On 09/12/2010 06:45 PM, [email protected] 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 > [email protected] > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
