <- sapply(mget(ioGeneID, org.Hs.egSYMBOL, ifnotfound=NA), > "[[",1) > > } else { > > nodesNames <- names(ios) > > } > > names(nodesNames) <- names(ios) > > > > nAttrs <- list(); > > nAttrs$fillcolor <- makeAttr(mapkGsub, "lightgrey", > list(orange=names(ios)[ios])) > > nAttrs$label <- nodesNames > > > Everything is fine so far, and the sessionInfo() is following: > > > > R version 2.10.1 (2009-12-14) > > i386-pc-mingw32 > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > base > > > > other attached packages: > > [1] org.Hs.eg.db_2.3.6 RSQLite_0.8-4 DBI_0.2-5 > AnnotationDbi_1.8.2 > Biobase_2.6.1 > > [6] KEGGgraph_1.2.2 Rgraphviz_1.24.0 graph_1.26.0 > XML_2.6-0 > > > > > loaded via a namespace (and not attached): > > [1] tools_2.10.1 > > > > However when I run > > plot(mapkGsub, "neato", nodeAttrs=nAttrs, > > attrs=list(node=list(fillcolor="lightgreen", > > width="0.75", shape="ellipse"), > > edge=list(arrowsize="0.7"))) > > > > > The R GUI stopped, and shows that: > > R for windows GUI front-end has stopped working > > A problem caused the program to stop working correctly. Windows will > close > the program and notify you if a solution is available > > > > Anybody can tell me why this happens and how to solve it? > > Thanks, > > Grace > > On Sat, Dec 25, 2010 at 12:03 AM, Alessandro Magrini < > alessandro.magrini at hotmail.it> wrote: > > > mmh no...I have 32-bit Windows 7. > > > > graphviz works correctly, I have installed the version suggested > > (2.20.3.1)... > > > > _______________________________________________ > > 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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I still don't know the reason, but our IT paper helped me to install the packages in our Linux system and no such weird problem in this system.I can temportarily use the Linux version. Thank you, Grace On Mon, Dec 27, 2010 at 10:18 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > If your problem really is the same as the thread you replied to, I do not > think there is a solution yet. Martin > > ----- Original Message ----- > > Hi, I got the similar problem when I run the KEGGgraph package. Below > > is the > > detailed information. please note that I use 64-bit windows 7 > > > > I run the following codes: > > > > mapkKGML <- system.file("extdata/hsa04010.xml", > > package="KEGGgraph") > > > > > > > > > > > > ################################################### > > > > ### chunk number 4: parsemapk > > > > ################################################### > > > > mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE) > > > > mapkG > > > > > > > > > > > > ################################################### > > > > ### chunk number 5: parsemapk2 > > > > ################################################### > > > > mapkpathway <- parseKGML(mapkKGML) > > > > mapkpathway > > > > mapkG2 <- KEGGpathway2Graph(mapkpathway, expandGenes=TRUE) > > > > mapkG2 > > > > > > > > > > > > ################################################### > > > > ### chunk number 6: nodeandedge > > > > ################################################### > > > > mapkNodes <- nodes(mapkG) > > > > nodes(mapkG)[1:3] > > > > mapkEdges <- edges(mapkG) > > > > edges(mapkG)[1] > > > > > > > > > > > > ################################################### > > > > ### chunk number 7: keggnodedata > > > > ################################################### > > > > mapkGnodedata <- getKEGGnodeData(mapkG) > > > > mapkGnodedata[[2]] > > > > > > > > > > > > ################################################### > > > > ### chunk number 8: keggnodedataalt eval=FALSE > > > > ################################################### > > > > ## getKEGGnodeData(mapkG, 'hsa:5924') > > > > > > > > > > > > ################################################### > > > > ### chunk number 9: keggedgedata > > > > ################################################### > > > > mapkGedgedata <- getKEGGedgeData(mapkG) > > > > mapkGedgedata[[4]] > > > > > > > > > > > > ################################################### > > > > ### chunk number 10: keggedgedataalt eval=FALSE > > > > ################################################### > > > > ## getKEGGedgeData(mapkG,'hsa:627~hsa:4915') > > > > > > > > > > > > ################################################### > > > > ### chunk number 11: inout > > > > ################################################### > > > > mapkGoutdegrees <- sapply(edges(mapkG), length) > > > > mapkGindegrees <- sapply(inEdges(mapkG), length) > > > > topouts <- sort(mapkGoutdegrees, decreasing=T) > > > > topins <- sort(mapkGindegrees, decreasing=T) > > > > topouts[1:3] > > > > topins[1:3] > > > > > > > > > > > > ################################################### > > > > ### chunk number 12: subsetprepare > > > > ################################################### > > > > library(Rgraphviz) > > > > set.seed(123) > > > > randomNodes <- sample(nodes(mapkG), 25) > > > > mapkGsub <- subGraph(randomNodes, mapkG) > > > > mapkGsub > > > > > > > > > > > > ################################################### > > > > ### chunk number 13: makeattr > > > > ################################################### > > > > makeAttr <- function(graph, default, valNodeList) { > > > > tmp <- nodes(graph) > > > > x <- rep(default, length(tmp)); names(x) <- tmp > > > > > > > > if(!missing(valNodeList)) { > > > > stopifnot(is.list(valNodeList)) > > > > allnodes <- unlist(valNodeList) > > > > stopifnot(all(allnodes %in% tmp)) > > > > for(i in seq(valNodeList)) { > > > > x[valNodeList[[i]]] <- names(valNodeList)[i] > > > > } > > > > } > > > > return(x) > > > > } > > > > > > > > > > > > ################################################### > > > > ### chunk number 14: subsetplot > > > > ################################################### > > > > outs <- sapply(edges(mapkGsub), length) > 0 > > > > ins <- sapply(inEdges(mapkGsub), length) > 0 > > > > ios <- outs | ins > > > > > > > > ## translate the KEGG IDs into Gene Symbol > > > > if(require(org.Hs.eg.db)) { > > > > ioGeneID <- translateKEGGID2GeneID(names(ios)) > > > > nodesNames <- sapply(mget(ioGeneID, org.Hs.egSYMBOL, ifnotfound=NA), > > "[[",1) > > > > } else { > > > > nodesNames <- names(ios) > > > > } > > > > names(nodesNames) <- names(ios) > > > > > > > > nAttrs <- list(); > > > > nAttrs$fillcolor <- makeAttr(mapkGsub, "lightgrey", > > list(orange=names(ios)[ios])) > > > > nAttrs$label <- nodesNames > > > > > > Everything is fine so far, and the sessionInfo() is following: > > > > > > > > R version 2.10.1 (2009-12-14) > > > > i386-pc-mingw32 > > > > > > > > locale: > > > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > States.1252 > > > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > > > > > [5] LC_TIME=English_United States.1252 > > > > > > > > attached base packages: > > > > [1] grid stats graphics grDevices utils datasets methods > > base > > > > > > > > other attached packages: > > > > [1] org.Hs.eg.db_2.3.6 RSQLite_0.8-4 DBI_0.2-5 > > AnnotationDbi_1.8.2 > > Biobase_2.6.1 > > > > [6] KEGGgraph_1.2.2 Rgraphviz_1.24.0 graph_1.26.0 > > XML_2.6-0 > > > > > > > > > > loaded via a namespace (and not attached): > > > > [1] tools_2.10.1 > > > > > > > > However when I run > > > > plot(mapkGsub, "neato", nodeAttrs=nAttrs, > > > > attrs=list(node=list(fillcolor="lightgreen", > > > > width="0.75", shape="ellipse"), > > > > edge=list(arrowsize="0.7"))) > > > > > > > > > > The R GUI stopped, and shows that: > > > > R for windows GUI front-end has stopped working > > > > A problem caused the program to stop working correctly. Windows will > > close > > the program and notify you if a solution is available > > > > > > > > Anybody can tell me why this happens and how to solve it? > > > > Thanks, > > > > Grace > > > > On Sat, Dec 25, 2010 at 12:03 AM, Alessandro Magrini < > > alessandro.magrini@hotmail.it> wrote: > > > > > mmh no...I have 32-bit Windows 7. > > > > > > graphviz works correctly, I have installed the version suggested > > > (2.20.3.1)... > > > > > > _______________________________________________ > > > 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]] > > > > _______________________________________________ > > 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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Hi Grace, It looks like you're using an old version of R. You should upgrade to 2.12.1. What version of graphviz do you have installed? What happens when you run "library(Rgraphviz)"? Cheers, Fraser -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of zhiqun tang Sent: Monday, December 27, 2010 2:02 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Rgraphviz in windows 7 - problem with GUI? Hi, I got the similar problem when I run the KEGGgraph package. Below is the detailed information. please note that I use 64-bit windows 7 I run the following codes: