[BioC] crlmm and snpMatrix
beniltoncarvalho at gmail.com
Tue Jun 15 15:47:04 CEST 2010
I'll look into this and get back to the list once the issue is
identified (and hopefully solved).
On 15 June 2010 14:36, Tim Rayner <tfrayner at gmail.com> wrote:
> 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.
> 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)
>  en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> attached base packages:
>  splines tools stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  snpMatrix_1.12.0 survival_2.35-8 crlmm_1.6.0
>  oligoClasses_1.10.0 Biobase_2.8.0 snow_0.3-3
>  ff_2.1-2 bit_1.1-4
> loaded via a namespace (and not attached):
>  affyio_1.16.0 annotate_1.26.0 AnnotationDbi_1.10.0
>  Biostrings_2.16.0 DBI_0.2-5 ellipse_0.3-5
>  genefilter_1.30.0 IRanges_1.6.6 mvtnorm_0.9-9
>  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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