Mitigate non-backward comptible changes in matrixStats 1.0.0 (issue #32)

Modify calls to matrixStats functions to mitigate non-backward comptible changes in matrixStats 1.0.0. More precisely: - 'useNames=NA' became deprecated in matrixStats 1.0.0 so we make sure to never pass 'useNames=NA' when calling a matrixStats function; - furthermore, we make sure to pass a 'useNames' value that preserves the pre-matrixStats 1.0.0 behavior in order to avoid disruption. See #31 for a discussion of these changes.
Bioconductor · Jun 8, 2023 · f7b7354 · f7b7354
1 parent 442fde2
commit f7b7354
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,7 +10,7 @@ Description: S4 generic functions modeled after the 'matrixStats' API
 biocViews: Infrastructure, Software
 URL: https://bioconductor.org/packages/MatrixGenerics
 BugReports: https://github.com/Bioconductor/MatrixGenerics/issues
-Version: 1.12.0
+Version: 1.12.1
 License: Artistic-2.0
 Encoding: UTF-8
 Authors@R: c(person("Constantin", "Ahlmann-Eltze",
@@ -21,7 +21,7 @@ Authors@R: c(person("Constantin", "Ahlmann-Eltze",
                 comment = c(ORCID = "0000-0002-8153-6258")),
             person("Hervé", "Pagès", email = "[email protected]",
                 role = "aut"))
-Depends: matrixStats (>= 0.60.1)
+Depends: matrixStats (>= 1.0.0)
 Imports: methods
 Suggests:
     Matrix,

diff --git a/R/rowAlls.R b/R/rowAlls.R
@@ -37,7 +37,7 @@ setGeneric("rowAlls", function(x, rows = NULL, cols = NULL, value = TRUE, na.rm
 )
 
 .matrixStats_rowAlls <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowAlls(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowAlls(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -58,7 +58,7 @@ setGeneric("colAlls", function(x, rows = NULL, cols = NULL, value = TRUE, na.rm
 )
 
 .matrixStats_colAlls <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colAlls(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colAlls(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowAnyNAs.R b/R/rowAnyNAs.R
@@ -33,7 +33,7 @@ setGeneric("rowAnyNAs", function(x, rows = NULL, cols = NULL,  ..., useNames = N
 )
 
 .matrixStats_rowAnyNAs <- function(x, rows = NULL, cols = NULL, ..., useNames = NA){
-  matrixStats::rowAnyNAs(x, rows = rows, cols = cols, ..., useNames = useNames)
+  matrixStats::rowAnyNAs(x, rows = rows, cols = cols, ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -54,7 +54,7 @@ setGeneric("colAnyNAs", function(x, rows = NULL, cols = NULL, ..., useNames = NA
 )
 
 .matrixStats_colAnyNAs <- function(x, rows = NULL, cols = NULL, ..., useNames = NA){
-  matrixStats::colAnyNAs(x, rows = rows, cols = cols, ..., useNames = useNames)
+  matrixStats::colAnyNAs(x, rows = rows, cols = cols, ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowAnys.R b/R/rowAnys.R
@@ -38,7 +38,7 @@ setGeneric("rowAnys", function(x, rows = NULL, cols = NULL, value = TRUE, na.rm
 )
 
 .matrixStats_rowAnys <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowAnys(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowAnys(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -59,7 +59,7 @@ setGeneric("colAnys", function(x, rows = NULL, cols = NULL, value = TRUE, na.rm
 )
 
 .matrixStats_colAnys <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colAnys(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colAnys(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowCollapse.R b/R/rowCollapse.R
@@ -46,7 +46,7 @@ setGeneric("rowCollapse", function(x, idxs, rows = NULL, ..., useNames = NA) sta
 )
 
 .matrixStats_rowCollapse <- function(x, idxs, rows = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowCollapse(x, idxs = idxs, rows = rows, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowCollapse(x, idxs = idxs, rows = rows, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -62,12 +62,12 @@ setMethod("rowCollapse", "ANY", make_default_method_def("rowCollapse"))
 
 #' @export
 #' @rdname rowCollapse
-setGeneric("colCollapse", function(x, idxs = idxs, cols = NULL, ..., useNames = NA) standardGeneric("colCollapse"),
+setGeneric("colCollapse", function(x, idxs, cols = NULL, ..., useNames = NA) standardGeneric("colCollapse"),
            signature = "x"
 )
 
 .matrixStats_colCollapse <- function(x, idxs, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colCollapse(x, idxs = idxs, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::colCollapse(x, idxs = idxs, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowCounts.R b/R/rowCounts.R
@@ -42,7 +42,7 @@ setGeneric("rowCounts", function(x, rows = NULL, cols = NULL, value = TRUE, na.r
 )
 
 .matrixStats_rowCounts <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowCounts(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowCounts(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -63,7 +63,7 @@ setGeneric("colCounts", function(x, rows = NULL, cols = NULL, value = TRUE, na.r
 )
 
