Browse code

Tweak DESCRIPTION and NAMESPACE

- HDF5Array and beachmat in Imports rather than Suggests

Peter Hickey authored on 14/06/2018 20:43:20
Showing 4 changed files

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@@ -8,7 +8,7 @@ Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
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     email = "kasperdanielhansen@gmail.com"),
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     person("Peter", "Hickey", role = "aut", email = "peter.hickey@gmail.com"))
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 Depends:
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-    R (>= 3.3),
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+    R (>= 3.5),
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     methods,
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     BiocGenerics,
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     GenomicRanges (>= 1.29.14),
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@@ -25,25 +25,25 @@ Imports:
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     data.table,
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     S4Vectors,
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     R.utils (>= 2.0.0),
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-    DelayedMatrixStats (>= 1.1.12),
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+    DelayedMatrixStats (>= 1.3.1),
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     permute,
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     limma,
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-    DelayedArray (>= 0.5.34),
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+    DelayedArray (>= 0.7.6),
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     Rcpp,
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     BiocParallel,
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     readr,
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     BSgenome,
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     Biostrings,
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-    utils
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+    utils,
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+    HDF5Array,
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+    beachmat
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 Suggests:
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     testthat,
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     bsseqData,
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     BiocStyle,
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     rmarkdown,
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     knitr,
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-    beachmat,
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     Matrix,
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-    HDF5Array,
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     doParallel
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 Collate:
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     utils.R
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@@ -3,6 +3,14 @@
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 ##
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 import(methods)
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+import(S4Vectors)
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+import(IRanges)
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+import(GenomicRanges)
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+import(SummarizedExperiment)
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+import(DelayedArray)
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+import(HDF5Array)
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+import(BiocParallel)
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+import(limma)
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 importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames",
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            "combine", "density", "intersect", "lapply", "ncol",
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            "nrow", "order", "paste", "pmax", "pmin", "rbind",
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@@ -18,9 +26,7 @@ import(parallel)
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 importFrom(locfit, "locfit", "lp")
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 importFrom(DelayedMatrixStats, "rowSds", "rowVars", "colMeans2", "colSums2",
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            "rowSums2", "rowMeans2", "rowAlls")
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-import(IRanges)
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-import(GenomicRanges)
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-import(SummarizedExperiment)
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+
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 importFrom(scales, "alpha")
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 importClassesFrom(Biobase, "AnnotatedDataFrame")
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 importMethodsFrom(Biobase, "annotatedDataFrameFrom",
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@@ -31,15 +37,11 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
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                   "seqinfo<-", "seqnames", "seqnames<-", "seqlevels",
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                   "seqlevels<-", "sortSeqlevels")
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 importFrom(GenomeInfoDb, "Seqinfo")
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-import(S4Vectors)
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 importFrom(gtools, "combinations")
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 # NOTE: data.table has some NAMESPACE clashes with functions in Bioconductor,
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 #       e.g., shift(). If new ones are discovered, add them to this list.
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 import(data.table, except = c(shift, first, second))
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-import(limma)
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 importFrom(permute, "shuffleSet", "how")
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-import(DelayedArray)
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-import(BiocParallel)
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 importFrom(readr, "cols", "cols_only", "col_character", "col_integer",
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            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")
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 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")
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@@ -226,11 +226,7 @@ BSmooth <- function(BSseq,
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         se.coef_sink <- NULL
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         sink_lock <- NULL
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     } else if (BACKEND == "HDF5Array") {
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-        if (!requireNamespace("HDF5Array", quietly = TRUE)) {
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-            stop("HDF5Array package required for HDF5Array backend",
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-                 call. = FALSE)
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-        }
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-        coef_sink <- HDF5Array::HDF5RealizationSink(
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+        coef_sink <- HDF5RealizationSink(
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             dim = dim(M),
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             # NOTE: Never allow dimnames.
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             dimnames = NULL,
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@@ -241,13 +241,7 @@
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         Cov_sink <- NULL
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         sink_lock <- NULL
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     } else if (BACKEND == "HDF5Array") {
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-        if (!requireNamespace("HDF5Array", quietly = TRUE)) {
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-            stop("HDF5Array package required for HDF5Array backend",
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-                 call. = FALSE)
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-        }
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-        # TODO: HDF5Array is only in suggests, so need to qualify the use of
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-        #       HDF5RealizationSink()
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-        M_sink <- HDF5Array::HDF5RealizationSink(
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+        M_sink <- HDF5RealizationSink(
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             dim = c(ans_nrow, ans_ncol),
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             # NOTE: Never allow dimnames.
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             dimnames = NULL,