[Rd] R CMD check tells me 'no visible binding for globalvariable ', what does it mean?

[William Dunlap]

> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Henrik Bengtsson
> Sent: Monday, April 12, 2010 8:24 AM
> To: Duncan Murdoch
> Cc: r-devel; Michael Dewey
> Subject: Re: [Rd] R CMD check tells me 'no visible binding 
> for globalvariable ', what does it mean?
> 
> On Mon, Apr 12, 2010 at 5:08 PM, Duncan Murdoch 
> <murdoch at stats.uwo.ca> wrote:
> > On 12/04/2010 10:51 AM, Michael Dewey wrote:
> >>
> >> When I run R CMD check on a package I have recently 
> started work on I get
> >> the following:
> >>
> >> * checking R code for possible problems ... NOTE
> >> addlinear: no visible binding for global variable 'x'
> >>
> >> I appreciate that this is only a NOTE and so I assume is 
> R's equivalent of
> >> 'This is perfectly legal but I wonder whether it is really what you
> >> intended' but I would like to understand it.
> >>
> >> In the relevant function addlinear the following function 
> is defined
> >> locally:
> >>
> >>    orfun <- function(x, oddsratio) {1/(1+1/(oddsratio * 
> (x/(1-x))))}
> >>
> >> and then used later in curve
> >>
> >>       curve(orfun(x, exp(estimate)), from = 0.001, to = 
> 0.999, add = TRUE)
> >>
> >> These are the only occurrences of 'x'.
> >>
> >> Is it just telling me that I have never assigned a value 
> to x? Or is it
> >> more sinister than that? As far as I can tell the function 
> does what I
> >> intended.
> >
> > The curve() function evaluates the first argument in a 
> strange way, and this
> > confuses the code checking.  (The variable name "x" is 
> special to curve().)
> >
> > I think you can avoid the warning by rewriting that call to 
> curve() as
> >
> > curve(function(x) orfun(x, exp(estimate)), from = 0.001, to 
> = 0.999, add =
> > TRUE)
> 
> ...or
> 
> x <- NULL; rm(x); # Dummy to trick R CMD check
> curve(orfun(x, exp(estimate)), from = 0.001, to = 0.999, add = TRUE)

Or we could come up with a scheme to telling the usage checking functions
in codetools that some some or all arguments of certain functions
are evaluated in odd ways so it should not check them.  E.g.,
   irregularUsage(curve, expr)
   irregularUsage(lm, subset, formula) # subset and formula arguments of lm
   irregularUsage(expression, ...) # ... arguments to expression
Perhaps one could add such indications to the NAMESPACE file
or to a new file in a package.  The former is kludgy but the
latter requires changes to the packaging system.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  


> 
> /Henrik
> 
> >
> > Duncan Murdoch
> >
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> >
> 
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