After being deprecated in BioC 3.1, GIntervalTree objects and the

"intervaltree" algorithm in findOverlaps() are now defunct. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@103336 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · May 1, 2015 · 2e5dd9e · 2e5dd9e
1 parent f85dd91
commit 2e5dd9e
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diff --git a/R/GIntervalTree-class.R b/R/GIntervalTree-class.R
@@ -117,11 +117,11 @@ setMethod("width", "GIntervalTree",
 setAs("GRanges", "GIntervalTree",
       function(from) {
         msg <- c("GIntervalTree objects and the \"intervaltree\" algorithm ",
-                 "used in findOverlaps() and family are deprecated. Please ",
+                 "used in findOverlaps() and family are defunct. Please ",
                  "use GNCList objects or the \"nclist\" algorithm instead. ",
                  "See ?GNCList and the 'algorithm' argument in ?findOverlaps ",
                  "for more information.")
-        .Deprecated(msg=wmsg(msg))
+        .Defunct(msg=wmsg(msg))
 
         if (any(isCircular(from), na.rm=TRUE))
           stop("'GIntervalTree' objects not supported for circular sequences")

diff --git a/man/GIntervalTree-class.Rd b/man/GIntervalTree-class.Rd
@@ -38,7 +38,7 @@
   The GIntervalTree class is a container for the genomic locations and
   their associated annotations.
 
-  WARNING: GIntervalTree objects are deprecated. Please use \link{GNCList}
+  WARNING: GIntervalTree objects are defunct. Please use \link{GNCList}
   objects instead. See \code{?\link{GNCList}} for more information.
 }
 
@@ -233,46 +233,6 @@
 }
 
 \examples{
-if (interactive()) {
-  ## GIntervalTree objects are deprecated. Please use GNCList objects
-  ## instead. See ?GNCList for more information.
-  seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
-  gr <-
-    GRanges(seqnames =
-          Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
-          ranges = IRanges(
-            1:10, width = 10:1, names = head(letters,10)),
-          strand = Rle(
-            strand(c("-", "+", "*", "+", "-")),
-            c(1, 2, 2, 3, 2)),
-          score = 1:10,
-          GC = seq(1, 0, length=10),
-          seqinfo=seqinfo)
-  tree <- GIntervalTree(gr)
-  tree
-
-  ## Summarizing elements
-  table(seqnames(tree))
-  sum(width(tree))
-  summary(mcols(tree)[,"score"])
-
-  ## find Overlaps
-  subject <-
-    GRanges(seqnames =
-              Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
-            ranges =
-              IRanges(1:10, width = 10:1, names = head(letters,10)),
-            strand =
-              Rle(strand(c("-", "+", "*", "+", "-")),
-                  c(1, 2, 2, 3, 2)),
-            score = 1:10,
-            GC = seq(1, 0, length=10))
-  query <-
-    GRanges(seqnames = "chr2", ranges = IRanges(4:3, 6),
-            strand = "+", score = 5:4, GC = 0.45)
-
-  stree <- GIntervalTree(subject)
-  findOverlaps(query, stree)
-  countOverlaps(query, stree)
-}
+## GIntervalTree objects are defunct. Please use GNCList objects
+## instead. See ?GNCList for more information.
 }
diff --git a/man/GNCList-class.Rd b/man/GNCList-class.Rd
@@ -50,7 +50,7 @@ GNCList(x)
   Containment Lists.
 
   Note that GNCList objects are replacements for \link{GIntervalTree} objects.
-  The latter are deprecated starting with BioC 3.1.
+  The latter are defunct starting with BioC 3.2.
 
   See \code{?\link[IRanges]{NCList}} in the \pkg{IRanges} package for
   some important differences between the new algorithm based on Nested