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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