[Vegan-commits] r2642 - in pkg/vegan: R inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Nov 3 15:34:21 CET 2013
Author: jarioksa
Date: 2013-11-03 15:34:20 +0100 (Sun, 03 Nov 2013)
New Revision: 2642
Modified:
pkg/vegan/R/adonis.R
pkg/vegan/R/anosim.R
pkg/vegan/R/bioenv.default.R
pkg/vegan/R/mantel.R
pkg/vegan/R/mantel.partial.R
pkg/vegan/R/metaMDSiter.R
pkg/vegan/R/mrpp.R
pkg/vegan/R/oecosimu.R
pkg/vegan/R/permutest.cca.R
pkg/vegan/R/simper.R
pkg/vegan/inst/ChangeLog
pkg/vegan/vignettes/decision-vegan.Rnw
Log:
do not use setDefaultCluster() clusters in parallel processing
Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/adonis.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -107,8 +107,6 @@
## Apply permutations for each term
## This is the new f.test (2011-06-15) that uses fewer arguments
## Set first parallel processing for all terms
- 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")
Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/anosim.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -48,8 +48,6 @@
permutations <- nrow(permat)
}
## Parallel processing
- 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")
Modified: pkg/vegan/R/bioenv.default.R
===================================================================
--- pkg/vegan/R/bioenv.default.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/bioenv.default.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -71,8 +71,6 @@
comdis <- vegdist(comm, method = index)
}
## Prepare for parallel processing
- 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")
Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/mantel.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -41,8 +41,6 @@
drop(cor(permvec, ydis, method = method, use = use))
}
## Parallel processing
- 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")
Modified: pkg/vegan/R/mantel.partial.R
===================================================================
--- pkg/vegan/R/mantel.partial.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/mantel.partial.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -49,8 +49,6 @@
part.cor(rxy, rxz, ryz)
}
## parallel processing
- 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")
Modified: pkg/vegan/R/metaMDSiter.R
===================================================================
--- pkg/vegan/R/metaMDSiter.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/metaMDSiter.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -73,8 +73,6 @@
monostop(s0)
tries <- 0
## Prepare for parallel processing
- 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")
Modified: pkg/vegan/R/mrpp.R
===================================================================
--- pkg/vegan/R/mrpp.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/mrpp.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -50,8 +50,6 @@
ncol(perms), N))
}
## Parallel processing
- 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")
Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/oecosimu.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -86,11 +86,7 @@
## start with empty simind
simind <- NULL
## Go to parallel processing if 'parallel > 1' or 'parallel' could
- ## be a pre-defined socket cluster or 'parallel = NULL' in which
- ## case it could be setDefaultCluster (or a user error)
- if (is.null(parallel) && getRversion() >= "2.15.0")
- parallel <- get("default", envir = parallel:::.reg)
- ## still NULL? was not a defaultCluster, so make to non-parallel
+ ## be a pre-defined socket cluster or 'parallel = NULL'.
if (is.null(parallel) || getRversion() < "2.14.0")
parallel <- 1
hasClus <- inherits(parallel, "cluster")
Modified: pkg/vegan/R/permutest.cca.R
===================================================================
--- pkg/vegan/R/permutest.cca.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/permutest.cca.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -124,8 +124,6 @@
}
nperm <- nrow(permutations)
## Parallel processing (similar as in oecosimu)
- 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")
Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/R/simper.R 2013-11-03 14:34:20 UTC (rev 2642)
@@ -38,8 +38,6 @@
if (nperm > 0)
perm.contr <- matrix(nrow=P, ncol=nperm)
## Parallel processing ?
- 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")
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/inst/ChangeLog 2013-11-03 14:34:20 UTC (rev 2642)
@@ -25,6 +25,11 @@
(testing theory requires nesting, but this is commonly violated by
users: here nesting is necessary).
+ * parellel: default cluster defined by setDefaultCluster() is no
+ longer used in functions with parallel processing. Using default
+ cluster would need querying an unexported environment
+ parellel:::.reg, and this gives a NOTE in R CMD check.
+
* specaccum, renyiaccum, tsallisaccum: gained argument to select a
'subset' of sites (looks like my student would need them).
Modified: pkg/vegan/vignettes/decision-vegan.Rnw
===================================================================
--- pkg/vegan/vignettes/decision-vegan.Rnw 2013-10-31 20:24:59 UTC (rev 2641)
+++ pkg/vegan/vignettes/decision-vegan.Rnw 2013-11-03 14:34:20 UTC (rev 2642)
@@ -92,10 +92,8 @@
package is loaded.
\R{} allows\footnote{Since \R{} version 2.15.0.}
-setting up a default socket cluster (\code{setDefaultCluster}). In
-that case \pkg{vegan} will perform parallel processing with that
-default cluster. If the \code{mc.cores} is also set, it takes
-precedence.
+setting up a default socket cluster (\code{setDefaultCluster}), but
+this will not be used in \pkg{vegan}.
\subsubsection{Setting up socket clusters}
\label{sec:parallel:socket}
@@ -201,31 +199,7 @@
\begin{enumerate}
\item \code{NULL}: The function is called with argument \code{parallel
= getOption("mc.cores")}. The option \code{mc.cores} is normally
- unset and then the default is \code{parallel = NULL}. This is
- interpreted as \code{parallel = 1} in \R-2.14.x. In \R-2.15.x the
- function inspects if a default socket cluster is defined. \R-2.15.0
- has a non-exported environment \code{parallel:::.reg} with variable
- \code{default} that is either \code{NULL} (default) or a socket
- cluster. Querying this environment is an error in \R-2.14.x so that
- we also need to test the \R{} version. In the following
- \code{oecosimu} code we first see if the default cluster is set when
- \code{parallel = NULL}, and if it is unset, the \code{parallel} will
- still be \code{NULL} and will be changed to \code{1}. After this,
- the value of \code{parallel} will be either an integer or a socket
- cluster, and information on the type is saved in variable
- \code{hasClus}:
-\begin{Schunk}
-\begin{Soutput}
-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")
-\end{Soutput}
-\end{Schunk}
+ unset and then the default is \code{parallel = NULL}.
\item Integer: An integer value is taken as the number of created
parallel processes. In unix-like systems this is the number of
forked multicore processes, and in Windows this is the number of
@@ -244,16 +218,12 @@
\item Explicitly given argument value of \code{parallel} will always
be used.
\item If \code{mc.cores} is set, it will be used. In Windows this
- means creating and stopping socket clusters even when a default
- cluster is set if \code{mc.cores} is not \code{NULL}. Please note
+ means creating and stopping socket clusters. Please note
that the \code{mc.cores} is only set from the environmental
variable \code{MC_CORES} when you load the \pkg{parallel} package,
and it is always unset before first
- \code{require(parallel)}.\footnote{The behaviour of
- \code{mc.cores} option is untested in Windows.}
- \item The default socket cluster will be used if
- set.\footnote{Default cluster is available since \R{} 2.15.0.}
- \item The fall back behaviour is no parallel processing.
+ \code{require(parallel)}.
+ \item The fall back behaviour is no parallel processing.
\end{enumerate}
\section{Nestedness and Null models}
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