Entering edit mode
Hi all,
I am using foreach and doMC packages to do some parallel GO analyses
with GOstats.
If I use 3 or less processors at the same time (i.e. the foreach loop
goes up to n=3) all works fine but when I want to use n>3 I get this
error:
"RSQLite driver: (RS_SQLite_fetch: failed: database disk image is
malformed)"
I assume that the error comes from the multiple connections to the
annotation packages used by GOstats. Is there a way to overcome this
problem?
Thanks
Adi L. Tarca
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.2.1 multicore_0.1-3 foreach_1.3.0
[4] codetools_0.2-2 iterators_1.0.3 GOstats_2.16.0
[7] RSQLite_0.9-3 DBI_0.2-5 graph_1.28.0
[10] Category_2.16.0 AnnotationDbi_1.12.0 Biobase_2.10.0
[13] limma_3.6.6
loaded via a namespace (and not attached):
[1] annotate_1.28.0 genefilter_1.32.0 GO.db_2.4.5
GSEABase_1.12.1
[5] RBGL_1.26.0 splines_2.12.0 survival_2.35-8 tools_2.12.0
[9] XML_3.2-0 xtable_1.5-6
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