Hopefully to too much of a tangent: A related problem this check doesn’t catch
is accidental top-level redefinitions in package code, such as
## a.R:
helper <- function() 1
f <- function() {
helper()
}
# “cool, f() must return 1"
## b.R:
helper <- function(x) 2
g <- function() {
helper()
}
# “cool, g() must return 2"
## Runtime:
# > c(pkg::f(), pkg::g())
# [1] 2 2
# “oh right, only the last definition of helper() is used”
I’ve seen several variants of this issue in code from folks who are new to
package development, especially if they're naively refactoring something that
started out as an interactively-run analysis. Collaborators who are puzzled by
it get my “packages are collections of objects not sequences of expressions,
yes that needs to be in your mental model, here’s the link to RWE again” talk,
but I would be happy to be able to point them to a check result to go along
with it.
I don’t think this is grounds on its own to change a 20-year precedent, but in
case anyone is collecting wishlist reasons to make the check look harder...
Thanks,
Chris
> On Feb 6, 2024, at 3:17 PM, Martin Morgan <mtmorgan....@gmail.com> wrote:
>
> I went looking and found this in codetools, where it's been for 20 years
>
> https://gitlab.com/luke-tierney/codetools/-/blame/master/R/codetools.R?ref_type=heads#L951
>
> I think the call stack in codetools is checkUsagePackage -> checkUsageEnv ->
> checkUsage, and these are similarly established. The call from the tools
> package
> https://github.com/wch/r-source/blame/95146f0f366a36899e4277a6a722964a51b93603/src/library/tools/R/QC.R#L4585
> is also quite old.
>
> I'm not sure this had been said explicitly, but perhaps the original intent
> was to protect against accidentally redefining a local function. Obviously
> one could do this with a local variable too, though that might less often be
> an error…
>
> toto <- function(mode) {
> tata <- function(a, b) a * b # intended
> tata <- function(a, b) a / b # oops
> …
> }
>
> Another workaround is to actually name the local functions
>
> toto <- function(mode) {
> tata <- function(a, b) a * b
> titi <- function(u, v, w) (u + v) / w
> if (mode == 1)
> tata
> else
> titi
> }
>
> … or to use a switch statement
>
> toto <- function(mode) {
> ## fun <- switch(…) for use of `fun()` in toto
> switch(
> mode,
> tata = function(a, b) a * b,
> titi = function(u, v, w) (u + v) / w,
> stop("unknown `mode = '", mode, "'`")
> )
> }
>
> … or similarly to write `fun <- if … else …`, assigning the result of the
> `if` to `fun`. I guess this last formulation points to the fact that a more
> careful analysis of Hervé's original code means that `fun` can only take one
> value (only one branch of the `if` can be taken) so there can only be one
> version of `fun` in any invocation of `toto()`.
>
> Perhaps the local names (and string-valued 'mode') are suggestive of special
> case, so serve as implicit documentation?
>
> Adding `…` to `tata` doesn't seem like a good idea; toto(1)(3, 5, 7) no
> longer signals an error.
>
> There seems to be a lot in common with S3 and S4 methods, where `toto`
> corresponds to the generic, `tata` and `titi` to methods. This 'dispatch' is
> brought out by using `switch()`. There is plenty of opportunity for thinking
> that you're invoking one method but actually you're invoking the other. For
> instance with dplyr, I like that I can tbl |> print(n = 2) so much that I
> find myself doing this with data.frame df |> print(n = 2), which is an error
> (`n` partially matches `na.print`, and 2 is not a valid value); both methods
> silently ignore the typo print(m = 2).
>
> Martin Morgan
>
> From: R-devel <r-devel-boun...@r-project.org> on behalf of Henrik Bengtsson
> <henrik.bengts...@gmail.com>
> Date: Tuesday, February 6, 2024 at 4:34 PM
> To: Izmirlian, Grant (NIH/NCI) [E] <izmir...@mail.nih.gov>
> Cc: r-devel@r-project.org <r-devel@r-project.org>
> Subject: Re: [Rd] [EXTERNAL] Re: NOTE: multiple local function definitions
> for ?fun? with different formal arguments
> Here's a dummy example that I think illustrates the problem:
>
> toto <- function() {
> if (runif(1) < 0.5)
> function(a) a
> else
> function(a,b) a+b
> }
>
>> fcn <- toto()
>> fcn(1,2)
> [1] 3
>> fcn <- toto()
>> fcn(1,2)
> [1] 3
>> fcn <- toto()
>> fcn(1,2)
> Error in fcn(1, 2) : unused argument (2)
>
> How can you use the returned function, if you get different arguments?
>
> In your example, you cannot use the returned function without knowing
> 'mode', or by inspecting the returned function. So, the warning is
> there to alert you to a potential bug. Anecdotally, I'm pretty sure
> this R CMD check NOTE has caught at least one such bug in one of
> my/our packages.
>
> If you want to keep the current design pattern, one approach could be
> to add ... to your function definitions:
>
> toto <- function(mode)
> {
> if (mode == 1)
> fun <- function(a, b, ...) a*b
> else
> fun <- function(u, v, w) (u + v) / w
> fun
> }
>
> to make sure that toto() returns functions that accept the same
> minimal number of arguments.
