[proteowizard-commit] SF.net SVN: proteowizard:[772] trunk/pwiz/pwiz

[<br...@us...>]

Revision: 772
          http://proteowizard.svn.sourceforge.net/proteowizard/?rev=772&view=rev
Author:   broter
Date:     2009-04-10 22:02:13 +0000 (Fri, 10 Apr 2009)

Log Message:
-----------
Added explicit includes for c-libraries, as required by gcc 4.x

Modified Paths:
--------------
    trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp
    trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp
    trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianParametersTest.cpp
    trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianTest.cpp
    trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp
    trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp
    trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp
    trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp
    trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp
    trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp
    trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp
    trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp
    trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp
    trunk/pwiz/pwiz/data/misc/CalibrationParametersTest.cpp
    trunk/pwiz/pwiz/data/misc/SampleDatumTest.cpp
    trunk/pwiz/pwiz/data/msdata/BinaryDataEncoderTest.cpp
    trunk/pwiz/pwiz/data/msdata/CVParamTest.cpp
    trunk/pwiz/pwiz/data/msdata/CVTranslatorTest.cpp
    trunk/pwiz/pwiz/data/msdata/DiffTest.cpp
    trunk/pwiz/pwiz/data/msdata/LegacyAdapterTest.cpp
    trunk/pwiz/pwiz/data/msdata/ReaderTest.cpp
    trunk/pwiz/pwiz/data/msdata/Serializer_mzML_Test.cpp
    trunk/pwiz/pwiz/data/msdata/Serializer_mzXML_Test.cpp
    trunk/pwiz/pwiz/data/msdata/SpectrumInfoTest.cpp
    trunk/pwiz/pwiz/data/msdata/SpectrumIteratorTest.cpp
    trunk/pwiz/pwiz/data/msdata/cvtest.cpp
    trunk/pwiz/pwiz/data/msdata/obotest.cpp
    trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp
    trunk/pwiz/pwiz/utility/math/LinearLeastSquaresTest.cpp
    trunk/pwiz/pwiz/utility/math/LinearSolverTest.cpp
    trunk/pwiz/pwiz/utility/math/MatchedFilterTest.cpp
    trunk/pwiz/pwiz/utility/math/ParabolaTest.cpp
    trunk/pwiz/pwiz/utility/math/StatsTest.cpp
    trunk/pwiz/pwiz/utility/math/erfTest.cpp
    trunk/pwiz/pwiz/utility/math/qrTest.cpp
    trunk/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp
    trunk/pwiz/pwiz/utility/misc/Base64Test.cpp
    trunk/pwiz/pwiz/utility/misc/IntegerSetTest.cpp
    trunk/pwiz/pwiz/utility/misc/IterationListenerTest.cpp
    trunk/pwiz/pwiz/utility/misc/Jamfile.jam
    trunk/pwiz/pwiz/utility/misc/SHA1CalculatorTest.cpp
    trunk/pwiz/pwiz/utility/misc/TabReader.cpp
    trunk/pwiz/pwiz/utility/misc/TabReaderTest.cpp
    trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabase.cpp
    trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabaseTest.cpp
    trunk/pwiz/pwiz/utility/proteome/IsotopeCalculatorTest.cpp
    trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimatorTest.cpp
    trunk/pwiz/pwiz/utility/proteome/IsotopeTableTest.cpp
    trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Test.cpp
    trunk/pwiz/pwiz_aux/sfcap/transient/TransientData.cpp
    trunk/pwiz/pwiz_aux/sfcap/transient/TransientDataTest.cpp
    trunk/pwiz/pwiz_aux/sfcap/transient/TransientGeneratorTest.cpp
    trunk/pwiz/pwiz_tools/common/MSDataAnalyzerApplicationTest.cpp

