Package: affxparser

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affxparser_1.32.0.tar.gz

StartedAt: 2013-05-01 01:49:29 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 01:52:04 -0700 (Wed, 01 May 2013)

EllapsedTime: 154.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: affxparser.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/affxparser.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affxparser/DESCRIPTION' ... OK
* this is package 'affxparser' version '1.32.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileBufferWriter.cpp
  affxparser/src/fusion_sdk/calvin_files/writers/src/CalvinCHPQuantificationDetectionFileBufferWriter.h

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package 'affxparser' can be installed ... [78s/83s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/affxparser.Rcheck/affxparser/libs/affxparser.so':
  Found '__ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'fusion_sdk/util/Verbose.o'
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'fusion_sdk/file/TsvFile/TsvFile.o',
      'fusion_sdk/util/Err.o'
  Found '___stdoutp', possibly from 'stdout' (C)
    Object: 'fusion_sdk/util/Util.o'
  Found '_exit', possibly from 'exit' (C)
    Objects: 'fusion_sdk/util/Err.o', 'R_affx_clf_pgf_parser.o'
  Found '_printf', possibly from 'printf' (C)
    Object: 'fusion_sdk/file/TsvFile/TsvFile.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... [20s/21s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testWriteAndReadEmptyCdf.R' [1s/1s]
  Running 'testWriteAndReadEmptyCel.R' [1s/1s]
 [3s/3s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/affxparser.Rcheck/00check.log'
for details.

* installing *source* package 'affxparser' ...
** libs
rm -f fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/calvin_files/data/src/CDFData.o
In file included from fusion_sdk/calvin_files/data/src/CDFData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CDFData.cpp:125:9: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        return GetUInt32FromGenericHdr(CDF_SETS_PARAM);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CDFData.cpp:130:22: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        SetDataTypeId(type, cnt);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜
fusion_sdk/calvin_files/data/src/CDFData.cpp:208:12: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
                result = paramType.GetValueUInt32();
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CDFData.cpp:210:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        return result;
        ˜˜˜˜˜˜ ^˜˜˜˜˜
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:31:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:31:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.h:31:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:24:
fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:47:32: warning: implicit conversion changes signedness: 'const u_int32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        int GetExpos() const { return indexPos; }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:30:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:30:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:30:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21:
fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:47:32: warning: implicit conversion changes signedness: 'const u_int32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        int GetExpos() const { return indexPos; }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:83:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        groupCnt = dgh.GetDataSetCnt();
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:109:15: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if (groupIdx < 0 || groupIdx >= groupCnt)
            ˜˜˜˜˜˜˜˜ ^ ˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:31:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:31:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.h:31:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk/calvin_files/data/src/CELData.o
In file included from fusion_sdk/calvin_files/data/src/CELData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CELData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CELData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/data/src/CELData.cpp:26:
fusion_sdk/calvin_files/utils/src/FileUtils.h:86:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/data/src/CELData.cpp:985:14: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                s.erase(0, len);
                ˜          ^˜˜
fusion_sdk/calvin_files/data/src/CELData.cpp:1014:14: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                s.erase(0, len);
                ˜          ^˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:23:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPData.cpp -o fusion_sdk/calvin_files/data/src/CHPData.o
In file included from fusion_sdk/calvin_files/data/src/CHPData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:23:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp -o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:20:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:29:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:20:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:29:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:20:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:30:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:342:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return dataSetInfo[dataType].metricColumns[col].GetLength();
               ˜˜˜˜˜˜˜˜˜˜˜                         ^˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:354:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return dataSetInfo[dataType].metricColumns[colIndex].GetName();
               ˜˜˜˜˜˜˜˜˜˜˜                         ^˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:803:17: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        metrics.resize(ncols);
        ˜˜˜˜˜˜˜        ^˜˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:806:11: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                metrics[icol].SetName(ds->metricColumns[icol].GetName());
                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:806:43: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                metrics[icol].SetName(ds->metricColumns[icol].GetName());
                                      ˜˜                ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:807:29: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                switch (ds->metricColumns[icol].GetColumnType())
                        ˜˜                ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:813:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueInt8(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:821:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueUInt8(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:829:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueInt16(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:837:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueUInt16(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:845:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueInt32(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:853:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueUInt32(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:861:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueFloat(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:869:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueAscii(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:877:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                metrics[icol].SetValueText(val);
                                ˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:1256:21: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
                else if (dataType = CytoGenotypeCallMultiDataType)
                         ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:1256:21: note: place parentheses around the assignment to silence this warning
                else if (dataType = CytoGenotypeCallMultiDataType)
                                  ^
                         (                                       )
fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp:1256:21: note: use '==' to turn this assignment into an equality comparison
                else if (dataType = CytoGenotypeCallMultiDataType)
                                  ^
                                  ==
19 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPTilingData.cpp -o fusion_sdk/calvin_files/data/src/CHPTilingData.o
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:23:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:23:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/CHPTilingData.cpp:166:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        entries = genericData.DataSet(0, index);
                  ˜˜˜˜˜˜˜˜˜˜˜            ^˜˜˜˜
fusion_sdk/calvin_files/data/src/CHPTilingData.cpp:220:42: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        param.SetName( param.GetName().substr(len, param.GetName().length()-len));
                                       ˜˜˜˜˜                  ^˜˜
fusion_sdk/calvin_files/data/src/CHPTilingData.cpp:220:72: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
                        param.SetName( param.GetName().substr(len, param.GetName().length()-len));
                                                                                           ˜^˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/ColumnInfo.cpp -o fusion_sdk/calvin_files/data/src/ColumnInfo.o
fusion_sdk/calvin_files/data/src/ColumnInfo.cpp:52:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      len = (totalSize - overhead) / sizeof(int16_t);
             ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜  ˜
fusion_sdk/calvin_files/data/src/ColumnInfo.cpp:55:36: warning: implicit conversion changes signedness: 'unsigned long' to 'int32_t' (aka 'int') [-Wsign-conversion]
      len = (totalSize - overhead) / sizeof(int8_t);
          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/ColumnInfo.cpp:55:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      len = (totalSize - overhead) / sizeof(int8_t);
             ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜  ˜
fusion_sdk/calvin_files/data/src/ColumnInfo.cpp:60:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_sdk/calvin_files/data/src/DataGroup.o
In file included from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fusion_sdk/calvin_files/data/src/DataGroupHeader.o
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:78:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if(dataSetHdrs[i].GetName() == p.GetName())
                   ˜˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:80:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        dataSetHdrs[i] = p;
                        ˜˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:88:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return dataSetHdrs[index];
               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:93:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return dataSetHdrs[index];
               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk/calvin_files/data/src/DataSet.o
In file included from fusion_sdk/calvin_files/data/src/DataSet.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/DataSet.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/DataSet.cpp:21:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/data/src/DataSet.cpp:26:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:151:49: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        if (MapDataPosix(header.GetDataStartFilePos(), header.GetDataSize()) == false)
            ˜˜˜˜˜˜˜˜˜˜˜˜                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:166:11: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        mapLen = header.GetDataSize();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:264:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        u_int32_t page_start = PAGE_TRUNC(start);
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:48:31: note: expanded from macro 'PAGE_TRUNC'
#define PAGE_TRUNC(ptr) (ptr&(PAGE_MASK))
                            ˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:44:19: note: expanded from macro 'PAGE_MASK'
#define PAGE_MASK ˜(PAGE_SIZE-1)
                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:273:21: warning: implicit conversion loses integer precision: 'long long' to 'u_int32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
