[BioC] bug in beadarray::setWeights

[Mark Dunning]

Hi,

You may need to upgrade your version of beadarray. I recall this bug
being present in older versions, but it should now be fixed for
Bioconductor 2.5 (beadarray 1.14.0).

Regards,

Mark

On Sun, Nov 22, 2009 at 6:46 PM, Mehrdad Shamsi
<Mehrdad.Shamsi at oicr.on.ca> wrote:
> Hi,
>
> Passing a list of weights, that has one vector of weights as the only component,
> to beadarray::setWeights causes R to aquire the entire available memory.
> After grabbing the maximum available memory, the function produces insufficient memory error and quits.
>
> Example:
> library(beadarray)
> data(BLData);
> output <- BASH(BLData, array = 1);
> BLData <- setWeights(BLData, wts = output$wts, array = 1);
>
> Error: cannot allocate vector of size 389 Kb
> In addition: Warning messages:
> 1: In class(x) <- NULL :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 2: In class(x) <- NULL :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 3: In x[[name]] <- value :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 4: In x[[name]] <- value :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 5: In x[[name]] <- value :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 6: In x[[name]] <- value :
>  Reached total allocation of 1535Mb: see help(memory.size)
>
> Source of the problem:
> The way the special case of "length(array) == 1" is dealth with in is the source of the problem.
>
>
> Best regards
> -- M. S.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>