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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