Hi,

I was just trying out the rtracklayer package with the example given in the 
bioinformatics paper on rtracklayer. Here is my code and the error statement:

> library(IRanges)
> library(rtracklayer)
> data(targets)
> tt <- 
>with(targets,GenomicData(IRanges(start,end),target,strand=strand,chrom=chrom))
> class(tt)
[1] "RangedData"
attr(,"package")
[1] "IRanges"

> session <- browserSession()
> session$targets <- tt
Error in FUN(X[[1L]], ...) : 
  Invalid chromosomes for hg19: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 
15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT


My sessionInfo and traceback for the error are:


> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   
base     


other attached packages:
 [1] hash_2.1.0         biomaRt_2.8.0      rtracklayer_1.12.2 RCurl_1.5-0        
bitops_1.0-4.1    

 [6] IRanges_1.10.4     pvclust_1.2-2      les_1.2.0          fdrtool_1.2.7      
ggplot2_0.8.9     

[11] proto_0.3-9.2      reshape_0.8.4      plyr_1.5.2        

loaded via a namespace (and not attached):
 [1] Biostrings_2.20.1   boot_1.2-43         BSgenome_1.20.0     
gdata_2.8.1         GenomicRanges_1.4.6
 [6] gplots_2.8.0        gtools_2.6.2        RColorBrewer_1.0-2  
tools_2.13.0        XML_3.4-0          




> traceback()
15: stop("Invalid chromosomes for ", genome(session), ": ", paste(badSpaces, 
        collapse = ", "))
14: FUN(X[[1L]], ...)
13: lapply(split(X, group), FUN, ...)
12: tapply(value, unlist(genomes), function(tracks) {
        genome <- genome(tracks[[1]])
        if (length(genome)) 
            genome(session) <- genome
        spaces <- unlist(lapply(tracks, names))
        badSpaces <- setdiff(spaces, seqnames(session))
        if (length(badSpaces)) 
            stop("Invalid chromosomes for ", genome(session), ": ", 
                paste(badSpaces, collapse = ", "))
    })
11: normArgTrackData(value, session)
10: .local(object, ..., value = value)
9: `track<-`(`*tmp*`, name, ..., value = <S4 object of class "RangedDataList">)
8: `track<-`(`*tmp*`, name, ..., value = <S4 object of class "RangedDataList">)
7: .local(object, ..., value = value)
6: `track<-`(`*tmp*`, i, ..., value = <S4 object of class "RangedData">)
5: `track<-`(`*tmp*`, i, ..., value = <S4 object of class "RangedData">)
4: `[[<-`(`*tmp*`, name, value = <S4 object of class "RangedData">)
3: `[[<-`(`*tmp*`, name, value = <S4 object of class "RangedData">)
2: `$<-`(`*tmp*`, "targets", value = <S4 object of class "RangedData">)
1: `$<-`(`*tmp*`, "targets", value = <S4 object of class "RangedData">)
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