                        mapLen = fileLen - page_start;
                               ˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:388:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        u_int32_t startByte = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos();
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:388:67: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        u_int32_t startByte = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos();
                                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:440:24: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        mapLen = BytesPerRow()*rowCount;
               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:441:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        mapStart = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos();
                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:441:56: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        mapStart = BytesPerRow()*rowStart + columnByteOffsets[col] + header.GetDataStartFilePos();
                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:578:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadUInt8(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:583:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadInt8(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:588:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadUInt16(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:593:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadInt16(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:598:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadUInt32(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:603:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadInt32(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:608:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadFloat(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:613:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadString8(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:618:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        values[index] = FileInput::ReadString16(instr);
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:787:72: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
        return (mapLen+(mapStart-header.GetDataStartFilePos()))/BytesPerRow() - 1;
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:787:58: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
        return (mapLen+(mapStart-header.GetDataStartFilePos()))/BytesPerRow() - 1;
                                                               ˜^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:623:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<unsigned char, std::allocator<unsigned char> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:628:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<signed char, std::allocator<signed char> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:633:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<unsigned short, std::allocator<unsigned short> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:638:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<short, std::allocator<short> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:643:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<unsigned int, std::allocator<unsigned int> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:648:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<int, std::allocator<int> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:653:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<float, std::allocator<float> > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:658:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
        GetDataT(col, startRow, count, values);
        ^
fusion_sdk/calvin_files/data/src/DataSet.cpp:548:35: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        ClearAndSizeVector(values, endRow-startRow);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜         ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSet.cpp:663:2: note: in instantiation of function template specialization 'affymetrix_calvin_io::DataSet::GetDataT<std::vector<std::basic_string<wchar_t>, std::allocator<std::basic_string<wchar_t> > > >' requested here
        GetDataT(col, startRow, count, values);
        ^
33 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusion_sdk/calvin_files/data/src/DataSetHeader.o
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:67:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
                result += GetColumnInfo(i).GetSize();
                       ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:69:9: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        return result;
        ˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:156:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return columnTypes[index];
               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_sdk/calvin_files/data/src/FileHeader.o
In file included from fusion_sdk/calvin_files/data/src/FileHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/FileHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/data/src/FileHeader.cpp:67:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return dataGroupHdrs[index];
               ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/FileHeader.cpp:72:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return dataGroupHdrs[index];
               ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion_sdk/calvin_files/data/src/GenericData.o
In file included from fusion_sdk/calvin_files/data/src/GenericData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/GenericData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/GenericData.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/data/src/GenericData.cpp:27:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/calvin_files/data/src/GenericData.cpp:109:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        return header.GetDataGroupCnt();
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:132:45: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        DataGroupHeader* dch = FindDataGroupHeader(dataGroupIdx);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:134:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                return dch->GetDataSetCnt();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:149:10: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                return dch->GetDataSetCnt();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:162:45: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        DataGroupHeader* dch = FindDataGroupHeader(dataGroupIdx);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:212:45: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        DataGroupHeader* dch = FindDataGroupHeader(dataGroupIdx);
                               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:388:18: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
                if (dataSetIdx >= 0 && (int32_t)dataSetIdx < dch->GetDataSetCnt())
                    ˜˜˜˜˜˜˜˜˜˜ ^  ˜
fusion_sdk/calvin_files/data/src/GenericData.cpp:390:27: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
                        dph = &dch->GetDataSet(dataSetIdx);
                               ˜˜˜             ^˜˜˜˜˜˜˜˜˜
12 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp:21:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp:21:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp:112:40: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'mapped_type' (aka 'int') [-Wshorten-64-to-32]
                        paramNameIdxMap[entry.GetName()] =  nameValParams.size();
                                                         ˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp:118:39: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'mapped_type' (aka 'int') [-Wshorten-64-to-32]
                paramNameIdxMap[entry.GetName()] =  nameValParams.size();
                                                 ˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp:125:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return nameValParams[index];
               ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp:157:25: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return GenericDataHdrs[index];
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:140:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                result = algParams.at(index).GetName();
                         ˜˜˜˜˜˜˜˜˜    ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:438:34: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        calvinCel.GetIntensities(index, intensities.size(), intensities);
        ˜˜˜˜˜˜˜˜˜                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:23:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:30:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:30:
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:506:38: warning: implicit conversion changes signedness: 'const int8_t' (aka 'const signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t GetReason() const { return reason; }
                                     ˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:511:40: warning: implicit conversion changes signedness: 'u_int8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        void SetReason(u_int8_t r) { reason = r; }
                                            ˜ ^
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:30:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:35:
fusion_sdk/file/CHPFileData.h:266:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetCols(int n) { m_Cols=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:271:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetRows(int n) { m_Rows=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:596:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char GetCalledBase(int index) { return calledBases[index]; }
                                               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:606:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeCalledBases(int size) { calledBases.resize(size); }
                                           ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:612:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetCalledBase(int index, char call) { calledBases[index] = call; }
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:623:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        float GetScore(int index) { return scores[index]; }
                                           ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:633:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeScores(int size) { scores.resize(size); }
                                      ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:639:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetScore(int index, float score) { scores[index] = score; }
                                                ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:650:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ForceCallType GetForceCall(int index) { return forceCalls[index]; }
                                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:660:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeForceCalls(int size) { forceCalls.resize(size); }
                                          ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:666:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetForceCall(int index, ForceCallType call) { forceCalls[index] = call; }
                                                           ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:677:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        BaseCallType GetOrigCall(int index) { return origCalls[index]; }
                                                     ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:687:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeOrigCalls(int size) { origCalls.resize(size); }
                                         ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:693:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetOrigCall(int index, BaseCallType call) { origCalls[index] = call; }
                                                         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:32:
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:29:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:411:57: warning: implicit conversion changes signedness: 'char' to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
