- 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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