diff -Nru r-bioc-biocgenerics-0.14.0/debian/changelog r-bioc-biocgenerics-0.16.0/debian/changelog
--- r-bioc-biocgenerics-0.14.0/debian/changelog	2015-05-09 05:30:15.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/debian/changelog	2015-10-29 15:48:07.000000000 +0000
@@ -1,3 +1,10 @@
+r-bioc-biocgenerics (0.16.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Add missing r-cran-runit to debian/test/control
+
+ -- Andreas Tille <tille@debian.org>  Thu, 29 Oct 2015 16:30:20 +0100
+
 r-bioc-biocgenerics (0.14.0-1) unstable; urgency=medium
 
   * New upstream version
diff -Nru r-bioc-biocgenerics-0.14.0/debian/tests/control r-bioc-biocgenerics-0.16.0/debian/tests/control
--- r-bioc-biocgenerics-0.14.0/debian/tests/control	2015-05-09 05:30:15.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/debian/tests/control	2015-10-29 15:48:07.000000000 +0000
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @
+Depends: @, r-cran-runit
 Restrictions: allow-stderr
diff -Nru r-bioc-biocgenerics-0.14.0/DESCRIPTION r-bioc-biocgenerics-0.16.0/DESCRIPTION
--- r-bioc-biocgenerics-0.14.0/DESCRIPTION	2015-04-17 03:42:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/DESCRIPTION	2015-10-14 02:13:19.000000000 +0000
@@ -1,7 +1,7 @@
 Package: BiocGenerics
 Title: S4 generic functions for Bioconductor
 Description: S4 generic functions needed by many Bioconductor packages.
-Version: 0.14.0
+Version: 0.16.0
 Author: The Bioconductor Dev Team
 Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
 biocViews: Infrastructure
@@ -11,15 +11,16 @@
         oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase,
         annotate, RUnit
 License: Artistic-2.0
-Collate: S3-classes-as-S4-classes.R normarg-utils.R update-utils.R
-        show-utils.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 is.unsorted.R lapply.R mapply.R match.R nrow.R order.R
-        paste.R rank.R rep.R row_colnames.R sets.R sort.R start.R
-        table.R tapply.R unique.R unlist.R unsplit.R relist.R boxplot.R
-        image.R density.R residuals.R weights.R xtabs.R clusterApply.R
-        annotation.R combine.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
+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
+        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: 2015-04-17 03:42:27 UTC; biocbuild
+Packaged: 2015-10-14 02:13:19 UTC; biocbuild
diff -Nru r-bioc-biocgenerics-0.14.0/man/BiocGenerics-package.Rd r-bioc-biocgenerics-0.16.0/man/BiocGenerics-package.Rd
--- r-bioc-biocgenerics-0.14.0/man/BiocGenerics-package.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/BiocGenerics-package.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -58,6 +58,8 @@
       \item \code{BiocGenerics::\link[BiocGenerics]{lapply}},
             \code{BiocGenerics::\link[BiocGenerics]{sapply}}
 
+      \item \code{BiocGenerics::\link[BiocGenerics]{lengths}}
+
       \item \code{BiocGenerics::\link[BiocGenerics]{mapply}}
 
       \item \code{BiocGenerics::\link[BiocGenerics]{match}}
@@ -94,6 +96,8 @@
             \code{BiocGenerics::\link[BiocGenerics]{width}},
             \code{BiocGenerics::\link[BiocGenerics]{width<-}}
 
+      \item \code{BiocGenerics::\link[BiocGenerics]{subset}}
+
       \item \code{BiocGenerics::\link[BiocGenerics]{table}}
 
       \item \code{BiocGenerics::\link[BiocGenerics]{tapply}}
@@ -152,6 +156,9 @@
 
       \item \code{\link[BiocGenerics]{combine}}
 
+      \item \code{\link[BiocGenerics]{dbconn}},
+            \code{\link[BiocGenerics]{dbfile}}
+
       \item \code{\link[BiocGenerics]{fileName}}
 
       \item \code{\link[BiocGenerics]{normalize}}
diff -Nru r-bioc-biocgenerics-0.14.0/man/cbind.Rd r-bioc-biocgenerics-0.16.0/man/cbind.Rd
--- r-bioc-biocgenerics-0.14.0/man/cbind.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/cbind.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -53,7 +53,7 @@
     \item \code{\link[methods]{selectMethod}} for getting the definition of
           a specific method.
 
-    \item \link[IRanges]{cbind,DataFrame-method} in the \pkg{IRanges}
+    \item \link[S4Vectors]{cbind,DataFrame-method} in the \pkg{S4Vectors}
           package for an example of a specific \code{cbind} method (defined
           for \link[S4Vectors]{DataFrame} objects).
 
