[Phylobase-commits] r840 - in pkg: . tests

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

Author: bbolker
Date: 2012-11-24 21:22:08 +0100 (Sat, 24 Nov 2012)
New Revision: 840

Modified:
   pkg/DESCRIPTION
   pkg/tests/plottest.R
   pkg/tests/plottest.Rout.save
Log:

  version bump
  fix check output



Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-11-23 20:26:17 UTC (rev 839)
+++ pkg/DESCRIPTION	2012-11-24 20:22:08 UTC (rev 840)
@@ -1,7 +1,7 @@
 Package: phylobase
 Type: Package
 Title: Base package for phylogenetic structures and comparative data
-Version: 0.6.4
+Version: 0.6.5
 Date: 2012-11-21
 Depends:
     methods,

Modified: pkg/tests/plottest.R
===================================================================
--- pkg/tests/plottest.R	2012-11-23 20:26:17 UTC (rev 839)
+++ pkg/tests/plottest.R	2012-11-24 20:22:08 UTC (rev 840)
@@ -15,7 +15,8 @@
 plot(g2, show.node.label=TRUE)
 
 
-g2B <- as(extractTree(g2), "phylog")
+## commented out since phylog objects are deprecated anyway
+## g2B <- as(extractTree(g2), "phylog")
 ##  Note the numbering differences!
 
 ## round trip 
@@ -32,6 +33,7 @@
 
 ## Playing with new ways of plotting
 
+if (FALSE) {
 if(require(MASS)){
     dist1 <- cophenetic.phylo(as(g2, "phylo"))
     mdspos <- isoMDS(dist1)$points
@@ -45,8 +47,8 @@
 }
 ## never mind, I don't know how to construct a useful
 ##  2D color space anyway ...
+}
 
-
 treePlot(g2,plot.at.tip=TRUE,tip.plot.fun=
          function(x,...) {
            grid.points(seq(along=x),x)})

Modified: pkg/tests/plottest.Rout.save
===================================================================
--- pkg/tests/plottest.Rout.save	2012-11-23 20:26:17 UTC (rev 839)
+++ pkg/tests/plottest.Rout.save	2012-11-24 20:22:08 UTC (rev 840)
@@ -45,11 +45,8 @@
 > plot(g2, show.node.label=TRUE)
 > 
 > 
-> g2B <- as(extractTree(g2), "phylog")
-Warning messages:
-1: In asMethod(object) : trees with unknown order may be unsafe in ape
-2: In asMethod(object) :
-  ade4::phylog objects are deprecated, please use the adephylo package instead
+> ## commented out since phylog objects are deprecated anyway
+> ## g2B <- as(extractTree(g2), "phylog")
 > ##  Note the numbering differences!
 > 
 > ## round trip 
@@ -68,7 +65,8 @@
 > 
 > ## Playing with new ways of plotting
 > 
-> if(require(MASS)){
+> if (FALSE) {
++ if(require(MASS)){
 +     dist1 <- cophenetic.phylo(as(g2, "phylo"))
 +     mdspos <- isoMDS(dist1)$points
 +     par(mfrow=c(2, 2))
@@ -79,31 +77,14 @@
 +     ## plot(cmdpos,type="n")
 +     ## text(cmdpos[,1],cmdpos[,2],abbreviate(rownames(mdspos)))
 + }
-Loading required package: MASS
-initial  value 12.162947 
-iter   5 value 3.201793
-iter  10 value 1.433796
-iter  15 value 1.147120
-iter  20 value 0.914894
-iter  25 value 0.705057
-iter  30 value 0.376895
-iter  35 value 0.256479
-iter  40 value 0.091883
-iter  45 value 0.024262
-iter  50 value 0.010918
-final  value 0.010918 
-stopped after 50 iterations
-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
-> ## never mind, I don't know how to construct a useful
-> ##  2D color space anyway ...
++ ## never mind, I don't know how to construct a useful
++ ##  2D color space anyway ...
++ }
 > 
-> 
 > treePlot(g2,plot.at.tip=TRUE,tip.plot.fun=
 +          function(x,...) {
 +            grid.points(seq(along=x),x)})
 > 
 > proc.time()
    user  system elapsed 
-  2.352   2.468   4.674 
+  2.136   2.312   4.300