[BioC] multicore package and AnnotationDbi

[Vincent Carey]

You aren't supplying many details, but there is a principle that
should help you get around this problem.

I can reproduce your error message with the following:

library(org.Hs.eg.db)
library(multicore)
g = function(x) get("1", org.Hs.egSYMBOL)
mclapply(1:3, g)

on the other hand, if, in a fresh session, i define

f = function(x) {library(org.Hs.eg.db); get("1", org.Hs.egSYMBOL)}
library(multicore)
mclapply(1:3, f)

all is well.  the principle is to fork before building the
connections.  there may be other solutions.


On Wed, Mar 17, 2010 at 4:48 AM,  <stephen.rudd at orionpharma.com> wrote:
> 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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>
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