[med-svn] [SCM] r-bioc-biocgenerics.git branch, upstream, updated. upstream/0.6.0

[Charles Plessy]

The following commit has been merged in the upstream branch:
commit 3f86ed7bd044ed0b94f1e2c3fc331a3bc919a6e2
Author: Charles Plessy <plessy at debian.org>
Date:   Sat Apr 6 13:35:51 2013 +0900

    Imported Upstream version 0.4.0

diff --git a/DESCRIPTION b/DESCRIPTION
index 2110815..d31aae3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BiocGenerics
 Title: Generic functions for Bioconductor
 Description: S4 generic functions needed by many other Bioconductor packages.
-Version: 0.2.0
+Version: 0.4.0
 Author: The Bioconductor Dev Team
 Maintainer: Bioconductor Package Maintainer
         <maintainer at bioconductor.org>
@@ -9,11 +9,13 @@ biocViews: Infrastructure
 Depends: methods, graphics, stats
 Imports: methods, graphics, stats
 Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,
-        oligo, affyPLM, flowClust, RUnit
+        oligo, affyPLM, RUnit
 License: Artistic-2.0
 Collate: connection-classes.R boxplot.R cbind.R density.R duplicated.R
         eval.R Extremes.R funprog.R get.R image.R lapply.R mapply.R
         nrow.R order.R paste.R rep.R residuals.R row_colnames.R sets.R
-        table.R tapply.R unique.R weights.R xtabs.R combine.R strand.R
-        updateObject.R testPackage.R test_BiocGenerics_package.R zzz.R
-Packaged: 2012-03-31 07:08:17 UTC; biocbuild
+        table.R tapply.R unique.R weights.R xtabs.R annotation.R
+        combine.R strand.R updateObject.R testPackage.R
+        test_BiocGenerics_package.R zzz.R
+Packaged: 2012-10-02 05:09:36 UTC; biocbuild
+InstallableEverywhere: yes
diff --git a/NAMESPACE b/NAMESPACE
index 658dc8d..08de67d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -91,6 +91,9 @@ export(
 ### --------------------------------------------------------------------------
 
 export(
+    ## from R/annotation.R:
+    annotation, "annotation<-",
+
     ## from R/combine.R:
     combine,
 
diff --git a/R/annotation.R b/R/annotation.R
new file mode 100644
index 0000000..f8ae829
--- /dev/null
+++ b/R/annotation.R
@@ -0,0 +1,9 @@
+### =========================================================================
+### The annotation() and `annotation<-`() generics
+### -------------------------------------------------------------------------
+
+setGeneric("annotation", 
+    function(object, ...) standardGeneric("annotation"))
+
+setGeneric("annotation<-", 
+    function(object, ..., value) standardGeneric("annotation<-"))
diff --git a/R/testPackage.R b/R/testPackage.R
index 10a5aed..8c63151 100644
--- a/R/testPackage.R
+++ b/R/testPackage.R
@@ -14,6 +14,8 @@ testPackage <- function(pkgname, subdir="unitTests", pattern="^test_.*\\.R$")
         } 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")
diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd
index c101a9d..0c17095 100644
--- a/man/BiocGenerics-package.Rd
+++ b/man/BiocGenerics-package.Rd
@@ -97,6 +97,9 @@
 
   \subsection{(2) Bioconductor specific generics}{
     \itemize{
+      \item \code{\link[BiocGenerics]{annotation}},
+            \code{\link[BiocGenerics]{annotation<-}}
+
       \item \code{\link[BiocGenerics]{combine}}
 
       \item \code{\link[BiocGenerics]{strand}},
diff --git a/man/annotation.Rd b/man/annotation.Rd
new file mode 100644
index 0000000..fc5ba53
--- /dev/null
+++ b/man/annotation.Rd
@@ -0,0 +1,53 @@
+\name{annotation}
+
+\alias{annotation}
+\alias{annotation<-}
+
+\title{Accessing annotation information}
+
+\description{
+    Get or set the annotation information contained in an object.
+}
+
+\usage{
+annotation(object, ...)
+annotation(object, ...) <- value
+}
+
+\arguments{
+  \item{object}{
+    An object containing annotation information.
+  }
+  \item{...}{
+    Additional arguments, for use in specific methods.
+  }
+  \item{value}{
+    The annotation information to set on \code{object}.
+  }
+}
+
+\seealso{
+  \code{\link[methods]{showMethods}} for displaying a summary of the
+  methods defined for a given generic function.
+
+  \code{\link[methods]{selectMethod}} for getting the definition of
+  a specific method.
+
+  \link[Biobase]{annotation,eSet-method} in the Biobase 
+  package for the method defined for \link[Biobase]{eSet}
+  objects.
+
+  \link{BiocGenerics} for a summary of all the generics defined
+  in the BiocGenerics package.
+}
+
+\examples{
+annotation
+showMethods("annotation")
+
+library(Biobase)
+showMethods("annotation")
+selectMethod("annotation", "eSet")
+}
+
+\keyword{methods}

-- 
generic functions for Bioconductor