[med-svn] [r-bioc-biocgenerics] 01/04: Imported Upstream version 0.16.1

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-biocgenerics.

commit 1820e1a33393b13e0a36afb9c23645372c48ffac
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 27 20:59:10 2016 +0200

    Imported Upstream version 0.16.1
---
 DESCRIPTION                 | 12 ++++++------
 R/is.unsorted.R             | 14 +++++++++++++-
 man/BiocGenerics-package.Rd |  3 +++
 man/is.unsorted.Rd          | 10 ++++++++--
 4 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8168ee6..b32c706 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BiocGenerics
 Title: S4 generic functions for Bioconductor
 Description: S4 generic functions needed by many Bioconductor packages.
-Version: 0.16.0
+Version: 0.16.1
 Author: The Bioconductor Dev Team
 Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
 biocViews: Infrastructure
@@ -14,13 +14,13 @@ License: Artistic-2.0
 Collate: S3-classes-as-S4-classes.R normarg-utils.R replaceSlots.R
         append.R as.data.frame.R as.list.R as.vector.R cbind.R
         do.call.R duplicated.R eval.R Extremes.R funprog.R get.R grep.R
-        IQR.R is.unsorted.R lapply.R lengths.R mad.R mapply.R match.R
-        nrow.R order.R paste.R rank.R rep.R row_colnames.R sets.R
-        sort.R start.R subset.R table.R tapply.R unique.R unlist.R
-        unsplit.R relist.R boxplot.R image.R density.R residuals.R
+        is.unsorted.R lapply.R lengths.R mapply.R match.R nrow.R
+        order.R paste.R rank.R rep.R row_colnames.R sets.R sort.R
+        start.R subset.R table.R tapply.R unique.R unlist.R unsplit.R
+        relist.R boxplot.R image.R density.R IQR.R mad.R residuals.R
         weights.R xtabs.R clusterApply.R annotation.R combine.R
         dbconn.R dge.R fileName.R normalize.R organism_species.R
         plotMA.R plotPCA.R score.R strand.R updateObject.R
         testPackage.R test_BiocGenerics_package.R zzz.R
 NeedsCompilation: no
-Packaged: 2015-10-14 02:13:19 UTC; biocbuild
+Packaged: 2015-11-06 03:02:04 UTC; biocbuild
diff --git a/R/is.unsorted.R b/R/is.unsorted.R
index 9f9abe9..0c60cbe 100644
--- a/R/is.unsorted.R
+++ b/R/is.unsorted.R
@@ -2,4 +2,16 @@
 ### The is.unsorted() generic
 ### -------------------------------------------------------------------------
 
-setGeneric("is.unsorted", signature = "x")
+### base::is.unsorted() doesn't have the ellipsis. We add it to the generic
+### function defined below so methods can support additional arguments (e.g.
+### the 'ignore.strand' argument for the method for GenomicRanges objects).
+
+.is.unsorted.useAsDefault <- function(x, na.rm=FALSE, strictly=FALSE, ...)
+    base::is.unsorted(x, na.rm, strictly, ...)
+
+setGeneric("is.unsorted", signature="x",
+    function(x, na.rm=FALSE, strictly=FALSE, ...)
+        standardGeneric("is.unsorted"),
+    useAsDefault=.is.unsorted.useAsDefault
+)
+
diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd
index b0e6d7a..4e28266 100644
--- a/man/BiocGenerics-package.Rd
+++ b/man/BiocGenerics-package.Rd
@@ -53,6 +53,9 @@
       \item \code{BiocGenerics::\link[BiocGenerics]{get}},
             \code{BiocGenerics::\link[BiocGenerics]{mget}}
 
+      \item \code{BiocGenerics::\link[BiocGenerics]{grep}},
+            \code{BiocGenerics::\link[BiocGenerics]{grepl}}
+
       \item \code{BiocGenerics::\link[BiocGenerics]{is.unsorted}}
 
       \item \code{BiocGenerics::\link[BiocGenerics]{lapply}},
diff --git a/man/is.unsorted.Rd b/man/is.unsorted.Rd
index 332a86d..b9b4dc4 100644
--- a/man/is.unsorted.Rd
+++ b/man/is.unsorted.Rd
@@ -12,11 +12,11 @@
   See \code{?base::\link[base]{is.unsorted}} for the default method
   (defined in the \pkg{base} package).
   Bioconductor packages can define specific methods for objects
-  not supported by the default method.
+  (typically vector-like) not supported by the default method.
 }
 
 \usage{
-is.unsorted(x, na.rm=FALSE, strictly=FALSE)
+is.unsorted(x, na.rm=FALSE, strictly=FALSE, ...)
 }
 
 \arguments{
@@ -27,6 +27,12 @@ is.unsorted(x, na.rm=FALSE, strictly=FALSE)
     See \code{?base::\link[base]{is.unsorted}} for a description of
     these arguments.
   }
+  \item{...}{
+    Additional arguments, for use in specific methods.
+
+    Note that \code{base::\link[base]{is.unsorted}} (the default method) only
+    takes the \code{x}, \code{na.rm}, and \code{strictly} arguments.
+  }
 }
 
 \value{

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