pass NBCORES bash script param to R scripts

rtest.sh

@@ -461,7 +461,7 @@ echo
 printLeftPurple "Generation of depends.R ... started at `date '+%H:%M:%S'` ... "
 # generate depends.R
 echo 'if (!"tools" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
-    install.packages("tools",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
+    install.packages("tools",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=$NBCORES)
 }
 
 old <- getOption("defaultPackages"); r <- getOption("repos")
@@ -518,7 +518,7 @@ if [ -n "$R_LIBS_USER" ]; then
     R_LIBS_USER_PARAM=", lib=Sys.getenv(\"R_LIBS_USER\")"
 fi
 echo '
-install.packages("'$PACKAGE_TO_TEST'"'$REPO_R_PARAM''$R_LIBS_USER_PARAM', dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
+install.packages("'$PACKAGE_TO_TEST'"'$REPO_R_PARAM''$R_LIBS_USER_PARAM', dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=$NBCORES)
 
 ff <- file("pkg.version", open = "w")
 cat( paste(sep=",",packageVersion("'$PACKAGE_TO_TEST'")), file=ff)
@@ -556,7 +556,7 @@ if [[ "$SKIPINSTALLFLAG" == "0" ]]; then
     update.packages(lib.loc=Sys.getenv("R_LIBS_USER"), repos=c("'$DEFAULT_REPOSITORY'"),ask=FALSE)
 
     if (!"XML" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
-        install.packages("XML",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
+        install.packages("XML",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=$NBCORES)
     }
     source("http://bioconductor.org/biocLite.R")
     biocLite("Biostrings", ask=FALSE, lib.loc=Sys.getenv("R_LIBS_USER"), suppressUpdates=TRUE)
@@ -602,7 +602,7 @@ if [[ "$SKIPINSTALLFLAG" == "0" ]]; then
         echo 'chooseBioCmirror(ind=3)
 setRepositories(ind=c(1, 2, 5, 6))
 if (!"'$pname'" %in% installed.packages(lib.loc=Sys.getenv("R_LIBS_USER"))) {
-    install.packages("'$pname'",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=7)
+    install.packages("'$pname'",repos=c("'$DEFAULT_REPOSITORY'"), lib=Sys.getenv("R_LIBS_USER"), dependencies=c("Depends", "Imports", "LinkingTo", "Suggests"), Ncpus=$NBCORES)
 }
 ' > ${pname}_install.R