[Bioc-devel] flank function with start argument a named vector

Dear Bioc developers,

I ran into problems when using the flank function with the start
argument set to a named vector.

This returns an IRanges with named starts and ends, which causes
problems downstream. Please see example below.

Thanks for your help

Leonard

ir <- IRanges(1, 1)
fl <- flank(ir, 1, c(a = FALSE))
fl

IRanges of length 1
    start end width
[1]     2   2     1

start(fl)

a
2

end(fl)

a
2

findOverlaps(ir, fl)

Error in findOverlaps(query, IntervalTree(subject), maxgap = maxgap,
minoverlap = minoverlap,  :
  error in evaluating the argument 'subject' in selecting a method for
function 'findOverlaps': Error in validObject(from) :
  invalid class "IRanges" object: 'start(x)' must be an unnamed
integer vector with no NAs

sessionInfo()

R Under development (unstable) (2013-12-03 r64376)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] IRanges_1.21.36    BiocGenerics_0.9.3

loaded via a namespace (and not attached):
[1] stats4_3.1.0