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?) 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
[Bioc-devel] Avoiding pkgs in Depends
3 messages · Benilton Carvalho, Vincent Carey, Hervé Pagès
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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... Cheers, H.
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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