[R] segfault when running heatmap()

Uwe Ligges ligges at statistik.tu-dortmund.de
Wed Mar 25 14:01:45 CET 2009


- Does it still happen with R-2.9.0 alpha?
- If so, can you please send us reproducible code in order to make able 
to see the error on our systems?

Best wishes,
uwe Ligges


Andrew Yee wrote:
> 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
> 
> 	[[alternative HTML version deleted]]
> 
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