diff -Nru r-bioc-biocgenerics-0.14.0/man/dbconn.Rd r-bioc-biocgenerics-0.16.0/man/dbconn.Rd
--- r-bioc-biocgenerics-0.14.0/man/dbconn.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/dbconn.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,60 @@
+\name{dbconn}
+
+\alias{dbconn}
+\alias{dbfile}
+
+\title{Accessing SQLite DB information}
+
+\description{
+  Get a connection object or file path for a SQLite DB
+}
+
+\usage{
+dbconn(x)
+dbfile(x)
+}
+
+\arguments{
+  \item{x}{
+    An object with a SQLite connection.
+  }
+}
+
+\value{
+  \code{dbconn} returns a connection object to the SQLite DB containing
+  \code{x}'s data.
+
+  \code{dbfile} returns a path (character string) to the SQLite DB (file)
+  containing \code{x}'s data.
+}
+
+\seealso{
+  \itemize{
+    \item \code{\link[methods]{showMethods}} for displaying a summary of the
+          methods defined for a given generic function.
+
+    \item \code{\link[methods]{selectMethod}} for getting the definition of
+          a specific method.
+
+    \item \link[AnnotationDbi]{dbconn,AnnotationDb-method} in the
+          \pkg{AnnotationDbi} package for an example of a specific
+          \code{dbconn} method (defined for \link[AnnotationDbi]{dbconn}
+          objects).
+
+    \item \link{BiocGenerics} for a summary of all the generics defined
+          in the \pkg{BiocGenerics} package.
+  }
+}
+
+\examples{
+dbconn
+showMethods("dbconn")
+dbfile
+showMethods("dbfile")
+
+library(AnnotationDbi)
+showMethods("dbconn")
+selectMethod("dbconn", "AnnotationDb")
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/grep.Rd r-bioc-biocgenerics-0.16.0/man/grep.Rd
--- r-bioc-biocgenerics-0.14.0/man/grep.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/grep.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,70 @@
+\name{grep}
+
+\alias{grep}
+\alias{grepl}
+
+\title{Pattern Matching and Replacement}
+
+\description{
+  Search for matches to argument 'pattern' within each element of a character
+  vector.
+  
+  NOTE: This man page is for the \code{grep} and \code{grepl}
+  \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
+  See \code{?base::\link[base]{grep}} for the default methods
+  (defined in the \pkg{base} package).
+  Bioconductor packages can define specific methods for objects
+  not supported by the default method.
+}
+
+\usage{
+grep(pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE,
+          fixed = FALSE, useBytes = FALSE, invert = FALSE)
+grepl(pattern, x, ignore.case = FALSE, perl = FALSE,
+          fixed = FALSE, useBytes = FALSE)
+}
+
+\arguments{
+  \item{pattern}{
+    The pattern for searching in \code{x}, such as a regular expression.
+  }
+  \item{x}{
+    The character vector (in the general sense) to search.
+  }
+  \item{ignore.case, perl, value, fixed, useBytes, invert}{
+    See \code{?base::\link[base]{grep}} for a description of
+    these arguments.
+  }
+}
+
+\value{
+  See \code{?base::\link[base]{grep}} for the value returned
+  by the default method.
+
+  Specific methods defined in Bioconductor packages should
+  behave as consistently as possible with the default method.
+}
+
+\seealso{
+  \itemize{
+    \item \code{base::\link[base]{grep}} for the default
+          \code{grep} and \code{grepl} methods.
+
+    \item \code{\link[methods]{showMethods}} for displaying a summary of the
+          methods defined for a given generic function.
+
+    \item \code{\link[methods]{selectMethod}} for getting the definition of
+          a specific method.
+
+    \item \link{BiocGenerics} for a summary of all the generics defined
+          in the \pkg{BiocGenerics} package.
+  }
+}
+
+\examples{
+grep  # note the dispatch on 'pattern' and 'x' args only
+showMethods("grep")
+selectMethod("grep", "ANY")  # the default method
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/IQR.Rd r-bioc-biocgenerics-0.16.0/man/IQR.Rd
--- r-bioc-biocgenerics-0.14.0/man/IQR.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/IQR.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,58 @@
+\name{IQR}
+
+\alias{IQR}
+
+\title{The Interquartile Range}
+
+\description{
+  Compute the interquartile range for a vector.
+
+  NOTE: This man page is for the \code{IQR} \emph{S4 generic function}
+  defined in the \pkg{BiocGenerics} package.
+  See \code{?stats::\link[stats]{IQR}} for the default method
+  (defined in the \pkg{stats} package).
+  Bioconductor packages can define specific methods for objects
+  not supported by the default method.
+}
+
+\usage{
+IQR(x, na.rm = FALSE, type = 7)
+}
+
+\arguments{
+  \item{x, na.rm, type}{
+    See \code{?stats::\link[stats]{IQR}}.
+  }
+}
+
+\value{
+  See \code{?stats::\link[stats]{IQR}} for the value returned by the
+  default method.
+
+  Specific methods defined in Bioconductor packages should
+  behave as consistently as possible with the default method.
+}
+
+\seealso{
+  \itemize{
+    \item \code{stats::\link[stats]{IQR}} for the default
+          \code{IQR} method.
+
+    \item \code{\link[methods]{showMethods}} for displaying a summary of the
+          methods defined for a given generic function.
+
+    \item \code{\link[methods]{selectMethod}} for getting the definition of
+          a specific method.
+
+    \item \link{BiocGenerics} for a summary of all the generics defined
+          in the \pkg{BiocGenerics} package.
+  }
+}
+
+\examples{
+IQR
+showMethods("IQR")
+selectMethod("IQR", "ANY")  # the default method
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/is.unsorted.Rd r-bioc-biocgenerics-0.16.0/man/is.unsorted.Rd
--- r-bioc-biocgenerics-0.14.0/man/is.unsorted.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/is.unsorted.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -38,7 +38,7 @@
 }
 
 \note{
-  TO DEVELOPPERS:
+  TO DEVELOPERS:
 
