Pass CHECK.

knncolle · Jul 29, 2024 · 448186c · 448186c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BiocNeighbors
-Version: 1.21.2
-Date: 2022-12-17
+Version: 1.21.3
+Date: 2024-07-28
 Title: Nearest Neighbor Detection for Bioconductor Packages
 Authors@R: c(person("Aaron", "Lun", role=c("aut", "cre", "cph"),
     email="infinite.monkeys.with.keyboards@gmail.com"))

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -5,9 +5,10 @@ setGeneric("buildIndex", signature=c("X", "BNPARAM"), function(X, transposed=FAL
 # This is explicitly a S4 generic so that developers can extend it at the R
 # level, not at the C++ level. We need to support dispatch on both X and
 # BNPARAM as X could be an arbitrary index structure (i.e., not an external
-# pointer). If we only dispatched on BNPARAM, the developer wouldn't be able to
-# select the correct method based on the type of a prebuilt non-pointer index
-# without also being supplied the BNPARAM, which is not ergonomic for the user.
+# pointer). If we only dispatched on BNPARAM, a user could call the method with
+# a prebuilt X that doesn't match the BNPARAM. This means that the developer of
+# the BNPARAM method would be responsible for figuring out what to do with a X
+# that they don't know anything about, which is pretty weird.
 
 #' @export
 #' @rdname findKNN

diff --git a/R/AnnoyParam.R b/R/AnnoyParam.R
@@ -85,7 +85,7 @@ setMethod("show", "AnnoyParam", function(object) {
 
 #' @export
 #' @rdname AnnoyParam
-setMethod("buildIndex", c("ANY", "AnnoyParam"), function(X, transposed = FALSE, ..., BNPARAM) {
+setMethod("buildIndex", c("matrix", "AnnoyParam"), function(X, transposed = FALSE, ..., BNPARAM) {
     X <- .coerce_matrix_build(X, transposed)
     build_annoy(X, num_trees=BNPARAM@ntrees, search_mult=BNPARAM@search.mult, distance=BNPARAM@distance)
 })
diff --git a/R/BiocNeighborParam-class.R b/R/BiocNeighborParam-class.R
@@ -4,12 +4,13 @@
 #' 
 #' @details
 #' The BiocNeighborParam class is a virtual base class on which other parameter objects are built.
-#' There are currently 4 concrete subclasses:
+#' There are currently 5 concrete subclasses in \pkg{BiocNeighbors}:
 #' \describe{
-#'     \item{}{\code{\link{KmknnParam}}: exact nearest-neighbor search with the KMKNN algorithm.}
-#'     \item{}{\code{\link{VptreeParam}}: exact nearest-neighbor search with the VP tree algorithm.}
-#'     \item{}{\code{\link{AnnoyParam}}: approximate nearest-neighbor search with the Annoy algorithm.}
-#'     \item{}{\code{\link{HnswParam}}: approximate nearest-neighbor search with the HNSW algorithm.}
+#' \item{\code{\link{KmknnParam}}:}{Exact nearest-neighbor search with the KMKNN algorithm.}
+#' \item{\code{\link{VptreeParam}}:}{Exact nearest-neighbor search with the tree algorithm.}
+#' \item{\code{\link{ExhaustiveParam}}:}{Exact nearest-neighbor search via brute-force.}
+#' \item{\code{\link{AnnoyParam}}:}{Approximate nearest-neighbor search with the Annoy algorithm.}
+#' \item{\code{\link{HnswParam}}:}{Approximate nearest-neighbor search with the HNSW algorithm.}
 #' }
 #' 
 #' These objects hold parameters specifying how each algorithm should be run on an arbitrary data set.
@@ -39,7 +40,7 @@
 #' @aliases
 #' BiocNeighborParam-class
 #' show,BiocNeighborParam-method
-#' bndistance,BiocNeighborParam-method
+#' bndistance
 #' [[,BiocNeighborParam-method
 #' [[<-,BiocNeighborParam-method
 #'

diff --git a/R/ExhaustiveParam.R b/R/ExhaustiveParam.R
@@ -43,7 +43,7 @@ ExhaustiveParam <- function(distance=c("Euclidean", "Manhattan", "Cosine")) {
 
