@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 1.25.3

+Version: 1.25.4

 Encoding: UTF-8

 Title: Analyze, manage and store bisulfite sequencing data

 Description: A collection of tools for analyzing and visualizing bisulfite

@@ -11,10 +11,10 @@ Depends:

     R (>= 3.5),

     methods,

     BiocGenerics,

-    GenomicRanges (>= 1.33.6),

-    SummarizedExperiment (>= 1.17.4)

+    GenomicRanges (>= 1.41.5),

+    SummarizedExperiment (>= 1.19.5)

 Imports:

-    IRanges (>= 2.23.5),

+    IRanges (>= 2.23.9),

     GenomeInfoDb,

     scales,

     stats,

@@ -23,7 +23,7 @@ Imports:

     locfit,

     gtools,

     data.table (>= 1.11.8),

-    S4Vectors (>= 0.25.14),

+    S4Vectors (>= 0.27.12),

     R.utils (>= 2.0.0),

     DelayedMatrixStats (>= 1.5.2),

     permute,

@@ -92,7 +92,7 @@ BSseq <- function(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,

     if (is.null(sampleNames)) {

         if (is.null(pData)) {

             # BSseq object will have no colnames.

-            pData <- S4Vectors:::new_DataFrame(nrows = ncol(M))

+            pData <- make_zero_col_DFrame(ncol(M))

         } else {

             # BSseq object will have 'sampleNames' as colnames.

             pData <- DataFrame(row.names = sampleNames)

@@ -251,8 +251,8 @@ blockApplyWithRealization <- function(x, FUN, ..., sink = NULL, x_grid = NULL,

     FUN <- match.fun(FUN)

     # Check conformable dots_grids and sinks_grids

-    x_grid <- DelayedArray:::.normarg_grid(x_grid, x)

-    sink_grid <- DelayedArray:::.normarg_grid(sink_grid, sink)

+    x_grid <- DelayedArray:::normarg_grid(x_grid, x)

+    sink_grid <- DelayedArray:::normarg_grid(sink_grid, sink)

     if (!identical(dim(x_grid), dim(sink_grid))) {

         stop("non-conformable 'x_grid' and 'sink_grid'")

     }

@@ -22,12 +22,12 @@

 # Internal methods -------------------------------------------------------------

-# NOTE: Combine the new "vertical slots" with those of the parent class. Make

-#       sure to put the new vertical slots **first**. See R/bindROWS.R file in

-#       the S4Vectors package for what slots should or should not be considered

-#       "vertical".

+# NOTE: Combine the new "parallel slots" with those of the parent class. Make

+#       sure to put the new parallel slots **first**. See R/Vector-class.R file

+#       in the S4Vectors package for what slots should or should not be

+#       considered "parallel".

 setMethod(

-    "vertical_slot_names",

+    "parallel_slot_names",

     "FWGRanges",

     function(x) {

         c(GenomicRanges:::extraColumnSlotNames(x), "seqnames", "ranges",

@@ -146,7 +146,7 @@ setMethod("update", "FWGRanges", function(object, ...) {

         s_space <- as.integer(strand(subject)) - 3L

     }

-    # IRanges:::NCList_find_overlaps_in_groups() ---------------------------

+    # IRanges:::find_overlaps_in_groups_NCList() ---------------------------

     q <- query@ranges

     s <- subject@ranges

     circle.length <- circle_length

@@ -186,7 +186,7 @@ setMethod("update", "FWGRanges", function(object, ...) {

         x = s,

         x_groups = s_groups,

         circle.length = s_circle_len)

-    .Call2("NCList_find_overlaps_in_groups",

+    .Call2("C_find_overlaps_in_groups_NCList",

            start(q), end(q), q_space, q_groups,

            start(s), end(s), s_space, s_groups,

            nclists, nclist_is_q,

@@ -281,7 +281,7 @@ setMethod("findOverlaps", c("FWGRanges", "FWGRanges"), .findOverlaps_FWGRanges)

     seqinfo <- Seqinfo(seqnames = levels(seqnames))

     ranges <- .FWIRanges(start = dt[["start"]], width = 1L)

     dt[, start := NULL]

-    mcols <- S4Vectors:::make_zero_col_DataFrame(length(ranges))

+    mcols <- make_zero_col_DFrame(length(ranges))

     if (is.null(dt[["strand"]])) {

         strand <- strand(Rle("*", length(seqnames)))

     } else {

@@ -35,7 +35,7 @@ setValidity2("FWIRanges", .valid.FWIRanges)

 # Internal methods -------------------------------------------------------------

-setMethod("vertical_slot_names", "FWIRanges",

+setMethod("parallel_slot_names", "FWIRanges",

           function(x) c("start", "NAMES", callNextMethod())

 )

@@ -53,10 +53,6 @@ setMethod("end", "FWIRanges", function(x) {

 setMethod("names", "FWIRanges", function(x) x@NAMES)

-setMethod("vertical_slot_names", "FWIRanges",

-          function(x) c("start", "NAMES", callNextMethod())

-)

-

 # TODO: Room for optmisation (e.g., write in C to reduce memory allocations).

 .set_FWIRanges_start <- function(x, value, check = TRUE) {

     if (!isTRUEorFALSE(check)) stop("'check' must be TRUE or FALSE")

@@ -180,7 +180,7 @@

     seqinfo <- Seqinfo(seqnames = levels(seqnames))

     ranges <- .FWIRanges(start = dt[["start"]], width = 1L)

     dt[, start := NULL]

-    mcols <- S4Vectors:::make_zero_col_DataFrame(length(ranges))

+    mcols <- make_zero_col_DFrame(length(ranges))

     if (is.null(dt[["strand"]])) {

         strand <- strand(Rle("*", length(seqnames)))

     } else {