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

 Package: affxparser

 Version: 1.7.1

-Date: 2006-11-01

+Date: 2006-11-03

 Title: Affymetrix File Parsing SDK

 Author: Henrik Bengtsson, James Bullard, Kasper Daniel Hansen

 Maintainer: Kasper Daniel Hansen <khansen@stat.berkeley.edu>

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

 Package: affxparser

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

-Version: 1.7.1 [2006-11-01]

+Version: 1.7.1 [2006-11-03]

 o Updated to Fusion SDK v1.0.8.

 o BUG FIX: In Fusion SDK (v1.0.5) that previous version of affxparser 

   used, a CDF file was never closed on Unix platforms (this bug was

@@ -10,6 +10,16 @@ o BUG FIX: In Fusion SDK (v1.0.5) that previous version of affxparser

   memory usage to blow up, when reading the same or different CDF

   files multiple times, because the memory was never deallocated.

   Thanks Seth Falcon and Ken Simpson for reporting this problem.

+o Windows build change: The Windows version is building against

+  the Windows code of Fusion SDK not the POSIX code. In order to do

+  this we have had to patch the preprocessor code in several of the

+  Fusion SDK source-code files, which has to be redone manually

+  whenever Fusion is updated.  Starting with this version, we instead 

+  set the _MSC_VER flag used in the Fusion code to indicate Windows

+  (set by the Microsoft Visual C++ compiler). Since we are using

+  MINGW this flag is obviously not set. Faking _MSC_VER this way

+  leaves us only having to patch one single file in the Fusion

+  release instead of 10-20. Hopefully there are no other side effects.

 Version: 1.7.0 [2006-10-25]

 o BUG FIX: writeCdf() would create an invalid CDF file if there were

@@ -36,11 +36,11 @@

   \code{"/usr/;usr/bin/;.;"}.

 }

-\section{Windows Shortcut links}{

-  If package \pkg{R.utils} is available, Windows Shortcut links (*.lnk)

-  are recognized and can be used to immitate links to directories

-  elsewhere.  For more details, see \code{\link[R.utils]{filePath}}.

-}

+% \section{Windows Shortcut links}{

+%   If package \pkg{R.utils} is available, Windows Shortcut links (*.lnk)

+%   are recognized and can be used to immitate links to directories

+%   elsewhere.  For more details, see \code{\link[R.utils]{filePath}}.

+% }

 \author{Henrik Bengtsson \url{http://www.braju.com/R/}}

@@ -16,7 +16,8 @@ PKG_CPPFLAGS+=\

  -Ifusion_sdk/calvin_files/writers/src\

  -Ifusion_sdk/file\

  -Ifusion_sdk/portability\

- -D_USE_MEM_MAPPING_

+ -D_USE_MEM_MAPPING_\

+ -D_MSC_VER

 SOURCES.fusion = \

 	fusion_sdk/calvin_files/data/src/CDFData.cpp\

@@ -174,7 +174,7 @@ extern "C" {

     int i_verboseFlag = INTEGER(verbose)[0];

     /** pointer to the name of the probeset. **/

-    const char* name;

+    char* name;

     char bfr[512];

     FusionCDFProbeSetInformation probeset;

@@ -234,11 +234,10 @@ extern "C" {

       /* Record its name */

       str = cdf.GetProbeSetName(iset);

       str_length = str.size();

-      cstr = Calloc(str_length+1, char);

-      strncpy(cstr, str.c_str(), str_length);

-      cstr[str_length] = '\0';

-      SET_STRING_ELT(names, ii, mkChar(cstr));

-      Free(cstr);

+      name = Calloc(str_length+1, char);

+      strncpy(name, str.c_str(), str_length);

+      name[str_length] = '\0';

+      SET_STRING_ELT(names, ii, mkChar(name));

       /* Get the number of groups in the unit */

       int ngroups = probeset.GetNumGroups();

@@ -282,7 +281,8 @@ extern "C" {

       /** pop the group list and group names of the stack. **/

       UNPROTECT(1);  /* 'r_group_names' */

-    }

+      Free(name);

+    } /* for (int ii=0 ...) */

     /** set the names down here at the end. **/

     setAttrib(probe_sets, R_NamesSymbol, names);

@@ -23,7 +23,7 @@

 using namespace affymetrix_calvin_io;

-#if !defined(_MSC_VER) && !defined(WIN32)

+#ifndef _MSC_VER

 #include <sys/mman.h>

 #endif

@@ -28,7 +28,6 @@ using namespace affymetrix_calvin_io;

 #ifndef _MSC_VER

 #include <unistd.h>

-#ifndef WIN32

 #include <sys/mman.h>

 #ifndef PAGE_SIZE

@@ -44,7 +43,6 @@ using namespace affymetrix_calvin_io;

 #define PAGE_TRUNC(ptr) (ptr&(PAGE_MASK))

 #endif

 #endif

-#endif

 /*

  * Initialize the object to use memory-mapping to access the file.

