[BioC] Gviz problem with chr16

[Adam Novak [guest]]

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

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