[med-svn] [r-bioc-biobase] 01/01: New upstream version 2.36.2

[Andreas Tille]

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tille pushed a commit to annotated tag upstream/2.36.2
in repository r-bioc-biobase.

commit d30b68f4610bf0bb6f125d18be5f5de9452ac549
Author: Andreas Tille <tille at debian.org>
Date:   Wed Aug 23 20:27:08 2017 +0200

    New upstream version 2.36.2
---
 DESCRIPTION                            |   4 ++--
 NAMESPACE                              |   7 ++++---
 NEWS                                   |   7 +++++++
 R/methods-ExpressionSet.R              |   2 ++
 R/methods-eSet.R                       |   2 +-
 build/vignette.rds                     | Bin 344 -> 343 bytes
 inst/doc/BiobaseDevelopment.pdf        | Bin 209348 -> 209687 bytes
 inst/doc/ExpressionSetIntroduction.pdf | Bin 157722 -> 157942 bytes
 inst/doc/esApply.pdf                   | Bin 86569 -> 87285 bytes
 9 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ad9f560..feec497 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Biobase
 Title: Biobase: Base functions for Bioconductor
-Version: 2.34.0
+Version: 2.36.2
 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
 Description: Functions that are needed by many other packages or which
         replace R functions.
@@ -22,4 +22,4 @@ Collate: tools.R strings.R environment.R vignettes.R packages.R
 LazyLoad: yes
 biocViews: Infrastructure
 NeedsCompilation: yes
-Packaged: 2016-10-17 22:07:44 UTC; biocbuild
+Packaged: 2017-05-03 22:15:53 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index 7438d16..09c21cd 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,7 +9,7 @@ importFrom(BiocGenerics,
 )
 
 importFrom(utils, head, tail, menu, packageDescription, read.table,
-           write.table)
+           write.table, .DollarNames)
 
 exportClasses(aggregator, container, eSet,
               MIAxE, MIAME, characterORMIAME,
@@ -49,8 +49,7 @@ exportMethods("[", "[[", "$", abstract, aggenv, aggfun,
               AnnotatedDataFrame,
               ExpressionSet)
 
-export(.DollarNames.eSet,
-       Aggregate, addVigs2WinMenu, anyMissing,
+export(Aggregate, addVigs2WinMenu, anyMissing,
        as.data.frame.ExpressionSet, assayDataNew,
        assayDataValidMembers, assayDataElementNames, assayDataElement,
        assayDataElementReplace, "assayDataElement<-", cache, copyEnv,
@@ -62,5 +61,7 @@ export(.DollarNames.eSet,
        selectSome, strbreak, subListExtract, testBioCConnection,
        lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery,
        validMsg, write.AnnotatedDataFrame)
+S3method(.DollarNames, "eSet")
+S3method(.DollarNames, "ExpressionSet")
 S3method(head, "AnnotatedDataFrame")
 S3method(tail, "AnnotatedDataFrame")
diff --git a/NEWS b/NEWS
index fd38adc..bec184b 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,10 @@
+CHANGES IN VERSION 2.36
+-----------------------
+
+BUG FIXES
+
+    o (v. 2.36.1) '$' completion on eSet and ExpressionSet works in RStudio.
+
 CHANGES IN VERSION 2.33
 -----------------------
 
diff --git a/R/methods-ExpressionSet.R b/R/methods-ExpressionSet.R
index 4394c22..db0dcff 100644
--- a/R/methods-ExpressionSet.R
+++ b/R/methods-ExpressionSet.R
@@ -258,3 +258,5 @@ setMethod(ExpressionSet, "matrix",
         featureData=featureData, experimentData=experimentData,
         annotation=annotation, protocolData=protocolData, ...)
 })
+
+.DollarNames.ExpressionSet <- .DollarNames.eSet
diff --git a/R/methods-eSet.R b/R/methods-eSet.R
index 2ef3923..c333556 100644
--- a/R/methods-eSet.R
+++ b/R/methods-eSet.R
@@ -407,7 +407,7 @@ setMethod("$", "eSet", function(x, name) {
     eval(substitute(phenoData(x)$NAME_ARG, list(NAME_ARG=name)))
 })
 
-.DollarNames.eSet <- function(x, pattern)
+.DollarNames.eSet <- function(x, pattern = "")
     grep(pattern, names(pData(x)), value=TRUE)
 
 setReplaceMethod("$", "eSet", function(x, name, value) {
diff --git a/build/vignette.rds b/build/vignette.rds
index 28c637f..4fcc59c 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/BiobaseDevelopment.pdf b/inst/doc/BiobaseDevelopment.pdf
index 677c6cd..8fe92ee 100644
Binary files a/inst/doc/BiobaseDevelopment.pdf and b/inst/doc/BiobaseDevelopment.pdf differ
diff --git a/inst/doc/ExpressionSetIntroduction.pdf b/inst/doc/ExpressionSetIntroduction.pdf
index 56fdf71..0a3c366 100644
Binary files a/inst/doc/ExpressionSetIntroduction.pdf and b/inst/doc/ExpressionSetIntroduction.pdf differ
diff --git a/inst/doc/esApply.pdf b/inst/doc/esApply.pdf
index 0b9f5ed..f82299a 100644
Binary files a/inst/doc/esApply.pdf and b/inst/doc/esApply.pdf differ

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