[R] R CMD check: no visible binding for global variable

[Rolf Turner]

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