DEPRECATION: Not specifying argument 'ties.method' for colRanks() and…

… rowRanks() will become deprecated in R (>= 4.4.0) [#142]

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: matrixStats
-Version: 1.2.0-9017
+Version: 1.2.0-9018
 Depends:
   R (>= 2.12.0)
 Suggests:

NEWS.md

@@ -11,6 +11,17 @@
 
 ## Deprecated and Defunct
 
+ * Calling `colRanks()` and `rowRanks()` without explicitly specifying
+   argument `ties.method` will be deprecated when using R (>=
+   4.4.0). The reason is that the current default is `ties.method =
+   "max"`, but we want to change that to `ties.method = "average"` to
+   align it with `base::rank()`. In order to minimize the risk for
+   sudden changes in results, we ask everyone to explicitly specify
+   their intent. The first notice will be through deprecation
+   warnings, which will only occur every 50:th call to keep the noise
+   level down.  We will make it more noisy in future releases, and
+   eventually also escalated to defunct errors.
+
  * Using a scalar value for argument `center` of `colSds()`,
    `rowSds()`, `colVars()`, `rowVars()`, `colMads()`, `rowMads()`,
    `colWeightedMads()`, and `rowWeightedMads()` is now defunct.

R/options.R

@@ -48,7 +48,7 @@
 #'    If \code{"defunct"}, an error is produced, if not.
 #'    If \code{"deprecated"}, a warning is signalled.
 #'    If \code{"ignore"}, it's silently ignored.
-#'    (Default: \code{"ignore"})}
+#'    (Default: \code{"deprecated"} in R (>= 4.4.0), otherwise \code{"ignore"})}
 #' }
 #'
 #' \describe{
@@ -213,7 +213,7 @@ update_package_options <- function() {
 
   update_package_option("matrixStats.useNames.NA", default = "defunct", choices = c("deprecated", "defunct"))
 
-  update_package_option("matrixStats.ties.method.missing", default = "ignore", choices = c("deprecated", "defunct", "ignore"))
+  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 = "50")
 }