   The \code{is.unsorted} method for specific vector-like objects should
   adhere to the same underlying order used by the
diff -Nru r-bioc-biocgenerics-0.14.0/man/lengths.Rd r-bioc-biocgenerics-0.16.0/man/lengths.Rd
--- r-bioc-biocgenerics-0.14.0/man/lengths.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/lengths.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,99 @@
+\name{lengths}
+
+\alias{lengths}
+
+\title{Lengths of the list elements of a list-like object}
+
+\description{
+  Get the length of each list element of a list-like object.
+
+  NOTE: This man page is for the \code{lengths} \emph{S4 generic
+  function} defined in the \pkg{BiocGenerics} package.
+  See \code{?base::\link[base]{lengths}} for the default method
+  (defined in the \pkg{base} package).
+  Bioconductor packages can define specific methods for list-like
+  objects not supported by the default method.
+}
+
+\usage{
+lengths(x, use.names=TRUE)
+}
+
+\arguments{
+  \item{x}{
+    A list-like object. Can also be a vector-like object that is not
+    list-like, in which case the result is trivial.
+  }
+  \item{use.names}{
+    See \code{?base::\link[base]{lengths}} for a description of
+    this argument.
+  }
+}
+
+\value{
+  See \code{?base::\link[base]{lengths}} for the value returned by the
+  default method.
+
+  Specific methods defined in Bioconductor packages should
+  behave as consistently as possible with the default method.
+}
+
+\note{
+  IMPORTANT: The default method (\code{base::\link[base]{lengths}})
+  is equivalent to \code{sapply(x, length)}. However, because the
+  \code{lengths} method for \link[S4Vectors]{Vector} objects is currently
+  defined as an alias for \code{S4Vectors::\link[S4Vectors]{elementLengths}},
+  it's equivalent to \code{sapply(x, NROW)}, not to \code{sapply(x, length)}.
+
+  This makes a difference if \code{x} has array-like list elements.
+  See \code{?base::\link[base]{NROW}} for the difference between
+  \code{length()} and \code{NROW()}.
+  This difference is illustrated in the Examples section below.
+
+  This is a temporary situation that will be addressed in BioC 3.3.
+}
+
+\seealso{
+  \itemize{
+    \item \code{base::\link[base]{lengths}} for the default \code{lengths} 
+          method.
+
+    \item \code{\link[methods]{showMethods}} for displaying a summary of the
+          methods defined for a given generic function.
+
+    \item \code{\link[methods]{selectMethod}} for getting the definition of
+          a specific method.
+
+    \item \link[S4Vectors]{lengths,Vector-method} in the \pkg{S4Vectors}
+          package for an example of a specific \code{lengths} method (defined
+          for \link[S4Vectors]{Vector} objects).
+
+    \item \link{BiocGenerics} for a summary of all the generics defined
+          in the \pkg{BiocGenerics} package.
+  }
+}
+
+\examples{
+lengths  # note the dispatch on the 'x' arg only
+showMethods("lengths")
+selectMethod("lengths", "ANY")  # the default method
+
+library(S4Vectors)
+showMethods("lengths")
+selectMethod("lengths", "Vector")  # the "lengths" method for Vector
+                                   # objects
+
+## Difference between default method and method for Vector objects:
+groups <- c("group1", "group2")
+df <- data.frame(
+    a=letters[1:10],
+    i=101:110,
+    group=rep(factor(groups, levels=groups), c(6, 4))
+)
+x1 <- split(df, df$group)
+x2 <- split(DataFrame(df), df$group)
+lengths(x1)  # dispatch on default method
+lengths(x2)  # dispatch on method for Vector objects
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/mad.Rd r-bioc-biocgenerics-0.16.0/man/mad.Rd
--- r-bioc-biocgenerics-0.14.0/man/mad.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/mad.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,60 @@
+\name{mad}
+
+\alias{mad}
+
+\title{Median Absolute Deviation}
+
+\description{
+  Compute the median absolute deviation for a vector, dispatching only
+  on the first argument, \code{x}.
+
+  NOTE: This man page is for the \code{mad} \emph{S4 generic function}
+  defined in the \pkg{BiocGenerics} package.
+  See \code{?stats::\link[stats]{mad}} for the default method
+  (defined in the \pkg{stats} package).
+  Bioconductor packages can define specific methods for objects
+  not supported by the default method.
+}
+
+\usage{
+mad(x, center = median(x), constant = 1.4826,
+    na.rm = FALSE, low = FALSE, high = FALSE)
+}
+
+\arguments{
+  \item{x, center, constant, na.rm, low, high}{
+    See \code{?stats::\link[stats]{mad}}.
+  }
+}
+
+\value{
+  See \code{?stats::\link[stats]{mad}} for the value returned by the
+  default method.
+
+  Specific methods defined in Bioconductor packages should
+  behave as consistently as possible with the default method.
+}
+
+\seealso{
+  \itemize{
+    \item \code{stats::\link[stats]{mad}} for the default
+          \code{mad} method.
+
+    \item \code{\link[methods]{showMethods}} for displaying a summary of the
+          methods defined for a given generic function.
+
+    \item \code{\link[methods]{selectMethod}} for getting the definition of
+          a specific method.
+
+    \item \link{BiocGenerics} for a summary of all the generics defined
+          in the \pkg{BiocGenerics} package.
+  }
+}
+
+\examples{
+mad
+showMethods("mad")
+selectMethod("mad", "ANY")  # the default method
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/order.Rd r-bioc-biocgenerics-0.16.0/man/order.Rd
--- r-bioc-biocgenerics-0.14.0/man/order.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/order.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -43,7 +43,7 @@
 }
 
 \note{
-  TO DEVELOPPERS:
+  TO DEVELOPERS:
 
