@@ -115,8 +115,6 @@ makeClusters <- function(hasGRanges, maxGap = 10^8) {

 # Exported functions -----------------------------------------------------------

 # TODO: BSmooth() should warn if BSseq object contains mix of strands.

-# TODO: Make 'mc.cores', 'mc.preschedule', and 'verbose' defunct one release

-#       cycle with them deprecated.

 # TODO: Consider having BSmooth() create a 'smoothed' assay in addition to or

 #       instead of the 'coef' and 'se.coef' assays.

 BSmooth <- function(BSseq,

@@ -127,10 +125,7 @@ BSmooth <- function(BSseq,

                     verbose = TRUE,

                     BPPARAM = bpparam(),

                     BACKEND = getRealizationBackend(),

-                    ...,

-                    parallelBy = c("sample", "chromosome"),

-                    mc.preschedule = FALSE,

-                    mc.cores = 1) {

+                    ...) {

     # Argument checks-----------------------------------------------------------

     # Check validity of 'BSseq' argument

@@ -143,40 +138,6 @@ BSmooth <- function(BSseq,

     if (is.unsorted(BSseq)) {

         stop("'BSseq' must be sorted before smoothing. Use 'sort(BSseq)'.")

     }

-    # Check for deprecated arguments and issue warning(s) if found.

-    if (!missing(parallelBy)) {

-        warning(

-            "'parallelBy' is deprecated and ignored.\n",

-            "See help(\"BSmooth\") for details.",

-            call. = FALSE,

-            immediate. = TRUE)

-    }

-    if (!missing(mc.preschedule)) {

-        warning(

-            "'mc.preschedule' is deprecated and ignored.\n",

-            "See help(\"BSmooth\") for details.",

-            call. = FALSE,

-            immediate. = TRUE)

-    }

-    if (!missing(mc.cores)) {

-        # TODO: What if user has provided a BPPARAM?

-        warning(

-            "'mc.cores' is deprecated.\n",

-            "Replaced with 'BPPARAM = MulticoreParam(workers = mc.cores)'",

-            ".\nSee help(\"BSmooth\").",

-            call. = FALSE,

-            immediate. = TRUE)

-        BPPARAM <- MulticoreParam(workers = mc.cores)

-    }

-    if (!missing(verbose)) {

-        warning(

-            "'verbose' is deprecated.\n",

-            "Replaced by setting 'bpprogressbar(BPPARAM) <- TRUE'.\n",

-            "See help(\"BSmooth\") for details.",

-            call. = FALSE,

-            immediate. = TRUE)

-        if (verbose) bpprogressbar(BPPARAM) <- TRUE

-    }

     # Register 'BACKEND' and return to current value on exit

     current_BACKEND <- getRealizationBackend()

     on.exit(setRealizationBackend(current_BACKEND), add = TRUE)

@@ -25,7 +25,7 @@

     guessed_file_types

 }

-# NOTE: In brief  benchmarking, readr::read_csv() is ~1.3-1.6x faster than

+# NOTE: In brief benchmarking, readr::read_csv() is ~1.3-1.6x faster than

 #       utils::read.delim() when reading a gzipped file, albeit it with ~1.6-2x

 #       more total memory allocated. Therefore, there may be times users prefer

 #       to trade off faster speed for lower memory usage.

@@ -383,7 +383,7 @@

 #       bpworkers() = N in the BPPARAM or nThread = N and use

 #       data.table::fread()? Or something in between?

 # TODO: Support passing a colData so that metadata is automatically added to

-#       samples?

+#       samples? Yes, do this.

 # TODO: Document that `...` are used to pass filepath, chunkdim, level, etc. to

 #       HDF5RealizationSink().

 # TODO: (long term) Formalise `...` by something analogous to the

@@ -403,32 +403,10 @@ read.bismark <- function(files,

                          verbose = TRUE,

                          BPPARAM = bpparam(),

                          BACKEND = getRealizationBackend(),

-                         is_zcat_available = TRUE,

                          nThread = 1L,

-                         ...,

-                         fileType = c("cov", "oldBedGraph", "cytosineReport"),

-                         mc.cores = 1) {

+                         ...) {

     # Argument checks ----------------------------------------------------------

-    # Check for deprecated arguments and issue warning(s) if found.

-    if (!missing(fileType)) {

-        warning(

-            "'filetype' is deprecated.\n",

-            "Replaced with automatic detection of file types.\n",

-            "See help(\"read.bismark\") for details.",

-            call. = FALSE,

-            immediate. = TRUE)

-    }

-    if (!missing(mc.cores)) {

-        # TODO: What if user has provided a BPPARAM?

-        warning(

-            "'mc.cores' is deprecated.\n",

-            "Replaced with 'BPPARAM = MulticoreParam(workers = mc.cores)'",

-            ".\nSee help(\"BSmooth\").",

-            call. = FALSE,

-            immediate. = TRUE)

-        BPPARAM <- MulticoreParam(workers = mc.cores)

-    }

     # Check 'files' is valid.

     # TODO: Allow duplicate files? Useful in testing/debugging but generally a

     #       bad idea.