[BioC] parallel and GSVA

[David Iles]

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