[BioC] Bug in GenomicRanges 1.14.3, as(from, "GRanges") not working for RleViewsList

[Hervé Pagès]

Hi George,

Thanks for the report. This should be fixed in IRanges 1.20.5 (release)
and 1.21.8 (devel), which should become available tru biocLite() in the
next 24 hours or so.

Cheers,
H.

On 11/04/2013 03:59 AM, George Baskozos wrote:
> 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
>
> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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