@@ -58,7 +56,7 @@ DataSet::DataSet(const std::string& fileName_, const DataSetHeader& header_, voi

 	data = 0;

 	isOpen = false;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	fileMapHandle = handle;

 #else

 	fp = 0;

@@ -82,7 +80,7 @@ DataSet::DataSet(const std::string& fileName_, const affymetrix_calvin_io::DataS

 	data = 0;

 	isOpen = false;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	fileMapHandle = 0;

 #else

 	fp = 0;

@@ -134,7 +132,7 @@ bool DataSet::Open()

  */

 bool DataSet::OpenMM()

 {

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	if (MapDataWin32(header.GetDataStartFilePos(), header.GetDataSize()) == false)

 		return false;

 #else

@@ -179,7 +177,7 @@ void DataSet::Close()

 		ClearStreamData();

 }

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 std::string GetErrorMsg()

 {

@@ -291,7 +289,7 @@ bool DataSet::MapDataPosix(u_int32_t start, u_int32_t bytes)

  */

 void DataSet::UnmapFile()

 {

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	// Unmap the view

 	if (mappedData != 0 )

@@ -385,7 +383,7 @@ char* DataSet::FilePosition(int32_t rowStart, int32_t col, int32_t rowCount)

 	// Byte offset in data set + byte offset of data set in file

 	u_int32_t startByte = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos();

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	if (useMemoryMapping)

 	{

@@ -28,7 +28,7 @@

 #include <string>

 #include <fstream>

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #include <windows.h>

 #endif

@@ -272,7 +272,7 @@ protected:

 	int32_t LastRowMapped();

 	/*! Platform specific memory-mapping method */

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	bool MapDataWin32(u_int32_t start, u_int32_t bytes);

@@ -341,7 +341,7 @@ protected:

 	 */

 	Int32Vector columnByteOffsets;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	/*! Handle returned by CreateFileMapping */

 	HANDLE fileMapHandle;

@@ -21,7 +21,7 @@

 #include "ParameterNameValueType.h"

 #include "StringUtils.h"

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma warning(disable: 4996) // don't show deprecated warnings.

 #include <winsock2.h>

 #else

@@ -22,7 +22,7 @@

 #include <stdio.h>

 #include <stdlib.h>

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #include <winsock2.h>

 #pragma warning(disable: 4996)

 #else

@@ -25,7 +25,7 @@

 #include <stdio.h>

 #include <sstream>

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma warning(disable: 4996) // ignore deprecated functions warning

 #include <winsock2.h>

 #include <process.h>

@@ -135,7 +135,7 @@ std::wstring StringUtils::ConvertMBSToWCS(const std::string& source)

  */

 std::wstring StringUtils::ToString(int value, int digits, wchar_t fill)

 {

-#if defined(_GLIBCPP_USE_WCHAR_T) || defined(_GLIBCXX_USE_WCHAR_T) || defined(_MSC_VER)

+#if !defined(__MINGW32__) && (defined(_GLIBCPP_USE_WCHAR_T) || defined(_GLIBCXX_USE_WCHAR_T) || defined(_MSC_VER))

 	std::wostringstream str;

 	str << std::setw(digits) << std::setfill(fill) << value;

 	return str.str();

@@ -26,7 +26,7 @@

 #include <math.h>

 #include <stdio.h>

-#if !defined(_MSC_VER) && !defined(WIN32)

+#ifndef _MSC_VER

 #include <sys/mman.h>

 #endif

@@ -75,7 +75,7 @@ CBPMAPFileData::CBPMAPFileData() :

 	m_bFileOpen(false),

 	m_bFileMapped(false)

 {

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	m_hFileMap = INVALID_HANDLE_VALUE;

 	m_hFile = INVALID_HANDLE_VALUE;

 #else

@@ -99,7 +99,7 @@ void CBPMAPFileData::Close()

 	m_NumberSequences = 0;

 	m_SequenceItems.erase(m_SequenceItems.begin(), m_SequenceItems.end());

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	if (m_bFileOpen)

 	{

 		if (m_bFileMapped)

@@ -439,7 +439,7 @@ bool CBPMAPFileData::ReadDataSection()

 	m_bFileOpen = false;

 	m_bFileMapped = false;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	// Create the file.

 	m_hFile = CreateFile(m_FileName.c_str(), GENERIC_READ, FILE_SHARE_READ,

@@ -25,7 +25,7 @@

 //////////////////////////////////////////////////////////////////////

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma warning(disable: 4786) // identifier was truncated in the debug information

 #include <windows.h>

 #endif

@@ -275,7 +275,7 @@ protected:

 	/*! Pointer to the data in the memory mapped file. */

 	char  *m_lpData;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	/*! Windows handle to the file. */

 	HANDLE m_hFileMap;

@@ -28,7 +28,7 @@

 #include "CDFFileData.h"

 #include "FileIO.h"

 #include <stdio.h>

-#if !defined(_MSC_VER) && !defined(WIN32)

+#ifndef _MSC_VER

 #include <sys/mman.h>

 #endif

@@ -67,7 +67,7 @@ CCDFFileData::CCDFFileData() :

 	m_bFileOpen(false),

 	m_bFileMapped(false)

