HI Gus,

The same problem here but using parallel. The problem lies in sqlite
threadsafe mode (Single-thread, Multi-thread, Serialized). As far as I
know, in windows the default binary comes with Serialized (thread safe) and
in unix no, thus you have to compile it from the source. But, if you are
using fork to parallelize, as in parallel or multicore library it stills
breaks the database conection. I don't know if for foreach works. Maybe you
should give it a try.

At present, the workaround I am using is to manualy split HyperGTest into
two functions: one to access annotation packages and other for the actual
hypergeometric test. So, in the code first secuentially access all the
annotation package/s to build the GO graphs and then run the tests in
parallel. This workaround is pretty much what you have been doing so far.

Regards,

Cristobal


2012/11/15 Gustavo Fernández Bayón <gbayon@gmail.com>

> Hi everybody.
>
> A simple question: is there any way I can perform a GO enrichment analysis
> without using the annotation packages?
>
> Problem is, I am trying to perform a series of GO analyses in parallel
> (with foreach), and I am experiencing problems with every call trying to
> access the same SqLite database. For now, I have solved it by putting
> "library(GOstats)" inside the inner foreach, but I was wondering if there
> is a better way.
>
> Regards,
> Gus
>
> ---------------------------
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