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

 Package: affxparser

-Version: 1.23.0

-Date: 2010-10-05

+Version: 1.23.1

+Date: 2010-12-16

 Title: Affymetrix File Parsing SDK

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

 Maintainer: Kasper Daniel Hansen <[email protected]>

@@ -82,7 +82,7 @@ readCdf <- function(filename, units=NULL, readXY=TRUE, readBases=TRUE,

                     stop("Number of PM and MM probes differ in probeset #", uu,

                          ": ", length(pm), " != ", length(mm));

                 }

-                pmmm <- .Internal(matrix(c(pm, mm), 2, npm, TRUE));

+                pmmm <- matrix(c(pm, mm), nrow=2L, ncol=npm, byrow=TRUE);

                 ## Re-order cell elements according to PM/MM.

                 ngroup <- length(group);

@@ -175,3 +175,10 @@ readCdf <- function(filename, units=NULL, readXY=TRUE, readBases=TRUE,

     cdf;

 } # readCdfUnits()

+

+############################################################################

+# HISTORY:

+# 2010-12-12

+# o ROBUSTNESS: Replaces .Internal(matrix(...)) with matrix().

+#   In the upcoming R 2.13.0 matrix() has less overhead.

+############################################################################

@@ -134,7 +134,7 @@ readCdfCellIndices <- function(filename, units=NULL, stratifyBy=c("nothing", "pm

           stop("Number of PM and MM probes differ in probeset #", uu,

                                      ": ", length(pm), " != ", length(mm));

         }

-        pmmm <- .Internal(matrix(c(pm, mm), 2, npm, TRUE));

+        pmmm <- matrix(c(pm, mm), nrow=2L, ncol=npm, byrow=TRUE);

 #        dimnames(pmmm) <- dimnames;

         # Re-order cell elements according to PM/MM.

@@ -206,6 +206,9 @@ readCdfCellIndices <- function(filename, units=NULL, stratifyBy=c("nothing", "pm

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

 # HISTORY:

+# 2010-12-12

+# o ROBUSTNESS: Replaces .Internal(matrix(...)) with matrix().

+#   In the upcoming R 2.13.0 matrix() has less overhead.

 # 2006-12-10

 # o BUG FIX: Same stratifyBy="mm" bug here as in readCdfUnits().

 # 2006-07-22

@@ -177,7 +177,7 @@ readCdfUnits <- function(filename, units=NULL, readXY=TRUE, readBases=TRUE, read

           stop("Number of PM and MM probes differ in probeset #", uu,

                                      ": ", length(pm), " != ", length(mm));

         }

-        pmmm <- .Internal(matrix(c(pm, mm), 2, npm, TRUE));

+        pmmm <- matrix(c(pm, mm), nrow=2L, ncol=npm, byrow=TRUE);

 #        dimnames(pmmm) <- dimnames;

         # Re-order cell elements according to PM/MM.

@@ -250,6 +250,9 @@ readCdfUnits <- function(filename, units=NULL, readXY=TRUE, readBases=TRUE, read

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

 # HISTORY:

+# 2010-12-12

+# o ROBUSTNESS: Replaces .Internal(matrix(...)) with matrix().

+#   In the upcoming R 2.13.0 matrix() has less overhead.

 # 2006-12-30

 # o Now 'readDirection=TRUE' also return group directions.

 # 2006-03-28

@@ -78,9 +78,9 @@ readCel <- function(filename,

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

     if (reorder) {

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

-      o <- .Internal(qsort(indices, TRUE));

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

       indices <- o$x;

-      o <- .Internal(qsort(o$ix, TRUE))$ix;

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

     }

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

@@ -276,9 +276,9 @@ readCelUnits <- function(filenames, units=NULL, stratifyBy=c("nothing", "pmmm",

   if (reorder) {

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

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

-    o <- .Internal(qsort(indices, TRUE));

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

     indices <- o$x;

-    o <- .Internal(qsort(o$ix, TRUE))$ix;

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

     verbose && exit(verbose);

   }

@@ -1,6 +1,18 @@

 Package: affxparser

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

+Version: 1.23.1 [2009-12-16]

+o ROBUSTNESS: Now matrix(...) is used instead of .Interal(matrix(...)).

+

+

+Version: 1.23.0 [2009-10-17]

+o The version number was bumped for the Bioconductor devel version.

+

+

+Version: 1.22.0 [2009-10-17]

+o The version number was bumped for the Bioconductor release version.

+

+

 Version: 1.21.1 [2010-10-05]

 o Now readCdfDataFrame() also returns the cell field 'expos'.