                        FusionForceCallType fusionType(f.position, f.call, f.reason);
                                            ˜˜˜˜˜˜˜˜˜˜                     ˜˜^˜˜˜˜˜
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:29:
fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:47:32: warning: implicit conversion changes signedness: 'const u_int32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        int GetExpos() const { return indexPos; }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:25:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:26:
fusion_sdk/calvin_files/utils/src/FileUtils.h:86:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:82:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinData->GetArrayCols();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:95:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinData->GetArrayRows();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:404:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinProbe->GetListIndex();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:597:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinGroup->GetNumLists();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:610:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinGroup->GetNumCells();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:639:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return probeInfo.GetListIndex();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:655:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
                calvinGroup->GetCell(calvinGroup->GetNumCells()-1, probeInfo);
                ˜˜˜˜˜˜˜˜˜˜˜          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:656:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return probeInfo.GetListIndex();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:809:33: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        calvinSet->GetGroupInformation(index, *calvinGroup);
        ˜˜˜˜˜˜˜˜˜                      ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:964:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinSet->GetNumLists();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:977:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinSet->GetNumGroups();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:990:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinSet->GetNumCells();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:1016:10: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                return calvinSet->GetProbeSetNumber();
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
19 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:30:
In file included from fusion_sdk/file/CELFileData.h:33:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:30:
fusion_sdk/file/CELFileData.h:120:75: warning: extra ';' inside a struct [-Wextra-semi]
        unsigned char Pixels; /* \cond */ /* STRUCT_ALIGNMENT */ /*! \endcond */ ;
                                                                                 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:26:
fusion_sdk/calvin_files/utils/src/FileUtils.h:86:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:28:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:492:10: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'unsigned int' [-Wshorten-64-to-32]
  return Fs::fileSize(filename);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:24:
fusion_sdk/calvin_files/utils/src/FileUtils.h:86:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:21:
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:506:38: warning: implicit conversion changes signedness: 'const int8_t' (aka 'const signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t GetReason() const { return reason; }
                                     ˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:511:40: warning: implicit conversion changes signedness: 'u_int8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        void SetReason(u_int8_t r) { reason = r; }
                                            ˜ ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:23:
fusion_sdk/file/CHPFileData.h:266:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetCols(int n) { m_Cols=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:271:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetRows(int n) { m_Rows=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:596:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char GetCalledBase(int index) { return calledBases[index]; }
                                               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:606:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeCalledBases(int size) { calledBases.resize(size); }
                                           ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:612:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetCalledBase(int index, char call) { calledBases[index] = call; }
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:623:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        float GetScore(int index) { return scores[index]; }
                                           ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:633:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeScores(int size) { scores.resize(size); }
                                      ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:639:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetScore(int index, float score) { scores[index] = score; }
                                                ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:650:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ForceCallType GetForceCall(int index) { return forceCalls[index]; }
                                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:660:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeForceCalls(int size) { forceCalls.resize(size); }
                                          ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:666:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetForceCall(int index, ForceCallType call) { forceCalls[index] = call; }
                                                           ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:677:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        BaseCallType GetOrigCall(int index) { return origCalls[index]; }
                                                     ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:687:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeOrigCalls(int size) { origCalls.resize(size); }
                                         ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:693:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetOrigCall(int index, BaseCallType call) { origCalls[index] = call; }
                                                         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:425:11: warning: implicit conversion changes signedness: 'u_int8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        reason = r;
               ˜ ^
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:491:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return calledBases[index];
               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:502:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        calledBases.resize(size);
        ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:507:14: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        calledBases[index] = call;
        ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:522:16: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return scores[index];
               ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:532:16: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        scores.resize(size);
        ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:537:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        scores[index] = score;
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:552:20: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return forceCalls[index];
               ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:562:20: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        forceCalls.resize(size);
        ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:567:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        forceCalls[index] = call;
        ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:582:19: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return origCalls[index];
               ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:592:19: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        origCalls.resize(size);
        ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp:597:12: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        origCalls[index] = call;
        ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
29 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:30:
In file included from fusion_sdk/file/CELFileData.h:33:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:30:
fusion_sdk/file/CELFileData.h:120:75: warning: extra ';' inside a struct [-Wextra-semi]
        unsigned char Pixels; /* \cond */ /* STRUCT_ALIGNMENT */ /*! \endcond */ ;
                                                                                 ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:28:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:28:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:28:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:23:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:30:
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:506:38: warning: implicit conversion changes signedness: 'const int8_t' (aka 'const signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t GetReason() const { return reason; }
                                     ˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:511:40: warning: implicit conversion changes signedness: 'u_int8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        void SetReason(u_int8_t r) { reason = r; }
                                            ˜ ^
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:35:
fusion_sdk/file/CHPFileData.h:266:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetCols(int n) { m_Cols=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:271:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetRows(int n) { m_Rows=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:596:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char GetCalledBase(int index) { return calledBases[index]; }
                                               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:606:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeCalledBases(int size) { calledBases.resize(size); }
                                           ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:612:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetCalledBase(int index, char call) { calledBases[index] = call; }
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:623:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        float GetScore(int index) { return scores[index]; }
                                           ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:633:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeScores(int size) { scores.resize(size); }
                                      ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:639:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetScore(int index, float score) { scores[index] = score; }
                                                ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:650:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ForceCallType GetForceCall(int index) { return forceCalls[index]; }
                                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:660:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeForceCalls(int size) { forceCalls.resize(size); }
                                          ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:666:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetForceCall(int index, ForceCallType call) { forceCalls[index] = call; }
                                                           ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:677:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        BaseCallType GetOrigCall(int index) { return origCalls[index]; }
