[BioC] parallel and GSVA

[Robert Castelo]

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