@@ -1,5 +1,5 @@

 Package: GSVA

-Version: 1.23.2

+Version: 1.23.3

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Author: Justin Guinney with contributions from Robert Castelo

 Maintainer: Justin Guinney <justin.guinney@sagebase.org>

@@ -299,7 +299,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),

 	if(parallel.sz > 0 && no.bootstraps > 0){

 		if((no.bootstraps %% parallel.sz) != 0){

-			stop("'parrallel.sz' must be an integer divisor of 'no.bootsraps'" )

+			stop("'parallel.sz' must be an integer divisor of 'no.bootsraps'" )

 		}

 	}

 	n.samples <- ncol(expr)

@@ -332,7 +332,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),

 		es.bootstraps <- array(NaN, c(n.gset, n.samples, no.bootstraps))

 		if(parallel.sz > 1){

-		  if(!.isPackageLoaded("snow")) {

+		  if(!.isPackageLoaded("snow")) { ## FIXME: should also open parallelism via 'parallel'

 			  stop("Please load the 'snow' library")

 		  }

       ## copying ShortRead's strategy, the calls to the 'get()' are

@@ -344,15 +344,16 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),

       stopCl <- get("stopCluster", mode="function")

 			cl <- makeCl(parallel.sz, type = parallel.type) 

-			.GlobalEnv[["expr"]] <- expr

-			.GlobalEnv[["bootstrap.nsamples"]] <- bootstrap.nsamples

-			.GlobalEnv[["n.samples"]] <- n.samples

-			.GlobalEnv[["gset.idx.list"]] <- gset.idx.list

-			clExport(cl,"expr")

-			clExport(cl,"bootstrap.nsamples")

-			clExport(cl, "n.samples")

-			clExport(cl, "gset.idx.list")

-			clExport(cl, "compute.geneset.es")

+			clExport(cl,"expr", envir=environment())

+			clExport(cl,"bootstrap.nsamples", envir=environment())

+			clExport(cl, "n.samples", envir=environment())

+			clExport(cl, "gset.idx.list", envir=environment())

+			clExport(cl, "rnaseq", envir=environment())

+			clExport(cl, "abs.ranking", envir=environment())

+			clExport(cl, "mx.diff", envir=environment())

+			clExport(cl, "tau", envir=environment())

+			clExport(cl, "kernel", envir=environment())

+			clExport(cl, "verbose", envir=environment())

 			clEvalQ(cl, library(GSVA))

 			clSetupRNG(cl)

@@ -362,10 +363,10 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),

 			n.cycles <- floor(no.bootstraps / parallel.sz)

 			for(i in 1:n.cycles){

 				if(verbose) cat("bootstrap cycle ", i, "\n")

-				r <- clEvalQ(cl, compute.geneset.es(expr, gset.idx.list, 

+				r <- clEvalQ(cl, GSVA:::compute.geneset.es(expr, gset.idx.list, 

 								sample(n.samples, bootstrap.nsamples, replace=T),

 								rnaseq=rnaseq, abs.ranking=abs.ranking, mx.diff=mx.diff,

-                tau=tau, kernel=kernel, verbose=verbose))

+                tau=tau, kernel=kernel, verbose=FALSE, parallel.sz=1))

 				for(j in 1:length(r)){

 					es.bootstraps[,,(parallel.sz * (i-1) + j)] <- r[[j]]

 				}	

@@ -377,7 +378,7 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),

 				es.bootstraps[,,i] <- compute.geneset.es(expr, gset.idx.list,

 						sample(n.samples, bootstrap.nsamples, replace=T),

 						rnaseq=rnaseq, abs.ranking=abs.ranking, mx.diff=mx.diff,

-            tau=tau, kernel=kernel, verbose=verbose)

+            tau=tau, kernel=kernel, verbose=verbose, parallel.sz=1)

 			}

 		}

@@ -469,7 +470,7 @@ compute.geneset.es <- function(expr, gset.idx.list, sample.idxs, rnaseq=FALSE,

 			stop("In order to run calculations in parallel either the 'snow', or the 'parallel' library, should be loaded first")

 		}

-    if (!haveParallel) {  ## use snow

+    if (haveSnow) {  ## use snow

       ## copying ShortRead's strategy, the calls to the 'get()' are

       ## employed to quieten R CMD check, and for no other reason

       makeCl <- get("makeCluster", mode="function")

@@ -498,7 +499,7 @@ compute.geneset.es <- function(expr, gset.idx.list, sample.idxs, rnaseq=FALSE,

         cat("Cleaning up\n")

 		  stopCl(cl)

-    } else {             ## use parallel

+    } else if (haveParallel) {             ## use parallel

       mclapp <- get('mclapply', envir=getNamespace('parallel'))

       detCor <- get('detectCores', envir=getNamespace('parallel'))

@@ -525,7 +526,8 @@ compute.geneset.es <- function(expr, gset.idx.list, sample.idxs, rnaseq=FALSE,

       if (verbose) {

         close(get("progressBar", envir=globalenv()))

       }

-    }

+    } else

+			stop("In order to run calculations in parallel either the 'snow', or the 'parallel' library, should be loaded first")

 	} else {

 		if (verbose) {