[Bioc-devel] Avoiding pkgs in Depends

Hervé Pagès hpages at fhcrc.org
Wed Mar 21 23:05:53 CET 2012

Hi Benilton,

On 03/21/2012 01:12 PM, Benilton Carvalho wrote:
> Hi,
> say I need a few functions from Biobase and for a number of reasons I
> don't want it in Depends.
> So I add it to Imports and, in my NAMESPACE file, I add something like:
> importFrom(Biobase, assayDataElementNames)
> Everything works as expected...
> But if I want to use assayDataElementNames in one of the examples, it
> won't be available for obvious reasons.
> What is the proper strategy to follow?
> 1) Do a library(Biobase) explicitly in the example? (Maybe
> library(pkg) is only bad within methods/functions, but acceptable in
> examples?)

I would do 1). The user also needs to be able to access the man page
for the things s/he is using. Does that mean that maybe you should
also put Biobase in Suggests? I'm not sure: technically it's not
needed since Biobase will get installed anyway when your package is
installed but...


> 2) Use Biobase::assayDataElementNames in the example?
> 3) Export, from my package, assayDataElementNames??? This seems
> incorrect/inappropriate and will even bug me to write a man page for
> assayDataElementNames, which already exists in Biobase.
> Thanks,
> benilton
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Hervé Pagès

Program in Computational Biology
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