R help - May 2011 - R CMD check: no visible binding for global variable

Dear All,
              I have built a package which has a data.frame "annotIndex.rda
in its "data" folder.
              I am using this data frame within two functions in my package.

              Though my package works fine, yet when I do a
              R CMD check

              to my package I get the following two notes

              get.affy.ensembl: no visible binding for global variable
‘annotIndex’
              get.affy.id: no visible binding for global variable
‘annotIndex’

              I need help in understanding these notes, and how can I avoid
them.

yours sincerely,
Swaraj Basu

	[[alternative HTML version deleted]]

On 17/05/11 06:05, swaraj basu wrote:
> Dear All,
>                I have built a package which has a data.frame
"annotIndex.rda
> in its "data" folder.
>                I am using this data frame within two functions in my
package.
>
>                Though my package works fine, yet when I do a
>                R CMD check
>
>                to my package I get the following two notes
>
>                get.affy.ensembl: no visible binding for global variable
> ?annotIndex?
>                get.affy.id: no visible binding for global variable
> ?annotIndex?
>
>                I need help in understanding these notes, and how can I
avoid
> them.
This may be a case of the blind leading the blind, but here goes.

Understanding is simple (I think!). You are referring to an object 
"annotIndex"
inside a function, as in

foo <- function(x) {
x + annotIndex # Don't worry about the fact that this doesn't make
sense!
}

When the package checker looks at this it says "Hmmmm, annotIndex has never
been defined (inside "foo") so it might not exist. There *could* be a 
problem here."

What to do about it: One solution is just to ignore the note; it's only 
a note,
not an error, nor even a warning, and you know that there isn't actually
a problem.

The solution that is often suggested --- see

RSiteSearch("{no visible
binding}",restrict=c("Rhelp02","Rhelp08"))

of assigning annotIndex a value, e.g. annotIndex <- NULL, at the beginning
of your function doesn't work here since that local NULL value will 
over-ride the
global value that you really want.

You might try (the appropriate analogue of) x + 
get("annotIndex",envir=.GlobalEnv).

That should satisfy the package checker. (I haven't tested it, but.)

Dunno if this has an adverse impact on the efficiency of your code.

HTH

cheers,

Rolf Turner

Follow-up to my previous message; just remembered another work-around
for the ``no visible binding'' note.

Wrap up your calls that involve "annotIndex" in text strings and then
evaluate these strings.

E.g.:

     xxx <- "y <- x + annotIndex"
     eval(parse(text=xxx))

That will fool the package checker! :-)

Might be more efficient than my suggestion of using ``get()''.

     cheers,

         Rolf Turner

If you install you package does the following work
in a fresh R session
   library(yourPackage)
   annotIndex
or do you need to say data(annotIndex) before using
that object?  (This may depend on whether yourPackage
uses a namespace or not.)  If so then adding the line
   LazyData: yes
to DESCRIPTION should eliminate the need for the call
to data(annotIndex) and make check happy as well.
It works for me with R 2.13.0 on Linux.

I am not an expert on the details of the DESCRIPTION
and NAMESPACE files in R packages and others who know
better will probably chime in.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of swaraj basu
> Sent: Monday, May 16, 2011 11:06 AM
> To: r-help at r-project.org
> Subject: [R] R CMD check: no visible binding for global variable
> 
> Dear All,
>               I have built a package which has a data.frame 
> "annotIndex.rda
> in its "data" folder.
>               I am using this data frame within two functions 
> in my package.
> 
>               Though my package works fine, yet when I do a
>               R CMD check
> 
>               to my package I get the following two notes
> 
>               get.affy.ensembl: no visible binding for global variable
> 'annotIndex'
>               get.affy.id: no visible binding for global variable
> 'annotIndex'
> 
>               I need help in understanding these notes, and 
> how can I avoid
> them.
> 
> yours sincerely,
> Swaraj Basu
> 
> 	[[alternative HTML version deleted]]
> 
>