No visible binding for global variable Note in R CMD check

Question

I noticed in checking a package that I obtain notes "no visible binding for global variable" when I use functions like subset that use verbatim names of list elements as arguments.

For example with a data frame:

foo <- data.frame(a=c(TRUE,FALSE,TRUE),b=1:3)

I can do silly things like:

subset(foo,a)
transform(foo,a=b)

Which work as expected. The R code check in R CMD however doesn't understand that these refer to elements and complains about there not being any visible bindings of global variables.

While this works ok, I don't really like having notes in my package and prefer for it to pass the check with no errors, warnings and notes at all. I also don't really want to rework my code too much. Is there a way to write these codes so that it is clear the arguments do not refer to global variables?

Answer 1

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.

Answer 2

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.

Answer 3

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

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

Answer 4

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, ])

Answer 5

I had this issue and traced it to my ggplot2 section.

This code provided the error:

ggplot2::ggplot(data = spec.df, ggplot2::aes(E.avg, fraction)) +
  ggplot2::geom_line() +
    ggplot2::ggtitle(paste0(title))

Adding the data name to the parameters eliminated the not:

ggplot2::ggplot(data = spec.df, ggplot2::aes(spec.df$E.avg, spec.df$fraction)) +
  ggplot2::geom_line() +
    ggplot2::ggtitle(paste0(title))