[Bioc-devel] using data() inside a package function

[Martin Morgan]

On 08/30/2011 10:17 AM, Stephanie M. Gogarten wrote:
> I stored the results of a calculation in the data directory of my
> package, so it can be loaded when needed by a function.
>
> data/relationsMeanVar.RData
>
> I then refer to this in the function as
> data(relationsMeanVar)
> FS <- relationsMeanVar$FullSibs

Hi Stephanie --

a little speculative on my part but data() as invoked above loads the 
data into the global environment, which would be a bad thing (e.g. 
clobbering variables of the same name the user might have created, but 
in generally having a side-effect). So maybe

   env = new.env(parent=emptyenv())
   data(relationsMeanVar, envir=env)
   FS = env[["relationsMeanVar"]]$FullSibs

I'm not sure whether this calms R CMD check or not, but is probably 
better regardless.

Martin

>
> This generates a NOTE in R CMD check:
> * checking R code for possible problems ... NOTE
> ibdPlot: no visible binding for global variable ‘relationsMeanVar’
>
> Is there a better way to do this?
>
> thanks,
> Stephanie Gogarten
>
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