Modified: trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/frequency/MagnitudeLorentzianTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -33,6 +33,7 @@
 #include <stdexcept>
 #include <limits>
 #include <algorithm>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/frequency/ParametrizedFunctionTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,6 +25,7 @@
 #include "TruncatedLorentzian.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianParametersTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianParametersTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianParametersTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,6 +25,7 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include <boost/filesystem/operations.hpp>
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/frequency/TruncatedLorentzianTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -33,6 +33,7 @@
 
 #include <iostream>
 #include <iomanip>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/passive/MSDataAnalyzerTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "MSDataAnalyzer.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/passive/MSDataCacheTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "pwiz/data/msdata/examples.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 #include "boost/lexical_cast.hpp"
 
 

Modified: trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/passive/RegionAnalyzerTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,6 +25,7 @@
 #include "pwiz/data/msdata/TextWriter.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_flatTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -23,6 +23,7 @@
 #include <iostream>
 #include <fstream>
 #include <string>
+#include <cstring>
 #include <exception>
 #include <boost/shared_ptr.hpp>
 

Modified: trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/peptideid/PeptideID_pepXMLTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -23,6 +23,7 @@
 #include <iostream>
 #include <fstream>
 #include <string>
+#include <cstring>
 
 #include "PeptideID_pepXML.hpp"
 #include "pwiz/utility/minimxml/SAXParser.hpp"

Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumListFactoryTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "SpectrumListFactory.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace pwiz::analysis;

Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_FilterTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "pwiz/utility/misc/IntegerSet.hpp"
 #include "boost/lexical_cast.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace pwiz::msdata;

Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_PrecursorRecalculatorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include "boost/filesystem/path.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace pwiz::msdata;

Modified: trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/analysis/spectrum_processing/SpectrumList_SorterTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <vector>
 #include <iostream>
 #include <iterator>
+#include <cstring>
 #include "pwiz/data/msdata/examples.hpp"
 #include "pwiz/data/msdata/TextWriter.hpp"
 #include "boost/logic/tribool.hpp"

Modified: trunk/pwiz/pwiz/data/misc/CalibrationParametersTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/misc/CalibrationParametersTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/misc/CalibrationParametersTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "CalibrationParameters.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/misc/SampleDatumTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/misc/SampleDatumTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/misc/SampleDatumTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,7 @@
 #include <vector>
 #include <iterator>
 #include <complex>
+#include <cstring>
 
 
 using namespace pwiz::util;

Modified: trunk/pwiz/pwiz/data/msdata/BinaryDataEncoderTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/BinaryDataEncoderTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/BinaryDataEncoderTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -28,6 +28,7 @@
 #include <iomanip>
 #include <iterator>
 #include <fstream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/CVParamTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/CVParamTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/CVParamTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <iostream>
 #include <iterator>
 #include <algorithm>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/CVTranslatorTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/CVTranslatorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/CVTranslatorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "CVTranslator.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/DiffTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/DiffTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/DiffTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "examples.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/LegacyAdapterTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/LegacyAdapterTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/LegacyAdapterTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -29,6 +29,7 @@
 #include "boost/lambda/bind.hpp"
 #include <iostream>
 #include <algorithm>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/ReaderTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/ReaderTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/ReaderTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "Reader.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/Serializer_mzML_Test.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/Serializer_mzML_Test.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/Serializer_mzML_Test.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -28,6 +28,7 @@
 #include "boost/iostreams/positioning.hpp"
 #include <iostream>
 #include <fstream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/Serializer_mzXML_Test.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/Serializer_mzXML_Test.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/Serializer_mzXML_Test.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -29,6 +29,7 @@
 #include "boost/iostreams/positioning.hpp"
 #include <iostream>
 #include <fstream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/SpectrumInfoTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/SpectrumInfoTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/SpectrumInfoTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,6 +25,7 @@
 #include "pwiz/data/msdata/examples.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/msdata/SpectrumIteratorTest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/SpectrumIteratorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/SpectrumIteratorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -29,6 +29,7 @@
 #include <iostream>
 #include <algorithm>
 #include <iterator>
+#include <cstring>
 
 
 using namespace pwiz::msdata;

