resync with latest changes in IRanges/S4Vectors

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@93886 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Sep 6, 2014 · d70ad74 · d70ad74
1 parent 92c2703
commit d70ad74
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,13 +7,13 @@ Description: The ability to efficiently represent and manipulate genomic
 	intervals. Specialized containers for representing and manipulating
 	short alignments against a reference genome are defined in the
 	GenomicAlignments package.
-Version: 1.17.38
+Version: 1.17.39
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage, 
          GenomeAnnotation
 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.11.3),
-	S4Vectors (>= 0.2.0), IRanges (>= 1.99.26), GenomeInfoDb (>= 1.1.19)
+	S4Vectors (>= 0.2.2), IRanges (>= 1.99.27), GenomeInfoDb (>= 1.1.19)
 Imports: methods, utils, stats, BiocGenerics, IRanges, XVector
 LinkingTo: S4Vectors, IRanges
 Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub,

diff --git a/R/GenomicRangesList-class.R b/R/GenomicRangesList-class.R
@@ -21,7 +21,7 @@ GenomicRangesList <- function(...) {
   args <- list(...)
   if (length(args) == 1 && is.list(args[[1]]))
     args <- args[[1]]
-  IRanges:::new_SimpleList_from_list("SimpleGenomicRangesList", args)
+  S4Vectors:::new_SimpleList_from_list("SimpleGenomicRangesList", args)
 }
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/man/SummarizedExperiment-class.Rd b/man/SummarizedExperiment-class.Rd
@@ -572,7 +572,7 @@ exptData(x, ...) <- value
 \seealso{
   \link{GRanges},
   \link[IRanges]{DataFrame},
-  \link[IRanges]{SimpleList},
+  \link[S4Vectors]{SimpleList},
 }
 
 \examples{