 #' @export
 #' @rdname ExhaustiveParam
-setMethod("buildIndex", c("ANY", "ExhaustiveParam"), function(X, transposed = FALSE, ..., BNPARAM) {
+setMethod("buildIndex", c("matrix", "ExhaustiveParam"), function(X, transposed = FALSE, ..., BNPARAM) {
     X <- .coerce_matrix_build(X, transposed)
     build_exhaustive(X, distance=BNPARAM@distance)
 })
diff --git a/R/HnswParam.R b/R/HnswParam.R
@@ -4,7 +4,6 @@
 #' 
 #' @param nlinks Integer scalar, number of bi-directional links per element for index generation.
 #' @param ef.construction Integer scalar, size of the dynamic list for index generation.
-#' @param directory String specifying the directory in which to save the index.
 #' @param ef.search Integer scalar, size of the dynamic list for neighbor searching.
 #' @param distance A string specifying the distance metric to use.
 #' @inheritParams ExhaustiveParam
@@ -89,7 +88,7 @@ setMethod("show", "HnswParam", function(object) {
 
 #' @export
 #' @rdname HnswParam
-setMethod("buildIndex", c("ANY", "HnswParam"), function(X, transposed = FALSE, ..., BNPARAM) {
+setMethod("buildIndex", c("matrix", "HnswParam"), function(X, transposed = FALSE, ..., BNPARAM) {
     X <- .coerce_matrix_build(X, transposed)
     build_hnsw(X, nlinks=BNPARAM@nlinks, ef_construct=BNPARAM@ef.construction, ef_search=BNPARAM@ef.search, distance=BNPARAM@distance)
 })
diff --git a/R/KmknnParam.R b/R/KmknnParam.R
@@ -2,7 +2,6 @@
 #'
 #' A class to hold parameters for the k-means k-nearest-neighbors (KMKNN) algorithm for exact nearest neighbor identification.
 #'
-#' @param search.mult Numeric scalar, multiplier for the number of points to search.
 #' @inheritParams ExhaustiveParam
 #' @param BNPARAM A KmknnParam instance.
 #'
@@ -48,7 +47,7 @@ KmknnParam <- function(..., distance=c("Euclidean", "Manhattan", "Cosine")) {
 
 #' @export
 #' @rdname KmknnParam
-setMethod("buildIndex", c("ANY", "KmknnParam"), function(X, transposed = FALSE, ..., BNPARAM) {
+setMethod("buildIndex", c("matrix", "KmknnParam"), function(X, transposed = FALSE, ..., BNPARAM) {
     X <- .coerce_matrix_build(X, transposed)
     build_kmknn(X, distance=BNPARAM@distance)
 })
diff --git a/R/VptreeParam.R b/R/VptreeParam.R
@@ -49,7 +49,7 @@ VptreeParam <- function(distance=c("Euclidean", "Manhattan", "Cosine")) {
 
 #' @export
 #' @rdname VptreeParam
-setMethod("buildIndex", c("ANY", "VptreeParam"), function(X, transposed=FALSE, ..., BNPARAM) {
+setMethod("buildIndex", c("matrix", "VptreeParam"), function(X, transposed=FALSE, ..., BNPARAM) {
     X <- .coerce_matrix_build(X, transposed)
     build_vptree(X, BNPARAM@distance)
 })
diff --git a/R/buildIndex.R b/R/buildIndex.R
@@ -25,10 +25,10 @@
 #' Aaron Lun
 #' 
 #' @seealso
-#' \code{\link{buildIndex,KmknnParam-method}},
-#' \code{\link{buildIndex,VptreeParam-method}},
-#' \code{\link{buildIndex,AnnoyParam-method}} 
-#' and \code{\link{buildIndex,HnswParam-method}} for specific methods. 
+#' \code{\link{buildIndex,matrix,KmknnParam-method}},
+#' \code{\link{buildIndex,matrix,VptreeParam-method}},
+#' \code{\link{buildIndex,matrix,AnnoyParam-method}} 
+#' and \code{\link{buildIndex,matrix,HnswParam-method}} for specific methods. 
 #' 
 #' @examples
 #' Y <- matrix(rnorm(100000), ncol=20)

