Questions on use of setGenericImplicit()

[PeteHaitch]

Martin Maechler urged for the use of implicit generics in the earlier email discussion (https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012308.html). Admittedly, I feel like I'm fumbling around a bit here with an incomplete understanding of the methods package, but I have tried to implement this, e.g.,

MatrixGenerics/R/rowMedians.R

Lines 41 to 55 in 584e237

	setGeneric(
	"rowMedians",
	function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x),
	...) standardGeneric("rowMedians"),
	signature = "x",
	useAsDefault = function(x, rows = NULL, cols = NULL, na.rm = FALSE,
	dim. = dim(x), ...) {
	if (!requireNamespace("matrixStats", quietly = TRUE)) {
	stop("'matrixStats' package required for matrix operations",
	call. = FALSE)
	}
	matrixStats::rowMedians(x, rows = rows, cols = cols, na.rm = na.rm,
	dim. = dim., ...)
	})
	setGenericImplicit("rowMedians")

The design pattern of setGeneric() followed by setGenericImplicit() is modelled on ddr; for example, https://github.com/vertica/ddR/blob/f6d7056fded5ae15385d5a16802b67116c30c188/ddR/R/ops.R#L203-L204.

Notably, this is different from that used by BiocGenerics. For example, https://github.com/Bioconductor/BiocGenerics/blob/2f85d3a0de8ab541e55d03ee6ea73d343349a7b8/R/matrix-summary.R#L6

Questions

So the first question is, have I got the use of setGeneric() and/or setGenericImplicit() correct?

Some other questions:

• Should restore be TRUE (the default) or FALSE in setGenericImplicit()?
• Should the appropriate matrixStats function (or function from other package, as needed) be used in useAsDefault argument of setGeneric()?
• Is having matrixStats in Suggests and making its use conditional on it being available the right design?