[R] R CMD check warning

[Uwe Ligges]

On 05.05.2011 21:20, Ray Brownrigg wrote:
> On 6/05/2011 6:06 a.m., swaraj basu wrote:
>> Dear All,
>> I am trying to build a package for a set of functions. I am
>> able to build the package and its working fine. When I check it with
>> R CMD check
>>
>> I get a following warning : no visible global function
>> definition for ‘biocLite’
>>
>> I have used biocLite to load a user defined library from
>> within a function if that library is not pre-installed
>>
>> if(is.element(annotpkg, installed.packages()[,1]) == "FALSE"){
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite(annotpkg)
>> library(annotpkg,character.only=TRUE)
>> }
>>
>> Should I ignore this error or there is a workaround for the
>> warning. My package is working fine though still I guess the warning
>> has to
>> have significance. Please help in clarifying this
>> warning.
>>
> Your source() call generates the function biocLite() in such a way that
> R CMD check cannot know, so a workaround is to precede the source()
> statement with something like:
> biocLite <- function(x) 0
>
> [I don't know if there is a 'best' way to do this.]
>
> In general Warnings are just that - they point you to a possible fault,
> but there is not enough information for the code to make a final
> determination.


Or just set ask people (or try yourself) to use install.packages() with 
the corresponding BioC repository selected. I still do not get the point 
why install.packages() and friends are not sufficient.

Best,
Uwe


> HTH
> Ray Brownrigg
>
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