Rgraphviz warnings in R-2.0
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SAURIN ★ 1.1k
@saurin-799
Last seen 7.2 years ago
Hi, I am using R-2.0 and trying to do: > install.packages2("Rgraphviz",develOK = TRUE); I have graphviz version 1.12 installed from AT&T website. I get below output: > install.packages2("Rgraphviz",develOK = TRUE); Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download Rgraphviz from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing Rgraphviz" * Installing *source* package 'Rgraphviz' ... checking for graphviz... checking for dotneato-config... /usr/local/bin/dotneato-config /usr/local/bin/dotneato-config configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/usr/local/lib/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_1_12 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o In file included from /usr/local/include/graphviz/render.h:49, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/macros.h:28:1: warning: "NEW" redefined In file included from common.h:13, from Rgraphviz.c:1: /usr/local/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition In file included from /usr/local/include/graphviz/types.h:11, from /usr/local/include/graphviz/render.h:51, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/pathplan.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/pathplan.h:16, from /usr/local/include/graphviz/types.h:11, from /usr/local/include/graphviz/render.h:51, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/pathgeom.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/render.h:52, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/render.h:55, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/gvrender.h:12: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/gvrender.h:19, from /usr/local/include/graphviz/render.h:55, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/gvrenderint.h:12: warning: ignoring #pragma prototyped In file included from common.h:23, from Rgraphviz.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from common.h:26, from Rgraphviz.c:1: /usr/local/include/graphviz/adjust.h:11: warning: ignoring #pragma prototyped In file included from common.h:28, from Rgraphviz.c:1: /usr/local/include/graphviz/gvrender.h:12: warning: ignoring #pragma prototyped gcc -I/usr/local/lib/R/include -I/usr/local/include/graphviz -DGRAPHVIZ_1_12 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o In file included from /usr/local/include/graphviz/render.h:49, from common.h:22, from RgraphvizInit.c:1: /usr/local/include/graphviz/macros.h:28:1: warning: "NEW" redefined In file included from common.h:13, from RgraphvizInit.c:1: /usr/local/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition In file included from /usr/local/include/graphviz/types.h:11, from /usr/local/include/graphviz/render.h:51, from common.h:22, from RgraphvizInit.c:1: /usr/local/include/graphviz/pathplan.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/pathplan.h:16, from /usr/local/include/graphviz/types.h:11, from /usr/local/include/graphviz/render.h:51, from common.h:22, from RgraphvizInit.c:1: /usr/local/include/graphviz/pathgeom.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/render.h:52, from common.h:22, from RgraphvizInit.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/render.h:55, from common.h:22, from RgraphvizInit.c:1: /usr/local/include/graphviz/gvrender.h:12: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/gvrender.h:19, from /usr/local/include/graphviz/render.h:55, from common.h:22, from RgraphvizInit.c:1: /usr/local/include/graphviz/gvrenderint.h:12: warning: ignoring #pragma prototyped In file included from common.h:23, from RgraphvizInit.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from common.h:26, from RgraphvizInit.c:1: /usr/local/include/graphviz/adjust.h:11: warning: ignoring #pragma prototyped In file included from common.h:28, from RgraphvizInit.c:1: /usr/local/include/graphviz/gvrender.h:12: warning: ignoring #pragma prototyped common.h:33: warning: `gvc' defined but not used gcc -shared -L/usr/local/lib -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -Wl -L/usr/local/lib/graphviz -ldotneato -lm ** R ** inst ** save image Loading required package: cluster Loading required package: Ruuid Creating a new generic function for "print" in "Ruuid" Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Creating a new generic function for "lines" in "Rgraphviz" Creating a new generic function for "plot" in "Rgraphviz" Warning messages: 1: Undefined slot classes in definition of "Ragraph": boundBox (class " boundingBox ") in: .completeClassSlots(ClassDef, where) 2: Undefined slot classes in definition of "boundingBox": botLeft (class " xyPoint "), upRight (class " xyPoint ") in: .completeClassSlots(ClassDef, where) 3: Undefined slot classes in definition of "AgNode": center (class " xyPoint "), txtLabel (class " AgTextLabel ") in: .completeClassSlots(ClassDef, where) 4: Undefined slot classes in definition of "AgEdge": sp (class " xyPoint "), ep (class " xyPoint "), txtLabel (class " AgTextLabel ") in: .completeClassSlots(ClassDef, where) ** help >>> Building/Updating help pages for package 'Rgraphviz' Formats: text html latex example AgEdge-class text html latex example AgNode-class text html latex example AgTextLabel-class text html latex example BezierCurve-class text html latex example GraphvizAttributes text html latex example GraphvizLayouts text html latex example Ragraph-class text html latex example agopen text html latex example agwrite text html latex example boundingBox-class text html latex example buildNodeList text html latex example getDefaultAttrs text html latex example graphvizVersion text html latex example imageMap text html latex example layoutGraph text html latex example pEdge-class text html latex example pNode-class text html latex example pieGlyph text html latex example plot-methods text html latex example removedEdges text html latex example toDot-methods text html latex example xyPoint-class text html latex example * DONE (Rgraphviz) [1] "Installation complete" >From URL: http://www.bioconductor.org/repository/devel/package/Source Rgraphviz version 1.4.23 Thank you, Saurin
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 7.2 years ago
> Warning messages: > 1: Undefined slot classes in definition of "Ragraph": > boundBox (class " boundingBox ") in: > .completeClassSlots(ClassDef, where) <snip other="" warnings=""> These are from the order of the file collation but don't really have any ill effect with the package usage. There are actually quite a few packages running around w/ these sorts of warnings, I fix them when I find them.