mapkKGML <- system.file("extdata/hsa04010.xml", package="KEGGgraph") ################################################### ### chunk number 4: parsemapk ################################################### mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE) mapkG ################################################### ### chunk number 5: parsemapk2 ################################################### mapkpathway <- parseKGML(mapkKGML) mapkpathway mapkG2 <- KEGGpathway2Graph(mapkpathway, expandGenes=TRUE) mapkG2 ################################################### ### chunk number 6: nodeandedge ################################################### mapkNodes <- nodes(mapkG) nodes(mapkG)[1:3] mapkEdges <- edges(mapkG) edges(mapkG)[1] ################################################### ### chunk number 7: keggnodedata ################################################### mapkGnodedata <- getKEGGnodeData(mapkG) mapkGnodedata[[2]] ################################################### ### chunk number 8: keggnodedataalt eval=FALSE ################################################### ## getKEGGnodeData(mapkG, 'hsa:5924') ################################################### ### chunk number 9: keggedgedata ################################################### mapkGedgedata <- getKEGGedgeData(mapkG) mapkGedgedata[[4]] ################################################### ### chunk number 10: keggedgedataalt eval=FALSE ################################################### ## getKEGGedgeData(mapkG,'hsa:627~hsa:4915') ################################################### ### chunk number 11: inout ################################################### mapkGoutdegrees <- sapply(edges(mapkG), length) mapkGindegrees <- sapply(inEdges(mapkG), length) topouts <- sort(mapkGoutdegrees, decreasing=T) topins <- sort(mapkGindegrees, decreasing=T) topouts[1:3] topins[1:3] ################################################### ### chunk number 12: subsetprepare ################################################### library(Rgraphviz) set.seed(123) randomNodes <- sample(nodes(mapkG), 25) mapkGsub <- subGraph(randomNodes, mapkG) mapkGsub ################################################### ### chunk number 13: makeattr ################################################### makeAttr <- function(graph, default, valNodeList) { tmp <- nodes(graph) x <- rep(default, length(tmp)); names(x) <- tmp if(!missing(valNodeList)) { stopifnot(is.list(valNodeList)) allnodes <- unlist(valNodeList) stopifnot(all(allnodes %in% tmp)) for(i in seq(valNodeList)) { x[valNodeList[[i]]] <- names(valNodeList)[i] } } return(x) } ################################################### ### chunk number 14: subsetplot ################################################### outs <- sapply(edges(mapkGsub), length) > 0 ins <- sapply(inEdges(mapkGsub), length) > 0 ios <- outs | ins ## translate the KEGG IDs into Gene Symbol if(require(org.Hs.eg.db)) { ioGeneID <- translateKEGGID2GeneID(names(ios)) nodesNames <- sapply(mget(ioGeneID, org.Hs.egSYMBOL, ifnotfound=NA), "[[",1) } else { nodesNames <- names(ios) } names(nodesNames) <- names(ios) nAttrs <- list(); nAttrs$fillcolor <- makeAttr(mapkGsub, "lightgrey", list(orange=names(ios)[ios])) nAttrs$label <- nodesNames Everything is fine so far, and the sessionInfo() is following: R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.3.6 RSQLite_0.8-4 DBI_0.2-5 AnnotationDbi_1.8.2 Biobase_2.6.1 [6] KEGGgraph_1.2.2 Rgraphviz_1.24.0 graph_1.26.0 XML_2.6-0 loaded via a namespace (and not attached): [1] tools_2.10.1 However when I run plot(mapkGsub, "neato", nodeAttrs=nAttrs, attrs=list(node=list(fillcolor="lightgreen", width="0.75", shape="ellipse"), edge=list(arrowsize="0.7"))) The R GUI stopped, and shows that: R for windows GUI front-end has stopped working A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available Anybody can tell me why this happens and how to solve it? Thanks, Grace On Sat, Dec 25, 2010 at 12:03 AM, Alessandro Magrini < alessandro.magrini at hotmail.it> wrote: > mmh no...I have 32-bit Windows 7. > > graphviz works correctly, I have installed the version suggested > (2.20.3.1)... > > _______________________________________________ > 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 > [[alternative HTML version deleted]] _______________________________________________ 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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