                                                     ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:687:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeOrigCalls(int size) { origCalls.resize(size); }
                                         ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:693:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetOrigCall(int index, BaseCallType call) { origCalls[index] = call; }
                                                         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
19 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:28:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:29:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:30:
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:506:38: warning: implicit conversion changes signedness: 'const int8_t' (aka 'const signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t GetReason() const { return reason; }
                                     ˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:511:40: warning: implicit conversion changes signedness: 'u_int8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        void SetReason(u_int8_t r) { reason = r; }
                                            ˜ ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:29:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:35:
fusion_sdk/file/CHPFileData.h:266:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetCols(int n) { m_Cols=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:271:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetRows(int n) { m_Rows=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:596:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char GetCalledBase(int index) { return calledBases[index]; }
                                               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:606:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeCalledBases(int size) { calledBases.resize(size); }
                                           ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:612:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetCalledBase(int index, char call) { calledBases[index] = call; }
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:623:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        float GetScore(int index) { return scores[index]; }
                                           ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:633:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeScores(int size) { scores.resize(size); }
                                      ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:639:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetScore(int index, float score) { scores[index] = score; }
                                                ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:650:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ForceCallType GetForceCall(int index) { return forceCalls[index]; }
                                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:660:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeForceCalls(int size) { forceCalls.resize(size); }
                                          ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:666:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetForceCall(int index, ForceCallType call) { forceCalls[index] = call; }
                                                           ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:677:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        BaseCallType GetOrigCall(int index) { return origCalls[index]; }
                                                     ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:687:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeOrigCalls(int size) { origCalls.resize(size); }
                                         ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:693:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetOrigCall(int index, BaseCallType call) { origCalls[index] = call; }
                                                         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:23:
In file included from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:32:
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:29:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.cpp:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:22:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:22:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:22:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:72:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    calls.resize(nchps);
    ˜˜˜˜˜        ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:73:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    confidences.resize(nchps);
    ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:78:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    vector<int> snpIndicies(nsnps);
                ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:81:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        snpIndicies[isnp] = snpNameIndexMap[snps[isnp]];
        ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:81:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        snpIndicies[isnp] = snpNameIndexMap[snps[isnp]];
                                            ˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:90:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        chp = FusionCHPDataReg::Read(chpFileNames[ichp]);
                                     ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:94:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            calls[ichp].clear();
            ˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:95:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            confidences[ichp].clear();
            ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:103:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        calls[ichp].resize(nsnps);
        ˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:103:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        calls[ichp].resize(nsnps);
        ˜˜˜˜˜              ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:104:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        confidences[ichp].resize(nsnps);
        ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:104:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        confidences[ichp].resize(nsnps);
        ˜˜˜˜˜˜˜˜˜˜˜              ^˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:107:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            calls[ichp][isnp] = mchp->GetGenoCall(GenotypeMultiDataType, snpIndicies[isnp]);
            ˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:107:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            calls[ichp][isnp] = mchp->GetGenoCall(GenotypeMultiDataType, snpIndicies[isnp]);
            ˜˜˜˜˜       ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:107:86: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            calls[ichp][isnp] = mchp->GetGenoCall(GenotypeMultiDataType, snpIndicies[isnp]);
                                                                         ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:108:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            confidences[ichp][isnp] = mchp->GetGenoConfidence(GenotypeMultiDataType, snpIndicies[isnp]);
            ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:108:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            confidences[ichp][isnp] = mchp->GetGenoConfidence(GenotypeMultiDataType, snpIndicies[isnp]);
            ˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp:108:98: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            confidences[ichp][isnp] = mchp->GetGenoConfidence(GenotypeMultiDataType, snpIndicies[isnp]);
                                                                                     ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:29:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:29:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:30:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:23:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:23:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.cpp:24:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp:21:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:137:50: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
  : Name(name), Type(mimeType), Value(mimeValue, mimeValueSize)
                                ˜˜˜˜˜            ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:173:13: warning: implicit conversion changes signedness: 'int8_t' (aka 'signed char') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToValue(value, Int8MIMEType);
        ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:193:13: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToValue(value, Int16MIMEType);
        ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:213:13: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToValue(value, Int32MIMEType);
        ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:230:18: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
                int32_t ival = ValueToInt(FloatMIMEType);
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:246:17: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToValue(pun.v_int32, FloatMIMEType);
        ˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:331:19: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
                for(int32_t i = len; i < reserve; ++i)
                            ˜   ^˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:334:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                Value.SetValue(buf, reserve);
                ˜˜˜˜˜               ^˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:511:31: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        Value = MIMEValue(mimeValue, mimeValueSize);
                ˜˜˜˜˜˜˜˜˜            ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:513:45: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        defaultValue = MIMEValue(defaultMimeValue, defaultMimeValueSize);
                       ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:566:20: warning: implicit conversion changes signedness: 'int8_t' (aka 'signed char') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToDefaultValue(value, Int8MIMEType);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:588:20: warning: implicit conversion changes signedness: 'int16_t' (aka 'short') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToDefaultValue(value, Int16MIMEType);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:610:20: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToDefaultValue(value, Int32MIMEType);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:628:18: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
                int32_t ival = DefaultValueToInt(FloatMIMEType);
                        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:645:24: warning: implicit conversion changes signedness: 'int' to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
        IntToDefaultValue(pun.v_int32, FloatMIMEType);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:728:19: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
                for(int32_t i = len; i < reserve; ++i)
                            ˜   ^˜˜
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:731:30: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                defaultValue.SetValue(buf, reserve);
                ˜˜˜˜˜˜˜˜˜˜˜˜               ^˜˜˜˜˜˜
17 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:29:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CelFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CELData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:23:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:28:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:28:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:22:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:28:
In file included from fusion_sdk/calvin_files/data/src/CHPData.h:24:
In file included from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:23:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:29:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:29:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:29:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPMultiDataData.h:30:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:23:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:23:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPTilingData.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:24:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.h:25:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:126:31: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'u_int32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        grpHdr.SetHeaderStartFilePos(fileStream.tellg());