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Hi Jeff, Thank you so much. I asked question because when I do below code R-1.9 then with graphviz 1.12 and Rgraphviz 1.4.0 it was working great. But now I have R-2.0 and same graphviz and Rgraphviz I get error message. -------------------------------------- if(require(Rgraphviz)){ + + opar = par(xpd = NA) + plotPieChart <- function(curPlot,counts,main) { + + renderNode <- function(x) { + + force(x) + y <- x * 100 + 1 + function(node,ur,attrs = list(),radConv = 1) { + nodeCenter <- getNodeCenter(node) + pieGlyph(y,xpos = getX(nodeCenter),ypos = getY(nodeCenter), + radius = getNodeRW(node),col = c("pink","green")) + #drawTxtLabel(txtLabel(node),getX(nodeCenter),getY(nodeCenter)) + } + + } + drawing <- vector(mode = "list",length = nrow(counts)); + for(i in 1:length(drawing)){ + drawing[[i]] <- renderNode(counts[i,]) + } + if(missing(main)) + main = "GO: Cellular Component : Mouse Embryo Fibroblast Pie Chart Plot" + plot(curPlot,drawNode = drawing,main = main) + legend(300,65,legend = c("KO","WT"), fill = c("pink","green")) + } + + plotPieChart(pgLayoutCC,ctmat) + par(opar) + } ----------------------------------- Error in FUN(X[[1]], ...) : couldn't find function "convertRadius" ------------------------------------ Thank you, Saurin
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> Thank you so much. I asked question because when I do > below code R-1.9 then with graphviz 1.12 and > Rgraphviz 1.4.0 it was working great. > ----------------------------------- > Error in FUN(X[[1]], ...) : couldn't find function > "convertRadius" > ------------------------------------ convertRadius is an old function that no longer exists, but you're not calling it directly. Can you provide a 'traceback()', because the string 'convertRadius' doesn't show up anywhere in the current R code so I have no idea where you're piciking that up from.
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Hi Jeff, I am collecting Differentially Expressed Genes (DEscores) : m.ranks <- rank(-abs(DEscores[,2])); names(m.ranks) <- rownames(DEscores); t.ranks <- rank(-abs(DEscores[,3])); names(t.ranks) <- rownames(DEscores); All_Ranks <- cbind(m.ranks,t.ranks)[TRUE,]; temp1.genes <- as.matrix(All_Ranks[,1] < 10); temp2.genes <- as.matrix(All_Ranks[,2] < 10); topgenes_m <- myDEGenes[temp1.genes]; topgenes_t <- myDEGenes[temp2.genes]; tmp <- unique(rbind(as.matrix(topgenes_m),as.matrix(topgenes_t))); topgenesGO <- as.character(unique(tmp)); topgenesGO <- as.matrix(as.character(unique(topgenesGO))); #collected top 10 highly ranked genes from whole DE genes # get locus link IDs myLL <- getLL(topgenesGO,"moe430a"); myUNQLL <- as.character(na.omit(unique(unlist(myLL)))); gGOCC <- makeGOGraph(myUNQLL,"CC"); gGOMF <- makeGOGraph(myUNQLL,"MF"); gGOBP <- makeGOGraph(myUNQLL,"BP"); CCnodes = nodes(gGOCC); MFnodes = nodes(gGOMF); BPnodes = nodes(gGOBP); c1 <- c("KO","KO","KO","WT","WT","WT"); mns <- apply(exprs(esetFeature),1,function(x) sapply(split(x,c1),mean)); whismax <- apply(mns,2,function(x) match(max(x),x)); maxNames <- names(mns[,1])[whismax]; names(maxNames) = names(whismax); table(maxNames); # cellular component GO graph CCnodes2affy = mget(CCnodes,moe430aGO2ALLPROBES); cts = sapply(CCnodes2affy,function(x) { wh = names(whismax) %in% x table(maxNames[wh]) }) KOcts = sapply(cts,function(x) x["KO"]); KOcts = ifelseis.na(KOcts),0,KOcts); names(KOcts) = names(cts); WTcts = sapply(cts,function(x) x["WT"]); WTcts = ifelseis.na(WTcts),0,WTcts); names(WTcts) = names(cts); ctmat = cbind(KOcts,WTcts); pgLayoutCC <- agopen(gGOCC,"LayoutgGOCC"); jpeg(filename="goGraph_CC1.jpeg",width=1300,height=1300); if(require(Rgraphviz)){ opar = par(xpd = NA) plotPieChart <- function(curPlot,counts,main) { renderNode <- function(x) { force(x) y <- x * 100 + 1 function(node,ur,attrs = list(),radConv = 1) { nodeCenter <- getNodeCenter(node) pieGlyph(y,xpos = getX(nodeCenter),ypos = getY(nodeCenter), radius = getNodeRW(node),col = c("pink","green")) #drawTxtLabel(txtLabel(node),getX(nodeCenter),getY(nodeCenter)) } } drawing <- vector(mode = "list",length = nrow(counts)); for(i in 1:length(drawing)){ drawing[[i]] <- renderNode(counts[i,]) } if(missing(main)) main = "GO: Cellular Component : Mouse Embryo Fibroblast Pie Chart Plot" plot(curPlot,drawNode = drawing,main = main) legend(300,65,legend = c("KO","WT"), fill = c("pink","green")) } plotPieChart(pgLayoutCC,ctmat) par(opar) } dev.off(); Thank you, Saurin --- Jeff Gentry <jgentry@jimmy.harvard.edu> wrote: > > Thank you so much. I asked question because when I > do > > below code R-1.9 then with graphviz 1.12 and > > Rgraphviz 1.4.0 it was working great. > > ----------------------------------- > > Error in FUN(X[[1]], ...) : couldn't find function > > "convertRadius" > > ------------------------------------ > > convertRadius is an old function that no longer > exists, but you're not > calling it directly. Can you provide a > 'traceback()', because the string > 'convertRadius' doesn't show up anywhere in the > current R code so I have > no idea where you're piciking that up from. > >
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> I am collecting Differentially Expressed Genes > (DEscores) : That's good, but could you send me the results of a 'traceback()' after you get the error as I originally asked?
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Hi Jeff, Extreemly sorry about lack of information. Here, is traceback() results: > traceback(); 6: FUN(X[[1]], ...) 5: lapply(AgEdge(x), function(x, rad, edgemode, ur, attrs) { if (!is(x, "AgEdge")) stop(paste("Class:", class("AgEdge"))) rad <- convertRadius(rad, ur) lines(x, len = (rad/3), edgemode = edgemode, attrs = attrs) }, rad, edgemode(x), ur, edgeAttrs) 4: .local(x, y, ...) 3: plot(curPlot, drawNode = drawing, main = main) 2: plot(curPlot, drawNode = drawing, main = main) 1: plotPieChart(pgLayoutCC, ctmat) Thanks, Saurin --- Jeff Gentry <jgentry@jimmy.harvard.edu> wrote: > > I am collecting Differentially Expressed Genes > > (DEscores) : > > That's good, but could you send me the results of a > 'traceback()' after > you get the error as I originally asked? > >
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Hi , In addition to privious message I see nodes but I don't see edges conneted to nodes. Thank you, Saurin if(require(Rgraphviz)){ + + opar = par(xpd = NA) + plotPieChart <- function(curPlot,counts,main) { + + renderNode <- function(x) { + + force(x) + y <- x * 100 + 1 + function(node,ur,attrs = list(),radConv = 1) { + nodeCenter <- getNodeCenter(node) + pieGlyph(y,xpos = getX(nodeCenter),ypos = getY(nodeCenter), + radius = getNodeRW(node),col = c("pink","green")) + #drawTxtLabel(txtLabel(node),getX(nodeCenter),getY(nodeCenter)) + } + + } + drawing <- vector(mode = "list",length = nrow(counts)); + for(i in 1:length(drawing)){ + drawing[[i]] <- renderNode(counts[i,]) + } + if(missing(main)) + main = "GO: Cellular Component : Mouse Embryo Fibroblast Pie Chart Plot" + plot(curPlot,drawNode = drawing,main = main) + legend(300,65,legend = c("KO","WT"), fill = c("pink","green")) + } + + plotPieChart(pgLayoutCC,ctmat) + par(opar) + } Error in FUN(X[[1]], ...) : couldn't find function "convertRadius" Thank you, Saurin
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