Merge pull request #206 from ropensci/silence-s3-warnings

Silences warnings about undeclared/unknown classes in method defs

Author: cboettig

DESCRIPTION

@@ -52,6 +52,7 @@ Collate:
     'add_characters.R'
     'add_meta.R'
     'add_namespaces.R'
+    'nexmlTree.R'
     'add_trees.R'
     'character_classes.R'
     'concatenate_nexml.R'
@@ -71,7 +72,6 @@ Collate:
     'internal_name_by_id.R'
     'internal_nexml_id.R'
     'meta.R'
-    'nexmlTree.R'
     'nexml_add.R'
     'nexml_get.R'
     'nexml_methods.R'

R/add_trees.R

@@ -1,3 +1,6 @@
+#' @include nexmlTree.R
+NULL
+
 #' add_trees
 #' 
 #' add_trees

R/get_trees.R

@@ -1,3 +1,6 @@
+#' @include nexmlTree.R
+NULL
+
 #' extract all phylogenetic trees in ape format
 #' 
 #' extract all phylogenetic trees in ape format

R/nexmlTree.R

@@ -4,9 +4,11 @@ setClass("phyloS4",
                         tip.label = "character",
                         edge.length = "numeric"))
 setOldClass("phylo", S4Class="phyloS4")
-# FIXME repeat selectMethod for all ape, geiger, etc methods(??)
-selectMethod("show", "phylo")
-removeClass("phyloS4")
+
+## multiPhylo and multiPhyloList are used in other files, but perhaps it is
+## best to keep the definitions all here
+setOldClass("multiPhylo")
+setOldClass("multiPhyloList")
 
 setClass("nexmlTree", slots = c(nexml = "nexml"), contains="phylo")
 setMethod("show", "nexmlTree", function(object) print.phylo(object))