[Vegan-commits] r2063 - in pkg/vegan: . R inst

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

Author: jarioksa
Date: 2012-02-05 08:32:54 +0100 (Sun, 05 Feb 2012)
New Revision: 2063

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/adonis.R
   pkg/vegan/R/anosim.R
   pkg/vegan/R/mantel.R
   pkg/vegan/R/mantel.partial.R
   pkg/vegan/R/mrpp.R
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/inst/ChangeLog
Log:
not all socket clusters need clusterEvalQ(..., library(vegan))

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/DESCRIPTION	2012-02-05 07:32:54 UTC (rev 2063)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 2.1-10
-Date: January 22, 2012
+Version: 2.1-11
+Date: February 5, 2012
 Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, 
    Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, 
    M. Henry H. Stevens, Helene Wagner  

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/R/adonis.R	2012-02-05 07:32:54 UTC (rev 2063)
@@ -118,7 +118,6 @@
     isMulticore <- .Platform$OS.type == "unix" && !hasClus
     if (isParal && !isMulticore && !hasClus) {
         parallel <- makeCluster(parallel)
-        clusterEvalQ(parallel, library(vegan))
     }
     if (isParal) {
         if (isMulticore) {

Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/R/anosim.R	2012-02-05 07:32:54 UTC (rev 2063)
@@ -61,7 +61,6 @@
         } else {
             if (!hasClus) {
                 parallel <- makeCluster(parallel)
-                clusterEvalQ(parallel, library(vegan))
             }
             perm <- parRapply(parallel, permat, ptest)
             if (!hasClus)

Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/R/mantel.R	2012-02-05 07:32:54 UTC (rev 2063)
@@ -46,7 +46,6 @@
             } else {
                 if (!hasClus) {
                     parallel <- makeCluster(parallel)
-                    clusterEvalQ(parallel, library(vegan))
                 }
                 perm <- parRapply(parallel, permat, ptest)
                 if (!hasClus)

Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/R/mantel.partial.R	2012-02-05 07:32:54 UTC (rev 2063)
@@ -54,7 +54,6 @@
             } else {
                 if (!hasClus) {
                     parallel <- makeCluster(parallel)
-                    clusterEvalQ(parallel, library(vegan))
                 }
                 perm <- parRapply(parallel, permat, ptest)
                 if (!hasClus)

Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/R/mrpp.R	2012-02-05 07:32:54 UTC (rev 2063)
@@ -63,8 +63,7 @@
         } else {
             if (!hasClus) {
                 parallel <- makeCluster(parallel)
-                clusterEvalQ(parallel, library(vegan))
-            }
+             }
             m.ds <- parCapply(parallel, perms, function(x)
                               mrpp.perms(x, dmat, indls, w))
             if (!hasClus)

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/R/permutest.cca.R	2012-02-05 07:32:54 UTC (rev 2063)
@@ -129,7 +129,6 @@
             ## if hasClus, do not set up and stop a temporary cluster
             if (!hasClus) {
                 parallel <- makeCluster(parallel)
-                clusterEvalQ(parallel, library(vegan))
             }
             tmp <- parRapply(parallel, permutations, function(i) getF(i))
             tmp <- matrix(tmp, ncol=3, byrow=TRUE)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-02-04 16:35:31 UTC (rev 2062)
+++ pkg/vegan/inst/ChangeLog	2012-02-05 07:32:54 UTC (rev 2063)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Vegan 2.1-10 (opened January 22, 2012)
+Version 2.1-11 (opened February 5, 2012)
 
+	* adonis, anosim, mantel, mantel.partial, mrpp, permutest.cca: do
+	not need clusterEvalQ(parallel, library(vegan)) for socket
+	clusters. 
+	
+Version 2.1-10 (closed February 5, 2012)
+
 	* adonis: print info that terms are added sequentially -- this
 	seems to confuse users. Make this change in adonis() instead of
 	print.adonis to be prepared to add other policies.