[CHNOSZ-commits] r319 - in pkg/CHNOSZ: . R data inst man

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

Author: jedick
Date: 2018-05-14 07:08:15 +0200 (Mon, 14 May 2018)
New Revision: 319

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/palply.R
   pkg/CHNOSZ/data/opt.csv
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/data.Rd
Log:
add thermo$opt$maxcores


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2018-05-06 06:41:29 UTC (rev 318)
+++ pkg/CHNOSZ/DESCRIPTION	2018-05-14 05:08:15 UTC (rev 319)
@@ -1,6 +1,6 @@
-Date: 2018-05-06
+Date: 2018-05-14
 Package: CHNOSZ
-Version: 1.1.3-26
+Version: 1.1.3-27
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/R/palply.R
===================================================================
--- pkg/CHNOSZ/R/palply.R	2018-05-06 06:41:29 UTC (rev 318)
+++ pkg/CHNOSZ/R/palply.R	2018-05-14 05:08:15 UTC (rev 319)
@@ -6,7 +6,7 @@
   if(length(X) >= get("thermo")$opt$paramin) {
     # Use option mc.cores to choose an appropriate cluster size.
     # and set max at 2 for now (per CRAN policies)
-    nCores <- min(getOption("mc.cores"), 2)
+    nCores <- min(getOption("mc.cores"), get("thermo")$opt$maxcores)
     # don't load methods package, to save startup time - ?makeCluster
     cl <- parallel::makeCluster(nCores, methods=FALSE)
     # export the variables and notify the user

Modified: pkg/CHNOSZ/data/opt.csv
===================================================================
--- pkg/CHNOSZ/data/opt.csv	2018-05-06 06:41:29 UTC (rev 318)
+++ pkg/CHNOSZ/data/opt.csv	2018-05-14 05:08:15 UTC (rev 319)
@@ -1,2 +1,2 @@
-cutoff,E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Berman
-1E-10,cal,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Helgeson,NA
+cutoff,E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Berman,maxcores
+1E-10,cal,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Helgeson,NA,2

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2018-05-06 06:41:29 UTC (rev 318)
+++ pkg/CHNOSZ/inst/NEWS	2018-05-14 05:08:15 UTC (rev 319)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-26 (2018-05-06)
+CHANGES IN CHNOSZ 1.1.3-27 (2018-05-14)
 ---------------------------------------
 
 THERMODYNAMIC DATA
@@ -84,6 +84,9 @@
 - Add demo/bison.R (average oxidation state of carbon of metagenome-
   derived proteins in different microbial phyla at Bison Pool)
 
+- Add thermo$opt$maxcores (default 2) to specify maximum number of
+  cores for parallel calculations with palply().
+
 CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd	2018-05-06 06:41:29 UTC (rev 318)
+++ pkg/CHNOSZ/man/data.Rd	2018-05-14 05:08:15 UTC (rev 319)
@@ -59,7 +59,8 @@
       \code{ideal.H} \tab logical \tab Should \code{\link{nonideal}} ignore the proton? [\code{TRUE}] \cr
       \code{ideal.e} \tab logical \tab Should \code{\link{nonideal}} ignore the electron? [\code{TRUE}] \cr
       \code{nonideal} \tab character \tab Method for \code{\link{nonideal}} [\code{Helgeson}] \cr
-      \code{Berman} \tab character \tab User data file for mineral parameters in the Berman equations [\code{NA}]
+      \code{Berman} \tab character \tab User data file for mineral parameters in the Berman equations [\code{NA}] \cr
+      \code{maxcores} \tab numeric \tab Maximum number of cores for parallel calculations with \code{\link{palply}} [\code{2}]
 }
 
     \item \code{thermo$element}