Add sort option (issue #180)

o Add option sortMethod that defaults to "auto" on R < 3.3 and "radix" otherwise.
lgatto · Jan 3, 2017 · 67278d0 · 67278d0
1 parent 0f18ae6
commit 67278d0
Show file tree

Hide file tree

Showing 4 changed files with 14 additions and 4 deletions.
diff --git a/R/functions-OnDiskMSnExp.R b/R/functions-OnDiskMSnExp.R
@@ -392,7 +392,8 @@ precursorValue_OnDiskMSnExp <- function(object, column) {
         res <- vector("list", nrow(ms1fd))
         for (i in 1:nrow(ms1fd)) {
             currentMat <- allSpect[[i]]
-            o <- order(currentMat[, 1], method = "radix")
+            ## issue #180: use radix sorting for R >= 3.3
+            o <- order(currentMat[, 1], method = MSnbaseOptions()$sortMethod)
             currentMat <- currentMat[o, ]
             res[[i]] <- Spectrum1(peaksCount = nrow(currentMat),
                                   scanIndex = ms1fd[i, "spIdx"],
@@ -424,7 +425,9 @@ precursorValue_OnDiskMSnExp <- function(object, column) {
         res2 <- vector("list", nrow(msnfd))
         for (i in 1:nrow(msnfd)) {
             currentMat <- allSpect[[i]]
-            o <- order(currentMat[, 1], method = "radix")
+            ## issue #180: use radix sorting for R >= 3.3
+            ## o <- order(currentMat[, 1], method = "radix")
+            o <- order(currentMat[, 1], method = MSnbaseOptions()$sortMethod)
             currentMat <- currentMat[o, ]
             res2[[i]] <- Spectrum2(peaksCount = nrow(currentMat),
                                    scanIndex = msnfd[i, "spIdx"],

diff --git a/R/methods-Spectrum.R b/R/methods-Spectrum.R
@@ -9,7 +9,9 @@ setMethod("initialize",
               if (xor(!missing(mz), !missing(intensity)))
                   stop("'mz' and 'intensity' or none required.")
               if (!missing(mz) & !missing(intensity)) {
-                  o <- base::order(mz, method = "radix")
+                  ## issue #180: use radix sorting for R >= 3.3
+                  ## o <- base::order(mz, method = "radix")
+                  o <- base::order(mz, method = MSnbaseOptions()$sortMethod)
                   .Object <- callNextMethod(.Object,
                                             ...,
                                             mz = mz[o],

diff --git a/R/options.R b/R/options.R
@@ -12,7 +12,7 @@
 ##' There are also setters to set options individually. When run
 ##' without argument, the verbosity setter inverts the current value
 ##' of the option.
-##' 
+##'
 ##' @title MSnbase options
 ##' @param opt The value of the new option
 ##' @return A \code{list} of MSnbase options and the single option

diff --git a/R/zzz.R b/R/zzz.R
@@ -12,7 +12,12 @@
 
 .onLoad <- function(libname, pkgname) {
     ## Add MSnbase options.
+    ## Use radix sorting for R >= 3.3
+    sortMeth <- "auto"
+    if (as.numeric(R.Version()$major) >= 3 & as.numeric(R.Version()$minor) >= 3)
+        sortMeth <- "radix"
     msOps <- list(PARALLEL_THRESH = 1000,
+                  sortMethod = sortMeth,
                   verbose = FALSE)
     options(MSnbase = msOps)
 }