Merge branch 'release/1.5.0'

.gitattributes

@@ -0,0 +1,8 @@
+## -------------------------------------------------------------------------
+## Ensure that all text files have LF line endings.
+##
+## If an editor introduces CRLF line endings, git will automatically
+## convert those to LF.  The 'auto' tells git to decide which
+## files are text files and which are not.
+## -------------------------------------------------------------------------
+* text=auto eol=lf

.github/workflows/R-CMD-check-valgrind.yaml

@@ -15,12 +15,9 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       ## R CMD check
       _R_CHECK_CRAN_INCOMING_: false
-      _R_CHECK_LENGTH_1_CONDITION_: true
-      _R_CHECK_LENGTH_1_LOGIC2_: true
       _R_CHECK_MATRIX_DATA_: true
       ## Specific to package
       _R_CHECK_USE_VALGRIND_: true
@@ -33,50 +30,43 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: release
+          use-public-rspm: true
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: Install system dependencies
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
           sudo apt-get install --yes valgrind
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
       - name: Session info
         run: |
           options(width = 100)
+          capabilities()
           pkgs <- installed.packages()[, "Package"]
           sessioninfo::session_info(pkgs, include_base = TRUE)
+          ## Verify LANGUAGE settings by generating a translatable error
+          cat(sprintf("LANGUAGE=%s\n", sQuote(Sys.getenv("LANGUAGE"))))
+          cat(sprintf("locales: %s\n", sQuote(Sys.getlocale())))
+          tryCatch(log("a"), error = conditionMessage)
         shell: Rscript {0}
 
       - name: Check with valgrind
-        run: rcmdcheck::rcmdcheck(build_args = "--no-build-vignettes", args = c("--use-valgrind", "--no-codoc", "--no-examples", "--no-manual", "--ignore-vignettes"), error_on = "warning", check_dir = "check")
+        run: |
+          rcmdcheck::rcmdcheck(
+            build_args = "--no-build-vignettes",
+            args = c("--use-valgrind", "--no-codoc", "--no-examples",
+                     "--no-manual", "--ignore-vignettes"),
+            error_on = "warning",
+            check_dir = "check"
+          )
         shell: Rscript {0}
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-rrelease-results
           path: check

.github/workflows/covr.yaml → .github/workflows/test-coverage.yaml

@@ -1,24 +1,24 @@
 on: [push]
 
-name: test-coverage
+name: test-coverage.yaml
 
 permissions: read-all
 
 jobs:
   test-coverage:
-    name: covr
-
-    timeout-minutes: 30
-
     runs-on: ubuntu-latest
-
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Assert CODECOV_TOKEN is set
+        run: |
+          if [[ -z "${{secrets.CODECOV_TOKEN}}" ]]; then
+            >&2 echo "::error::ERROR: 'secrets.CODECOV_TOKEN' not set"
+            exit 1
+          fi
 
       - uses: r-lib/actions/setup-r@v2
         with:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: matrixStats
-Version: 1.4.1
+Version: 1.5.0
 Depends:
-  R (>= 2.12.0)
+  R (>= 3.4.0)
 Suggests:
   utils,
   base64enc,

NEWS.md

@@ -1,10 +1,37 @@
+# Version 1.5.0 [2025-01-07]
+
+## Significant Changes
+
+ * Package now requires R (>= 3.4.0) [2017-04-21], because the next
+   release of R will have stricter C header requirements that are not
+   backward compatible with older versions of R.
+
+## Deprecated and Defunct
+
+ * The hidden R options for deescalating the error for using `useNames
+   = NA` to a warning has been removed; `useNames = NA` is now always
+   an error.
+
+ * Calling `colRanks()` and `rowRanks()` without explicitly specifying
+   argument `ties.method` is deprecated since version 1.3.0
+   [2024-04-10]. If not explicitly specified, a deprecation warning is
+   now produced every 10:th call not specifying the `ties.method`
+   argument.
+
+## Bug Fixes
+
+ * The error message of `colTabulates()` and `rowTabulates()`
+   asserting that double values are passed, reported on the class of
+   the input data, not the storage type.
+
+
 # Version 1.4.1 [2024-09-06]
 
 ## Bug Fixes
 
- * Fix a potential `runtime error: null pointer passed as argument 1,
-   which is declared to never be null` bug introduced in v1.4.0 that
-   was detected by the UndefinedBehaviorSanitizer (UBSan) running on CRAN.
+ * Fix a `runtime error: null pointer passed as argument 1, which is
+   declared to never be null` bug introduced in v1.4.0 that was
+   detected by the UndefinedBehaviorSanitizer (UBSan) running on CRAN.
 
