topGO graph visualization functions crashing under R 2.13.2 with Graphviz 2.20.3.1
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Joseph Skaf ▴ 20
@joseph-skaf-4053
Last seen 7.1 years ago
Dear Bioconductor mailing group, I have been trying to get the topGO graph visualization tools to work on my Windows 7 PC with R 2.13.2 installed, but I've been encountering a crippling crash. Just as a little bit of background, I have Rgraphviz_1.30.1 installed in R and Graphviz 2.20.3.1 installed for my PC (the bin folder is declared in the Environmental Path variable as 'C:\Program Files (x86)\Graphviz2.20\bin'). Loading Rgraphviz in the library works fine (so does example(Layout) after loading), but whenever I try to use a topGO function calling something from Rgraphviz (such as showSigOfNodes() ), R crashes immediately with no error message. The problem occurs even with the example data in the topGO package: library(topGO) > library(Rgraphviz) > data(GOdata) > data(results.tGO) > showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo = > 'all') #Crashes > printGraph(GOdata, resultFisher, firstSigNodes = 5, fn.prefix = > "sampleFile", useInfo = "all", pdfSW = TRUE) #Crashes I have tried all advice that I have seen in older responses (installing visual c++ redistribution package, trying older and newer versions of graphviz, uninstalling and re-installing R and graphviz, updating packages), but nothing seems to work. If anyone has any suggestions on how to fix this crash, it would be very much appreciated! Thanks and all the best, Joseph Skaf > sessionInfo() R version 2.13.2 (2011-09-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rgraphviz_1.30.1 topGO_2.4.0 SparseM_0.89 [4] GO.db_2.5.0 RSQLite_0.10.0 DBI_0.2-5 [7] AnnotationDbi_1.14.1 Biobase_2.12.2 graph_1.30.0 loaded via a namespace (and not attached): [1] lattice_0.19-33 tools_2.13.2 [[alternative HTML version deleted]]
GO Visualization graph Rgraphviz topGO GO Visualization graph Rgraphviz topGO • 679 views
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