>
> /Henrik
>
> On Tue, Feb 6, 2024 at 1:15 PM Izmirlian, Grant (NIH/NCI) [E] via
> R-devel <r-devel@r-project.org> wrote:
>>
>> Because functions get called and therefore, the calling sequence matters.
>> It’s just protecting you from yourself, but as someone pointed out, there’s
>> a way to silence such notes.
>> G
>>
>>
>> From: Hervé Pagès <hpages.on.git...@gmail.com>
>> Sent: Tuesday, February 6, 2024 2:40 PM
>> To: Izmirlian, Grant (NIH/NCI) [E] <izmir...@mail.nih.gov>; Duncan Murdoch
>> <murdoch.dun...@gmail.com>; r-devel@r-project.org
>> Subject: Re: [EXTERNAL] Re: [Rd] NOTE: multiple local function definitions
>> for ?fun? with different formal arguments
>>
>>
>> On 2/6/24 11:19, Izmirlian, Grant (NIH/NCI) [E] wrote:
>> The note refers to the fact that the function named ‘fun’ appears to be
>> defined in two different ways.
>>
>> Sure I get that. But how is that any different from a variable being defined
>> in two different ways like in
>>
>> if (mode == 1)
>> x <- -8
>> else
>> x <- 55
>>
>> This is such a common and perfectly fine pattern. Why would this be
>> considered a potential hazard when the variable is a function?
>>
>> H.
>>
>> From: Hervé Pagès
>> <hpages.on.git...@gmail.com><mailto:hpages.on.git...@gmail.com>
>> Sent: Tuesday, February 6, 2024 2:17 PM
>> To: Duncan Murdoch
>> <murdoch.dun...@gmail.com><mailto:murdoch.dun...@gmail.com>; Izmirlian,
>> Grant (NIH/NCI) [E] <izmir...@mail.nih.gov><mailto:izmir...@mail.nih.gov>;
>> r-devel@r-project.org<mailto:r-devel@r-project.org>
>> Subject: [EXTERNAL] Re: [Rd] NOTE: multiple local function definitions for
>> ?fun? with different formal arguments
>>
>>
>> Thanks. Workarounds are interesting but... what's the point of the NOTE in
>> the first place?
>>
>> H.
>> On 2/4/24 09:07, Duncan Murdoch wrote:
>> On 04/02/2024 10:55 a.m., Izmirlian, Grant (NIH/NCI) [E] via R-devel wrote:
>>
>>
>> Well you can see that yeast is exactly weekday you have. The way out is to
>> just not name the result
>>
>> I think something happened to your explanation...
>>
>>
>>
>>
>> toto <- function(mode)
>> {
>> ifelse(mode == 1,
>> function(a,b) a*b,
>> function(u, v, w) (u + v) / w)
>> }
>>
>> It's a bad idea to use ifelse() when you really want if() ... else ... . In
>> this case it works, but it doesn't always. So the workaround should be
>>
>>
>> toto <- function(mode)
>> {
>> if(mode == 1)
>> function(a,b) a*b
>> else
>> function(u, v, w) (u + v) / w
>> }
>>
>>
>>
>>
>>
>>
>> ________________________________
>> From: Grant Izmirlian <izmirlidr...@gmail.com><mailto:izmirlidr...@gmail.com>
>> Date: Sun, Feb 4, 2024, 10:44 AM
>> To: "Izmirlian, Grant (NIH/NCI) [E]"
>> <izmir...@mail.nih.gov><mailto:izmir...@mail.nih.gov>
>> Subject: Fwd: [EXTERNAL] R-devel Digest, Vol 252, Issue 2
>>
>> Hi,
>>
>> I just ran into this 'R CMD check' NOTE for the first time:
>>
>> * checking R code for possible problems ... NOTE
>> toto: multiple local function definitions for �fun� with different
>> formal arguments
>>
>> The "offending" code is something like this (simplified from the real code):
>>
>> toto <- function(mode)
>> {
>> if (mode == 1)
>> fun <- function(a, b) a*b
>> else
>> fun <- function(u, v, w) (u + v) / w
>> fun
>> }
>>
>> Is that NOTE really intended? Hard to see why this code would be
>> considered "wrong".
>>
>> I know it's just a NOTE but still...
>>
>> I agree it's a false positive, but the issue is that you have a function
>> object in your function which can't be called unconditionally. The
>> workaround doesn't create such an object.
>>
>> Recognizing that your function never tries to call fun requires global
>> inspection of toto(), and most of the checks are based on local inspection.
>>
>> Duncan Murdoch
>>
>> ______________________________________________
>> R-devel@r-project.org<mailto:R-devel@r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> --
>>
>> Hervé Pagès
>>
>>
>>
>> Bioconductor Core Team
>>
>> hpages.on.git...@gmail.com<mailto:hpages.on.git...@gmail.com>
>> CAUTION: This email originated from outside of the organization. Do not
>> click links or open attachments unless you recognize the sender and are
>> confident the content is safe.
>>
>>
>> --
>>
>> Hervé Pagès
>>
>>
>>
>> Bioconductor Core Team
>>
>> hpages.on.git...@gmail.com<mailto:hpages.on.git...@gmail.com>
>> CAUTION: This email originated from outside of the organization. Do not
>> click links or open attachments unless you recognize the sender and are
>> confident the content is safe.
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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>
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>
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