Modified: trunk/pwiz/pwiz/data/msdata/cvtest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/cvtest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/cvtest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "cv.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace pwiz::msdata;

Modified: trunk/pwiz/pwiz/data/msdata/obotest.cpp
===================================================================
--- trunk/pwiz/pwiz/data/msdata/obotest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/msdata/obotest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,7 @@
 #include <iostream>
 #include <fstream>
 #include <stdexcept>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp
===================================================================
--- trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/data/vendor_readers/Reader_Thermo_Test.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
 #include <fstream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/LinearLeastSquaresTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/LinearLeastSquaresTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/LinearLeastSquaresTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -1,6 +1,7 @@
 #include "LinearLeastSquares.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/LinearSolverTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/LinearSolverTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/LinearSolverTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <boost/numeric/ublas/matrix_sparse.hpp>
 #include <boost/numeric/ublas/banded.hpp>
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/MatchedFilterTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/MatchedFilterTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/MatchedFilterTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,8 +25,9 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
 #include <complex>
+#include <cstring>
+#include <typeinfo>
 
-
 using namespace pwiz::math;
 using namespace pwiz::util;
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/ParabolaTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/ParabolaTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/ParabolaTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -28,6 +28,7 @@
 #include <iomanip>
 #include <cmath>
 #include <limits>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/StatsTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/StatsTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/StatsTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -24,6 +24,7 @@
 #include "Stats.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/erfTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/erfTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/erfTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <iostream>
 #include <iomanip>
 #include <limits>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/math/qrTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/math/qrTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/math/qrTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -16,6 +16,7 @@
 #include <boost/numeric/ublas/io.hpp>
 
 #include <iostream>
+#include <cstring>
 #include <iomanip>
 //#include <execinfo.h>
 

Modified: trunk/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/minimxml/SAXParserTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,7 @@
 #include <vector>
 #include <iterator>
 #include <algorithm>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/misc/Base64Test.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/misc/Base64Test.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/Base64Test.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <iostream>
 #include <vector>
 #include <algorithm>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/misc/IntegerSetTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/misc/IntegerSetTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/IntegerSetTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <iostream>
 #include <vector>
 #include <iterator>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/misc/IterationListenerTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/misc/IterationListenerTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/IterationListenerTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,6 +25,7 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
 #include <string>
+#include <cstring>
 #include <ctime>
 
 

Modified: trunk/pwiz/pwiz/utility/misc/Jamfile.jam
===================================================================
--- trunk/pwiz/pwiz/utility/misc/Jamfile.jam	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/Jamfile.jam	2009-04-10 22:02:13 UTC (rev 772)
@@ -41,8 +41,8 @@
         random_access_compressed_ifstream.cpp
         SHA1Calculator.cpp
         SHA1.cpp
-        #TabReader.cpp
-        #MSIHandler.cpp
+        TabReader.cpp
+        MSIHandler.cpp
     : # requirements
         <warnings>all
         <toolset>msvc:<source>COMInitializer.cpp
@@ -82,13 +82,13 @@
 unit-test SHA1_ostream_test : SHA1_ostream_test.cpp pwiz_utility_misc ;
 unit-test mru_list_test : mru_list_test.cpp ;
 
-#run TabReaderTest.cpp pwiz_utility_misc
-#    : # args
-#    : TabReaderTest.data/TabTest.tab # input-files
-#    : # requirements
-#    : TabReaderTest # target name
-#    : # default-build
-#    ;
+run TabReaderTest.cpp pwiz_utility_misc
+    : # args
+    : TabReaderTest.data/TabTest.tab # input-files
+    : # requirements
+    : TabReaderTest # target name
+    : # default-build
+    ;
 
 
 import modules ;

Modified: trunk/pwiz/pwiz/utility/misc/SHA1CalculatorTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/misc/SHA1CalculatorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/SHA1CalculatorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,7 @@
 #include <iostream>
 #include <fstream>
 #include <string>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/misc/TabReader.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/misc/TabReader.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/TabReader.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,9 +25,6 @@
 #include <stdexcept>
 #include <iostream>
 
