[Bioc-devel] Slicing Throws Interger Overflow

Sorry about the version numbers. I replicated it on another computer, that had old versions of packages without realising this, as you pointed out, and pasted those session details into the report. However, the problem does occur on my main computer with the latest versions, too. Here is a specific and runnable example :

library(Rsamtools)
reads<- readBamGappedAlignments("http://129.94.136.7/file_dump/dario/RNA.bam") # 1.1 GB
heights<- coverage(reads)
low.counts<- slice(heights, upper = 2)

I used :

R version 2.13.2 (2011-09-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
     ...                         ...
other attached packages:
[1] Rsamtools_1.4.3     Biostrings_2.20.4   GenomicRanges_1.4.8
[4] IRanges_1.10.6

---- Original message ----

Date: Mon, 31 Oct 2011 10:42:55 -0700
From: Valerie Obenchain<vobencha at fhcrc.org>
Subject: Re: [Bioc-devel] Slicing Throws Interger Overflow
To: D.Strbenac at garvan.org.au
Cc: bioc-devel at r-project.org

Dario,

I can't reproduce the problem in R-2.13 or 2.14 with any value of
'upper'. Could I get a copy of the file you're working with?  Is it
publicly available?

I noticed your Rsamtools and Biostrings are quite old - even older than
the versions available for R-2.13. To cover all bases, please biocLite
up the most recent versions and try again.


Valerie


## With 2.13 :

summary(galn)

           Length            Class             Mode
         72727432 GappedAlignments               S4

  cov<- coverage(galn)
sl<- slice(cov, upper=2)
sessionInfo()

R version 2.13.0 Patched (2011-04-14 r55448)
Platform: x86_64-unknown-linux-gnu (64-bit)
...
...
other attached packages:
[1] Rsamtools_1.4.3       Biostrings_2.20.0     GenomicFeatures_1.4.5
[4] GenomicRanges_1.4.8   IRanges_1.10.6



## With 2.14 :

summary(galn)

           Length            Class             Mode
         72727432 GappedAlignments               S4

cov<- coverage(galn)
sl<- slice(cov, upper=2)
sessionInfo()

R Under development (unstable) (2011-10-26 r57443)
Platform: x86_64-unknown-linux-gnu (64-bit)
...
...
other attached packages:
[1] Rsamtools_1.5.82       Biostrings_2.21.11     GenomicFeatures_1.5.39
[4] AnnotationDbi_1.15.48  Biobase_2.13.12        GenomicRanges_1.5.58
[7] IRanges_1.11.33



On 10/29/2011 11:04 AM, Valerie Obenchain wrote:

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