From info at aghmed.fsnet.co.uk  Mon Apr 19 13:48:16 2010
From: info at aghmed.fsnet.co.uk (Michael Dewey)
Date: Mon, 19 Apr 2010 12:48:16 +0100
Subject: [Rd] R CMD check tells me 'no visible binding for
 globalvariable ', what does it mean?
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	<77EB52C6DD32BA4D87471DCD70C8D70002C34E95@NA-PA-VBE03.na.tibco.com>
	<alpine.LFD.2.00.1004151239120.12182@nokomis.stat.uiowa.edu>
	<62C82B39B8A85E4B95A18F7F7B852F8705658B333C@exvic-mbx03.nexus.csiro.au>
Message-ID: <Zen-1O3pST-0002On-RQ@smarthost01.mail.zen.net.uk>

At 01:09 16/04/2010, Mark.Bravington at csiro.au wrote:

>Speaking as a copious generator of CMD CHECK notes: I don't see that 
>there's a problem to be solved here-- i.e. I don't see why it's 
>worth changing good code or adding conventions just to circumvent 
>CMD CHECK notes. (If the code is bad, of course it should be 
>changed!) As the original poster said, the CMD CHECK note is only a 
>note, not a warning-- it's checking for "*possible* problems". With 
>my packages, especially debug & mvbutils, CHECK issues 100s of lines 
>of "notes", which (after inspection) I don't worry about-- they 
>arise from RCMD CHECK not understanding my code (eg non-default 
>scopings), not from coding errors. I would be very unhappy at having 
>to add enormous amounts of "explanation" to the packages simply to 
>alleviate a non-problem!
>
>Similarly, some compilers give notes about possibly non-initialized 
>variables etc, but these are often a result of the compiler not 
>understanding the code. I do look at them, and decide whether there 
>are problems that need fixing or not-- it's no big deal to ignore 
>them if not useful. Presumably the RCMD CHECK notes are useful to 
>some coders, in which case good; but nothing further really seems needed.

As the original poster can I endorse that, I was trying to improve my 
understanding. I was not worried by it.

Just to follow up on the suggestions made for eliminating the note I 
posted that Duncan's suggestion worked.

> >>>> 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)

  It does remove the note but then throws an error when called
Error in xy.coords(x, y) : 'x' and 'y' lengths differ

Henrik's suggestion of setting x to a value and then removing it 
works but in the light of the discussions I think I will just leave 
the note in place.

Thanks to everyone for their help and suggestions


>Mark
>
>--
>Mark Bravington
>CSIRO Mathematical & Information Sciences
>Marine Laboratory
>Castray Esplanade
>Hobart 7001
>TAS
>
>ph (+61) 3 6232 5118
>fax (+61) 3 6232 5012
>mob (+61) 438 315 623
>
>luke at stat.uiowa.edu wrote:
> > On Mon, 12 Apr 2010, William Dunlap wrote:
> >
> >>
> >>> -----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.
> >>
> >
> > 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
> >>>>
> >>>> ______________________________________________
> >>>> R-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>>
> >>>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel

Michael Dewey
http://www.aghmed.fsnet.co.uk



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