Package evolution - changing stuff in your package

Making packages is a great way to organize R code, whether it’s a set of scripts for personal use, a set of functions for internal company use or a lab group, or to distribute your new cool framework foobar to the masses. There’s a number of guides to writing packages, including http://r-pkgs.had.co.nz/.

As you develop packages there’s a number of issues that don’t often get much air time. I’ll cover some of them here.

Philosophy of changes

Everyone’s free to have their own opinion about how freely parameters/functions/etc. are changed in a library - rules about package changes are not enforced by CRAN or otherwise. Generally, as a library gets more mature, changes to user facing methods (i.e., exported functions in an R package) should become very rare. Libraries that are depended on by many other libraries are likely to be more careful, and should be, about changes.

Parameters: changing parameter names

Sometimes parameter names must be changed for clarity, or some other reason.

An approach I often use is to catch all parameters passed in to the function and check against some list of parameters, and stop or warn with a meaningful message.

foo_bar <- function(x, y) {
    calls <- names(sapply(match.call(), deparse))[-1]
    if(any("x" %in% calls)) {
        stop("use 'y' instead of 'x'")
    }
    y^2
}

foo_bar(x = 5)
#> Error in foo_bar(x = 5) : use 'y' instead of 'x' 

Or instead of stopping with error, you could check for use of x parameter and set it to y internally.

foo_bar <- function(x, y) {
    calls <- names(sapply(match.call(), deparse))[-1]
    if(any("x" %in% calls)) {
        y <- x
    }
    y^2
}

foo_bar(x = 5)
#> 25

Be aware of the parameter .... If your function has ..., and you have already removed a parameter (lets call it z), a user may have older code that uses z. When they pass in z, it’s not a parameter in the function definition, and will likely be silently ignored - not what you want. So do make sure to always check for removed parameters moving forward since you can’t force users to upgrade.

Functions: changing function names

If you must change a function name, do it gradually, as with any package changes.

Let’s say you have a function foo.

foo <- function(x) x + 1

However, you want to change the function name to bar.

Instead of simply changing the function name and foo no longer existing straight away, in the first version of the package that bar appears, make an alias like:

#' foo - add 1 to an input
#' @export
foo <- function(x) x + 1

#' @export
#' @rdname foo
bar <- foo

With the above, the user can use either foo() or bar() - either will do the same thing, as they are the same function.

It’s also useful to have a message but then you’ll only want to throw that message when they use the old function name, e.g.,

#' foo - add 1 to an input
#' @export
foo <- function(x) {
    if (as.character(match.call()[[1]]) == "foo") {
        warning("please use bar() instead of foo()", call. = FALSE)
    }
    x + 1
}

#' @export
#' @rdname foo
bar <- foo

After users have used the package version for a while (with both foo and bar), in the next version you can remove the old function name (foo), and only have bar.

#' bar - add 1 to an input
#' @export
bar <- function(x) x + 1

Functions: deprecate & defunct

To remove a function from a package (let’s say your package name is helloworld), I use the following protocol:

• Mark the function as deprecated in package version x (e.g., v0.2.0)

In the function itself, use .Deprecated() like:

foo <- function() {
    .Deprecated(msg = "'foo' will be removed in the next version")
}

There’s options in .Deprecated for specifying a new function name, as well as a new package name, which I do use when moving functions into different packages.

The message that’s given by .Deprecated is a warning, so can be suppressed by users with suppressWarnings() if desired.

Make a man page for deprecated functions like:

#' Deprecated functions in helloworld
#' 
#' These functions still work but will be removed (defunct) in the next version.
#' 
#' \itemize{
#'  \item \code{\link{foo}}: This function is deprecated, and will
#'  be removed in the next version of this package.
#' }
#' 
#' @name helloworld-deprecated
NULL

This creates a man page that users can access like ?helloworld-deprecated and they’ll see in the documentation index. Add any functions to this page as needed, and take away as a function moves to defunct (see below).

• In the next version (v0.3.0) you can make the function defunct (that is, completely gone from the package, except for a man page with a note about it).

In the function itself, use .Defunct() like:

foo <- function() {
    .Defunct(msg = "'foo' has been removed from this package")
}

Note that the message in .Defunct is an error, so the function stops - whereas .Deprecated returned a warning, letting the function proceed.

In addition, I like to add ... to all defunct functions so that if users pass in any parameters they’ll get the same defunct message instead of a unused argument message, so like:

foo <- function(...) {
    .Defunct(msg = "'foo' has been removed from this package")
}

Without ... gives:

foo(x = 5)
#> Error in foo(x = 5) : unused argument (x = 5)

And with ... gives:

foo(x = 5)
#> Error: 'foo' has been removed from this package

Make a man page for defunct functions like:

#' Defunct functions in helloworld
#' 
#' These functions are gone, no longer available.
#' 
#' \itemize{
#'  \item \code{\link{foo}}: This function is defunct.
#' }
#' 
#' @name helloworld-defunct
NULL

This creates a man page that users can access like ?helloworld-defunct and they’ll see in the documentation index. Add any functions to this page as needed. You’ll likely want to keep this man page indefinitely.

Others?

What are some other less discussed aspects of how to make changes in your packages?