r - Error in heatmap.2 (gplots) -

ive moved on new server , installed r version 3.0 on it. (gplots library no longer available 2.14)

using script worked version 2.14 encounter problem generating heatmap.

in r version 3 error:

error in lapply(args, is.character) : node stack overflow error in dev.flush() : node stack overflow error in par(op) : node stack overflow 

in r version 2.14 error:

error: evaluation nested deeply: infinite recursion / options(expressions=)? 

which can resolve increasing options(expressions=500000)

in r version 3 increasing option not resolve issue. , im still stuck same error.

the script same both:

y=read.table("test", row.names=1, sep="\t", header=true) hr <- hclust(dist(as.matrix(y))) hc <- hclust(dist(as.matrix(t(y)))) mycl <- cutree(hr, k=7); mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9); mycolhc     <- mycolhc[as.vector(mycl)]   install.packages("gplots") library("gplots", character.only=true) myheatcol <- redgreen(75)  pdf("heatmap.pdf") heatmap.2(as.matrix(y), rowv=as.dendrogram(hr), colv=as.dendrogram(hc), col=myheatcol,scale="none", density.info="none", trace="none", rowsidecolors=mycolhc, labrow=false) dev.off() 

where "test" tdl file headers , row names , 40*5000 0/1 matrix

any appreciated

ps: when reduce data set 2000 lines no longer error.

pss: increasing dataset 2500 lines resulted in same error; however, removing non-informative lines (all 1s) left me 3700 lines. using data set did not result in error.

i'm author of gplots package. 'node stack overflow' error occurs when byte-compiled function has many recursive calls.

in case, occurs because function plots dendrogram objects (stats:::plotnode) implemented using recursive algorithm , dendrogram object nested.

ultimately, correct solution modify plotnode use iterative algorithm, prevent recursion depth error occuring.

in short term, possible force stats:::plotnode run interpreted code rather byte-compiled code via nasty hack.

here's recipe:

## convert byte-compiled function interpreted-code function  unbytecode <- function(fun)     {         fun <- eval(parse(text=deparse(fun)))         environment(fun) <- environment(fun)         fun     }  ## replace function definition inside of locked environment **hack**  assignedgewise <- function(name, env, value)     {         unlockbinding(name, env=env)         assign( name, envir=env, value=value)         lockbinding(name, env=env)         invisible(value)     }  ## replace byte-compiled function in locked environment interpreted-code ## function unbytecodeassign <- function(fun)     {         name <- gsub('^.*::+','', deparse(substitute(fun)))         fun <- unbytecode(fun)         retval <- assignedgewise(name=name,                                  env=environment(fun),                                  value=fun                                  )         invisible(retval)     }  ## use above functions convert stats:::plotnode interpreted-code: unbytecodeassign(stats:::plotnode)  ## raise interpreted code recursion limit (you may need adjust this, ##  decreasing if uses memory, increasing if recursion depth error ). options(expressions=5e4)  ## heatmap.2 should work  heatmap.2( ... )