[Bioc-devel] Slicing Throws Interger Overflow

[Dario Strbenac]

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