[CHNOSZ-commits] r68 - in pkg/CHNOSZ: . R inst

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

Author: jedick
Date: 2014-12-08 15:23:52 +0100 (Mon, 08 Dec 2014)
New Revision: 68

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/R/util.program.R
   pkg/CHNOSZ/R/wjd.R
   pkg/CHNOSZ/inst/NEWS
Log:
fixes for R CMD check


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2014-12-08 13:07:30 UTC (rev 67)
+++ pkg/CHNOSZ/DESCRIPTION	2014-12-08 14:23:52 UTC (rev 68)
@@ -1,6 +1,6 @@
-Date: 2014-11-20
+Date: 2014-12-08
 Package: CHNOSZ
-Version: 1.0.3-5
+Version: 1.0.3-6
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2014-12-08 13:07:30 UTC (rev 67)
+++ pkg/CHNOSZ/R/diagram.R	2014-12-08 14:23:52 UTC (rev 68)
@@ -144,6 +144,9 @@
     dim(predominant) <- dim(pv[[1]])
   }
 
+  ## where we'll put extra output for predominance diagrams (lx, ly, is)
+  out2D <- list()
+
   ### now on to the plotting ###
 
   if(plot.it) {
@@ -189,8 +192,6 @@
       }
     }
 
-    out2D <- list()
-
     if(nd==0) {
 
       ### 0-D diagram - bar graph of properties of species or reactions
@@ -406,6 +407,7 @@
         zs <- plotvals[[1]]
         if(length(plotvals) > 1) warning("showing only first species in 2-D property diagram")
         contour(xs, ys, zs, add=TRUE, col=col, lty=lty, lwd=lwd, labcex=cex)
+        pn <- list(lx=NULL, ly=NULL, is=NULL)
       } else {
         # put predominance matrix in the right order for image() etc
         zs <- t(predominant[, ncol(predominant):1])

Modified: pkg/CHNOSZ/R/util.program.R
===================================================================
--- pkg/CHNOSZ/R/util.program.R	2014-12-08 13:07:30 UTC (rev 67)
+++ pkg/CHNOSZ/R/util.program.R	2014-12-08 14:23:52 UTC (rev 68)
@@ -25,11 +25,11 @@
     ## Use option mc.cores to choose an appropriate cluster size.
     # or detectCores if that is NULL, and set max at 2 for now
     # (to be nice to CRAN etc.)
-    nCores <- max(getOption("mc.cores", detectCores()), 2)
+    nCores <- max(getOption("mc.cores", parallel::detectCores()), 2)
     # don't load methods package, to save startup time - ?makeCluster
-    cl <- makeCluster(nCores, methods=FALSE)
-    out <- parLapply(cl, X, FUN, ...)
-    stopCluster(cl)
+    cl <- parallel::makeCluster(nCores, methods=FALSE)
+    out <- parallel::parLapply(cl, X, FUN, ...)
+    parallel::stopCluster(cl)
   } else out <- lapply(X, FUN, ...)
   return(out)
 }

Modified: pkg/CHNOSZ/R/wjd.R
===================================================================
--- pkg/CHNOSZ/R/wjd.R	2014-12-08 13:07:30 UTC (rev 67)
+++ pkg/CHNOSZ/R/wjd.R	2014-12-08 14:23:52 UTC (rev 68)
@@ -270,7 +270,7 @@
       # minX is the minimum mole number we will accept
       H <- rep(minX, nrow(A))
       # get a solution
-      X <- xranges(E=t(A), F=B, G=G, H=H, central=TRUE, full=TRUE)[, "central"]
+      X <- limSolve::xranges(E=t(A), F=B, G=G, H=H, central=TRUE, full=TRUE)[, "central"]
       return(X)
     }
   }

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2014-12-08 13:07:30 UTC (rev 67)
+++ pkg/CHNOSZ/inst/NEWS	2014-12-08 14:23:52 UTC (rev 68)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-5 (2014-11-20)
+CHANGES IN CHNOSZ 1.0.3-6 (2014-12-08)
 --------------------------------------
 
 - Add files with average amino acid compositions of proteins from Bison