Add sort method option

o Add sort method option that defaults to "auto" on R versions < 3.3. See
  lgatto/MSnbase#180 for more info.

R/functions-binning.R

@@ -171,7 +171,8 @@ binYonX <- function(x, y, breaks, nBins, binSize, binFromX,
         stop("One of 'breaks', 'nBins' or 'binSize' has to be defined!")
     if (!sortedX) {
         message("'x' is not sorted, will sort 'x' and 'y'.")
-        o <- order(x, method = "radix")
+        ## Sort method; see issue #180 for MSnbase
+        o <- order(x, method = options()$BioC$xcms$sortMethod)
         x <- x[o]
         y <- y[o]
     }

R/init.R

@@ -70,12 +70,17 @@
 
     ## getEIC method
     getEIC.method="getEICOld"
+
+    ## Sort method; see issue #180 for MSnbase
+    sortMeth <- "auto"
+    if (as.numeric(R.Version()$major) >= 3 & as.numeric(R.Version()$minor) >= 3)
+        sortMeth <- "radix"
     xcms.opt <- list(findPeaks.method=findPeaks.method, findPeaks.methods=findPeaks.methods,
                      group.method=group.method, group.methods=group.methods,
                      retcor.method=retcor.method, retcor.methods=retcor.methods,
                      fillPeaks.method=fillPeaks.method, fillPeaks.methods=fillPeaks.methods,
                      specDist.methods=specDist.methods, getEIC.method=getEIC.method,
-                     useOriginalCode = FALSE)
+                     useOriginalCode = FALSE, sortMethod = sortMeth)
 
     class(xcms.opt) <- "BioCPkg"