Browse code

fixing warnings

Kasper Daniel Hansen authored on 30/10/2018 00:57:46
Showing4 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 1.17.7
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+Version: 1.17.8
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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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@@ -35,7 +35,7 @@ Imports:
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     Biostrings,
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     utils,
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     HDF5Array,
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-    beachmat
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+    rhdf5
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 Suggests:
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     testthat,
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     bsseqData,
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@@ -45,7 +45,8 @@ Suggests:
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     Matrix,
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     doParallel,
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     rtracklayer,
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-    BSgenome.Hsapiens.UCSC.hg38
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+    BSgenome.Hsapiens.UCSC.hg38,
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+    beachmat
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 Collate:
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     utils.R
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     hasGRanges.R
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@@ -38,6 +38,8 @@ importMethodsFrom(GenomeInfoDb, "seqlengths", "seqlengths<-", "seqinfo",
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                   "seqlevels<-", "sortSeqlevels")
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 importFrom(GenomeInfoDb, "Seqinfo")
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 importFrom(gtools, "combinations")
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+importFrom(Rcpp, sourceCpp)
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+
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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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@@ -35,13 +35,13 @@ makeClusters <- function(hasGRanges, maxGap = 10^8) {
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     # Load packages on worker (required for SnowParam) -------------------------
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     suppressPackageStartupMessages({
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-        library(BiocParallel)
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+        requireNamespace("BiocParallel")
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     })
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     suppressPackageStartupMessages({
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-        library(locfit)
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+        requireNamespace("locfit")
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     })
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     suppressPackageStartupMessages({
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-        library(DelayedArray)
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+        requireNamespace("DelayedArray")
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     })
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     # Construct inputs for smoothing -------------------------------------------
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@@ -4,17 +4,19 @@
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 \section{Version 1.17.x}{
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   \itemize{
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     \item{\code{BSseq()} will no longer reorder inputs. Previously, the
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-    returned \emph{BSseq} object was ordered by ordering the loci, although
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-    this behaviour was not documented. \code{BSseq()} may still filter out loci
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-    if \code{rmZeroCov = FALSE} or collapse loci if
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-    \code{strandCollapse = FALSE} or duplicate loci are detected, but the
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-    relative order of loci in the output will match that of the input.
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+      returned \emph{BSseq} object was ordered by ordering the loci, although
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+      this behaviour was not documented. \code{BSseq()} may still filter out loci
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+      if \code{rmZeroCov = FALSE} or collapse loci if
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+      \code{strandCollapse = FALSE} or duplicate loci are detected, but the
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+      relative order of loci in the output will match that of the input.
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     }
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     \item{Fix bug with \code{maxGap} argument of \code{BSmooth()}. The bug
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-    meant that the 'maximum gap between two methylation loci' was incorrectly
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-    set to \code{2 * maxGap + 1} instead of \code{maxGap}. This likely did not
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-    affect results for users who left the default value of \code{maxGap = 10^8}
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-    but may have affected results for small values of \code{maxGap}.
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+      meant that the 'maximum gap between two methylation loci' was incorrectly
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+      set to \code{2 * maxGap + 1} instead of \code{maxGap}. This likely did not
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+      affect results for users who left the default value of \code{maxGap = 10^8}
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+      but may have affected results for small values of \code{maxGap}.
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+    }
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+    \item{Cleaning up Imports and Suggests.
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     }
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   }
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 }