   Specific \code{order} methods should preferably be made "stable" for
   consistent behavior across platforms and consistency with
diff -Nru r-bioc-biocgenerics-0.14.0/man/organism_species.Rd r-bioc-biocgenerics-0.16.0/man/organism_species.Rd
--- r-bioc-biocgenerics-0.14.0/man/organism_species.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/organism_species.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -42,7 +42,7 @@
 }
 
 \note{
-  TO DEVELOPPERS:
+  TO DEVELOPERS:
 
   \code{species} has been historically misused in many places in Bioconductor
   and is redundant with \code{organism}. So implementing the \code{species}
diff -Nru r-bioc-biocgenerics-0.14.0/man/rank.Rd r-bioc-biocgenerics-0.16.0/man/rank.Rd
--- r-bioc-biocgenerics-0.14.0/man/rank.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/rank.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -40,7 +40,7 @@
 }
 
 \note{
-  TO DEVELOPPERS:
+  TO DEVELOPERS:
 
   See note in \code{?BiocGenerics::\link[BiocGenerics]{order}} 
   about "stable" order.
diff -Nru r-bioc-biocgenerics-0.14.0/man/rep.Rd r-bioc-biocgenerics-0.16.0/man/rep.Rd
--- r-bioc-biocgenerics-0.14.0/man/rep.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/rep.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -16,18 +16,16 @@
 }
 
 \usage{
-## Unlike the standard rep.int() function defined in base (default method),
-## the generic function described here have a '...' argument (instead of
-## 'times').
-rep.int(x, ...)
+rep.int(x, times)
 }
 
 \arguments{
   \item{x}{
     The object to replicate (typically vector-like).
   }
-  \item{...}{
-    Additional arguments, for use in specific \code{rep.int} methods.
+  \item{times}{
+    See \code{?base::\link[base]{rep.int}} for a description of
+    this argument.
   }
 }
 
diff -Nru r-bioc-biocgenerics-0.14.0/man/sort.Rd r-bioc-biocgenerics-0.16.0/man/sort.Rd
--- r-bioc-biocgenerics-0.14.0/man/sort.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/sort.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -38,7 +38,7 @@
 }
 
 \note{
-  TO DEVELOPPERS:
+  TO DEVELOPERS:
 
   See note in \code{?BiocGenerics::\link[BiocGenerics]{order}}
   about "stable" order.
diff -Nru r-bioc-biocgenerics-0.14.0/man/subset.Rd r-bioc-biocgenerics-0.16.0/man/subset.Rd
--- r-bioc-biocgenerics-0.14.0/man/subset.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/subset.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,69 @@
+\name{subset}
+
+\alias{subset}
+
+\title{Subsetting vector-like, matrix-like and data-frame-like objects}
+
+\description{
+  Return subsets of vector-like, matrix-like or data-frame-like objects
+  which meet conditions.
+
+  NOTE: This man page is for the \code{subset} \emph{S4 generic function}
+  defined in the \pkg{BiocGenerics} package.
+  See \code{?base::\link[base]{subset}} for the \code{subset} S3 generic
+  defined in the \pkg{base} package.
+}
+
+\usage{
+subset(x, ...)
+}
+
+\arguments{
+  \item{x}{
+    A vector-like, matrix-like or data-frame-like object to be subsetted.
+  }
+  \item{...}{
+    Additional arguments (e.g. \code{subset}, \code{select}, \code{drop}),
+    for use in specific methods. See \code{?base::\link[base]{subset}} for
+    more information.
+  }
+}
+
+\value{
+  An object similar to \code{x} containing just the selected elements (for a
+  vector-like object), or the selected rows and columns (for a matrix-like or
+  data-frame-like object).
+}
+
+\seealso{
+  \itemize{
+    \item \code{base::\link[base]{subset}} in the \pkg{base} package
+          for the \code{subset} S3 generic.
+
+    \item \code{\link[methods]{showMethods}} for displaying a summary of the
+          methods defined for a given generic function.
+
+    \item \code{\link[methods]{selectMethod}} for getting the definition of
+          a specific method.
+
+    \item \link[S4Vectors]{subset,DataTable-method} in the \pkg{S4Vectors}
+          package for an example of a specific \code{subset} method (defined
+          for \link[S4Vectors]{DataTable} objects).
+
+    \item \link{BiocGenerics} for a summary of all the generics defined
+          in the \pkg{BiocGenerics} package.
+  }
+}
+
+\examples{
+subset
+showMethods("subset")
+selectMethod("subset", "ANY")  # the default method
+
+library(S4Vectors)
+showMethods("subset")
+selectMethod("subset", "DataTable")  # the "subset" method for
+                                     # DataTable objects
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/testPackage.Rd r-bioc-biocgenerics-0.16.0/man/testPackage.Rd
--- r-bioc-biocgenerics-0.14.0/man/testPackage.Rd	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/testPackage.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,79 @@
+\name{testPackage}
+
+\alias{testPackage}
+
+\title{Run RUnit package unit tests}
+
+\description{
+  \code{testPackage} helps developers implement unit tests using the
+  \pkg{RUnit} testing conventions.
+}
+
+\usage{
+testPackage(pkgname=NULL, subdir="unitTests", pattern="^test_.*\\\\.R$",
+    path=getwd())
+}
+
+\arguments{
+  \item{pkgname}{
+    The name of the package whose installed unit tests are to be run. A
+    missing or NULL value implies that the \code{testPackage} command
+    will look for tests within the package source directory indicated by
+    \code{path}.
+  }
+  \item{subdir}{
+    A character(1) vector providing the subdirectory in which unit tests
+    are located. The directory is searched first in the (installed or
+    source) package root, or in a subdirectory \code{inst/} below the
+    root.
+  }
+  \item{pattern}{
+    A character(1) regular expression describing the file names to be
+    evaluated; typically used to restrict tests to a subset of all test
+    files.
+  }
+  \item{path}{
+    A character(1) directory path indicating, when \code{pkgname} is
+    missing or NULL, where unit tests will be searched. \code{path} can
+    be any location at or below the package root.
+  }
+}
+
+\details{
+  This function is not exported from the package namespace, and must be
+  invoked using triple colons, \code{BiocGenerics:::testPackage()}; it
+  is provided primarily for the convenience of developers.
+
+  When invoked with missing or NULL \code{pkgname} argument, the
+  function assumes that it has been invoked from within the package
+  source tree (or that the source tree is located above \code{path}),
+  and finds unit tests in \code{subdir="unitTests"} in either the base
+  or \code{inst/} directories at the root of the package source
+  tree. This mode is useful when developing unit tests, since the
+  package does not have to be re-installed to run an updated test.
+
+  When invoked with \code{pkgname} set to the name of an installed
+  package, unit tests are searched for in the installed package
+  directory.
+}
+
+\value{
+  The function returns the result of \code{RUnit::runTestSuite} invoked
+  on the unit tests specified in the function call.
+}
+
+\seealso{
+  \url{http://bioconductor.org/developers/how-to/unitTesting-guidelines/}
+}
+
+\examples{
+## Run unit tests found in the library location where
+## BiocGenerics is installed
+BiocGenerics:::testPackage("BiocGenerics")
+\dontrun{## Run unit tests for the package whose source tree implied
+## by getwd()
+BiocGenerics:::testPackage()
+}
+}
+
+\keyword{methods}
diff -Nru r-bioc-biocgenerics-0.14.0/man/unsplit.Rd r-bioc-biocgenerics-0.16.0/man/unsplit.Rd
--- r-bioc-biocgenerics-0.14.0/man/unsplit.Rd	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/man/unsplit.Rd	2015-10-13 20:31:17.000000000 +0000
@@ -18,7 +18,7 @@
 }
 
