[Bioc-sig-seq] X11 fatal IO error

[Martin Morgan]

On 09/12/2010 06:45 PM, 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
>   
To make this a little more reproducible...

I downloaded

 
http://bioconductor.org/help/course-materials/2010/SeattleJan10/day3/day3_0.0.3.tar.gz

and then installed it

  R CMD INSTALL --clean day3_0.0.3.tar.gz

And then ran the script generated from the vignette in the package

   R --vanilla -e "source(system.file('doc', 'CoverageEDA.R',  package='day3'),
verbose=TRUE, max=Inf)"

or starting R

  R --vanilla

and then entering the line

  > source(system.file('doc', 'CoverageEDA.R',  package='day3'), verbose=TRUE, max=Inf)

I didn't see any errors; do you if you do a similar set of steps? I
notice that your R-devel and packages are not completely up to date;
does the error persist if they are updated?

I'll also mention that I ran the code under valgrind (adding -d valgrind
to the R command above, before -e); this pointed to a small error in IRanges C code that should not cause a problem but that has been fixed, and a small error in R's grDevices library that might cause a problem if the output had been to a PDF file, but I don't think that is the case for you.

Here's the output of the equivalent of sessionInfo(), from the end of
the script


> > toLatex(sessionInfo())
>   
curr.fun: symbol toLatex
\begin{itemize}\raggedright
  \item R version 2.12.0 Under development (unstable) (2010-09-05
r52874), \verb|x86_64-unknown-linux-gnu|
  \item Locale: \verb|LC_CTYPE=en_US.UTF-8|, \verb|LC_NUMERIC=C|,
\verb|LC_TIME=en_US.UTF-8|, \verb|LC_COLLATE=en_US.UTF-8|,
\verb|LC_MONETARY=C|, \verb|LC_MESSAGES=en_US.UTF-8|,
\verb|LC_PAPER=en_US.UTF-8|, \verb|LC_NAME=C|, \verb|LC_ADDRESS=C|,
\verb|LC_TELEPHONE=C|, \verb|LC_MEASUREMENT=en_US.UTF-8|,
\verb|LC_IDENTIFICATION=C|
  \item Base packages: base, datasets, graphics,
    grDevices, methods, stats, utils
  \item Other packages: AnnotationDbi~1.11.4,
    Biobase~2.9.0, biomaRt~2.5.1, Biostrings~2.17.39,
    bitops~1.0-4.1, BSgenome~1.17.6,
    BSgenome.Scerevisiae.UCSC.sacCer2~1.3.16,
    day3~0.0.3, DBI~0.2-5, GenomicRanges~1.1.25,
    IRanges~1.7.32, lattice~0.18-8,
    org.Sc.sgd.db~2.4.1, RCurl~1.4-3,
    Rsamtools~1.1.15, RSQLite~0.9-2,
    rtracklayer~1.9.9, ShortRead~1.7.19
  \item Loaded via a namespace (and not attached):
    grid~2.12.0, hwriter~1.2, tools~2.12.0, XML~3.1-1
\end{itemize}



Martin

>


>   
>> 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
>
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>
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