From 0d199dba8a3608f86e89673cc4623755a3ff5a72 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Mon, 27 Apr 2009 07:00:32 +0000
Subject: [PATCH] fixed a small bug in read.tree

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@71 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 ChangeLog      | 2 ++
 DESCRIPTION    | 2 +-
 R/read.nexus.R | 5 +++--
 R/read.tree.R  | 4 ++--
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 3a9c02b..c154531 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -6,6 +6,8 @@ BUG FIXES
     o dist.gene() failed on most occasions with the default
       pairwise.deletion = FALSE.
 
+    o read.tree() failed to read correctly the tree name(s).
+
 
 
 		CHANGES IN APE VERSION 2.3
diff --git a/DESCRIPTION b/DESCRIPTION
index e89a11b..9bd41dc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.3-1
-Date: 2009-04-31
+Date: 2009-04-27
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
diff --git a/R/read.nexus.R b/R/read.nexus.R
index b8a17d8..3edcd3f 100644
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,4 +1,4 @@
-## read.nexus.R (2009-01-19)
+## read.nexus.R (2009-04-01)
 
 ##   Read Tree File in Nexus Format
 
@@ -228,7 +228,8 @@ read.nexus <- function(file, tree.names = NULL)
         class(trees) <- "multiPhylo"
     }
     if (length(grep("[\\/]", file)) == 1)
-        file <- paste(getwd(), file, sep = "/")
+        if (!file.exists(file)) # suggestion by Francois Michonneau
+            file <- paste(getwd(), file, sep = "/")
     attr(trees, "origin") <- file
     trees
 }
diff --git a/R/read.tree.R b/R/read.tree.R
index aa0b029..d19acae 100644
--- a/R/read.tree.R
+++ b/R/read.tree.R
@@ -1,4 +1,4 @@
-## read.tree.R (2009-03-29)
+## read.tree.R (2009-04-27)
 
 ##   Read Tree Files in Parenthetic Format
 
@@ -133,7 +133,7 @@ read.tree <- function(file = "", text = NULL, tree.names = NULL, skip = 0,
 
     tmp <- unlist(lapply(STRING, unname))
     tmpnames <- tmp[c(TRUE, FALSE)]
-    tree <- tmp[c(FALSE, TRUE)]
+    STRING <- tmp[c(FALSE, TRUE)]
     if (is.null(tree.names) && any(nzchar(tmpnames)))
         tree.names <- tmpnames
 
-- 
2.39.2