 \usage{
-unsplit(x, recursive=TRUE, use.names=TRUE)
+unsplit(value, f, drop=FALSE)
 }
 
 \arguments{
diff -Nru r-bioc-biocgenerics-0.14.0/NAMESPACE r-bioc-biocgenerics-0.16.0/NAMESPACE
--- r-bioc-biocgenerics-0.14.0/NAMESPACE	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/NAMESPACE	2015-10-13 20:31:17.000000000 +0000
@@ -57,12 +57,18 @@
     ## from R/get.R:
     get, mget,
 
+    ## from R/grepl.R:
+    grep, grepl,
+
     ## from R/is.unsorted.R:
     is.unsorted,
-    
+ 
     ## from R/lapply.R:
     lapply, sapply,
 
+    ## from R/lengths.R:
+    lengths,
+
     ## from R/mapply.R:
     mapply,
 
@@ -98,6 +104,9 @@
     end, "end<-",
     width, "width<-",
 
+    ## from R/subset.R:
+    subset,
+
     ## from R/table.R:
     table,
 
@@ -134,6 +143,12 @@
     ## from R/density.R:
     density,
 
+    ## from R/IQR.R:
+    IQR,
+
+    ## from R/mad.R:
+    mad,
+
     ## from R/residuals.R:
     residuals,
 
@@ -166,6 +181,9 @@
     ## from R/combine.R:
     combine,
 
+    ## from R/dbconn.R:
+    dbconn, dbfile,
+
     ## from R/fileName.R:
     fileName,
 
diff -Nru r-bioc-biocgenerics-0.14.0/R/dbconn.R r-bioc-biocgenerics-0.16.0/R/dbconn.R
--- r-bioc-biocgenerics-0.14.0/R/dbconn.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/dbconn.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,8 @@
+### =========================================================================
+### The dbconn() and dbfile() generics
+### -------------------------------------------------------------------------
+###
+
+setGeneric("dbconn", function(x) standardGeneric("dbconn"))
+
+setGeneric("dbfile", function(x) standardGeneric("dbfile"))
diff -Nru r-bioc-biocgenerics-0.14.0/R/grep.R r-bioc-biocgenerics-0.16.0/R/grep.R
--- r-bioc-biocgenerics-0.14.0/R/grep.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/grep.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,11 @@
+### =========================================================================
+### The grep() and grepl() generics
+### -------------------------------------------------------------------------
+###
+### Need to explicitly define those generics otherwise the implicit generics
+### in package "base" would dispatch on all their arguments. Here we set
+### dispatch on the first 2 args ('pattern', 'x').
+
+setGeneric("grep", signature = c("pattern", "x"))
+
+setGeneric("grepl", signature = c("pattern", "x"))
diff -Nru r-bioc-biocgenerics-0.14.0/R/IQR.R r-bioc-biocgenerics-0.16.0/R/IQR.R
--- r-bioc-biocgenerics-0.14.0/R/IQR.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/IQR.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,6 @@
+### =========================================================================
+### The IQR() generic
+### -------------------------------------------------------------------------
+###
+
+setGeneric("IQR", signature="x")
diff -Nru r-bioc-biocgenerics-0.14.0/R/is.unsorted.R r-bioc-biocgenerics-0.16.0/R/is.unsorted.R
--- r-bioc-biocgenerics-0.14.0/R/is.unsorted.R	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/is.unsorted.R	2015-10-13 20:31:17.000000000 +0000
@@ -2,7 +2,4 @@
 ### The is.unsorted() generic
 ### -------------------------------------------------------------------------
 
