[Bioc-devel] Slicing Throws Interger Overflow

[Valerie Obenchain]

Hi Dario,

Thanks for the report. I'll look into it.

Valerie


On 10/26/11 18:00, Dario Strbenac wrote:
> Hello,
>
> I have a problem when slicing a coverage object with a maximum bound. It gives an integer overflow error for a wide variety of upper values.
>
> e.g.
>
>> summary(reads)
>            Length            Class             Mode
>          19138567 GappedAlignments               S4
> genome.coverage<- coverage(reads)
>> low.counts<- slice(genome.coverage, upper = 2)
> Error in do.call(c, unname(x)) : negative length vectors are not allowed
> In addition: Warning message:
> In newCompressedList("CompressedLogicalList", listData) :
>    Integer overflow in 'cumsum'; use 'cumsum(as.numeric(.))'
>
> Is lapply over each chromosome necessary for this ? Using the lapply approach, it works well.
>
> other attached packages:
> [1] Rsamtools_1.3.34    Biostrings_2.19.18  GenomicRanges_1.4.8  IRanges_1.10.6
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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