-#include <unistd.h>
-#include <sys/param.h>
-
 #include "TabReader.hpp"
 
 namespace pwiz {
@@ -263,9 +260,6 @@
         th_ = default_th_.get();
     }
 
-    char path[MAXPATHLEN];
-    getcwd(path, MAXPATHLEN);
-
     ifstream in(filename);
 
     string line;

Modified: trunk/pwiz/pwiz/utility/misc/TabReaderTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/misc/TabReaderTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/misc/TabReaderTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "boost/filesystem/path.hpp"
 #include "boost/filesystem/fstream.hpp"
 #include <iostream>
+#include <cstring>
 
 using namespace pwiz::util;
 using namespace pwiz::utility;

Modified: trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabase.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabase.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabase.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -28,6 +28,7 @@
 #include <iomanip>
 #include <fstream>
 #include <stdexcept>
+#include <cstdlib>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabaseTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabaseTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/proteome/IPIFASTADatabaseTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include <boost/filesystem/operations.hpp>
 #include <iostream>
 #include <fstream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/proteome/IsotopeCalculatorTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/proteome/IsotopeCalculatorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/proteome/IsotopeCalculatorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,8 @@
 #include <iomanip>
 #include <numeric>
 #include <algorithm>
+#include <cstring>
+#include<iterator>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimatorTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimatorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/proteome/IsotopeEnvelopeEstimatorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -25,6 +25,7 @@
 #include "IsotopeCalculator.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz/utility/proteome/IsotopeTableTest.cpp
===================================================================
--- trunk/pwiz/pwiz/utility/proteome/IsotopeTableTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz/utility/proteome/IsotopeTableTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,7 @@
 #include <iomanip>
 #include <iterator>
 #include <algorithm>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Test.cpp
===================================================================
--- trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Test.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz_aux/isb/readers/waters/Reader_Waters_Test.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -3,6 +3,7 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
 #include <fstream>
+#include <cstring>
 
 
 using namespace std;

Modified: trunk/pwiz/pwiz_aux/sfcap/transient/TransientData.cpp
===================================================================
--- trunk/pwiz/pwiz_aux/sfcap/transient/TransientData.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz_aux/sfcap/transient/TransientData.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -36,6 +36,7 @@
 #include <sstream>
 #include <iterator>
 #include <cmath>
+#include <cstring>
 #include <algorithm>
 
 

Modified: trunk/pwiz/pwiz_aux/sfcap/transient/TransientDataTest.cpp
===================================================================
--- trunk/pwiz/pwiz_aux/sfcap/transient/TransientDataTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz_aux/sfcap/transient/TransientDataTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "pwiz/utility/misc/unit.hpp"
 #include <boost/filesystem/operations.hpp>
 #include <iostream>
+#include <cstring>
 #include <fstream>
 #include <stdexcept>
 #include <iterator>

Modified: trunk/pwiz/pwiz_aux/sfcap/transient/TransientGeneratorTest.cpp
===================================================================
--- trunk/pwiz/pwiz_aux/sfcap/transient/TransientGeneratorTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz_aux/sfcap/transient/TransientGeneratorTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -26,6 +26,7 @@
 #include "pwiz/data/misc/FrequencyData.hpp"
 #include "pwiz/utility/misc/unit.hpp"
 #include <iostream>
+#include <cstring>
 #include <iterator>
 
 

Modified: trunk/pwiz/pwiz_tools/common/MSDataAnalyzerApplicationTest.cpp
===================================================================
--- trunk/pwiz/pwiz_tools/common/MSDataAnalyzerApplicationTest.cpp	2009-04-09 02:24:13 UTC (rev 771)
+++ trunk/pwiz/pwiz_tools/common/MSDataAnalyzerApplicationTest.cpp	2009-04-10 22:02:13 UTC (rev 772)
@@ -27,6 +27,7 @@
 #include <boost/filesystem/operations.hpp>
 #include <iostream>
 #include <iterator>
+#include <cstring>
 
 
 using namespace std;


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