        ˜˜˜˜˜˜                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp:21:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o
In file included from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:120:28: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'u_int32_t' (aka 'unsigned int') [-Wshorten-64-to-32]
        dsh.SetHeaderStartFilePos(fileStream.tellg());
        ˜˜˜                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetReader.o
In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp:58:9: warning: implicit conversion loses integer precision: 'streamsize' (aka 'long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
        return fileStream.gcount();
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
In file included from fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/FileHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/FileHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/FileHeader.h:27:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp:66:29: warning: implicit conversion changes signedness: 'int8_t' (aka 'signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t fileMagicNumber = FileInput::ReadInt8(fileStream);
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp:80:31: warning: implicit conversion changes signedness: 'int8_t' (aka 'signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t fileVersionNumber = FileInput::ReadInt8(fileStream);
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp:94:26: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        header.SetNumDataGroups(dataGroupCnt);
        ˜˜˜˜˜˜                  ^˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:73:8: warning: operand of ? changes signedness: '__uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
        val = ntohs(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:126:18: note: expanded from macro 'ntohs'
#define ntohs(x)        __DARWIN_OSSwapInt16(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:75:32: note: expanded from macro '__DARWIN_OSSwapInt16'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt16(x) : _OSSwapInt16(x))
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:44:6: note: expanded from macro '__DARWIN_OSSwapConstInt16'
    ((__uint16_t)((((__uint16_t)(x) & 0xff00) >> 8) | \
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:73:8: warning: operand of ? changes signedness: '__uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
        val = ntohs(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:126:18: note: expanded from macro 'ntohs'
#define ntohs(x)        __DARWIN_OSSwapInt16(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:75:63: note: expanded from macro '__DARWIN_OSSwapInt16'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt16(x) : _OSSwapInt16(x))
                                                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:84:8: warning: operand of ? changes signedness: '__uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        val = ntohl(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:129:18: note: expanded from macro 'ntohl'
#define ntohl(x)        __DARWIN_OSSwapInt32(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:78:32: note: expanded from macro '__DARWIN_OSSwapInt32'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt32(x) : _OSSwapInt32(x))
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:48:6: note: expanded from macro '__DARWIN_OSSwapConstInt32'
    ((__uint32_t)((((__uint32_t)(x) & 0xff000000) >> 24) | \
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:84:8: warning: operand of ? changes signedness: '__uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        val = ntohl(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:129:18: note: expanded from macro 'ntohl'
#define ntohl(x)        __DARWIN_OSSwapInt32(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:78:63: note: expanded from macro '__DARWIN_OSSwapInt32'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt32(x) : _OSSwapInt32(x))
                                                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:127:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned int' [-Wsign-conversion]
        pun.v_uint32=ReadInt32(instr);
                    ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:232:8: warning: operand of ? changes signedness: '__uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
        val = ntohs(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:126:18: note: expanded from macro 'ntohs'
#define ntohs(x)        __DARWIN_OSSwapInt16(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:75:32: note: expanded from macro '__DARWIN_OSSwapInt16'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt16(x) : _OSSwapInt16(x))
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:44:6: note: expanded from macro '__DARWIN_OSSwapConstInt16'
    ((__uint16_t)((((__uint16_t)(x) & 0xff00) >> 8) | \
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:232:8: warning: operand of ? changes signedness: '__uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
        val = ntohs(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:126:18: note: expanded from macro 'ntohs'
#define ntohs(x)        __DARWIN_OSSwapInt16(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:75:63: note: expanded from macro '__DARWIN_OSSwapInt16'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt16(x) : _OSSwapInt16(x))
                                                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:243:8: warning: operand of ? changes signedness: '__uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        val = ntohl(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:129:18: note: expanded from macro 'ntohl'
#define ntohl(x)        __DARWIN_OSSwapInt32(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:78:32: note: expanded from macro '__DARWIN_OSSwapInt32'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt32(x) : _OSSwapInt32(x))
                               ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:48:6: note: expanded from macro '__DARWIN_OSSwapConstInt32'
    ((__uint32_t)((((__uint32_t)(x) & 0xff000000) >> 24) | \
     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:243:8: warning: operand of ? changes signedness: '__uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        val = ntohl(val);
            ˜ ^˜˜˜˜˜˜˜˜˜
/usr/include/sys/_endian.h:129:18: note: expanded from macro 'ntohl'
#define ntohl(x)        __DARWIN_OSSwapInt32(x)
                        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/libkern/_OSByteOrder.h:78:63: note: expanded from macro '__DARWIN_OSSwapInt32'
    (__builtin_constant_p(x) ? __DARWIN_OSSwapConstInt32(x) : _OSSwapInt32(x))
                                                              ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:282:30: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
        instr += (sizeof(u_int16_t)*len);
                                   ˜^˜˜
fusion_sdk/calvin_files/parsers/src/FileInput.cpp:383:21: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memcpy(buf, instr, len);
        ˜˜˜˜˜˜             ^˜˜
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
In file included from fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.h:27:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:27:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21:
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:28:
fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:90:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:28:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
In file included from fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:24:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:26:
fusion_sdk/calvin_files/utils/src/checksum.h:49:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/utils/src/DateTime.cpp -o fusion_sdk/calvin_files/utils/src/DateTime.o
fusion_sdk/calvin_files/utils/src/DateTime.cpp:163:11: warning: comparison of constant 18446744073709551615 with expression of type 'int32_t' (aka 'int') is always false [-Wtautological-constant-out-of-range-compare]
        if (posT == std::wstring::npos)
            ˜˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/utils/src/DateTime.cpp:169:38: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::wstring date = value.substr(0, posT);
                            ˜˜˜˜˜           ^˜˜˜
fusion_sdk/calvin_files/utils/src/DateTime.cpp:175:11: warning: comparison of constant 18446744073709551615 with expression of type 'int32_t' (aka 'int') is always true [-Wtautological-constant-out-of-range-compare]
        if (posZ != std::wstring::npos)
            ˜˜˜˜ ^  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/calvin_files/utils/src/DateTime.cpp:183:26: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                value = value.substr(0,posZ);   // remove the ZULU specifier
                        ˜˜˜˜˜          ^˜˜˜
fusion_sdk/calvin_files/utils/src/DateTime.cpp:186:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::wstring time = value.substr(posT+1);
                            ˜˜˜˜˜        ˜˜˜˜^˜
fusion_sdk/calvin_files/utils/src/DateTime.cpp:240:22: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                        date = FormatDate(y, m, d);
                               ˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/calvin_files/utils/src/DateTime.cpp:240:25: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                        date = FormatDate(y, m, d);
                               ˜˜˜˜˜˜˜˜˜˜    ^
fusion_sdk/calvin_files/utils/src/DateTime.cpp:240:28: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'u_int32_t' (aka 'unsigned int') [-Wsign-conversion]
                        date = FormatDate(y, m, d);
                               ˜˜˜˜˜˜˜˜˜˜       ^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o
In file included from fusion_sdk/calvin_files/utils/src/FileUtils.cpp:24:
fusion_sdk/calvin_files/utils/src/FileUtils.h:86:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/calvin_files/utils/src/FileUtils.cpp:26:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/calvin_files/utils/src/FileUtils.cpp:78:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/utils/src/StringUtils.cpp -o fusion_sdk/calvin_files/utils/src/StringUtils.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o
In file included from fusion_sdk/calvin_files/utils/src/checksum.cpp:21:
fusion_sdk/calvin_files/utils/src/checksum.h:49:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
In file included from fusion_sdk/file/BPMAPFileData.cpp:21:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:125:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        munmap(m_lpFileMap, m_MapLen);
                        ˜˜˜˜˜˜              ^˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:302:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        m_NumberSequences = uval;
                          ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:306:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        m_SequenceItems.resize(m_NumberSequences);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:309:24: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
        m_DataStartPosition = instr.tellg();
                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:341:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Name);
                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:346:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_ProbePairs = uval;
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:346:41: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_ProbePairs = uval;
                                                           ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:348:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_HitStartPosition = uval;
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:348:47: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_HitStartPosition = uval;
                                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:352:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_NumberHits = uval;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:352:40: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                m_SequenceItems[iSeq].m_NumberHits = uval;