-setGeneric("is.unsorted",
-           function(x, na.rm = FALSE, strictly = FALSE)
-           standardGeneric("is.unsorted"),
-           signature = "x")
+setGeneric("is.unsorted", signature = "x")
diff -Nru r-bioc-biocgenerics-0.14.0/R/lengths.R r-bioc-biocgenerics-0.16.0/R/lengths.R
--- r-bioc-biocgenerics-0.14.0/R/lengths.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/lengths.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,10 @@
+### =========================================================================
+### The lengths() generic
+### -------------------------------------------------------------------------
+###
+### Need to explicitly define this generic otherwise the implicit generic in
+### package "base" would dispatch on all its arguments. Here we set dispatch
+### on the first arg ('x') only.
+
+setGeneric("lengths", signature="x")
+
diff -Nru r-bioc-biocgenerics-0.14.0/R/mad.R r-bioc-biocgenerics-0.16.0/R/mad.R
--- r-bioc-biocgenerics-0.14.0/R/mad.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/mad.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,8 @@
+### =========================================================================
+### The mad() generic
+### -------------------------------------------------------------------------
+###
+### Dispatches only on 'x'
+###
+
+setGeneric("mad", signature="x")
diff -Nru r-bioc-biocgenerics-0.14.0/R/replaceSlots.R r-bioc-biocgenerics-0.16.0/R/replaceSlots.R
--- r-bioc-biocgenerics-0.14.0/R/replaceSlots.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/replaceSlots.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,54 @@
+### =========================================================================
+### Efficient multiple slots replacement of an S4 object
+### -------------------------------------------------------------------------
+###
+### NOTE: The stuff in this file (not exported) doesn't really belong to
+### BiocGenerics.
+###
+### TODO: This stuff would need to be moved to a more appropriate place (when
+### we have one).
+
+unsafe_replaceSlots <- function(object, ..., .slotList = list()) {
+  valid_argnames <- slotNames(object)
+  args <- extraArgsAsList(valid_argnames, ...)
+  firstTime <- TRUE
+  listUpdate <- function(object, l) {
+    for (nm in names(l)) {
+      ## Too risky! identical() is not reliable enough e.g. with objects
+      ## that contain external pointers. For example, DNAStringSet("A") and
+      ## DNAStringSet("T") are considered to be identical! identical() needs
+      ## to be fixed first.
+      ##if (identical(slot(object, nm), l[[nm]]))
+      ##  next
+      if (firstTime) {
+        ## Triggers a copy.
+        slot(object, nm, check=FALSE) <- l[[nm]]
+        firstTime <<- FALSE
+      } else {
+        ## In-place modification (i.e. no copy).
+        `slot<-`(object, nm, check=FALSE, l[[nm]])
+      }
+    }
+    object
+  }
+  listUpdate(listUpdate(object, args), .slotList)
+}
+
+### 'replaceSlots' is essentially a more efficient initialize for (value) S4
+### objects.
+replaceSlots <- function(object, ..., check = TRUE) {
+  if (!isTRUEorFALSE(check)) 
+    stop("'check' must be TRUE or FALSE")
+  object <- unsafe_replaceSlots(object, ...)
+  if (check) {
+    validObject(object)
+  }
+  object
+}
+
+updateS4 <- function(...)
+{
+    .Deprecated("replaceSlots")
+    replaceSlots(...)
+}
+
diff -Nru r-bioc-biocgenerics-0.14.0/R/rep.R r-bioc-biocgenerics-0.16.0/R/rep.R
--- r-bioc-biocgenerics-0.14.0/R/rep.R	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/rep.R	2015-10-13 20:31:17.000000000 +0000
@@ -1,39 +1,6 @@
 ### =========================================================================
-### The rep() and rep.int() generics
+### The rep.int() generic
 ### -------------------------------------------------------------------------
 
-### Actually, rep() seems to be already a generic function (that's what the
-### man page claims) but the reality is confusing. On a fresh R session (this
-### is with R-2.14.0):
-###
-###   > isGeneric("rep")
-###   [1] FALSE
-###   > showMethods("rep")
-###   Function: rep (package base)
-###
-###   > isGeneric("rep")
-###   [1] TRUE
-###
-#setGeneric("rep")
-
-### A more natural (and cleaner) thing to do for this generic would be to
-### use the same arguments as base::rep.int() (i.e. 'x', 'times') but then
-### 'R CMD check' would get confused and think that we are trying to define
-### an S3 method for base::rep and would complain (observed with R <= 2.12):
-###
-###   * checking S3 generic/method consistency ... WARNING
-###   rep:
-###     function(x, ...)
-###   rep.int:
-###     function(x, times)
-###
-### so we use the arguments of base::rep() (i.e. 'x', '...') just to make
-### 'R CMD check' happy :-) ... Kind of an ugly/silly hack though :-(
-
-.rep.int.useAsDefault <- function(x, ...) base::rep.int(x, ...)
-
-setGeneric("rep.int",
-    function(x, ...) standardGeneric("rep.int"),
-    useAsDefault=.rep.int.useAsDefault
-)
+setGeneric("rep.int")
 
