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

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 > > _______________________________________________ > 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 >