Browse code

Resync with latest internal changes to S4Vectors and IRanges

Hervé Pagès authored on 09/06/2020 01:36:15
Showing6 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 1.25.3
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+Version: 1.25.4
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 Encoding: UTF-8
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: A collection of tools for analyzing and visualizing bisulfite
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@@ -11,10 +11,10 @@ Depends:
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     R (>= 3.5),
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     methods,
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     BiocGenerics,
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-    GenomicRanges (>= 1.33.6),
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-    SummarizedExperiment (>= 1.17.4)
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+    GenomicRanges (>= 1.41.5),
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+    SummarizedExperiment (>= 1.19.5)
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 Imports:
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-    IRanges (>= 2.23.5),
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+    IRanges (>= 2.23.9),
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     GenomeInfoDb,
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     scales,
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     stats,
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@@ -23,7 +23,7 @@ Imports:
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     locfit,
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     gtools,
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     data.table (>= 1.11.8),
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-    S4Vectors (>= 0.25.14),
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+    S4Vectors (>= 0.27.12),
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     R.utils (>= 2.0.0),
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     DelayedMatrixStats (>= 1.5.2),
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     permute,
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@@ -92,7 +92,7 @@ BSseq <- function(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,
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     if (is.null(sampleNames)) {
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         if (is.null(pData)) {
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             # BSseq object will have no colnames.
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-            pData <- S4Vectors:::new_DataFrame(nrows = ncol(M))
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+            pData <- make_zero_col_DFrame(ncol(M))
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         } else {
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             # BSseq object will have 'sampleNames' as colnames.
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             pData <- DataFrame(row.names = sampleNames)
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@@ -251,8 +251,8 @@ blockApplyWithRealization <- function(x, FUN, ..., sink = NULL, x_grid = NULL,
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     FUN <- match.fun(FUN)
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     # Check conformable dots_grids and sinks_grids
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-    x_grid <- DelayedArray:::.normarg_grid(x_grid, x)
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-    sink_grid <- DelayedArray:::.normarg_grid(sink_grid, sink)
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+    x_grid <- DelayedArray:::normarg_grid(x_grid, x)
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+    sink_grid <- DelayedArray:::normarg_grid(sink_grid, sink)
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     if (!identical(dim(x_grid), dim(sink_grid))) {
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         stop("non-conformable 'x_grid' and 'sink_grid'")
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     }
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@@ -22,12 +22,12 @@
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 # Internal methods -------------------------------------------------------------
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-# NOTE: Combine the new "vertical slots" with those of the parent class. Make
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-#       sure to put the new vertical slots **first**. See R/bindROWS.R file in
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-#       the S4Vectors package for what slots should or should not be considered
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-#       "vertical".
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+# NOTE: Combine the new "parallel slots" with those of the parent class. Make
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+#       sure to put the new parallel slots **first**. See R/Vector-class.R file
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+#       in the S4Vectors package for what slots should or should not be
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+#       considered "parallel".
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 setMethod(
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-    "vertical_slot_names",
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+    "parallel_slot_names",
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     "FWGRanges",
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     function(x) {
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         c(GenomicRanges:::extraColumnSlotNames(x), "seqnames", "ranges",
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@@ -146,7 +146,7 @@ setMethod("update", "FWGRanges", function(object, ...) {
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         s_space <- as.integer(strand(subject)) - 3L
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     }
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-    # IRanges:::NCList_find_overlaps_in_groups() ---------------------------
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+    # IRanges:::find_overlaps_in_groups_NCList() ---------------------------
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     q <- query@ranges
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     s <- subject@ranges
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     circle.length <- circle_length
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@@ -186,7 +186,7 @@ setMethod("update", "FWGRanges", function(object, ...) {
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         x = s,
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         x_groups = s_groups,
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         circle.length = s_circle_len)
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-    .Call2("NCList_find_overlaps_in_groups",
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+    .Call2("C_find_overlaps_in_groups_NCList",
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            start(q), end(q), q_space, q_groups,
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            start(s), end(s), s_space, s_groups,
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            nclists, nclist_is_q,
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@@ -281,7 +281,7 @@ setMethod("findOverlaps", c("FWGRanges", "FWGRanges"), .findOverlaps_FWGRanges)
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     seqinfo <- Seqinfo(seqnames = levels(seqnames))
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     ranges <- .FWIRanges(start = dt[["start"]], width = 1L)
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     dt[, start := NULL]
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-    mcols <- S4Vectors:::make_zero_col_DataFrame(length(ranges))
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+    mcols <- make_zero_col_DFrame(length(ranges))
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     if (is.null(dt[["strand"]])) {
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         strand <- strand(Rle("*", length(seqnames)))
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     } else {
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@@ -35,7 +35,7 @@ setValidity2("FWIRanges", .valid.FWIRanges)
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 # Internal methods -------------------------------------------------------------
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-setMethod("vertical_slot_names", "FWIRanges",
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+setMethod("parallel_slot_names", "FWIRanges",
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           function(x) c("start", "NAMES", callNextMethod())
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 )
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@@ -53,10 +53,6 @@ setMethod("end", "FWIRanges", function(x) {
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 setMethod("names", "FWIRanges", function(x) x@NAMES)
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-setMethod("vertical_slot_names", "FWIRanges",
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-          function(x) c("start", "NAMES", callNextMethod())
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-)
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-
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 # TODO: Room for optmisation (e.g., write in C to reduce memory allocations).
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 .set_FWIRanges_start <- function(x, value, check = TRUE) {
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     if (!isTRUEorFALSE(check)) stop("'check' must be TRUE or FALSE")
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@@ -180,7 +180,7 @@
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     seqinfo <- Seqinfo(seqnames = levels(seqnames))
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     ranges <- .FWIRanges(start = dt[["start"]], width = 1L)
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     dt[, start := NULL]
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-    mcols <- S4Vectors:::make_zero_col_DataFrame(length(ranges))
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+    mcols <- make_zero_col_DFrame(length(ranges))
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     if (is.null(dt[["strand"]])) {
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         strand <- strand(Rle("*", length(seqnames)))
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     } else {