diff -Nru r-bioc-biocgenerics-0.14.0/R/show-utils.R r-bioc-biocgenerics-0.16.0/R/show-utils.R
--- r-bioc-biocgenerics-0.14.0/R/show-utils.R	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/show-utils.R	1970-01-01 00:00:00.000000000 +0000
@@ -1,99 +0,0 @@
-### =========================================================================
-### Utilities for showing object components in a systematic way
-### -------------------------------------------------------------------------
-###
-
-labeledLine <-
-  function(label, els, count = TRUE, labelSep = ":", sep = " ", ellipsis = "...",
-           ellipsisPos = c("middle", "end", "start"))
-{
-  if (count && !is.null(els))
-    label <- paste(label, "(", length(els), ")", sep = "")
-  label <- paste(label, labelSep, sep, sep = "")
-  width <- getOption("width") - nchar(label)
-  line <- ellipsize(els, width, sep, ellipsis, ellipsisPos)
-  paste(label, line, "\n", sep = "")
-}
-
-ellipsize <-
-  function(obj, width = getOption("width"), sep = " ", ellipsis = "...",
-           pos = c("middle", "end", "start"))
-{
-  pos <- match.arg(pos)
-  if (is.null(obj))
-    obj <- "NULL"
-  if (is.factor(obj))
-    obj <- as.character(obj)
-  ## get order selectSome() would print
-  if (pos == "middle") {
-    if (length(obj) > 2 * width)
-      obj <- c(head(obj, width), tail(obj, width))
-    half <- seq_len(ceiling(length(obj) / 2L))
-    ind <- as.vector(rbind(half, length(obj) - half + 1L))
-  } else if (pos == "end") {
-    obj <- head(obj, width)
-    ind <- seq_len(length(obj))
-  } else {
-    obj <- tail(obj, width)
-    ind <- rev(seq_len(length(obj)))
-  }
-  str <- encodeString(obj)
-  nc <- cumsum(nchar(str[ind]) + nchar(sep)) - nchar(sep)
-  last <- findInterval(width, nc)
-  if (length(obj) > last) {
-    ## make sure ellipsis fits
-    while (last &&
-           (nc[last] + nchar(sep)*2^(last>1) + nchar(ellipsis)) > width)
-      last <- last - 1L
-    if (last == 0) { ## have to truncate the first/last element
-      if (pos == "start") {
-        str <-
-          paste(ellipsis,
-                substring(tail(str, 1L),
-                          nchar(tail(str, 1L))-(width-nchar(ellipsis))+1L,
-                          nchar(ellipsis)),
-                sep = "")
-      } else {
-        str <-
-          paste(substring(str[1L], 1, width - nchar(ellipsis)), ellipsis,
-                sep = "")
-      }
-    }
-    else if (last == 1) { ## can only show the first/last
-      if (pos == "start")
-        str <- c(ellipsis, tail(str, 1L))
-      else str <- c(str[1L], ellipsis)
-    }
-    else {
-      str <- selectSome(str, last + 1L, ellipsis, pos)
-    }
-  }
-  paste(str, collapse = sep)
-}
-
-## taken directly from Biobase, then added 'ellipsisPos' argument
-selectSome <- function(obj, maxToShow = 5, ellipsis = "...",
-                       ellipsisPos = c("middle", "end", "start"), quote=FALSE) 
-{
-  if(is.character(obj) && quote)
-      obj <- sQuote(obj)
-  ellipsisPos <- match.arg(ellipsisPos)
-  len <- length(obj)
-  if (maxToShow < 3) 
-    maxToShow <- 3
-  if (len > maxToShow) {
-    maxToShow <- maxToShow - 1
-    if (ellipsisPos == "end") {
-      c(head(obj, maxToShow), ellipsis)
-    } else if (ellipsisPos == "start") {
-      c(ellipsis, tail(obj, maxToShow))
-    } else {
-      bot <- ceiling(maxToShow/2)
-      top <- len - (maxToShow - bot - 1)
-      nms <- obj[c(1:bot, top:len)]
-      c(as.character(nms[1:bot]), ellipsis, as.character(nms[-c(1:bot)]))
-    }
-  } else {
-    obj
-  }
-}
diff -Nru r-bioc-biocgenerics-0.14.0/R/subset.R r-bioc-biocgenerics-0.16.0/R/subset.R
--- r-bioc-biocgenerics-0.14.0/R/subset.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/subset.R	2015-10-13 20:31:17.000000000 +0000
@@ -0,0 +1,8 @@
+### =========================================================================
+### The subset() generic
+### -------------------------------------------------------------------------
+###
+### base::subset is an S3 generic.
+
+setGeneric("subset")
+
diff -Nru r-bioc-biocgenerics-0.14.0/R/testPackage.R r-bioc-biocgenerics-0.16.0/R/testPackage.R
--- r-bioc-biocgenerics-0.14.0/R/testPackage.R	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/testPackage.R	2015-10-13 20:31:17.000000000 +0000
@@ -1,6 +1,33 @@
-###
+### 
 
-testPackage <- function(pkgname, subdir="unitTests", pattern="^test_.*\\.R$")
+packageRoot <- function(path)
+{
+    hasDescription <- function(path) {
+        file.exists(file.path(path, "DESCRIPTION"))
+    }
+    isRoot <- function(path) {
+        identical(path, dirname(path))
+    }
+    while (!hasDescription(path) && !isRoot(path)) {
+        path <- dirname(path)
+    }
+    if (isRoot(path)) {
+        NULL
+    } else {
+        path
+    }
+}
+
+packageInfo <- function(path)
+{
+    as.data.frame(read.dcf(file.path(path, "DESCRIPTION")),
+                  stringsAsFactors=FALSE)
+}
+
+testPackage <- function(pkgname = NULL,
+                        subdir="unitTests",
+                        pattern="^test_.*\\.R$",
+                        path = getwd())
 {
     .failure_details <- function(result) {
         res <- result[[1L]]
@@ -14,17 +41,38 @@
         } else list()
     }
 
