Thanks, Dirk and Michael,
In my opinion, there are several reasons why you wouldn't want to just do
importFrom(stats, filter). Using devtools::load_all() typing "filte" in the
console now only brings up Base::Filter and stats::filter and not the
function that will actually be called from filter(),
i.e., my internal filter function. Additionally, you can't do this if the
reason you did pkg::foo() was to avoid nameclash between two different
packages, e.g., extend my example with also dplyr::filter. You can't add
importFrom(stats, filter)
importFrom(dplyr, filter)
How I see it, the only safe way to do it in this case is to use
stats::filter and dplyr::filter outside the R6 class, either by refactoring
(which might make the code more unreadable) or adding an unused function,
such as this:
avoid_cran_note() {
stats::filter(1:10, rep(1, 3))
my_data <- data.frame(
x = 1:5,
y = c(10, 20, 30, 40, 50)
)
dplyr::filter(my_data, my_data$x > 3)
}
Neither approach seems ideal to me.
Best regards,
Bjarke
Den tors. 12. feb. 2026 kl. 23.53 skrev Michael Chirico <
[email protected]>:
> R6 is a _build-time_ dependency for your package. It may be possible for a
> user without R6 installed to run your package without issue from the built
> tarball. R today doesn't really have a concept of a build-time dependency
> in the DESCRIPTION
>
> 'stats' is more of a false positive -- {codetools} simply doesn't know how
> to check the R6 object DataProcessor (which it sees as an environment and
> doesn't walk completely). It could find 'stats::' if it looked at
>
>
> body(getNamespace(<pkg>)$DataProcessor$public_methods$filter_data)[[3]][[3]][[1]]
>
> Anyway, Dirk's advice is correct: you can just add the entries to your
> NAMESPACE:
>
> importFrom(R6, R6class)
> importFrom(stats, filter)
>
> Once that's done, you can choose whether to continue namespace-qualifying
> the calls inside the sources.
>
> You could also explore if just putting the packages in Suggests, not
> Imports, works.
>
> Mike C
>
> On Thu, Feb 12, 2026 at 2:33 PM Dirk Eddelbuettel <[email protected]> wrote:
>
>>
>> On 12 February 2026 at 15:52, Bjarke Hautop wrote:
>> | Hi all,
>> |
>> | R CMD check gives a false positive locally when the only usage of an
>> | imported package is through pkg::foo() inside an R6 class. This GitHub
>> repo
>> | contains a full MWE, with log files and a more elaborate explanation:
>> | https://github.com/BjarkeHautop/RCMDcheckFalsePositive
>> |
>> | The R package contains a single .R file with this (I'm aware you don't
>> have
>> | to import base packages explicitly, but this is an MWE with only base
>> | packages (except R6)):
>> |
>> | filter <- function() {
>> | message("This is a custom filter function.")
>> | }
>> |
>> | DataProcessor <- R6::R6Class(
>> | "DataProcessor",
>> | public = list(
>> | data = NULL,
>> | initialize = function(data) self$data <- data,
>> |
>> | filter_data = function(data) {
>> | filter()
>> | self$data <- stats::filter(self$data, rep(1, 3))
>> | }
>> | )
>> | )
>> |
>> | When running R CMD check, it will generate the following NOTE:
>> |
>> | * checking dependencies in R code ... NOTE
>> | Namespaces in Imports field not imported from:
>> | ‘R6’ ‘stats’
>>
>> Thanks for posting a full and complete example! From a quick glance your
>> problem may be that while you DO have the the packages in DESCRIPTION you
>> DO NOT import them in NAMESPACE. The error message could arguably be more
>> explicit but that seems to be the case here.
>>
>> Hope this helps, Dirk
>>
>> | Interestingly, the NOTE disappears on CRAN release/dev winbuilder.
>> |
>> | My questions are:
>> |
>> | 1. Is this the intended behavior of R CMD check, or is it a bug that it
>> | fails to detect usage of packages inside
>> | R6 classes? If intended (e.g., due to it being too expensive to check
>> for
>> | :: in "hidden places") should this be
>> | mentioned somewhere on WRE? Currently
>> | [WRE](
>> |
>> https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Package-Dependencies-1
>> )
>> | says:
>> | *"The ‘Imports’ field should not contain packages which are not imported
>> | from (via the NAMESPACE file or :: or ::: operators)"*
>> | indicating that `::` usage should be fully supported.
>> |
>> | 2. How/Why does the NOTE disappear when checking on CRAN dev winbuilder?
>> | Can I replicate this behavior locally using R CMD check? Will it pass on
>> | CRAN?
>> |
>> | Best regards,
>> | Bjarke
>> |
>> | [[alternative HTML version deleted]]
>> |
>> | ______________________________________________
>> | [email protected] mailing list
>> | https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | [email protected]
>>
>> ______________________________________________
>> [email protected] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>
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