stuff that was Deprecated is now Defunct.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@89093 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Apr 16, 2014 · 74476bd · 74476bd
1 parent 052b17b
commit 74476bd
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/R/GRangesList-class.R b/R/GRangesList-class.R
@@ -499,7 +499,7 @@ setReplaceMethod("[[", "GRangesList", .dBracketReplaceGRList)
 setMethod("relistToClass", "GRanges", function(x) "GRangesList")
 
 setMethod("splitAsListReturnedClass", "GRanges",
-    function(x) {.Deprecated("relistToClass"); "GRangesList"}
+    function(x) {.Defunct("relistToClass"); "GRangesList"}
 )
 
 

diff --git a/R/makeSeqnameIds.R b/R/makeSeqnameIds.R
@@ -2,7 +2,7 @@ makeSeqnameIds <- function(seqnames, X.is.sexchrom=NA)
 {
      txt <- "'makeSeqnameIds' is deprecated.
            Use 'rankSeqlevels()' in 'GenomeInfoDb' instead." 
-    .Deprecated("rankSeqlevels", msg=paste(strwrap(txt), collapse="\n"))
+    .Defunct("rankSeqlevels", msg=paste(strwrap(txt), collapse="\n"))
     rankSeqlevels(seqnames, X.is.sexchrom=NA)
 }
 
diff --git a/R/seqinfo.R b/R/seqinfo.R
@@ -364,7 +364,7 @@ setGeneric("seqnameStyle", function(x) standardGeneric("seqnameStyle"))
 setMethod("seqnameStyle", "ANY",
     function(x)
     {
-        .Deprecated("seqlevelsStyle")
+        .Defunct("seqlevelsStyle")
         seqlevelsStyle(x)
     }
 )
@@ -376,7 +376,7 @@ setGeneric("seqnameStyle<-", signature="x",
 setReplaceMethod("seqnameStyle", "ANY",
     function(x, value)
     {
-        .Deprecated("seqlevelsStyle")
+        .Defunct("seqlevelsStyle")
         `seqlevelsStyle<-`(x, value)
     }
 )