 {

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	m_hFileMap = INVALID_HANDLE_VALUE;

 	m_hFile = INVALID_HANDLE_VALUE;

 #else

@@ -409,7 +409,7 @@ void CCDFFileData::Close()

 	m_QCProbeSets.clear();

 	m_ProbeSetNames.Clear();

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	if (m_bFileOpen)

 	{

 		if (m_bFileMapped)

@@ -668,7 +668,7 @@ bool CCDFFileData::ReadXDAFormatUsingMemMap(bool bReadHeaderOnly)

 	m_bFileOpen = false;

 	m_bFileMapped = false;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	// Create the file.

 	m_hFile = CreateFile(m_FileName.c_str(), GENERIC_READ, FILE_SHARE_READ,

@@ -26,7 +26,7 @@

 //////////////////////////////////////////////////////////////////////

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma warning(disable: 4786) // identifier was truncated in the debug information

 #include <windows.h>

 #endif

@@ -748,7 +748,7 @@ protected:

 	/*! A pointer to data in a memory mapped file. */

 	char  *m_lpData;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	/*! A windows handle used for memory mapping. */

 	HANDLE m_hFileMap;

@@ -29,7 +29,7 @@

 #include <iostream>

 #include <stdio.h>

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma warning(disable: 4996) // don't show deprecated warnings.

 #ifdef HAVE_SNPRINTF // If not using visual c++'s _snprintf include snprintf.

 extern "C" {

@@ -94,12 +94,12 @@ using namespace affxcel;

 /// Size of compact cel format identifier

 #define CCEL_HEADER_LEN 8

-#if defined(_MSC_VER) || defined(WIN32)

-/// Line separator for Windows

-#define LINE_SEPARATOR "\r\n"

-#else

+#ifndef WIN32

 /// Line separator for unix/linux

 #define LINE_SEPARATOR "\n"

+#else

+/// Line separator for Windows

+#define LINE_SEPARATOR "\r\n"

 #endif

 #ifndef PAGE_SIZE

@@ -836,7 +836,7 @@ bool CCELFileData::ReadXDABCel(bool bReadHeaderOnly)

   //#if defined(_USE_MEM_MAPPING_)

 #ifndef _DONT_USE_MEM_MAPPING_

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	// Memory map file on windows...

 	SYSTEM_INFO info;

 	GetSystemInfo(&info);

@@ -1134,7 +1134,7 @@ bool CCELFileData::ReadTranscriptomeBCel(bool bReadHeaderOnly)

 	instr.close();

 	// Memory map file

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	SYSTEM_INFO info;

 	GetSystemInfo(&info);

 	m_hFile = CreateFile(m_FileName.c_str(), GENERIC_READ, FILE_SHARE_READ,

@@ -1359,7 +1359,7 @@ bool CCELFileData::ReadCompactBCel(bool bReadHeaderOnly)

 		return true;

 	// Memory map file

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	SYSTEM_INFO info;

 	GetSystemInfo(&info);

 	m_hFile = CreateFile(m_FileName.c_str(), GENERIC_READ, FILE_SHARE_READ,

@@ -1850,7 +1850,7 @@ void CCELFileData::Munmap()

 	m_pMeanIntensities = NULL;

 	// free the map

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	if (m_lpFileMap != NULL)

 	{

 		UnmapViewOfFile(m_lpFileMap);

@@ -38,7 +38,7 @@

 ///  Set page mask value for memory mapping used under CYGWIN

 #define PAGE_MASK	(~(PAGE_SIZE-1))

-#elif defined (_MSC_VER) || defined (WIN32)

+#elif defined (_MSC_VER)

 #include <windows.h>

 ///  Structure alignment requirement for g++

 ///  @remark Structure alignment for Visual C++ is included in #pragma

@@ -70,7 +70,7 @@

 namespace affxcel

 {

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER 

 #pragma pack(push, 1)

 #endif

 ///////////////////////////////////////////////////////////////////////////////

@@ -101,7 +101,7 @@ typedef struct _CELFileTranscriptomeEntryType

 	unsigned char Pixels /* \cond */ STRUCT_ALIGNMENT /*! \endcond */ ;

 } CELFileTranscriptomeEntryType;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma pack(pop)

 #endif

@@ -567,7 +567,7 @@ protected:

 	/// Flag to determine if outlier data should be read

 	bool m_bReadOutliers;

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 	/// File handle used by CreateFileMapping in _MSC_VER

 	HANDLE m_hFile;

 	/// File map handle used by MapViewOfFile in _MSC_VER

@@ -27,7 +27,7 @@

 //////////////////////////////////////////////////////////////////////

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #pragma warning(disable: 4996) // don't show deprecated warnings.

 #include <winsock2.h>

 #else

@@ -26,7 +26,7 @@

 //////////////////////////////////////////////////////////////////////

-#if defined(_MSC_VER) || defined(WIN32)

+#ifdef _MSC_VER

 #include <winsock2.h>

 #else

 #include <inttypes.h>