[BioC] parallel and GSVA

Robert Castelo robert.castelo at upf.edu
Fri Jan 11 14:11:43 CET 2013


Dear David,

just to discard any other issue not related to the parallel execution in 
your system, could you try to call the gsva() function adding the 
argument parallel.sz=1? does it work?

cheers,
robert.

On 01/11/2013 01:18 PM, David Iles wrote:
> Hi Folks,
>
> I want to run a GSVA analysis on a set of Affymetrix hgu133plus2 arrays. To familiarise myself with the GSVA code, I worked through the example in the vignette, but encountered the following issue...
>
>> data(leukemia)
>> data(c2BroadSets)
>> library(parallel)
>> filtered_eset<- nsFilter(leukemia_eset, require.entrez=TRUE, remove.dupEntrez=TRUE,
> +                           var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
> +                           feature.exclude="^AFFX")
>> leukemia_filtered_eset<- filtered_eset$eset
>> leukemia_es<- gsva(leukemia_filtered_eset, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs
> Mapping identifiers between gene sets and feature names
>    |                                                                                                               |   0%)
>
> The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec().
> Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__() to debug.
>
> ....etcetcetc. The process hangs here.
>
> I get the same messages with my own data. I must have overlooked something. Any suggestions?
>
> Dr David Iles
> School of Biology
> University of Leeds
> Leeds LS2 9JT
>
> d.e.iles at leeds.ac.uk<mailto:d.e.iles at leeds.ac.uk>
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] parallel  grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] RBGL_1.34.0          BiocInstaller_1.8.3  GSVAdata_0.99.9      hgu95a.db_2.8.0      org.Hs.eg.db_2.8.0
>   [6] RSQLite_0.11.2       DBI_0.2-5            GSVA_1.6.1           GSEABase_1.20.1      annotate_1.36.0
> [11] AnnotationDbi_1.20.3 Rgraphviz_2.2.1      graph_1.36.1         RColorBrewer_1.0-5   limma_3.14.3
> [16] genefilter_1.40.0    Biobase_2.18.0       BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.4  splines_2.15.2  stats4_2.15.2   survival_2.37-2 tools_2.15.2    XML_3.95-0.1    xtable_1.7-0
>
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-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550



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