                                                   ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:356:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_GroupName);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:357:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_SeqVersion);
                                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:360:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_SequenceItems[iSeq].m_Parameters.resize(uval);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:363:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:363:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:364:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:364:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
                                                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:378:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  instr.seekg(m_SequenceItems[iSeq].m_HitStartPosition);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:380:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:380:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:384:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:384:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_Number = uval;
                                                 ˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:385:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                  m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:425:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:427:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_pHits = NULL;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:428:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                int offset = m_SequenceItems[iSeq].m_NumberHits * hitSize;
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:509:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        m_lpFileMap = mmap(NULL, m_MapLen, PROT_READ, MAP_SHARED, fileno(m_fp), 0);
                      ˜˜˜˜       ^˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:527:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_bMapped = true;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:528:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_lpData = m_lpData + m_SequenceItems[iSeq].m_HitStartPosition;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:528:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_SequenceItems[iSeq].m_lpData = m_lpData + m_SequenceItems[iSeq].m_HitStartPosition;
                                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:373:7: warning: unused variable 'probeOut' [-Wunused-variable]
        char probeOut[probeBufSize]="";
             ^
fusion_sdk/file/BPMAPFileData.cpp:372:16: warning: unused variable 'probeIn' [-Wunused-variable]
        unsigned char probeIn[PROBE_STORAGE_BUFFER_LENGTH]="";
                      ^
fusion_sdk/file/BPMAPFileData.cpp:385:48: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                  m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
                                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:505:17: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int' [-Wshorten-64-to-32]
                m_MapLen = st.st_size;
                         ˜ ˜˜˜^˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:540:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        seq.MakeShallowCopy(m_SequenceItems[index]);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:586:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          hit = (*m_pHits)[index];
                ˜          ^˜˜˜˜
fusion_sdk/file/BPMAPFileData.cpp:641:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          return m_Parameters[index];
                 ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
39 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
In file included from fusion_sdk/file/BPMAPFileWriter.cpp:22:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:220:55: warning: implicit conversion loses integer precision: 'unsigned int' to 'char' [-Wconversion]
        packedSequence[i] = ((packedSequence[i] << 2) | base);
                          ˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:220:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        packedSequence[i] = ((packedSequence[i] << 2) | base);
                              ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜  ˜
fusion_sdk/file/BPMAPFileWriter.cpp:226:45: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
      packedSequence[i] = packedSequence[i] << 2*(4-k);
                        ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:301:21: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
  hit.ProbeLength = (int)sequence.size();
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:626:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
            WriteUInt32_N(of, (*i).m_ProbePairsValue);// 2.3
            ˜˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:665:29: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
            WriteUInt32_N(of, (*i).m_HitStartPosition);   // 2.4 fixup
            ˜˜˜˜˜˜˜˜˜˜˜˜˜     ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/BPMAPFileWriter.cpp:642:32: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
            (*i).m_HitStartPosition = of.tellp();
                                    ˜ ^˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o
In file included from fusion_sdk/file/CDFFileData.cpp:23:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:148:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    info = (*m_pCells)[cell_index];
           ˜           ^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:191:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    info = (*m_pCells)[index];;
           ˜           ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:235:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    info.MakeShallowCopy((*m_pGroups)[index]);
                         ˜            ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:262:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return m_ProbeSetNames[index];
           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:269:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_ProbeSetNames.resize(size);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CDFFileData.cpp:276:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_ProbeSetNames[index] = name;
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:288:9: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
  seekg(loc, std::ios::beg);
  ˜˜˜˜˜ ^˜˜
fusion_sdk/file/CDFFileData.cpp:469:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return m_ProbeSets[index].GetProbeSetType();
               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:476:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  i_pos=(uint32_t) probeSetIndexPos + (index*sizeof(uint32_t));
                                       ^˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:493:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        info.MakeShallowCopy(m_ProbeSets[index]);
                             ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:507:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    i_pos = (uint32_t)probeSetIndexPos + (index*sizeof(uint32_t));
                                          ^˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:515:24: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
  m_probeSetIndex_last=index;
                      ˜^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:540:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  info.m_Groups.resize(info.m_NumGroups);
  ˜˜˜˜                 ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:544:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            pBlk = &info.m_Groups[j];
                    ˜˜˜˜          ^
fusion_sdk/file/CDFFileData.cpp:578:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            pBlk->m_Cells.resize(pBlk->m_NumCells);
            ˜˜˜˜                 ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:582:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                pCell = &pBlk->m_Cells[k];
                         ˜˜˜˜          ^
fusion_sdk/file/CDFFileData.cpp:594:34: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                pCell->m_PBase = ucval;
                               ˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:596:34: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'char' [-Wsign-conversion]
                pCell->m_TBase = ucval;
                               ˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:634:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        info.MakeShallowCopy(m_QCProbeSets[index]);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:638:46: warning: implicit conversion changes signedness: 'unsigned long' to 'int32_t' (aka 'int') [-Wsign-conversion]
        int32_t pos = (int32_t)qcSetIndexPos + (index*sizeof(int32_t));
                ˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:638:23: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'unsigned long' [-Wsign-conversion]
        int32_t pos = (int32_t)qcSetIndexPos + (index*sizeof(int32_t));
                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CDFFileData.cpp:638:49: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        int32_t pos = (int32_t)qcSetIndexPos + (index*sizeof(int32_t));
                                                ^˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:639:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        seekg(pos, std::ios::beg);
        ˜˜˜˜˜ ^˜˜
fusion_sdk/file/CDFFileData.cpp:641:15: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        seekg(pos, std::ios::beg);
        ˜˜˜˜˜ ^˜˜
fusion_sdk/file/CDFFileData.cpp:653:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        info.m_Cells.resize(info.m_NumCells);
        ˜˜˜˜                ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:660:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            info.m_Cells[j].m_X = usval;
            ˜˜˜˜         ^
fusion_sdk/file/CDFFileData.cpp:663:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            info.m_Cells[j].m_Y = usval;
            ˜˜˜˜         ^
fusion_sdk/file/CDFFileData.cpp:666:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            info.m_Cells[j].m_PLen = ucval;
            ˜˜˜˜         ^
fusion_sdk/file/CDFFileData.cpp:669:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            info.m_Cells[j].m_PMProbe = ucval;
            ˜˜˜˜         ^
fusion_sdk/file/CDFFileData.cpp:672:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            info.m_Cells[j].m_Background = ucval;
            ˜˜˜˜         ^
fusion_sdk/file/CDFFileData.cpp:796:37: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
    seekg(MAX_PROBE_SET_NAME_LENGTH * m_Header.m_NumProbeSets, std::ios::cur);
    ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:801:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    seekg(m_Header.m_NumQCProbeSets * sizeof(uint32_t), std::ios::cur);
          ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CDFFileData.cpp:908:23: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
    m_Header.m_Rows = atoi(subStr);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:911:23: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
    m_Header.m_Cols = atoi(subStr);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:940:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_QCProbeSets.resize(m_Header.m_NumQCProbeSets);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:945:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        pQCProbeSet = &m_QCProbeSets[iQCProbeSet];
                       ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:950:41: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        pQCProbeSet->m_QCProbeSetType = atoi( subStr);
                                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:961:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        pQCProbeSet->m_Cells.resize(pQCProbeSet->m_NumCells);
        ˜˜˜˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:964:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            pQCCell = &pQCProbeSet->m_Cells[iqccell];
                       ˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:974:28: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
            pQCCell->m_X = xqc;