 .matrixStats_colCounts <- function(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colCounts(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colCounts(x, rows = rows, cols = cols, value = value, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowCummaxs.R b/R/rowCummaxs.R
@@ -37,7 +37,7 @@ setGeneric("rowCummaxs", function(x, rows = NULL, cols = NULL, ..., useNames = N
 )
 
 .matrixStats_rowCummaxs <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowCummaxs(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowCummaxs(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -58,7 +58,7 @@ setGeneric("colCummaxs", function(x, rows = NULL, cols = NULL, ..., useNames = N
 )
 
 .matrixStats_colCummaxs <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colCummaxs(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::colCummaxs(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowCummins.R b/R/rowCummins.R
@@ -37,7 +37,7 @@ setGeneric("rowCummins", function(x, rows = NULL, cols = NULL, ..., useNames = N
 )
 
 .matrixStats_rowCummins <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowCummins(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowCummins(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -58,7 +58,7 @@ setGeneric("colCummins", function(x, rows = NULL, cols = NULL, ..., useNames = N
 )
 
 .matrixStats_colCummins <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colCummins(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::colCummins(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowCumprods.R b/R/rowCumprods.R
@@ -36,7 +36,7 @@ setGeneric("rowCumprods", function(x, rows = NULL, cols = NULL, ..., useNames =
 )
 
 .matrixStats_rowCumprods <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowCumprods(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowCumprods(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -57,7 +57,7 @@ setGeneric("colCumprods", function(x, rows = NULL, cols = NULL, ..., useNames =
 )
 
 .matrixStats_colCumprods <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colCumprods(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::colCumprods(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowCumsums.R b/R/rowCumsums.R
@@ -34,7 +34,7 @@ setGeneric("rowCumsums", function(x, rows = NULL, cols = NULL,  ..., useNames =
 )
 
 .matrixStats_rowCumsums <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowCumsums(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowCumsums(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -55,7 +55,7 @@ setGeneric("colCumsums", function(x, rows = NULL, cols = NULL, ..., useNames = N
 )
 
 .matrixStats_colCumsums <- function(x, rows = NULL, cols = NULL, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colCumsums(x, rows = rows, cols = cols, dim. = dim., ..., useNames = useNames)
+  matrixStats::colCumsums(x, rows = rows, cols = cols, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowDiffs.R b/R/rowDiffs.R
@@ -39,7 +39,7 @@ setGeneric("rowDiffs", function(x, rows = NULL, cols = NULL, lag = 1L, differenc
 )
 
 .matrixStats_rowDiffs <- function(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowDiffs(x, rows = rows, cols = cols, lag = lag, differences = differences, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowDiffs(x, rows = rows, cols = cols, lag = lag, differences = differences, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -60,7 +60,7 @@ setGeneric("colDiffs", function(x, rows = NULL, cols = NULL, lag = 1L, differenc
 )
 
 .matrixStats_colDiffs <- function(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colDiffs(x, rows = rows, cols = cols, lag = lag, differences = differences, dim. = dim., ..., useNames = useNames)
+  matrixStats::colDiffs(x, rows = rows, cols = cols, lag = lag, differences = differences, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowIQRDiffs.R b/R/rowIQRDiffs.R
@@ -37,7 +37,7 @@ setGeneric("rowIQRDiffs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, d
 )
 
 .matrixStats_rowIQRDiffs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ..., useNames = NA){
-  matrixStats::rowIQRDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff = diff, trim = trim, ..., useNames = useNames)
+  matrixStats::rowIQRDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff = diff, trim = trim, ..., useNames = !isFALSE(useNames))
 }
 
 #' @export
@@ -58,7 +58,7 @@ setGeneric("colIQRDiffs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, d
 )
 
 .matrixStats_colIQRDiffs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ..., useNames = NA){
-  matrixStats::colIQRDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff = diff, trim = trim, ..., useNames = useNames)
+  matrixStats::colIQRDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff = diff, trim = trim, ..., useNames = !isFALSE(useNames))
 }
 
 #' @export

diff --git a/R/rowIQRs.R b/R/rowIQRs.R
@@ -38,7 +38,7 @@ setGeneric("rowIQRs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
 )
 
 .matrixStats_rowIQRs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA){
-  matrixStats::rowIQRs(x, rows = rows, cols = cols, na.rm = na.rm, ..., useNames = useNames)
+  matrixStats::rowIQRs(x, rows = rows, cols = cols, na.rm = na.rm, ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -59,7 +59,7 @@ setGeneric("colIQRs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
 )
 
 .matrixStats_colIQRs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = NA){
-  matrixStats::colIQRs(x, rows = rows, cols = cols, na.rm = na.rm, ..., useNames = useNames)
+  matrixStats::colIQRs(x, rows = rows, cols = cols, na.rm = na.rm, ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowLogSumExps.R b/R/rowLogSumExps.R
@@ -40,7 +40,7 @@ setGeneric("rowLogSumExps", function(lx, rows = NULL, cols = NULL, na.rm = FALSE
 )
 
