@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.11.4

+Version: 1.11.5

 Date: 2010-12-10

 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -161,13 +161,13 @@ readIDAT <- function(idatFile){

   }

   versionNumber <- readBin(tempCon, "integer", n=1, size=8,

-                           endian="little", signed=FALSE)

+                           endian="little")

   if(versionNumber<3)

 	  stop("Older style IDAT files not supported:  consider updating your scanner settings")

   nFields <- readBin(tempCon, "integer", n=1, size=4,

-                     endian="little", signed=FALSE)

+                     endian="little")

   fields <- matrix(0,nFields,3);

   colnames(fields) <- c("Field Code", "Byte Offset", "Bytes")

@@ -175,7 +175,7 @@ readIDAT <- function(idatFile){

     fields[i1,"Field Code"] <-

       readBin(tempCon, "integer", n=1, size=2, endian="little", signed=FALSE)

     fields[i1,"Byte Offset"] <-

-      readBin(tempCon, "integer", n=1, size=8, endian="little", signed=FALSE)

+      readBin(tempCon, "integer", n=1, size=8, endian="little")

   }

   knownCodes <- c(1000, 102, 103, 104, 107, 200, 300, 400,

@@ -214,11 +214,11 @@ readIDAT <- function(idatFile){

   seek(tempCon, fields["nSNPsRead", "Byte Offset"])

   nSNPsRead <- readBin(tempCon, "integer", n=1, size=4,

-                       endian="little", signed=FALSE)

+                       endian="little")

   seek(tempCon, fields["IlluminaID", "Byte Offset"])

   IlluminaID <- readBin(tempCon, "integer", n=nSNPsRead, size=4,

-                       endian="little", signed=FALSE)

+                       endian="little")

   seek(tempCon, fields["SD", "Byte Offset"])

   SD <- readBin(tempCon, "integer", n=nSNPsRead, size=2,

@@ -233,13 +233,13 @@ readIDAT <- function(idatFile){

   seek(tempCon, fields["MidBlock", "Byte Offset"])

   nMidBlockEntries <- readBin(tempCon, "integer", n=1, size=4,

-                              endian="little", signed=FALSE)

+                              endian="little")

   MidBlock <- readBin(tempCon, "integer", n=nMidBlockEntries, size=4,

-                      endian="little", signed=FALSE)

+                      endian="little")

   seek(tempCon, fields["RunInfo", "Byte Offset"])

   nRunInfoBlocks <- readBin(tempCon, "integer", n=1, size=4,

-                            endian="little", signed=FALSE)

+                            endian="little")

   RunInfo <- matrix(NA, nRunInfoBlocks, 5)

   colnames(RunInfo) <- c("RunTime", "BlockType", "BlockPars",

                          "BlockCode", "CodeVersion")

@@ -252,7 +252,7 @@ readIDAT <- function(idatFile){

   seek(tempCon, fields["RedGreen", "Byte Offset"])

   RedGreen <- readBin(tempCon, "numeric", n=1, size=4,

-                      endian="little", signed=FALSE)

+                      endian="little")

   #RedGreen <- readBin(tempCon, "integer", n=4, size=1,

   #                    endian="little", signed=FALSE)

@@ -346,7 +346,7 @@ readBPM <- function(bpmFile){

   ## should be 1

   versionNumber <-

-    readBin(tempCon, "integer", n=1, size=4, endian="little", signed=FALSE)

+    readBin(tempCon, "integer", n=1, size=4, endian="little")

   ## should be 4

   nChars <- readBin(tempCon, "integer", n=1, size=1, signed=FALSE)

@@ -358,13 +358,13 @@ readBPM <- function(bpmFile){

   entriesByteOffset <- seek(tempCon);

   nEntries <- readBin(tempCon, "integer", n=1, size=4,

-                      endian="little", signed=FALSE)

+                      endian="little")

   if(FALSE){

     snpIndexByteOffset <- seek(tempCon)

     snpIndex <- readBin(tempCon, "integer", n=nEntries, size=4,

-                        endian="little", signed=FALSE)

+                        endian="little")

     ## for the 1M array, these are simply in order from 1 to 1072820.

     snpNamesByteOffset <- seek(tempCon)