Fixed in 1.21.38.


On Fri, Mar 28, 2014 at 9:15 AM, Leonard Goldstein <
goldstein.leonard@gene.com> wrote:

> 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
> >
>
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>

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