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R CMD check tells me 'no visible binding for global variable ', what does it mean?

13 messages · Michael Dewey, Duncan Murdoch, William Dunlap +6 more

Original
Michael Dewey
# 
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.


Michael Dewey
http://www.aghmed.fsnet.co.uk
Duncan Murdoch
#
On 12/04/2010 10:51 AM, Michael Dewey wrote:
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)

Duncan Murdoch
Henrik Bengtsson
#
On Mon, Apr 12, 2010 at 5:08 PM, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
...or

x <- NULL; rm(x); # Dummy to trick R CMD check
curve(orfun(x, exp(estimate)), from = 0.001, to = 0.999, add = TRUE)

/Henrik
William Dunlap
# 
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
1 day later
Michael Dewey
#
At 16:24 12/04/2010, Henrik Bengtsson wrote:

            

      
      
      
    

        
Just to draw a line under it my comment inline below

            

      
      
      
    

        
Yes, Duncan is correct that avoids the note.
I found this aesthetically more pleasing than Henrik's suggestion but 
other people's taste may be different.

Thanks for the prompt and interesting replies.

            

      
      
      
    

        

      
      
    

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

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Luke Tierney
    

    

      
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On Mon, 12 Apr 2010, William Dunlap wrote:

        

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Mark Bravington
    

    

      
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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.

Mark

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Henrik Bengtsson
    

    

      
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I think what people are also thinking about is that the policy for
publishing a package on CRAN is that it have to pass R CMD check with
no errors, warnings *or* notes.  So, in that sense notes are no
different from warnings.

At least that's why I go about and add some rare ad hoc code patching
in my code.

/Henrik

        
On Fri, Apr 16, 2010 at 2:09 AM,  <Mark.Bravington at csiro.au> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      John Fox
    

    

      
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Dear all,

I think that "notes" were introduced precisely to differentiate between
situations that may be innocuous and those that are more serious, the latter
producing "warnings" and "errors." The Rcmdr package, for example, generates
a whack of notes for code that works correctly and that I don't know how to
rewrite to get rid of the notes -- not to say that it would necessarily be
impossible to do so. Eliminating all packages that produce R CMD check notes
from CRAN is not a good idea, in my opinion.

Best,
 John

--------------------------------
John Fox
Senator William McMaster 
  Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
web: socserv.mcmaster.ca/jfox

            

      
      
      
    

        
On

            

      
      
      
    

        
globalvariable

            

      
      
      
    

        
notes.

            

      
      
      
    

        
poster

            

      
      
      
    

        
CHECK

            

      
      
      
    

        
non-default

            

      
      
      
    

        
add

            

      
      
      
    

        
non-

            

      
      
      
    

        
understanding

            

      
      
      
    

        
need

            

      
      
      
    

        
the

            

      
      
      
    

        
nothing

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Apr 16, 2010, at 4:38 AM, Henrik Bengtsson wrote:

        

            

      
      
      
    

        
Can you cite your reference, please? I see only (R-ext 1.5 Submitting a package to CRAN):

"Please ensure that you can run through the complete procedure with only warnings that you understand and have reasons not to eliminate. In principle, packages must pass R CMD check without warnings to be admitted to the main CRAN package area. If there are warnings you cannot eliminate (for example because you believe them to be spurious) send an explanatory note with your submission."

It talks explicitly about warnings, notes are not mentioned at all... That said, you should examine all notes and make sure they are not indications of problems.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Thomas Lumley
    

    

      
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On Fri, 16 Apr 2010, Simon Urbanek wrote:

        

            

      
      
      
    

        
In my experience, if a package is new or previously checked without notes, the CRAN maintainers will likely ask you to look at them to make sure they aren't problems, but there isn't any difficulty in getting a package on CRAN if it has notes.  A whole lot of packages on CRAN have notes even when checked on r-release.

CMD check notes are the R equivalent of old-time lint warnings in C, and as the First Commandment says:
 	 Thou shalt run lint frequently and study its pronouncements with care, for verily its perception and judgement oft exceed thine.
and the prophet (Henry Spencer) expands on this:
  ``Study'' doth not mean mindless zeal to eradicate every byte of lint output-if for no other reason, because thou just canst not shut it up about some things-but that thou should know the cause of its unhappiness and understand what worrisome sign it tries to speak of.


          -thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

  
  


  


      

    

    

      
      

        


  

        

      Henrik Bengtsson
    

    

      
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On Fri, Apr 16, 2010 at 5:51 PM, Thomas Lumley <tlumley at u.washington.edu> wrote:

            

      
      
      
    

        
WRONG: As already said by other, it is indeed possible to get packages
with 'notes' onto CRAN.

I have at some point in history became to believe this, but I went
back in my submission log and I only found one case and it is was more
Kurt H. kindly suggesting that I should fix an incorrectly formatted
license (reported as a NOTE).  Thanks for making me aware of this.

Sorry for adding noise!

/Henrik

            

      
      
      
    

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Michael Dewey
    

    

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

        

            

      
      
      
    

        
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.

            

      
      
      
    

        
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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

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