diff --git a/R/findKNN.R b/R/findKNN.R
@@ -19,7 +19,7 @@
 #' @param subset An integer, logical or character vector specifying the rows of \code{X} for which the nearest neighbors should be identified.
 #' This yields the same result as (but is more efficient than) subsetting the output matrices after running \code{findKmknn} with \code{subset=NULL}.
 #' @param ... Further arguments to pass to \code{\link{buildIndex}} when \code{X} is not an external pointer.
-#' @param BNPARAM A \linkS4class{BiocNeighborsParam} object specifying how the index should be constructed.
+#' @param BNPARAM A \linkS4class{BiocNeighborParam} object specifying how the index should be constructed.
 #' If \code{NULL}, this defaults to a \linkS4class{KmknnParam}.
 #' Ignored if \code{x} contains a prebuilt index.
 #' 
@@ -52,6 +52,8 @@
 #' @aliases
 #' findKNN,matrix,ANY-method
 #' findKNN,externalptr,ANY-method
+#' findKNN,matrix-method
+#' findKNN,externalptr-method
 #' 
 #' @examples
 #' Y <- matrix(rnorm(100000), ncol=20)

diff --git a/R/findNeighbors.R b/R/findNeighbors.R
@@ -51,6 +51,8 @@
 #' @aliases
 #' findNeighbors,matrix,ANY-method
 #' findNeighbors,externalptr,ANY-method
+#' findNeighbors,matrix-method
+#' findNeighbors,externalptr-method
 #'
 #' @name findNeighbors
 NULL

diff --git a/R/queryKNN.R b/R/queryKNN.R
@@ -37,6 +37,8 @@
 #' @aliases
 #' queryKNN,matrix,ANY-method
 #' queryKNN,externalptr,ANY-method
+#' queryKNN,matrix-method
+#' queryKNN,externalptr-method
 #'
 #' @examples
 #' Y <- matrix(rnorm(100000), ncol=20)

diff --git a/R/queryNeighbors.R b/R/queryNeighbors.R
@@ -54,12 +54,14 @@
 #' @aliases
 #' queryNeighbors,matrix,ANY-method
 #' queryNeighbors,externalptr,ANY-method
+#' queryNeighbors,matrix-method
+#' queryNeighbors,externalptr-method
 #'
 #' @name queryNeighbors
 NULL
 
 #' @export
-setMethod("queryNeighbors", c("ANY", "ANY"), function(X, query, threshold, get.index=TRUE, get.distance=TRUE, num.threads=1, subset=NULL, transposed=FALSE, ..., BPPARAM=NULL, BNPARAM=NULL) {
+setMethod("queryNeighbors", c("matrix", "ANY"), function(X, query, threshold, get.index=TRUE, get.distance=TRUE, num.threads=1, subset=NULL, transposed=FALSE, ..., BPPARAM=NULL, BNPARAM=NULL) {
     ptr <- buildIndex(X, transposed=transposed, ..., BNPARAM=BNPARAM)
     callGeneric(ptr, query=query, threshold=threshold, get.index=get.index, get.distance=get.distance, num.threads=num.threads, subset=subset, transposed=transposed, ..., BPPARAM=BPPARAM)
 })

diff --git a/man/AnnoyParam.Rd b/man/AnnoyParam.Rd
diff --git a/man/BiocNeighborParam.Rd b/man/BiocNeighborParam.Rd
diff --git a/man/ExhaustiveParam.Rd b/man/ExhaustiveParam.Rd
diff --git a/man/HnswParam.Rd b/man/HnswParam.Rd
diff --git a/man/KmknnParam.Rd b/man/KmknnParam.Rd
diff --git a/man/VptreeParam.Rd b/man/VptreeParam.Rd
diff --git a/man/buildIndex.Rd b/man/buildIndex.Rd
diff --git a/man/findKNN.Rd b/man/findKNN.Rd
diff --git a/man/findNeighbors.Rd b/man/findNeighbors.Rd
diff --git a/man/queryKNN.Rd b/man/queryKNN.Rd
diff --git a/man/queryNeighbors.Rd b/man/queryNeighbors.Rd