1. Biobase
  2. Commit 1952429d5ffcd3496ab0369d57bdccfb6528d8dd
Browse code

fix & patch .DollarNames for RStudio

- pattern = "", else fails when called with no first letter
- create and export derived methods, else RStudio does not recognize
inheritance (seems like a bug in RStudio)


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@129302 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 30/04/2017 14:40:40
Showing 5 changed files
DESCRIPTION
History View file @ 1952429
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: Biobase
2 2 
 Title: Biobase: Base functions for Bioconductor
3 
-Version: 2.37.0
3 
+Version: 2.37.1
4 4 
 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
5 5 
 Description: Functions that are needed by many other packages or which
6 6 
         replace R functions.
NAMESPACE
History View file @ 1952429
... ... 
@@ -49,8 +49,7 @@ exportMethods("[", "[[", "$", abstract, aggenv, aggfun,
49 49 
               AnnotatedDataFrame,
50 50 
               ExpressionSet)
51 51
52 
-export(.DollarNames.eSet,
53 
-       Aggregate, addVigs2WinMenu, anyMissing,
52 
+export(Aggregate, addVigs2WinMenu, anyMissing,
54 53 
        as.data.frame.ExpressionSet, assayDataNew,
55 54 
        assayDataValidMembers, assayDataElementNames, assayDataElement,
56 55 
        assayDataElementReplace, "assayDataElement<-", cache, copyEnv,
... ... 
@@ -62,5 +61,7 @@ export(.DollarNames.eSet,
62 61 
        selectSome, strbreak, subListExtract, testBioCConnection,
63 62 
        lcSuffix, lcPrefix, lcPrefixC, updateOldESet, userQuery,
64 63 
        validMsg, write.AnnotatedDataFrame)
64 
+S3method(.DollarNames, "eSet")
65 
+S3method(.DollarNames, "ExpressionSet")
65 66 
 S3method(head, "AnnotatedDataFrame")
66 67 
 S3method(tail, "AnnotatedDataFrame")
NEWS
History View file @ 1952429
... ... 
@@ -1,3 +1,10 @@
1 
+CHANGES IN VERSION 2.37
2 
+-----------------------
3 
+
4 
+BUG FIXES
5 
+
6 
+    o '$' completion on eSet and ExpressionSet works in RStudio.
7 
+
1 8 
 CHANGES IN VERSION 2.33
2 9 
 -----------------------
3 10
R/methods-ExpressionSet.R
History View file @ 1952429
... ... 
@@ -258,3 +258,5 @@ setMethod(ExpressionSet, "matrix",
258 258 
         featureData=featureData, experimentData=experimentData,
259 259 
         annotation=annotation, protocolData=protocolData, ...)
260 260 
 })
261 
+
262 
+.DollarNames.ExpressionSet <- .DollarNames.eSet
R/methods-eSet.R
History View file @ 1952429
... ... 
@@ -407,7 +407,7 @@ setMethod("$", "eSet", function(x, name) {
407 407 
     eval(substitute(phenoData(x)$NAME_ARG, list(NAME_ARG=name)))
408 408 
 })
409 409
410 
-.DollarNames.eSet <- function(x, pattern)
410 
+.DollarNames.eSet <- function(x, pattern = "")
411 411 
     grep(pattern, names(pData(x)), value=TRUE)
412 412
413 413 
 setReplaceMethod("$", "eSet", function(x, name, value) {