No visible binding for global variable Note in R CMD check

This is one of the potential "unanticipated consequences" of using subset non-interactively. As it says in the Warning section of ?subset:

This is a convenience function intended for use interactively. For programming it is better to use the standard subsetting functions like ‘[’, and in particular the non-standard evaluation of argument ‘subset’ can have unanticipated consequences.

From R version 2.15.1 onwards there is a way around this:

if(getRversion() >= "2.15.1")  utils::globalVariables(c("a", "othervar"))

As per the warning section of ?subset it is better to use subset interactively, and [ for programming.

I would replace a command like

subset(foo,a)

with

foo[foo$a]

or if foo is a dataframe:

foo[foo$a, ]

you might also like to use with if foo is a dataframe and the expression to be evaluated is complex:

with(foo, foo[a, ])

To get it past R CMD check you can either :

• Use get("b") (but that is onerous)
• Place a=b=NULL somewhere higher up in your function (that's what I do)

There was a thread on r-devel a while ago where somebody from r-core basically said (from memory) "NOTES are ok, you know. The assumption is that the author checked it and is ok with the NOTE.". But, I agree with you. I do prefer to have CRAN checks return a clean "OK" on all platforms. That way the user is left in no doubt that it passes checks ok.

EDIT :

Here is the r-devel thread I was remembering (from April 2010). So that appears to suggest that there are some situations where there is no known way to avoid the NOTE, but that's ok.