 
 # Version 1.4.0 [2024-09-03]
@@ -28,8 +55,8 @@
 ## Deprecated and Defunct
 
  * Calling `colRanks()` and `rowRanks()` without explicitly specifying
-   argument `ties.method` is deprecated since version 1.3.0. If not
-   explicitly specified, a deprecation warning is now produced every
+   argument `ties.method` is deprecated since version 1.3.0 [2024-04-10].
+   If not explicitly specified, a deprecation warning is now produced every
    25:th call not specifying the `ties.method` argument.
 
 

R/000.DEPRECATION.R

@@ -1,18 +1,3 @@
-isUseNamesNADefunct <- function() {
-  action <- getOption("matrixStats.useNames.NA", "defunct")
-  action <- match.arg(action, choices = c("deprecated", "defunct"))
-  (action == "defunct")
-}
-
-deprecatedUseNamesNA <- function() {
-  if (isUseNamesNADefunct()) {
-    .Defunct(msg = sprintf("[%s (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options", .packageName), package = .packageName)
-  } else {
-    .Deprecated(msg = sprintf("[%s (>= 1.2.0)] useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options", .packageName), package = .packageName)
-  }
-}
-
-
 defunctShouldBeMatrixOrDim <- function(x) {
   x_class <- sQuote(class(x)[1])
   x_name <- sQuote(as.character(substitute(x)))
@@ -31,16 +16,17 @@ defunctShouldBeMatrixOrVector <- function(x) {
   .Defunct(msg = sprintf("[%s] Argument %s is of class %s, but should be a matrix or a vector. The use of a %s is not supported, the correctness of the result is not guaranteed. Please update your code accordingly.", .packageName, x_name, x_class, x_class))  #nolint
 }
 
-validateScalarCenter <- function(center, n, dimname) {
-  onScalar <- getOption("matrixStats.center.onScalar", "defunct")
-  if (identical(onScalar, "ignore")) return()
-
+validateScalarCenter <- function(center, n, dimname) {  onScalar <- getOption("matrixStats.center.onScalar", "defunct") 
   action <- switch(onScalar,
     deprecated = .Deprecated,
        defunct = .Defunct,
-    function(...) NULL
+                 NULL
   )
 
+  if (is.null(action)) {
+    stop(sprintf("R option 'matrixStats.center.onScalar' must not be \"%s\"; the only valid values are \"defunct\" and \"deprecated\"", onScalar))
+  }
+
   msg <- sprintf("[%s (>= 0.58.0)] Argument '%s' should be of the same length as number of %s of '%s'. Use of a scalar value is %s: %s != %s (See also ?matrixStats::matrixStats.options)", .packageName, "center", dimname, "x", onScalar, length(center), n)
   action(msg = msg, package = .packageName)
 }
@@ -80,13 +66,16 @@ centerOnUse <- function(fcnname, calls = sys.calls(), msg = NULL) {
   value <- getOption("matrixStats.center.onUse", "ignore")
   if (identical(value, "ignore")) return()
 
-  value <- match.arg(value, c("deprecated", "defunct"))
   action <- switch(value,
     deprecated = .Deprecated,
        defunct = .Defunct,
-    function(...) NULL
+                 NULL
   )
 
+  if (is.null(action)) {
+    stop(sprintf("R option 'matrixStats.center.onScalar' must not be \"%s\"; the only valid values are \"defunct\", \"deprecated\", and \"ignore\"", value))
+  }
+
   if (is.null(msg)) {
     msg <- sprintf("[%s] Argument '%s' of %s::%s() is %s: %s (See also ?matrixStats::matrixStats.options)",
                    .packageName, "center", .packageName, fcnname,
@@ -102,7 +91,7 @@ validateTiesMethodMissing <- local({
   always <- structure(TRUE, when = "each time this function is called")
 
   function() {
-    freq <- getOption("matrixStats.ties.method.freq", 25L)
+    freq <- getOption("matrixStats.ties.method.freq", 10L)
 
     ## Nothing to do?
     if (is.null(freq)) return(FALSE)
@@ -128,18 +117,23 @@ validateTiesMethodMissing <- local({
 
 tiesMethodMissing <- local({
   function() {
-    action <- getOption("matrixStats.ties.method.missing", if (getRversion() >= "4.4.0") "deprecated" else "ignore")
-    if (action == "ignore") return()
+    value <- getOption("matrixStats.ties.method.missing", if (getRversion() >= "4.4.0") "deprecated" else "ignore")
+    if (value == "ignore") return()
 
