Change in expected argument type `findKNN(subset=...)`

[MikeDMorgan]

Hi @LTLA - there seems to be an undocumented change to findKNN. Previously the subset argument would take a character vector input, but in Bioc 3.20 this leads to C++ type error:

Error: Not compatible with requested type: [type=character; target=integer].

13 . | stop(structure(list(message = "Not compatible with requested type: [type=character; target=integer].", call = NULL, cppstack = NULL), class = c("Rcpp::not_compatible", "C++Error", "error", "condition")))
-- | --

12. | generic_find_knn(X@ptr, num_neighbors = as.integer(k), force_variable_neighbors = is(k, "AsIs"), chosen = subset, num_threads = num.threads, last_distance_only = FALSE, report_index = !isFALSE(get.index), report_distance = !isFALSE(get.distance))
-- | --

11. | .local(X, k, get.index, get.distance, num.threads, subset, ..., BNPARAM = BNPARAM)
-- | --

10. | findKNN(ptr, k = k, get.index = get.index, get.distance = get.distance, num.threads = num.threads, subset = subset, ..., BPPARAM = BPPARAM)
-- | --

9. | findKNN(ptr, k = k, get.index = get.index, get.distance = get.distance, num.threads = num.threads, subset = subset, ..., BPPARAM = BPPARAM)
-- | --

8. eval(call, parent.frame())

7. eval(call, parent.frame())

6. | callGeneric(ptr, k = k, get.index = get.index, get.distance = get.distance, num.threads = num.threads, subset = subset, ..., BPPARAM = BPPARAM)
-- | --

5. | .local(X, k, get.index, get.distance, num.threads, subset, ..., BNPARAM = BNPARAM)
-- | --

4. findKNN(all_reduced_dims, k = nrow(nh_reduced_dims) + 1, subset = rownames(nh_reduced_dims))

3. findKNN(all_reduced_dims, k = nrow(nh_reduced_dims) + 1, subset = rownames(nh_reduced_dims)) at makeNhoods.R#188

2. .refined_sampling(random_vertices, X_reduced_dims, k) at makeNhoods.R#110

1. makeNhoods(traj_milo, prop = 0.1, k = 10, d = 30, refined = TRUE)

The obvious get around is for me to switch to using an integer/logical vector in miloR, but then that also means I need to add in a few extra checks on dimnames setting, etc.

Could either the documentation be updated to reflect this change in behaviour, or allow character vector input to subset?

Cheers me 'ol mucker.

[LTLA]

Oops. Should be fixed in the HEAD, pushed to BioC-devel as 1.99.3.

[MikeDMorgan]

Cheers, much obliged.