On Mon, 12 Apr 2010, William Dunlap wrote:
-----Original Message-----
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@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
<murd...@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.
This is done at the moment in a very ad hoc way for functions in the
core packages. I will make a note to add something for curve. This
is an interesting case, as only the variable 'x' should be viewed as
special for code analysis purposes if I understand the intent in curve
properly.
Providing a mechanism for user functions to be annotated for code
analysis might be useful, and might help in making the handling of
core package functions with special evaluation rulesa little less ad
hloc. On the other hand I'm not sure I want to do anything that
encourages further use of nonstantard evaluation in new code.
luke
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
/Henrik
Duncan Murdoch
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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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