@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),

     email = "kasperdanielhansen@gmail.com"),

     person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com"))

 Depends:

-    R (>= 3.3),

+    R (>= 3.5),

     methods,

     BiocGenerics,

     GenomicRanges (>= 1.29.14),

@@ -25,25 +25,25 @@ Imports:

     data.table,

     S4Vectors,

     R.utils (>= 2.0.0),

-    DelayedMatrixStats (>= 1.1.12),

+    DelayedMatrixStats (>= 1.3.1),

     permute,

     limma,

-    DelayedArray (>= 0.5.34),

+    DelayedArray (>= 0.7.6),

     Rcpp,

     BiocParallel,

     readr,

     BSgenome,

     Biostrings,

-    utils

+    utils,

+    HDF5Array,

+    beachmat

 Suggests:

     testthat,

     bsseqData,

     BiocStyle,

     rmarkdown,

     knitr,

-    beachmat,

     Matrix,

-    HDF5Array,

     doParallel

 Collate:

     utils.R

@@ -3,6 +3,14 @@

 ##

 import(methods)

+import(S4Vectors)

+import(IRanges)

+import(GenomicRanges)

+import(SummarizedExperiment)

+import(DelayedArray)

+import(HDF5Array)

+import(BiocParallel)

+import(limma)

 importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",

            "combine", "density", "intersect", "lapply", "ncol",

            "nrow", "order", "paste", "pmax", "pmin", "rbind",

@@ -18,9 +26,7 @@ import(parallel)

 importFrom(locfit, "locfit", "lp")

 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",

            "rowSums2", "rowMeans2", "rowAlls")

-import(IRanges)

-import(GenomicRanges)

-import(SummarizedExperiment)

+

 importFrom(scales, "alpha")

 importClassesFrom(Biobase, "AnnotatedDataFrame")

 importMethodsFrom(Biobase, "annotatedDataFrameFrom",

@@ -31,15 +37,11 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",

                   "seqinfo<-", "seqnames", "seqnames<-", "seqlevels",

                   "seqlevels<-", "sortSeqlevels")

 importFrom(GenomeInfoDb, "Seqinfo")

-import(S4Vectors)

 importFrom(gtools, "combinations")

 # NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,

 #       e.g., shift(). If new ones are discovered, add them to this list.

 import(data.table, except = c(shift, first, second))

-import(limma)

 importFrom(permute, "shuffleSet", "how")

-import(DelayedArray)

-import(BiocParallel)

 importFrom(readr, "cols", "cols_only", "col_character", "col_integer",

            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")

 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")

@@ -226,11 +226,7 @@ BSmooth <- function(BSseq,

         se.coef_sink <- NULL

         sink_lock <- NULL

     } else if (BACKEND == "HDF5Array") {

-        if (!requireNamespace("HDF5Array", quietly = TRUE)) {

-            stop("HDF5Array package required for HDF5Array backend",

-                 call. = FALSE)

-        }

-        coef_sink <- HDF5Array::HDF5RealizationSink(

+        coef_sink <- HDF5RealizationSink(

             dim = dim(M),

             # NOTE: Never allow dimnames.

             dimnames = NULL,

@@ -241,13 +241,7 @@

         Cov_sink <- NULL

         sink_lock <- NULL

     } else if (BACKEND == "HDF5Array") {

-        if (!requireNamespace("HDF5Array", quietly = TRUE)) {

-            stop("HDF5Array package required for HDF5Array backend",

-                 call. = FALSE)

-        }

-        # TODO: HDF5Array is only in suggests, so need to qualify the use of

-        #       HDF5RealizationSink()

-        M_sink <- HDF5Array::HDF5RealizationSink(

+        M_sink <- HDF5RealizationSink(

             dim = c(ans_nrow, ans_ncol),

             # NOTE: Never allow dimnames.

             dimnames = NULL,