I am conducting GO enrichment using GOstats, and upon executing the hyperGTest function

overBP <- hyperGTest(params)

a series of warning messages are printed out:

## Warning in .local(name, pos, envir, all.names, pattern): ignoring 'pos' argument
## Warning in .local(name, pos, envir, all.names, pattern): ignoring 'envir' argument
## Warning in .local(name, pos, envir, all.names, pattern): ignoring 'all.names' argument

I've been unable to find anything about these warnings. The script seems to run fine otherwise; I'm using R 3.2 with Bioconductor 3.1. Any help on this matter would be appreciated.

The short answer is that you don't have to worry - these are just warnings and things are proceeding as expected. We do however probably need to make changes so people don't have to see these warnings.