[BioC] crlmm and snpMatrix

[Benilton Carvalho]

Thanks, Tim,

I'll look into this and get back to the list once the issue is
identified (and hopefully solved).

b

On 15 June 2010 14:36, Tim Rayner <tfrayner at gmail.com> wrote:
> Hi,
>
> I'm not sure if this really qualifies as a bug, but I've spent the
> morning tracking down an odd interaction between the crlmm and
> snpMatrix packages and I thought I should share it and maybe save
> others some time. It looks as though an object in the snpMatrix
> namespace is clobbering something needed by the crlmm2() call. When I
> run the following, crlmm2 runs indefinitely, slowly consuming memory
> until I eventually kill it:
>
> # celdir is a directory containing cel files.
> nclust=4
> clusttype='MPI'
> require(ff)
> require(snow)
> require(crlmm)
> require(snpMatrix)   # comment this line out to fix
> options(cluster=makeCluster(nclust, clusttype))
> cels <- list.celfiles(celdir, full.names=TRUE)
> result <- crlmm2(cels, verbose=TRUE)
>
> If I comment out the "require(snpMatrix)" line then everything runs fine.
>
> The typical output from hanging run looks like this:
>
> Loading required package: genomewidesnp6Crlmm
> Welcome togenomewidesnp6Crlmmversion 1.0.2
> Loading annotations and mixture model parameters.
> Initializing objects.
> Processing 64 files.
> Loading annotations.
> Determining gender.
> Calling 906600 SNPs for recalibration...
>
> And finally, the sessionInfo():
>
> R version 2.11.0 Patched (2010-04-30 r51866)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] snpMatrix_1.12.0    survival_2.35-8     crlmm_1.6.0
> [4] oligoClasses_1.10.0 Biobase_2.8.0       snow_0.3-3
> [7] ff_2.1-2            bit_1.1-4
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.16.0         annotate_1.26.0       AnnotationDbi_1.10.0
>  [4] Biostrings_2.16.0     DBI_0.2-5             ellipse_0.3-5
>  [7] genefilter_1.30.0     IRanges_1.6.6         mvtnorm_0.9-9
> [10] preprocessCore_1.10.0 RSQLite_0.8-4         xtable_1.5-6
>
> So to conclude: don't load snpMatrix until after you're done with
> crlmm2. I'm afraid I've no idea what the actual cause of this problem
> is, since I don't get any "The following object(s) are masked from"
> messages when loading snpMatrix.
>
> Best regards,
>
> Tim Rayner
>
> --
> Bioinformatician, Smith Lab
> CIMR, University of Cambridge
>
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