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

 Package: affxparser

-Version: 1.13.6

-Date: 2008-08-21

+Version: 1.13.7

+Date: 2008-08-23

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen

 Maintainer: Kasper Daniel Hansen <[email protected]>

@@ -521,22 +521,18 @@ readCcg <- function(pathname, verbose=0, .filter=NULL, ...) {

 ##      nchars <- nchars[1];

       nchars <- readInt(con=value, n=1);

       rm(value);

-      gc <- gc();

       ccs <- 1:(size-4);

       value <- raw[ccs,];

       raw <- raw[-ccs,,drop=FALSE];

-      gc <- gc();

       value <- rawToChar(value, multiple=TRUE);

       dim(value) <- c(nchars, nbrOfRows);

-      gc <- gc();

       # Build strings using vectorization (not apply()!)

       strs <- NULL;

       for (pp in seq(length=nrow(value))) {

         valuePP <- value[1,,drop=FALSE];

         value <- value[-1,,drop=FALSE];

-#        gc <- gc();

         if (pp == 1) {

           strs <- valuePP;

         } else {

@@ -550,16 +546,12 @@ readCcg <- function(pathname, verbose=0, .filter=NULL, ...) {

       ccs <- 1:size;

       value <- raw[ccs,,drop=FALSE];

       raw <- raw[-ccs,,drop=FALSE];

-      gc <- gc();

       value <- readBin(con=value, what=what, size=size, signed=signed, endian="big", n=nbrOfRows);

     }

-    # Garbage collect

-    gc <- gc();

-

     table[[cc]] <- value;

     colsOffset <- colsOffset + size;

-  }

+  } # for (cc ...)

   # Turn into a data frame

   attr(table, "row.names") <- .set_row_names(length(table[[1]]));

@@ -574,6 +566,8 @@ readCcg <- function(pathname, verbose=0, .filter=NULL, ...) {

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

 # HISTORY:

+# 2008-08-23

+# o SPEED UP: Removed all gc() calls.

 # 2008-01-13

 # o Removed dependency on intToChar() in R.utils.

 # o BUG FIX/UPDATE: The file format was updated between April 2006 and

@@ -1,8 +1,14 @@

 Package: affxparser

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

+Version: 1.13.7 [2008-08-23]

+o SPEED UP: readCcg() is substantially faster after removing 

+  all gc() calls.

+

+

 Version: 1.13.6 [2008-08-21]

-o Updated Fusion SDK from 1.10b to 1.11

+o Updated Fusion SDK from 1.0.10b (Jan 2008) to 1.0.11 (July 2008).

+

 Version: 1.13.x [2008-08-14]

 o Fixed typos and incorrect equation in help page