[BioC] crlmm and snpMatrix
tfrayner at gmail.com
Tue Jun 15 15:36:39 CEST 2010
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
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.
Processing 64 files.
Calling 906600 SNPs for recalibration...
And finally, the sessionInfo():
R version 2.11.0 Patched (2010-04-30 r51866)
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.
Bioinformatician, Smith Lab
CIMR, University of Cambridge
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