[Phylobase-commits] r532 - pkg/tests

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

Author: bbolker
Date: 2009-08-20 19:24:00 +0200 (Thu, 20 Aug 2009)
New Revision: 532

Modified:
   pkg/tests/misctests.Rout.save
Log:
  updating to match current results (some warnings now gone)



Modified: pkg/tests/misctests.Rout.save
===================================================================
--- pkg/tests/misctests.Rout.save	2009-08-20 16:18:31 UTC (rev 531)
+++ pkg/tests/misctests.Rout.save	2009-08-20 17:24:00 UTC (rev 532)
@@ -25,6 +25,12 @@
 > set.seed(1)
 > 
 > data(geospiza)
+> 
+> ## make sure geospiza is properly formatted
+> if(is.character(checkval <- checkPhylo4(geospiza)))
++   stop(checkval)
+>   
+> 
 > geospiza0 <-
 +   list(geospiza.tree=as(geospiza,"phylo"),geospiza.data=tdata(geospiza))
 Warning message:
@@ -58,9 +64,6 @@
 > p1C <- na.omit(p1)
 > 
 > labels(p1C) <- tolower(labels(p1C))
-Note: Method with signature "phylo4d#missing#ANY" chosen for function "labels<-",
- target signature "phylo4d#missing#character".
- "phylo4#ANY#character" would also be valid
 > 
 > ## 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);")
@@ -117,9 +120,6 @@
 > ## trace("plot", browser, signature = c("phylo4d","missing"))
 > tipLabels(q1) <- paste("q",1:5,sep="")
 > nodeLabels(q1) <- paste("n",1:4,sep="")
-Note: Method with signature "phylo4#character" chosen for function "nodeLabels<-",
- target signature "phylo4d#character".
- "phylo4d#ANY" would also be valid
 > p3 <- phylo4d(r1,tip.data=tipdat,node.data=data.frame(b=6:9), match.data=FALSE)
 > summary(p3)
 
@@ -334,4 +334,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.467   0.066   3.153 
+  3.464   0.076   3.520