I'm trying to use mclapply() with org.Hs.eg.db annotation package as
follows:

library('org.Hs.eg.db')
library('multicore')

foo <- list('EGFR', 'KRAS', 'TP53')

# the following works fine

result <- mclapply(foo, mc.cores=1, function(x) {
mget(x, env=revmap(org.Hs.egSYMBOL))
})

# however when you try using more than one core, you start generating error
messages

result <- mclapply(foo, mc.cores=2, function(x) {
mget(x, env=revmap(org.Hs.egSYMBOL))
})


> result
[[1]]
[1] "Error in sqliteExecStatement(con, statement, bind.data) : \n  RS-DBI
driver: (invalid dbManager handle)\n"

[[2]]
[1] "Error in sqliteExecStatement(con, statement, bind.data) : \n  RS-DBI
driver: (invalid dbManager handle)\n"

[[3]]
[1] "Error in sqliteExecStatement(con, statement, bind.data) : \n  RS-DBI
driver: (invalid dbManager handle)\n"


This question has been explored previously here
https://stat.ethz.ch/pipermail/r-sig-hpc/2009-August/000336.html on the HPC
mailing list, but I figured it may be worth while to try it on the
Bioconductor mailing list.  Any suggestions?

Thanks,
Andrew

> sessionInfo()
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] multicore_0.1-3     org.Hs.eg.db_2.3.6  RSQLite_0.8-3
[4] DBI_0.2-5           AnnotationDbi_1.8.1 Biobase_2.6.1
[7] Biostrings_2.14.12  IRanges_1.4.11

loaded via a namespace (and not attached):
[1] tools_2.10.1

	[[alternative HTML version deleted]]

