Entering edit mode
Andrew Yee
▴
350
@andrew-yee-2667
Last seen 10.4 years ago
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
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