[Vegan-commits] r1592 - in branches/1.17: R inst inst/doc

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

Author: jarioksa
Date: 2011-04-27 13:30:32 +0200 (Wed, 27 Apr 2011)
New Revision: 1592

Modified:
   branches/1.17/R/capscale.R
   branches/1.17/inst/ChangeLog
   branches/1.17/inst/doc/decision-vegan.Rnw
Log:
merge 1590,1: 2.13.0 fix and 2.14.0 (under devel) warning

Modified: branches/1.17/R/capscale.R
===================================================================
--- branches/1.17/R/capscale.R	2011-04-27 11:23:42 UTC (rev 1591)
+++ branches/1.17/R/capscale.R	2011-04-27 11:30:32 UTC (rev 1592)
@@ -76,7 +76,8 @@
     if (add) {
         X <- cmdscale(X, k = k, eig = TRUE, add = add)
         ## All eigenvalues *should* be positive, but see that they are
-        X$points <- X$points[, X$eig[-(k+1)] > 0]
+        if (getRversion() < "2.13.0")
+            X$points <- X$points[, X$eig[-(k+1)] > 0]
         X$eig <- X$eig[X$eig > 0]
     }
     else

Modified: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog	2011-04-27 11:23:42 UTC (rev 1591)
+++ branches/1.17/inst/ChangeLog	2011-04-27 11:30:32 UTC (rev 1592)
@@ -4,6 +4,12 @@
 
 Version 1.17-10 (opened April 10, 2011)
 
+	* merged 1591:R 2.14.0 test warnings in decision-vegan.Rnw.
+
+	* merged r1590: capscale failed in rank-deficit cases with option
+	add = TRUE due to changes in cmdsscale() in R 2.13.0, and this
+	made BiodiversityR fail the tests.
+
 	* merged r1204, 1206, 1209, 1568: speed-up of examples in Rd
 	files. 
 

Modified: branches/1.17/inst/doc/decision-vegan.Rnw
===================================================================
--- branches/1.17/inst/doc/decision-vegan.Rnw	2011-04-27 11:23:42 UTC (rev 1591)
+++ branches/1.17/inst/doc/decision-vegan.Rnw	2011-04-27 11:30:32 UTC (rev 1592)
@@ -22,7 +22,7 @@
 in \Sexpr{R.version.string} on \today}
 
 \begin{document}
-\SweaveOpts{strip.white=TRUE}
+\SweaveOpts{strip.white=true}
 \setkeys{Gin}{width=0.55\linewidth}
 <<echo=false,results=hide>>=
 figset <- function() par(mar=c(4,4,1,1)+.1)