Browse code

Regenerate NAMESPACE

Peter Hickey authored on 21/08/2018 03:47:21
Showing3 changed files

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@@ -25,7 +25,7 @@ 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 (>= 1.3.4),
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+    DelayedMatrixStats (>= 1.3.6),
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     permute,
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     limma,
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     DelayedArray (>= 0.7.15),
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@@ -79,3 +79,4 @@ biocViews: DNAMethylation
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 SystemRequirements: C++11
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 LinkingTo: Rcpp, Rhdf5lib, beachmat
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 NeedsCompilation: yes
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+RoxygenNote: 6.1.0
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@@ -25,7 +25,7 @@ importFrom(graphics, "abline", "axis", "layout", "legend", "lines",
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 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", "rowGrid", "colGrid")
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+           "rowSums2", "rowMeans2", "rowAlls", "rowsum", "colsum")
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 importFrom(scales, "alpha")
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 importClassesFrom(Biobase, "AnnotatedDataFrame")
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@@ -267,7 +267,7 @@
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             chunkdim = chunkdim,
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             level = level)
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         on.exit(close(M_sink), add = TRUE)
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-        Cov_sink <- HDF5Array::HDF5RealizationSink(
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+        Cov_sink <- HDF5RealizationSink(
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             dim = ans_dim,
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             dimnames = NULL,
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             type = "integer",
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@@ -352,6 +352,7 @@
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 #       (e.g., .cov files).
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 # TODO: (long term) Report a run-time warning/message if strandCollapse = TRUE
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 #       is used in conjunction with files without strand information.
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+# TODO: Try a bpiterate()-based approach to getting the set of loci from files.
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 read.bismark <- function(files,
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                          loci = NULL,
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                          colData = NULL,
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@@ -409,7 +410,7 @@ read.bismark <- function(files,
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         if (!.isSingleMachineBackend(BPPARAM)) {
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             stop("The parallelisation strategy must use a single machine ",
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                  "when using an on-disk realization backend.\n",
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-                 "See help(\"BSmooth\") for details.",
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+                 "See help(\"read.bismark\") for details.",
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                  call. = FALSE)
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         }
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     } else {
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@@ -419,12 +420,12 @@ read.bismark <- function(files,
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             #       ordinary matrix is returned rather than a matrix-backed
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             #       DelayedMatrix.
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             stop("The '", BACKEND, "' realization backend is not supported.",
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-                 "\n  See help(\"BSmooth\") for details.",
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+                 "\n  See help(\"read.bismark\") for details.",
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                  call. = FALSE)
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         }
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     }
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     # If using HDF5Array as BACKEND, check remaining options are sensible.
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-    if (!is.null(BACKEND) && BACKEND == "HDF5Array") {
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+    if (identical(BACKEND, "HDF5Array")) {
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         # NOTE: Most of this copied from
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         #       HDF5Array::saveHDF5SummarizedExperiment().
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         if (!isSingleString(dir)) {
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@@ -463,7 +464,6 @@ read.bismark <- function(files,
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             message("Done in ", round(stime, 1), " secs")
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         }
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     } else {
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-        ptime1 <- proc.time()
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         if (verbose) {
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             message("[read.bismark] Using 'loci' as candidate loci.")
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         }