-    require(pkgname, quietly=TRUE, character.only=TRUE) ||
-        stop("package '", pkgname, "' not found")
-    dir <- system.file(subdir, package=pkgname)
-    if (nchar(dir) == 0L)
-        stop("unable to find unit tests, no '", subdir, "' dir")
-    require("RUnit", quietly=TRUE) || stop("RUnit package not found")
+    if (is.null(pkgname)) {
+        root <- packageRoot(path)
+        if (is.null(root))
+            stop("could not infer package root directory")
+
+        pkgname0 <- packageInfo(root)$Package
+        if (is.null(pkgname)) {
+            pkgname <- pkgname0
+        } else if (!identical(pkgname, pkgname0)) {
+            stop("'pkgname' and inferred DESCRIPTION 'Package' differ")
+        }
+    } else {
+        root <- system.file(package=pkgname)
+    }
+
+    library(pkgname, character.only = TRUE, quietly=TRUE)
+
+    dir <- file.path(root, subdir)
+    if (!file.exists(dir)) {            # try inst/subdir
+        dir <- file.path(root, "inst", subdir)
+    }
+    if (!file.exists(dir)) {
+        stop("unable to find unit tests, no subdir ", sQuote(subdir))
+    }
+
+    library("RUnit", quietly=TRUE)
     RUnit_opts <- getOption("RUnit", list())
     RUnit_opts$verbose <- 0L
     RUnit_opts$silent <- TRUE
     RUnit_opts$verbose_fail_msg <- TRUE
-    options(RUnit = RUnit_opts)
+    oopt <- options(RUnit = RUnit_opts)
+    on.exit(options(oopt))
     suite <- RUnit::defineTestSuite(name=paste(pkgname, "RUnit Tests"),
                                     dirs=dir,
                                     testFileRegexp=pattern,
@@ -33,7 +81,7 @@
     result <- RUnit::runTestSuite(suite)
     cat("\n\n")
     RUnit::printTextProtocol(result, showDetails=FALSE)
-    if (length(details <- .failure_details(result)) >0) {
+    if (length(details <- .failure_details(result)) > 0) {
         cat("\nTest files with failing tests\n")
         for (i in seq_along(details)) {
             cat("\n  ", basename(names(details)[[i]]), "\n")
@@ -46,4 +94,3 @@
     }
     result
 }
-
diff -Nru r-bioc-biocgenerics-0.14.0/R/update-utils.R r-bioc-biocgenerics-0.16.0/R/update-utils.R
--- r-bioc-biocgenerics-0.14.0/R/update-utils.R	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/R/update-utils.R	1970-01-01 00:00:00.000000000 +0000
@@ -1,47 +0,0 @@
-### =========================================================================
-### Efficient update behavior for S4 objects
-### -------------------------------------------------------------------------
-###
-### NOTE: The stuff in this file (not exported) doesn't really belong to
-### BiocGenerics.
-###
-### TODO: This stuff would need to be moved to a more appropriate place (when
-### we have one).
-
-unsafe_updateS4 <- function(object, ..., .slotList = list()) {
-  valid_argnames <- slotNames(object)
-  args <- extraArgsAsList(valid_argnames, ...)
-  firstTime <- TRUE
-  listUpdate <- function(object, l) {
-    for (nm in names(l)) {
-      ## Too risky! identical() is not reliable enough e.g. with objects
-      ## that contain external pointers. For example, DNAStringSet("A") and
-      ## DNAStringSet("T") are considered to be identical! identical() needs
-      ## to be fixed first.
-      ##if (identical(slot(object, nm), l[[nm]]))
-      ##  next
-      if (firstTime) {
-        ## Triggers a copy.
-        slot(object, nm, check=FALSE) <- l[[nm]]
-        firstTime <<- FALSE
-      } else {
-        ## In-place modification (i.e. no copy).
-        `slot<-`(object, nm, check=FALSE, l[[nm]])
-      }
-    }
-    object
-  }
-  listUpdate(listUpdate(object, args), .slotList)
-}
-
-### 'updateS4' is essentially a more efficient initialize for (value) S4
-### objects.
-updateS4 <- function(object, ..., check = TRUE) {
-  if (!isTRUEorFALSE(check)) 
-    stop("'check' must be TRUE or FALSE")
-  object <- unsafe_updateS4(object, ...)
-  if (check) {
-    validObject(object)
-  }
-  object
-}
diff -Nru r-bioc-biocgenerics-0.14.0/TODO r-bioc-biocgenerics-0.16.0/TODO
--- r-bioc-biocgenerics-0.14.0/TODO	2015-04-16 20:12:27.000000000 +0000
+++ r-bioc-biocgenerics-0.16.0/TODO	2015-10-13 20:31:17.000000000 +0000
@@ -3,8 +3,6 @@
   made generics by the IRanges package):
 
   From package base:
-    - is.unsorted(): implicit generic dispatches on (x, na.rm, strictly).
-      Explicit generic should dispatch on (x) only.
     - split(): implicit generic dispatches on (x, f, drop).
       Explicit generic should dispatch on (x, f) only.
     - which(): implicit generic dispatches on (x, arr.ind, useNames).
@@ -45,6 +43,4 @@
     - runmed(): implicit generic dispatches on (x, k, endrule, algorithm,
       print.level). Explicit generic should dispatch on (x) only.
 
-o Move all the generics for count datasets defined in Biobase (and used by the
-  DESeq and DEXSeq packages) to BiocGenerics.