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stephen.rudd@orionpharma.com
▴
10
@stephenruddorionpharmacom-3965
Last seen 9.6 years ago
Dear BioC list,
I am trying to optimize the performance of some data reporting tools
and am struggling to deploy multi-threaded enrichment analysis
methods. If I attempt to use the multicore::mclapply method with
functions that utilize the AnnotationDbi package I am met with an
error
"Error in sqliteExecStatement(con, statement, bind.data) : \n RS-DBI
driver: (invalid dbManager handle)\n"
There has been brief mention of this in the past that "the child
processes that are forked by the mclapply function are not able to use
the database connection that they inherited from their parent." - are
there any solutions as to how this might be worked around?
I'm using a rather vanilla R installation
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
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] limma_3.2.1 XML_2.6-0 rat2302.db_2.3.5
[4] org.Rn.eg.db_2.3.5 affy_1.24.2 multicore_0.1-3
[7] GO.db_2.3.5 GOstats_2.12.0 RSQLite_0.8-2
[10] DBI_0.2-5 graph_1.24.2 Category_2.12.0
[13] AnnotationDbi_1.8.1 Biobase_2.6.1 OrionR_0.4.211
loaded via a namespace (and not attached):
[1] affyio_1.14.0 annotate_1.24.1 genefilter_1.28.2
[4] GSEABase_1.8.0 preprocessCore_1.8.0 RBGL_1.22.0
[7] splines_2.10.1 survival_2.35-8 tools_2.10.1
[10] xtable_1.5-6
Thanks - greetings from Finland
Stephen
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