Hi, I was wondering if someone in the mailing list has any insight into this
segfault error that I consistently find when running a script containing
heatmap() in R 2.8.1 and 2.8.0 on a Linux 64-bit machine.

Some points:

1. This occurs when running heatmap().
2. Interestingly, if I source() the script or copy and paste the script in
its entirety, this error occurs.  However, if I run the commands
individually, heatmap() will actually work.
3. I've had this error occur on two types of machines as follows.  Intel
64bit, linux kernel 2.6.18-92.1.22.el5, gcc version 4.1.2 as well as AMD
64bit, linux kernel 2.6.9-5.ELsmp, gcc version 3.4.3

Here is the error messages that I receive when I debug(heatmap) and source()
the script containing heatmap().  The sessionInfo() follows.


Browse[1]>
debug: op <- par(no.readonly = TRUE)
Browse[1]>

 *** caught segfault ***
address 0x103c93d53, cause 'memory not mapped'

Traceback:
 1: function (display = "", width, height, pointsize, gamma, bg,     canvas,
fonts, xpos, ypos, title, type, antialias) {    if (display == "" &&
.Platform$GUI == "AQUA" && is.na(Sys.getenv("DISPLAY",         NA)))
Sys.setenv(DISPLAY = ":0")    new <- list()    if (!missing(display))
  new$display <- display    if (!missing(width))         new$width <- width
   if (!missing(height))         new$height <- height    if
(!missing(gamma))         new$gamma <- gamma    if (!missing(pointsize))
    new$pointsize <- pointsize    if (!missing(bg))         new$bg <- bg
 if (!missing(canvas))         new$canvas <- canvas    if (!missing(xpos))
      new$xpos <- xpos    if (!missing(ypos))         new$ypos <- ypos    if
(!missing(title))         new$title <- title    if
(!checkIntFormat(new$title))         stop("invalid 'title'")    if
(!missing(type))         new$type <- match.arg(type, c("Xlib", "cairo",
"nbcairo"))    if (!missing(antialias)) {        new$antialias <-
pmatch(antialias, c("default", "none",             "gray", "subpixel"))
   if (is.na(new$antialias))             stop("invalid value for
'antialias'")    }    d <- check.options(new, name.opt = ".X11.Options",
envir = .X11env)    type <- if (capabilities("cairo"))
switch(d$type, cairo = 1, nbcairo = 2, 0)    else 0    if (display ==
"XImage")         type <- 0    .Internal(X11(d$display, d$width, d$height,
d$pointsize,         d$gamma, d$colortype, d$maxcubesize, d$bg, d$canvas,
      d$fonts, NA_integer_, d$xpos, d$ypos, d$title, type,
d$antialias))}()
 2: par(no.readonly = TRUE)
 3: heatmap(selected.matrix, distfun = cor.dist, zlim = zlim, col =
colors.for.heatmap)
 4: eval.with.vis(expr, envir, enclos)
 5: eval.with.vis(ei, envir)

Here is the sessionInfo()

> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     grid      stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] u133x3p.db_2.2.5    RSQLite_0.7-1       DBI_0.2-4
[4] AnnotationDbi_1.4.3 Biobase_2.2.2       vcd_1.2-3
[7] colorspace_1.0-0    MASS_7.2-46
>


Thanks,
Andrew

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