Browse code

Remove deprecated arguments

Kasper wants these removed without deprecation/defunct cycle

Peter Hickey authored on 10/07/2018 04:39:30
Showing2 changed files

... ...
@@ -115,8 +115,6 @@ makeClusters <- function(hasGRanges, maxGap = 10^8) {
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 # Exported functions -----------------------------------------------------------
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 # TODO: BSmooth() should warn if BSseq object contains mix of strands.
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-# TODO: Make 'mc.cores', 'mc.preschedule', and 'verbose' defunct one release
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-#       cycle with them deprecated.
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 # TODO: Consider having BSmooth() create a 'smoothed' assay in addition to or
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 #       instead of the 'coef' and 'se.coef' assays.
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 BSmooth <- function(BSseq,
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@@ -127,10 +125,7 @@ BSmooth <- function(BSseq,
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                     verbose = TRUE,
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                     BPPARAM = bpparam(),
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                     BACKEND = getRealizationBackend(),
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-                    ...,
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-                    parallelBy = c("sample", "chromosome"),
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-                    mc.preschedule = FALSE,
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-                    mc.cores = 1) {
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+                    ...) {
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     # Argument checks-----------------------------------------------------------
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     # Check validity of 'BSseq' argument
... ...
@@ -143,40 +138,6 @@ BSmooth <- function(BSseq,
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     if (is.unsorted(BSseq)) {
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         stop("'BSseq' must be sorted before smoothing. Use 'sort(BSseq)'.")
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     }
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-    # Check for deprecated arguments and issue warning(s) if found.
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-    if (!missing(parallelBy)) {
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-        warning(
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-            "'parallelBy' is deprecated and ignored.\n",
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-            "See help(\"BSmooth\") for details.",
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-            call. = FALSE,
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-            immediate. = TRUE)
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-    }
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-    if (!missing(mc.preschedule)) {
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-        warning(
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-            "'mc.preschedule' is deprecated and ignored.\n",
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-            "See help(\"BSmooth\") for details.",
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-            call. = FALSE,
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-            immediate. = TRUE)
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-    }
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-    if (!missing(mc.cores)) {
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-        # TODO: What if user has provided a BPPARAM?
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-        warning(
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-            "'mc.cores' is deprecated.\n",
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-            "Replaced with 'BPPARAM = MulticoreParam(workers = mc.cores)'",
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-            ".\nSee help(\"BSmooth\").",
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-            call. = FALSE,
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-            immediate. = TRUE)
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-        BPPARAM <- MulticoreParam(workers = mc.cores)
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-    }
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-    if (!missing(verbose)) {
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-        warning(
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-            "'verbose' is deprecated.\n",
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-            "Replaced by setting 'bpprogressbar(BPPARAM) <- TRUE'.\n",
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-            "See help(\"BSmooth\") for details.",
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-            call. = FALSE,
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-            immediate. = TRUE)
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-        if (verbose) bpprogressbar(BPPARAM) <- TRUE
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-    }
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     # Register 'BACKEND' and return to current value on exit
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     current_BACKEND <- getRealizationBackend()
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     on.exit(setRealizationBackend(current_BACKEND), add = TRUE)
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@@ -25,7 +25,7 @@
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     guessed_file_types
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 }
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-# NOTE: In brief  benchmarking, readr::read_csv() is ~1.3-1.6x faster than
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+# NOTE: In brief benchmarking, readr::read_csv() is ~1.3-1.6x faster than
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 #       utils::read.delim() when reading a gzipped file, albeit it with ~1.6-2x
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 #       more total memory allocated. Therefore, there may be times users prefer
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 #       to trade off faster speed for lower memory usage.
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@@ -383,7 +383,7 @@
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 #       bpworkers() = N in the BPPARAM or nThread = N and use
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 #       data.table::fread()? Or something in between?
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 # TODO: Support passing a colData so that metadata is automatically added to
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-#       samples?
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+#       samples? Yes, do this.
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 # TODO: Document that `...` are used to pass filepath, chunkdim, level, etc. to
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 #       HDF5RealizationSink().
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 # TODO: (long term) Formalise `...` by something analogous to the
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@@ -403,32 +403,10 @@ read.bismark <- function(files,
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                          verbose = TRUE,
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                          BPPARAM = bpparam(),
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                          BACKEND = getRealizationBackend(),
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-                         is_zcat_available = TRUE,
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                          nThread = 1L,
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-                         ...,
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-                         fileType = c("cov", "oldBedGraph", "cytosineReport"),
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-                         mc.cores = 1) {
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+                         ...) {
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     # Argument checks ----------------------------------------------------------
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-    # Check for deprecated arguments and issue warning(s) if found.
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-    if (!missing(fileType)) {
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-        warning(
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-            "'filetype' is deprecated.\n",
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-            "Replaced with automatic detection of file types.\n",
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-            "See help(\"read.bismark\") for details.",
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-            call. = FALSE,
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-            immediate. = TRUE)
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-    }
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-    if (!missing(mc.cores)) {
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-        # TODO: What if user has provided a BPPARAM?
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-        warning(
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-            "'mc.cores' is deprecated.\n",
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-            "Replaced with 'BPPARAM = MulticoreParam(workers = mc.cores)'",
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-            ".\nSee help(\"BSmooth\").",
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-            call. = FALSE,
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-            immediate. = TRUE)
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-        BPPARAM <- MulticoreParam(workers = mc.cores)
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-    }
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     # Check 'files' is valid.
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     # TODO: Allow duplicate files? Useful in testing/debugging but generally a
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     #       bad idea.