[Vegan-commits] r2048 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2012-01-18 12:19:13 +0100 (Wed, 18 Jan 2012)
New Revision: 2048

Modified:
   pkg/vegan/R/permutest.cca.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/anova.cca.Rd
Log:
parallel processing honours setDefatultCluster

Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R	2012-01-17 09:34:52 UTC (rev 2047)
+++ pkg/vegan/R/permutest.cca.R	2012-01-18 11:19:13 UTC (rev 2048)
@@ -7,7 +7,7 @@
 `permutest.cca` <-
     function (x, permutations = 99,
               model = c("reduced", "direct", "full"), first = FALSE,
-              strata = NULL, parallel = getOption("mc.cores", 1L) , ...) 
+              strata = NULL, parallel = getOption("mc.cores") , ...) 
 {
     model <- match.arg(model)
     isCCA <- !inherits(x, "rda")
@@ -114,7 +114,11 @@
     }
     nperm <- nrow(permutations)
     ## Parallel processing (similar as in oecosimu)
-    hasClus <- inherits(parallel, "cluster") || is.null(parallel)
+    if (is.null(parallel) && getRversion() >= "2.15.0")
+        parallel <- get("default", envir = parallel:::.reg)
+    if (is.null(parallel) || getRversion() < "2.14.0")
+        parallel <- 1
+    hasClus <- inherits(parallel, "cluster")
     if ((hasClus || parallel > 1)  && require(parallel)) {
         if(.Platform$OS.type == "unix" && !hasClus) {
             tmp <- do.call(rbind,

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-01-17 09:34:52 UTC (rev 2047)
+++ pkg/vegan/inst/ChangeLog	2012-01-18 11:19:13 UTC (rev 2048)
@@ -13,13 +13,12 @@
 	_R_CHECK_FORCE_SUGGESTS_=FALSE (see, e.g., discussion
 	https://stat.ethz.ch/pipermail/r-devel/2011-December/062827.html).
 
-	* oecosimu: new experimental parallel block which honours
+	* oecosimu, permutest.cca: new parallel block which honours
 	setDefaultCluster() in R-devel (becoming R 2.15.0) and
 	automatically uses parallel processing with socket clusters if
 	setDefaultCluster was defined. Tested in R (unstable) (2012-01-16
-	r58122) with full features, and in R version 2.13.1 (2011-07-08)
-	without parallel processing, but not yet in R 2.14.1 with parallel
-	processing but without setDefaultCluster().
+	r58122) with full features, in R 2.14.1 without setDefaultCluster,
+	and in R 2.13.1 (2011-07-08) without parallel processing
 
 	* anova.ccabymargin failed if none of the terms was analysed (all
 	were aliased) and no permutations were performed.  This would

Modified: pkg/vegan/man/anova.cca.Rd
===================================================================
--- pkg/vegan/man/anova.cca.Rd	2012-01-17 09:34:52 UTC (rev 2047)
+++ pkg/vegan/man/anova.cca.Rd	2012-01-18 11:19:13 UTC (rev 2048)
@@ -26,7 +26,7 @@
 \method{permutest}{cca}(x, permutations = 99,
           model = c("reduced", "direct", "full"),
           first = FALSE, strata = NULL, 
-	  parallel = getOption("mc.cores", 1L) , ...)
+	  parallel = getOption("mc.cores") , ...)
 }
 
 \arguments{