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

From: Hervé Pagès <>
Date: Fri, 06 Apr 2012 14:17:39 -0700

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

Phone:  (206) 667-5791
Fax:    (206) 667-1319

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