                         ˜ ^˜˜
fusion_sdk/file/CDFFileData.cpp:975:28: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
            pQCCell->m_Y = yqc;
                         ˜ ^˜˜
fusion_sdk/file/CDFFileData.cpp:976:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
            pQCCell->m_PLen = plenqc;
                            ˜ ^˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:986:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_ProbeSets.resize(m_Header.m_NumProbeSets);
    ˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1002:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    pProbeSet = &m_ProbeSets[iProbeSet];
                 ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1009:30: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
    pProbeSet->m_Direction = atoi(subStr);
                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1015:36: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
    pProbeSet->m_NumCellsPerList = NumCellsPerList;
                                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1110:70: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
                pProbeSet->m_NumCellsPerList = pProbeSet->m_NumCells / pProbeSet->m_NumLists;
                                             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1139:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    pProbeSet->m_Groups.resize(pProbeSet->m_NumGroups);
    ˜˜˜˜˜˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1142:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        pBlk = &pProbeSet->m_Groups[iGroup];
                ˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1198:33: warning: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Wconversion]
            pBlk->m_Direction = atoi(subStr);
                              ˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1206:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        pBlk->m_Cells.resize(pBlk->m_NumCells);
        ˜˜˜˜                 ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1255:24: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
            cell.m_X = x;
                     ˜ ^
fusion_sdk/file/CDFFileData.cpp:1256:24: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
            cell.m_Y = y;
                     ˜ ^
fusion_sdk/file/CDFFileData.cpp:1260:68: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cellIndex = (iCell / pProbeSet->m_NumCellsPerList) * pProbeSet->m_NumCellsPerList;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CDFFileData.cpp:1268:68: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                cellIndex = (iCell / pProbeSet->m_NumCellsPerList) * pProbeSet->m_NumCellsPerList;
                          ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
56 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o
In file included from fusion_sdk/file/CELFileData.cpp:21:
In file included from fusion_sdk/file/CELFileData.h:33:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/file/CELFileData.cpp:21:
fusion_sdk/file/CELFileData.h:120:75: warning: extra ';' inside a struct [-Wextra-semi]
        unsigned char Pixels; /* \cond */ /* STRUCT_ALIGNMENT */ /*! \endcond */ ;
                                                                                 ^
fusion_sdk/file/CELFileData.cpp:323:42: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        strncpy(str, pInfo + 10, pEnd - pInfo - 10);
                        ˜˜˜˜˜˜˜                  ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
fusion_sdk/file/CELFileData.cpp:358:30: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                strncpy(str, pInfo, pEnd - pInfo);
                                ˜˜˜˜˜˜˜             ˜˜˜˜˜^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:384:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ((m_Params.at(i) == ':') || (m_Params.at(i) == '='))
                             ˜˜˜˜˜˜˜˜    ^
fusion_sdk/file/CELFileData.cpp:384:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        if ((m_Params.at(i) == ':') || (m_Params.at(i) == '='))
                                                        ˜˜˜˜˜˜˜˜    ^
fusion_sdk/file/CELFileData.cpp:386:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                tag = m_Params.substr(iStart, (iEnd - iStart + 1));
                                      ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:386:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                tag = m_Params.substr(iStart, (iEnd - iStart + 1));
                                      ˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
fusion_sdk/file/CELFileData.cpp:390:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        else if ((m_Params.at(i) == ';') || (m_Params.at(i) == ' '))
                                  ˜˜˜˜˜˜˜˜    ^
fusion_sdk/file/CELFileData.cpp:390:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        else if ((m_Params.at(i) == ';') || (m_Params.at(i) == ' '))
                                                             ˜˜˜˜˜˜˜˜    ^
fusion_sdk/file/CELFileData.cpp:392:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                value = m_Params.substr(iStart, (iEnd - iStart + 1));
                                        ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:392:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                value = m_Params.substr(iStart, (iEnd - iStart + 1));
                                        ˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
fusion_sdk/file/CELFileData.cpp:400:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                value = m_Params.substr(iStart, (iEnd - iStart + 2));
                        ˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:400:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                value = m_Params.substr(iStart, (iEnd - iStart + 2));
                        ˜˜˜˜˜˜˜˜                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
fusion_sdk/file/CELFileData.cpp:708:9: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        return lSize;
        ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CELFileData.cpp:706:14: warning: implicit conversion loses integer precision: 'off_t' (aka 'long long') to 'int32_t' (aka 'int') [-Wshorten-64-to-32]
                lSize = st.st_size;
                      ˜ ˜˜˜^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1026:35: warning: implicit conversion changes signedness: 'unsigned int' to 'int32_t' (aka 'int') [-Wsign-conversion]
  int32_t datasize = GetFileSize()-iHeaderBytes;
          ˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1026:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  int32_t datasize = GetFileSize()-iHeaderBytes;
                                  ˜^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1028:32: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  size_t read=fread(m_lpData,1,datasize,m_File);
              ˜˜˜˜˜            ^˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1049:40: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
        int iOffset = m_HeaderData.GetCells() * (FLOAT_SIZE + FLOAT_SIZE + SHORT_SIZE);
            ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1049:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        int iOffset = m_HeaderData.GetCells() * (FLOAT_SIZE + FLOAT_SIZE + SHORT_SIZE);
                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1055:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        x = ((int16_t)MmGetUInt16_I((uint16_t*)(m_lpData + iOffset + iCell * 2 * SHORT_SIZE)));
                                                                                     ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1057:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        y = ((int16_t)MmGetUInt16_I((uint16_t*)(m_lpData + iOffset + iCell * 2 * SHORT_SIZE + SHORT_SIZE)));
                                                                                     ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1070:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        x = ((int16_t)MmGetUInt16_I((uint16_t*)(m_lpData + iOffset + iCell * 2 * SHORT_SIZE)));
                                                                                     ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1071:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        y = ((int16_t)MmGetUInt16_I((uint16_t*)(m_lpData + iOffset + iCell * 2 * SHORT_SIZE + SHORT_SIZE)));
                                                                                     ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1163:23: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        m_HeaderData.SetCols(ulValue);
        ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1165:23: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        m_HeaderData.SetRows(ulValue);
        ˜˜˜˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1171:21: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.upperleft.x = ulValue;
                         ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1173:21: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.upperleft.y = ulValue;
                         ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1175:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.upperright.x = ulValue;
                          ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1177:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.upperright.y = ulValue;
                          ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1179:21: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.lowerleft.x = ulValue;
                         ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1181:21: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.lowerleft.y = ulValue;
                         ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1183:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.lowerright.x = ulValue;
                          ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1185:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
        grid.lowerright.y = ulValue;
                          ˜ ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1243:16: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
        int iOffset = ulValue;
            ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1338:18: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
  int alloc_size=GetFileSize();
      ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1367:63: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
        iOffset = m_HeaderData.GetCells() * STRUCT_SIZE_FEATURE_DATA + UINT32_SIZE;
                ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1367:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        iOffset = m_HeaderData.GetCells() * STRUCT_SIZE_FEATURE_DATA + UINT32_SIZE;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1378:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        x = MmGetUInt32_N((uint32_t*) (m_lpData + iOffset + iCell * 2 * UINT32_SIZE));
                                                                            ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1379:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        y = MmGetUInt32_N((uint32_t*) (m_lpData + iOffset + iCell * 2 * UINT32_SIZE + UINT32_SIZE));
                                                                            ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1380:44: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        m_MaskedCells.insert(std::make_pair(y * m_HeaderData.GetCols() + x, true));
                                                              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1396:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        x = MmGetUInt32_N((uint32_t*) (m_lpData + iOffset + iCell * 2 * UINT32_SIZE));
                                                                            ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1397:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        y = MmGetUInt32_N((uint32_t*) (m_lpData + iOffset + iCell * 2 * UINT32_SIZE + UINT32_SIZE));
                                                                            ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1398:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        m_Outliers.insert(std::make_pair(y * m_HeaderData.GetCols() + x, true));
                                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1611:62: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
