[Phylobase-commits] r630 - pkg/tests

[noreply at r-forge.r-project.org]

Author: regetz
Date: 2009-09-09 17:50:58 +0200 (Wed, 09 Sep 2009)
New Revision: 630

Modified:
   pkg/tests/misctests.Rout.save
   pkg/tests/testprune.Rout.save
Log:
updated *.Rout.save test files to reflect changes in test output
resulting from recent code changes


Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save	2009-09-09 15:29:09 UTC (rev 629)
+++ pkg/tests/misctests.Rout.save	2009-09-09 15:50:58 UTC (rev 630)
@@ -33,8 +33,9 @@
 > 
 > geospiza0 <-
 +   list(geospiza.tree=as(geospiza,"phylo"),geospiza.data=tdata(geospiza))
-Warning message:
-In asMethod(object) : losing data while coercing phylo4d to phylo
+Warning messages:
+1: In asMethod(object) : losing data while coercing phylo4d to phylo
+2: In asMethod(object) : trees with unknown order may be unsafe in ape
 > ## push data back into list form as in geiger
 > 
 > t1 <-  try(p1 <- phylo4d(geospiza0$geospiza.tree,geospiza0$geospiza.data))
@@ -63,7 +64,7 @@
 > ## or ...
 > p1C <- na.omit(p1)
 > 
-> labels(p1C) <- tolower(labels(p1C))
+> labels(p1C, "allnode") <- tolower(labels(p1C, "all"))
 > 
 > ## trace("prune",browser,signature="phylo4d")
 > r1 <- read.tree(text="((t4:0.3210275554,(t2:0.2724586465,t3:0.2724586465):0.0485689089):0.1397952619,(t5:0.07551818331,t1:0.07551818331):0.385304634);")
@@ -177,8 +178,10 @@
 > 
 > example("phylo4d")
 
-phyl4d> tree.owls.bis <- read.tree(text = "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);")
+phyl4d> treeOwls <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
 
+phyl4d> tree.owls.bis <- read.tree(text=treeOwls)
+
 phyl4d> try(phylo4d(as(tree.owls.bis,"phylo4"),data.frame(wing=1:3)), silent=TRUE)
           label node ancestor edge.length node.type wing
 1   Strix_aluco    1        5         4.2       tip    1

Modified: pkg/tests/testprune.Rout.save
===================================================================
--- pkg/tests/testprune.Rout.save	2009-09-09 15:29:09 UTC (rev 629)
+++ pkg/tests/testprune.Rout.save	2009-09-09 15:50:58 UTC (rev 630)
@@ -72,8 +72,9 @@
 + }
 > 
 > plot.phylo(as(p2,"phylo"))
-Warning message:
-In asMethod(object) : losing data while coercing phylo4d to phylo
+Warning messages:
+1: In asMethod(object) : losing data while coercing phylo4d to phylo
+2: In asMethod(object) : trees with unknown order may be unsafe in ape
 > 
 > proc.time()
    user  system elapsed