Hi again,
I've run into a problem accessing elements of a GRangesList using single
brackets, but only if they have been added using double brackets after the
initial GRanges() call.
Happens in both 2.6 and devel branches.

> g1 <- GRanges("chr1", IRanges(5, width=1))
> glist <- GRangesList(g1)
> glist[[2]] <- g1
> glist[1]
GRangesList of length 1
[[1]]
GRanges with 1 range and 0 elementMetadata values
    seqnames    ranges strand |
       <Rle> <IRanges>  <Rle> |
[1]     chr1    [5, 5]      * |

seqlengths
 chr1
   NA
> glist[2]
Error in .bracket.Index(start, nrow(x), rownames(x), asRanges = TRUE) :
  range index out of bounds
> glist[[2]]
GRanges with 1 range and 0 elementMetadata values
    seqnames    ranges strand |
       <Rle> <IRanges>  <Rle> |
[1]     chr1    [5, 5]      * |

seqlengths
 chr1
   NA
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-07-06 r52460)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicRanges_1.1.20 IRanges_1.7.24

Thanks,
Aaron

-- 
Aaron Statham
Postgraduate Scholar, Cancer Epigenetics
Garvan Institute of Medical Research   Tel: (02) 9295 8393
384 Victoria St Darlinghurst 2010   Fax: (02) 9295 8316
NSW Australia         email: a.statham@garvan.org.au

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