Hi,
I have found a recently introduced bug. The bug is present in GenomicRanges
1.14.3 but not in GenomicRanges 1.12.5.

Example to illustrate the bug:


> example(GRanges)
> mycov = coverage(longGR)
>  rle.i = slice(mycov, lower=3)
>  gr = as (rle.i, "GRanges")
Error in normalizeSingleBracketSubscript(i, x) : invalid subscript type
>
> sessionInfo()
R version 3.0.2 (2013-09-25)
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] BiocInstaller_1.12.0 GenomicRanges_1.14.3 XVector_0.2.0
[4] IRanges_1.20.4       BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] stats4_3.0.2 tools_3.0.2


Using previous versions the example is working properly. Just to illustrate
it:

> example(GRanges)
> mycov = coverage(longGR)
>  rle.i = slice(mycov, lower=3)
>  gr = as (rle.i, "GRanges")
> gr
GRanges with 20 ranges and 2 metadata columns:
       seqnames     ranges strand   |     score      view
          <Rle>  <IRanges>  <Rle>   | <integer> <integer>
   [1]     chr1    [2,  2]      *   |         3         1
   [2]     chr1    [3,  4]      *   |         4         1
   [3]     chr1    [5,  6]      *   |         5         1
   [4]     chr1    [7,  7]      *   |         4         1
   [5]     chr1    [8, 10]      *   |         3         1
   ...      ...        ...    ... ...       ...       ...
  [16]     chr3 [  9,   9]      *   |         6         1
  [17]     chr3 [ 10,  10]      *   |         8         1
  [18]     chr3 [ 11,  11]      *   |         4         1
  [19]     chr3 [ 12,  12]      *   |         3         1
  [20]     chr3 [110, 117]      *   |         3         2
  ---
  seqlengths:
   chr1 chr2 chr3
     NA   NA   NA
>
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] GenomicRanges_1.12.5 IRanges_1.18.4       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] stats4_3.0.2 tools_3.0.2

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