@@ -1,6 +1,6 @@

 Package: affxparser

 Version: 1.29.2

-Date: 2012-05-18

+Date: 2012-05-22

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan

 Maintainer: Kasper Daniel Hansen <[email protected]>

@@ -10,6 +10,17 @@ readCel <- function(filename,

                     readMap = NULL, 

                     verbose = 0,

                     .checkArgs = TRUE) {

+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+    # Local functions

+    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+    qsort <- function(x) {

+  ##    o0 <- .Internal(qsort(x, TRUE));

+  ##    o <- sort.int(x, index.return=TRUE, method="quick");

+  ##    stopifnot(identical(o, o0));

+      sort.int(x, index.return=TRUE, method="quick");

+    } # qsort()

+

+

     # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

     # Validate arguments

     # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -77,10 +88,12 @@ readCel <- function(filename,

     # jumping around in the file.

     # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

     if (reorder) {

-      # About 10-15 times faster than using order()!

-      o <- .Internal(qsort(indices, TRUE));  # From base::sort.int()

+      # qsort() is about 10-15 times faster than using order()!

+      # WAS: o <- .Internal(qsort(indices, TRUE));  # From base::sort.int()

+      o <- qsort(indices);

       indices <- o$x;

-      o <- .Internal(qsort(o$ix, TRUE))$ix;  # From base::sort.int()

+      # WAS: o <- .Internal(qsort(o$ix, TRUE))$ix;  # From base::sort.int()

+      o <- qsort(o$ix)$ix;

     }

     # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

@@ -113,6 +126,9 @@ readCel <- function(filename,

 ############################################################################

 # HISTORY:

+# 2012-05-22 [HB]

+# o CRAN POLICY: readCel() and readCelUnits() are no longer calling

+#   .Internal(qsort(...)).

 # 2011-11-18

 # o ROBUSTNESS: Added sanity check that the native code did not return NULL.

 # 2007-12-01

@@ -78,6 +78,17 @@

 # @keyword "IO"

 #*/######################################################################### 

 readCelUnits <- function(filenames, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"), cdf=NULL, ..., addDimnames=FALSE, dropArrayDim=TRUE, transforms=NULL, readMap=NULL, verbose=FALSE) {

+  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+  # Local functions

+  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+  qsort <- function(x) {

+##    o0 <- .Internal(qsort(x, TRUE));

+##    o <- sort.int(x, index.return=TRUE, method="quick");

+##    stopifnot(identical(o, o0));

+    sort.int(x, index.return=TRUE, method="quick");

+  } # qsort()

+

+

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

   # Validate arguments

   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

@@ -275,10 +286,12 @@ readCelUnits <- function(filenames, units=NULL, stratifyBy=c("nothing", "pmmm",

   reorder <- TRUE;  # Hardwired from now on.

   if (reorder) {

     verbose && enter(verbose, "Reordering cell indices to optimize speed");

-    # About 10-15 times faster than using order()!

-    o <- .Internal(qsort(indices, TRUE));  # From base::sort.int()

+    # qsort() is about 10-15 times faster than using order()!

+    # WAS: o <- .Internal(qsort(indices, TRUE));  # From base::sort.int()

+    o <- qsort(indices);

     indices <- o$x;

-    o <- .Internal(qsort(o$ix, TRUE))$ix;  # From base::sort.int()

+    # WAS: o <- .Internal(qsort(o$ix, TRUE))$ix;  # From base::sort.int()

+    o <- qsort(o$ix)$ix;

     verbose && exit(verbose);

   }

@@ -452,6 +465,9 @@ readCelUnits <- function(filenames, units=NULL, stratifyBy=c("nothing", "pmmm",

 ############################################################################

 # HISTORY:

+# 2012-05-22 [HB]

+# o CRAN POLICY: readCel() and readCelUnits() are no longer calling

+#   .Internal(qsort(...)).

 # 2007-12-01 [HB]

 # o Removed argument 'reorder' from readCelUnits(). Reordering is now always

 #   done.

@@ -1,6 +1,13 @@

 Package: affxparser

 ===================

+Version: 1.29.2 [2012-05-22]

+o GENERALIZATION: Now system tests that launch another R process no

+  longer assumes R is on the OS's search path.

+o ROBUSTNESS/CRAN POLICY: readCel() and readCelUnits() are no longer

+  calling .Internal(qsort(...)).

+

+

 Version: 1.29.1 [2012-05-18]

 o Replaced several throw() with stop(), because the former assumes

   that R.methodsS3 is loaded, which it may not be.

@@ -1,5 +1,14 @@

-R_exe <- file.path(Sys.getenv("R_HOME"), "bin", "R")

-out <- system(paste(R_exe, '-e "affxparser:::.testWriteAndReadEmptyCdf()"'), intern=TRUE);

+systemR <- function(command="", ..., verbose=FALSE) {

+  # Locate the R executable

+  Rbin <- file.path(R.home("bin"), "R");

+

+  cmd <- sprintf('%s %s', Rbin, command);

+  if (verbose) cat("Command: ", cmd, "\n", sep="");

+  system(cmd, ...);

+} # systemR()

+

+

+out <- systemR('-e "affxparser:::.testWriteAndReadEmptyCdf()"', intern=TRUE, verbose=TRUE);

 cat(out, sep="\n");

 res <- any(regexpr("COMPLETE", out) != -1);

 cat("Test result: ", res, "\n", sep="");

@@ -7,6 +16,10 @@ cat("Test result: ", res, "\n", sep="");

 ############################################################################

 # HISTORY:

+# 2012-05-22

+# o ROBUSTNESS: Now launching R without assuming it is on the search path,

+#   cf. R-devel thread 'Best way to locate R executable from within R?'

+#   on May 22, 2012.

 # 2012-05-18

 # o Added because of the OSX build bug, cf.

 #   https://groups.google.com/d/topic/aroma-affymetrix/lEfDanThLEA/discussion