[R-pkg-devel] S3 generic/method consistency NOTE
This was the correct answer, thank you!
On Thu, Feb 6, 2025 at 00:10 Ivan Krylov <ikrylov at disroot.org> wrote:
? Wed, 5 Feb 2025 19:52:57 -0800 Zhian Kamvar <zkamvar at gmail.com> ?????:
Mismatches for methods registered for non-generic:
is:
function(object, class2)
is.genind:
function(x)
is:
function(object, class2)
is.genpop:
function(x)
sample:
function(x, size, replace, prob)
sample.haploGen:
function(x, n)
Neither methods::is nor base::sample are S3 generics, so these S3 method registrations are not needed: https://github.com/thibautjombart/adegenet/blob/e4874e73f0d39ebdddeca05b7eb1359fab771aaf/NAMESPACE#L50-L51 https://github.com/thibautjombart/adegenet/blob/e4874e73f0d39ebdddeca05b7eb1359fab771aaf/NAMESPACE#L73 In other words, calling is(new("genind", ...)) or sample(haploGen(...)) won't dispatch to is.genind() or sample.haploGen() anyway; these functions are probably intended to be called by their full names. Removing these lines and re-generating NAMESPACE should help: https://github.com/thibautjombart/adegenet/blob/e4874e73f0d39ebdddeca05b7eb1359fab771aaf/R/basicMethods.R#L546 https://github.com/thibautjombart/adegenet/blob/e4874e73f0d39ebdddeca05b7eb1359fab771aaf/R/basicMethods.R#L553 https://github.com/thibautjombart/adegenet/blob/e4874e73f0d39ebdddeca05b7eb1359fab771aaf/R/haploGen.R#L529 -- Best regards, Ivan