[BioC] Gviz problem with chr16

[Hahne, Florian]

Hi Adam,
thanks for reporting this bug. A fixed version should be available in the
next couple of days as soon as it passes the build system (1.4.2 in
release and 1.5.3 in devel)
Florian



Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com




On 5/10/13 8:53 PM, "Adam Novak [guest]" <guest at bioconductor.org> wrote:

>
>Dear Gviz developers,
>
>We have come across an issue while visualizing chromosome 16 of the human
>genome hg19 using IdeogramTrack and plotTracks. Plotting chr16 produces
>the following error:
>
>Error in lcS[[as.numeric(j) - 1]] : subscript out of bounds
>
>while this does not happen with other chromosomes. Please see the minimal
>example attached below.
>
>#####  beginning of script  ######
># produces an error with chr16 (but not with other chromosomes)
>library(Gviz)
>library(GenomicRanges)
>data(cpgIslands)
>cg = GRanges(seqnames = "chr16",ranges = ranges(cpgIslands))
>chr <- as.character(unique(seqnames(cg)))
>gen = "hg19"
>atrack <- AnnotationTrack(cg, name = "CpG")
>itrack <- IdeogramTrack(genome = "hg19", chromosome = chr)
>gtrack <- GenomeAxisTrack()
>plotTracks(list(itrack, gtrack, atrack))
>#####  end of script  ######
>
>We believe this must be an error in the plotting engine and/or the
>chromosome data.
>
>Thank you for looking into this, best wishes,
>
>Adam Novak
>Sophia Genetics SA
>
>ps. please CC me in the reply as I'm not subscribed to the list - thank
>you
>
> -- output of sessionInfo():
>
>R version 3.0.0 (2013-04-03)
>Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>locale:
>[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] parallel  grid      stats     graphics  grDevices utils     datasets
>[8] methods   base
>
>other attached packages:
>[1] GenomicRanges_1.12.2 IRanges_1.18.0       BiocGenerics_0.6.0
>[4] Gviz_1.4.1    
>
>loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.22.5   Biobase_2.20.0         biomaRt_2.16.0
> [4] Biostrings_2.28.0      biovizBase_1.8.0       bitops_1.0-5
> [7] BSgenome_1.28.0        cluster_1.14.4         colorspace_1.2-2
>[10] DBI_0.2-6              dichromat_2.0-0        GenomicFeatures_1.12.1
>[13] Hmisc_3.10-1.1         labeling_0.1           lattice_0.20-15
>[16] munsell_0.4            plyr_1.8               RColorBrewer_1.0-5
>[19] RCurl_1.95-4.1         Rsamtools_1.12.2       RSQLite_0.11.3
>[22] rtracklayer_1.20.2     scales_0.2.3           stats4_3.0.0
>[25] stringr_0.6.2          tools_3.0.0            XML_3.95-0.2
>[28] zlibbioc_1.6.0
>
>--
>Sent via the guest posting facility at bioconductor.org.