 .matrixStats_rowLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(lx), ..., useNames = NA){
-  matrixStats::rowLogSumExps(lx, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowLogSumExps(lx, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = !isFALSE(useNames))
 }
 
 #' @export
@@ -64,7 +64,7 @@ setGeneric("colLogSumExps", function(lx, rows = NULL, cols = NULL, na.rm = FALSE
 )
 
 .matrixStats_colLogSumExps <- function(lx, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(lx), ..., useNames = NA){
-  matrixStats::colLogSumExps(lx, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colLogSumExps(lx, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = !isFALSE(useNames))
 }
 
 #' @export

diff --git a/R/rowMadDiffs.R b/R/rowMadDiffs.R
@@ -36,7 +36,7 @@ setGeneric("rowMadDiffs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, d
 )
 
 .matrixStats_rowMadDiffs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ..., useNames = NA){
-  matrixStats::rowMadDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff = diff, trim = trim, ..., useNames = useNames)
+  matrixStats::rowMadDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff = diff, trim = trim, ..., useNames = !isFALSE(useNames))
 }
 
 #' @export
@@ -57,7 +57,7 @@ setGeneric("colMadDiffs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, d
 )
 
 .matrixStats_colMadDiffs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ..., useNames = NA){
-  matrixStats::colMadDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff =diff, trim = trim, ..., useNames = useNames)
+  matrixStats::colMadDiffs(x, rows = rows, cols = cols, na.rm = na.rm, diff =diff, trim = trim, ..., useNames = !isFALSE(useNames))
 }
 
 #' @export

diff --git a/R/rowMads.R b/R/rowMads.R
@@ -43,7 +43,7 @@ setGeneric("rowMads", function(x, rows = NULL, cols = NULL, center = NULL, const
 )
 
 .matrixStats_rowMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowMads(x, rows = rows, cols = cols, center = center, constant = constant, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowMads(x, rows = rows, cols = cols, center = center, constant = constant, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -64,7 +64,7 @@ setGeneric("colMads", function(x, rows = NULL, cols = NULL, center = NULL, const
 )
 
 .matrixStats_colMads <- function(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colMads(x, rows = rows, cols = cols, center = center, constant = constant, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colMads(x, rows = rows, cols = cols, center = center, constant = constant, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowMaxs.R b/R/rowMaxs.R
@@ -35,7 +35,7 @@ setGeneric("rowMaxs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
 )
 
 .matrixStats_rowMaxs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowMaxs(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowMaxs(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -56,7 +56,7 @@ setGeneric("colMaxs", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
 )
 
 .matrixStats_colMaxs <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colMaxs(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colMaxs(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowMeans2.R b/R/rowMeans2.R
@@ -39,7 +39,7 @@ setGeneric("rowMeans2", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...
 )
 
 .matrixStats_rowMeans2 <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowMeans2(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowMeans2(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -60,7 +60,7 @@ setGeneric("colMeans2", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...
 )
 
 .matrixStats_colMeans2 <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colMeans2(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colMeans2(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowMedians.R b/R/rowMedians.R
@@ -36,7 +36,7 @@ setGeneric("rowMedians", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..
 )
 
 .matrixStats_rowMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowMedians(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowMedians(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -57,7 +57,7 @@ setGeneric("colMedians", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ..
 )
 
 .matrixStats_colMedians <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colMedians(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colMedians(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowMins.R b/R/rowMins.R
@@ -35,7 +35,7 @@ setGeneric("rowMins", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
 )
 
 .matrixStats_rowMins <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowMins(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowMins(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -56,7 +56,7 @@ setGeneric("colMins", function(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
 )
 
 .matrixStats_colMins <- function(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colMins(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = useNames)
+  matrixStats::colMins(x, rows = rows, cols = cols, na.rm = na.rm, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export

diff --git a/R/rowOrderStats.R b/R/rowOrderStats.R
@@ -44,7 +44,7 @@ setGeneric("rowOrderStats", function(x, rows = NULL, cols = NULL, which, ..., us
 )
 
 .matrixStats_rowOrderStats <- function(x, rows = NULL, cols = NULL, which, dim. = dim(x), ..., useNames = NA){
-  matrixStats::rowOrderStats(x, rows = rows, cols = cols, which = which, dim. = dim., ..., useNames = useNames)
+  matrixStats::rowOrderStats(x, rows = rows, cols = cols, which = which, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export
@@ -65,7 +65,7 @@ setGeneric("colOrderStats", function(x, rows = NULL, cols = NULL, which, ..., us
 )
 
 .matrixStats_colOrderStats <- function(x, rows = NULL, cols = NULL, which, dim. = dim(x), ..., useNames = NA){
-  matrixStats::colOrderStats(x, rows = rows, cols = cols, which = which, dim. = dim., ..., useNames = useNames)
+  matrixStats::colOrderStats(x, rows = rows, cols = cols, which = which, dim. = dim., ..., useNames = isTRUE(useNames))
 }
 
 #' @export