[Bioc-devel] Different behavior of get() between 2.9.0 and later versions`

Seth Falcon seth at userprimary.net
Wed Nov 4 18:02:54 CET 2009

On 11/3/09 11:07 PM, Luigi Marchionni wrote:
> Maybe you all guys already discussed that, but the stringsAsFactors=TRUE
> as global setting for R in genomics can be a problem.

Yes, in general global configuration that changes the behavior of many R 
functions poses a potential problem.  I would generally recommend not 
modifying such global options.  The Bioconductor project, for example, 
tests all software using default options (at least as far as I know).

> Clearly this is not the case for the problem I raised (or maybe it is,,,
> in my .Rprofile I set it to FALSE..., il check this), however, for
> annotation purposes factors (and cbind, data.frame, and the like) do not
> work.
> I ask you to make a major philosophical decision here...
> Either everybody set the option to FALSE in the code, orx the base
> setting change. or. I do not know.
> Or maybe there is a shortcut I am not aware of.
> You cannot really anticipate what the end-user will do...
> but if stringsAsFactors=TRUE is the scenario, one must take to keep it
> in mind.
> Am I making too complicate?

You have not described very clearly a specific problem you are having so 
it is difficult to provide any further assistance.

+ seth

More information about the Bioc-devel mailing list