     ## How often should we check?
     if (!validateTiesMethodMissing()) return()
 
-    action <- switch(action,
+    action <- switch(value,
       deprecated = .Deprecated,
       defunct    = .Defunct,
-      function(...) NULL
+                   NULL
     )
-    msg <- sprintf("[%s (>= 1.3.0)] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of %s. This is because the current default ties.method=\"max\" will eventually be updated to ties.method=\"average\" in order to align with the default of base::rank(). See also ?matrixStats::matrixStats.options", .packageName, .packageName)
+
+    if (is.null(action)) {
+      stop(sprintf("R option 'matrixStats.ties.method.missing' must not be \"%s\"; the only valid values are \"defunct\", \"deprecated\", and \"ignore\"", value))
+    }
+
+    msg <- sprintf("[%s (>= 1.3.0)] Please explicitly specify argument 'ties.method' when calling colRanks() and rowRanks() of %s. This is because the current default ties.method=\"max\" will eventually be updated to ties.method=\"average\" in order to align with the default of base::rank(). If you are an end-user that cannot update the R code causing this, see ?matrixStats::matrixStats.options for how to temporarily disable this check", .packageName, .packageName)
     action(msg = msg, package = .packageName)
   }
 })

R/options.R

@@ -22,7 +22,6 @@
 #'    Action taken when argument \code{center} is a scalar.
 #'    If \code{"defunct"}, an error is thrown.
 #'    If \code{"deprecated"}, a warning is signaled.
-#'    If \code{"ignore"}, it's silently ignored.
 #'    (Default: \code{"deprecated"})}
 #' }
 #'
@@ -54,32 +53,22 @@
 #' \describe{
 #'  \item{\option{matrixStats.ties.method.freq}:}{(numeric)
 #'    Controls how often the above validation is checked.
-#'    (Default: \code{25} - every 25:th call starting with the first)}
-#' }
-#'
-#' \describe{
-#'  \item{\option{matrixStats.useNames.NA}:}{(string)
-#'    Action taken when argument \code{useNames} is set to \code{NA}.
-#'    If \code{"defunct"}, an error is thrown.
-#'    If \code{"deprecated"}, a warning is signaled.
-#'    (Default: \code{"defunct"})}
+#'    (Default: \code{10} - every 10:th call starting with the first)}
 #' }
 #'
 #' @section Environment variables that set R options:
 #' All of the above \R \option{matrixStats.*} options can be set by
 #' corresponding environment variable \env{R_MATRIXSTATS_*}
 #' \emph{when the \pkg{matrixStats} package is loaded}.
-#' For example, if \code{R_MATRIXSTATS_USENAMES_NA=defunct}, then option
-#' \option{matrixStats.useNames.NA} is set to \code{"defunct"} (string).
+#' For example, if \code{R_MATRIXSTATS_TIES_METHOD_FREQ=10}, then option
+#' \option{matrixStats.ties.method.freq} is set to \code{10} (integer).
 #'
 #' @examples
 #' \dontrun{
-#' options(matrixStats.useNames.NA = "defunct")
+#' options(matrixStats.ties.method.freq = 10L)
 #' }
 #'
 #' @aliases
-#' matrixStats.useNames.NA
-#' R_MATRIXSTATS_USENAMES_NA
 #' matrixStats.vars.formula.freq
 #' R_MATRIXSTATS_VARS_FORMULA_FREQ
 #' matrixStats.vars.formula.onMistake
@@ -209,11 +198,9 @@ update_package_options <- function() {
 
   update_package_option("matrixStats.vars.center.onUse", default = "ignore", choices = c("deprecated", "defunct", "ignore"))
 
-  update_package_option("matrixStats.center.onScalar", default = "defunct", choices = c("deprecated", "defunct", "ignore"))
+  update_package_option("matrixStats.center.onScalar", default = "defunct", choices = c("deprecated", "defunct"))
 
-  update_package_option("matrixStats.useNames.NA", default = "defunct", choices = c("deprecated", "defunct"))
-
   update_package_option("matrixStats.ties.method.missing", default = if (getRversion() >= "4.4.0") "deprecated" else "ignore", choices = c("deprecated", "defunct", "ignore"))
 
-  update_package_option("matrixStats.ties.method.freq", mode = "numeric", default = "25")
+  update_package_option("matrixStats.ties.method.freq", mode = "numeric", default = "10")
 }