This chapter presents our guidance for changing stuff in your package: changing parameter names, changing function names, deprecating functions, and even retiring and archiving packages.
This chapter was initially contributed as a tech note on rOpenSci website by Scott Chamberlain; you can read the original version here.
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 dependencies of many other libraries are likely to be more careful about changes, and should be.
This chapter presents solutions that do not require the lifecycle package but you might still find it useful. We recommend reading the lifecycle documentation.
Sometimes parameter names must be changed for clarity, or some other reason.
A possible approach is check if deprecated arguments are not missing, and stop providing a meaningful message.
foo_bar <- function(x, y) {
if (!missing(x)) {
stop("use 'y' instead of 'x'")
}
y^2
}
foo_bar(x = 5)
#> Error in foo_bar(x = 5) : use 'y' instead of 'x' If you want to be more helpful, you could emit a warning but automatically take the necessary action:
foo_bar <- function(x, y) {
if (!missing(x)) {
warning("use 'y' instead of 'x'")
y <- x
}
y^2
}
foo_bar(x = 5)
#> 25Be 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. Instead, leave the argument around, throwing an error if it used.
If you must change a function name, do it gradually, as with any other change in your package.
Let’s say you have a function foo.
foo <- function(x) x + 1However, 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 where bar appears, make an alias like:
#' foo - add 1 to an input
#' @export
foo <- function(x) x + 1
#' @export
#' @rdname foo
bar <- fooWith the above solution, 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, e.g.,
#' foo - add 1 to an input
#' @export
foo <- function(x) {
warning("please use bar() instead of foo()", call. = FALSE)
bar(x)
}
#' @export
#' @rdname foo
bar <- function(x) x + 1After 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 + 1To remove a function from a package (let’s say your package name is helloworld), you can use the following protocol:
x (e.g., v0.2.0)In the function itself, use .Deprecated() to point to the replacement function:
foo <- function() {
.Deprecated("bar")
}There’s options in .Deprecated for specifying a new function name, as well as a new package name, which makes sense 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
NULLThis 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).
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("bar")
}Note that the message in .Defunct is an error so that the function stops whereas .Deprecated uses a warning that let the function proceed.
In addition, it’s good 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("bar")
}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 packageMake 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
NULLThis 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.
You don’t have to change the tests of deprecated functions until they are made defunct.
.Deprecated inside the function, did you change the parameters at all in the deprecated function, or create a new function that replaces the deprecated function, etc. Those changes should be tested if any made.suppressWarnings() could be used to suppress the warning thrown from .Deprecated, but tests are not user facing, so it is not that bad if the warning is thrown in tests, and the warning could even be used as a reminder to the maintainer.Once a function is made defunct, its tests are simply removed.
Software generally has a finite lifespan, and packages may eventually need to be archived. Archived packages are archived and moved to a dedicated GitHub organization, ropensci-archive. Prior to archiving, the contents of the README file should be moved to an alternative location (such as “README-OLD.md”), and replaced with minimal contents including something like the following:
# <package name>
[](https://www.repostatus.org/#unsupported)
[](https://github.com/ropensci/software-review/issues/<issue_number>)
This package has been archived. The former README is now in [README-old](<link-to-README-old>).The repo status badge should be “unsupported” for formerly released packages, or “abandoned” for former concept or WIP packages, in which case the badge code above should be replaced with:
[](https://www.repostatus.org/#abandoned)An example of a minimal README in an archived package is in ropensci-archive/monkeylearn. Once the README has been copied elsewhere and reduced to minimal form, the following steps should be followed:
Archived packages may be unarchived if authors or a new person opt to resume maintenance. For that please contact rOpenSci. They are transferred to the ropenscilabs organization.