[Rd] R CMD check returns NOTE about package data set as global variable

Hervé Pagès hpages at fhcrc.org
Fri Apr 6 23:17:39 CEST 2012

Hi Brian,

On 04/06/2012 02:04 PM, Brian G. Peterson wrote:
> On Fri, 2012-04-06 at 13:23 -0700, Hervé Pagès wrote:
>> test<-function() {
>>      RutgersMapB36<- NULL
>>      data(RutgersMapB36)
>>      return(RutgersMapB36[,1])
>> }
> That won't work, but this should:
> RutgersMapB36<- NULL
> test<-function() {
>      data(RutgersMapB36)
>      return(RutgersMapB36[,1])
> }
> Honestly, this is just another example of a non-helpful 'global
> variable' NOTE.  I've removed many of these from our packages, often by
> resorting to useless workarounds like this one, but I have never once
> gotten a valid NOTE out of this message.  We provided other examples
> earlier in a different thread.

Other people might have a different experience. I've personally seen a
lot of true positive "no visible binding for global variable" notes in
the Bioconductor check results.

In that sense 'R CMD check' is no different from other code checking
tools like e.g. gcc -Wall. There are sometimes false positives, it's
unavoidable. Personally I can live with that.


Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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