[Bioc-sig-seq] X11 fatal IO error

[Ludo Pagie]

sounds a bit like
http://www.mail-archive.com/r-devel@r-project.org/msg18494.html

the corresponding bug-report (#14055) was closed as it was declared
not-reproducible and solely due to the X-server (although the same code
kills windows machines as well).

Does the error only occur when drawing large polygons, as in #14055?


Ludo

On 09/13/2010 03:45 AM, pterry at huskers.unl.edu wrote:
>  Dear bioc-sig-sequencing,
> 
> I received the following error message while running code from slide 17 from the workshop lab CoverageEDA.pdf, 01/29/10 in Seattle, (http://www.bioconductor.org/help/course-materials/2010/SeattleJan10/day3/CoverageEDA.pdf)
> 
>> plotCoverage <-
> + function (x, chrom, start = 1, end = length(x[[chrom]]), col = "blue",
> + xlab = "Index", ylab = "Coverage", main = chrom)
> + {
> + xWindow <- as.vector(window(x[[chrom]], start, end))
> + x <- start:end
> + xlim <- c(start, end)
> + ylim <- c(0, max(xWindow))
> + plot(x = start, y = 0, xlim = xlim, ylim = ylim, xlab = xlab,
> + ylab = ylab, main = main, type = "n")
> + polygon(c(start, x, end), c(0, xWindow, 0), col = col)
> + }
>> plotCoverage(cov.arabtest1_s8, "chr1")
> Error in polygon(c(start, x, end), c(0, xWindow, 0), col = col) :
>   X11 fatal IO error: please save work and shut down R
> 
>> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-08-02 r52661)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] chipseq_0.99.1       BSgenome_1.17.6      ShortRead_1.7.11
> [4] Rsamtools_1.1.11     lattice_0.18-8       Biostrings_2.17.27
> [7] GenomicRanges_1.1.20 IRanges_1.7.15
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.9.0 grid_2.12.0   hwriter_1.2
>>
> 
> The plot works fine with the 2.11 release vesion of R.  This is a linux Ubuntu laptop running 10.04, 8 Gb ram.
> 
> Thanks,
> P. Terry
> pterry at huskers.unl.edu
> 
> 	[[alternative HTML version deleted]]
> 
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