    ((SHORT_SIZE + SHORT_SIZE)             * GetNumMasked()) + // masked
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1610:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    ((SHORT_SIZE)*(GetRows()*GetCols())) + // row*col
                 ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1636:40: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
        int iOffset = m_HeaderData.GetCells() * USHORT_SIZE;
            ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1636:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        int iOffset = m_HeaderData.GetCells() * USHORT_SIZE;
                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1642:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        x = ((int16_t)MmGetUInt16_I((uint16_t*)(m_lpData + iOffset + iCell * 2 * USHORT_SIZE)));
                                                                                     ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1644:71: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        y = ((int16_t)MmGetUInt16_I((uint16_t*)(m_lpData + iOffset + iCell * 2 * USHORT_SIZE + USHORT_SIZE)));
                                                                                     ˜˜˜˜˜˜^˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1676:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                size_t bytecnt = GetCols() * GetRows() * sizeof(CELFileTranscriptomeEntryType);
                                 ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1691:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                size_t bytecnt = GetCols() * GetRows() * sizeof(CELFileEntryType);
                                 ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1706:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                size_t bytecnt = GetCols() * GetRows() * sizeof(unsigned short);
                                 ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/file/CELFileData.cpp:1907:22: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
                        SetPixels(t_x,t_y,t_pixels);
                        ˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1946:23: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
                                SetPixels(t_x,t_y,t_pixels);
                                ˜˜˜˜˜˜˜˜˜         ^˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:1965:26: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                m_HeaderData.SetMasked(nMasked);
                ˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:2003:28: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                m_HeaderData.SetOutliers(nOutliers);
                ˜˜˜˜˜˜˜˜˜˜˜˜             ^˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:2437:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int idx_end=idx_start+intensities.size();
              ^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:2445:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity);
      ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/file/CELFileData.cpp:2451:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity);
      ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/file/CELFileData.cpp:2457:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      intensities[idx]=MmGetUInt16_N(&m_pTransciptomeEntries[idx].Intensity);
      ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/file/CELFileData.cpp:2463:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      intensities[idx]=MmGetUInt16_I(&m_pMeanIntensities[idx]);
      ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/file/CELFileData.cpp:2437:24: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
  int idx_end=idx_start+intensities.size();
      ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:3064:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int startIndex = (int) strHeader.rfind(" ", endIndex);
                               ˜˜˜˜˜˜˜˜˜            ^˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:3067:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::string start = strHeader.substr(0, startIndex + 1);
                            ˜˜˜˜˜˜˜˜˜           ˜˜˜˜˜˜˜˜˜˜˜^˜˜
fusion_sdk/file/CELFileData.cpp:3068:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::string end = strHeader.substr(endIndex, length - endIndex);
                          ˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜
fusion_sdk/file/CELFileData.cpp:3068:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::string end = strHeader.substr(endIndex, length - endIndex);
                          ˜˜˜˜˜˜˜˜˜                  ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
68 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/CHPFileData.cpp -o fusion_sdk/file/CHPFileData.o
In file included from fusion_sdk/file/CHPFileData.cpp:20:
fusion_sdk/file/CHPFileData.h:266:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetCols(int n) { m_Cols=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:271:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetRows(int n) { m_Rows=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:596:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char GetCalledBase(int index) { return calledBases[index]; }
                                               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:606:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeCalledBases(int size) { calledBases.resize(size); }
                                           ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:612:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetCalledBase(int index, char call) { calledBases[index] = call; }
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:623:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        float GetScore(int index) { return scores[index]; }
                                           ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:633:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeScores(int size) { scores.resize(size); }
                                      ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:639:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetScore(int index, float score) { scores[index] = score; }
                                                ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:650:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ForceCallType GetForceCall(int index) { return forceCalls[index]; }
                                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:660:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeForceCalls(int size) { forceCalls.resize(size); }
                                          ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:666:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetForceCall(int index, ForceCallType call) { forceCalls[index] = call; }
                                                           ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:677:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        BaseCallType GetOrigCall(int index) { return origCalls[index]; }
                                                     ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:687:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeOrigCalls(int size) { origCalls.resize(size); }
                                         ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:693:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetOrigCall(int index, BaseCallType call) { origCalls[index] = call; }
                                                         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
In file included from fusion_sdk/file/CHPFileData.cpp:22:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/file/CHPFileData.cpp:24:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/file/CHPFileData.cpp:257:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                delete m_ProbeSetResults[i];
                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/file/CHPFileData.cpp:258:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                m_ProbeSetResults[i]=NULL;
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/file/CHPFileData.cpp:269:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                return (CExpressionProbeSetResults *) m_ProbeSetResults[index];
                                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:280:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                return (CGenotypeProbeSetResults *) m_ProbeSetResults[index];
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:298:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                return (CUniversalProbeSetResults *) m_ProbeSetResults[index];
                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:638:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_ProbeSetResults.resize(m_Header.m_NumProbeSets);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:654:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                m_ProbeSetResults[iset] = pResults;
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:702:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_ProbeSetResults.resize(m_Header.m_NumProbeSets);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:709:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                m_ProbeSetResults[iset] = pResults;
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:738:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_ProbeSetResults.resize(m_Header.m_NumProbeSets);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:745:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                m_ProbeSetResults[iset] = pResults;
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:821:36: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                ReadFixedCString(instr, vString, (int) strlen(AppName));
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:861:21: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned short' [-Wconversion]
                m_Header.m_Rows = ival;
                                ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:865:21: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned short' [-Wconversion]
                m_Header.m_Cols = ival;
                                ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:976:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_ProbeSetResults.resize(m_Header.m_NumProbeSets);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:980:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                m_ProbeSetResults[iset] = pResults;
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:983:26: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned short' [-Wconversion]
                                pResults->NumPairs = ival;
                                                   ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:986:30: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned short' [-Wconversion]
                                pResults->NumUsedPairs = ival;
                                                       ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:1011:27: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned char' [-Wconversion]
                                pResults->Detection = ival;
                                                    ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:1057:33: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned short' [-Wconversion]
                                        pResults->NumCommonPairs = ival;
                                                                 ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:1067:25: warning: implicit conversion loses integer precision: 'int32_t' (aka 'int') to 'unsigned char' [-Wconversion]
                                        pResults->Change = ival;
                                                         ˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:1109:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_ProbeSetResults.resize(m_Header.m_NumProbeSets);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:1113:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                m_ProbeSetResults[iset] = pResults;
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:1231:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                        m_ProbeSetResults.resize(m_Header.m_NumProbeSets);
                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/CHPFileData.cpp:1243:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                m_ProbeSetResults[iset] = pResults;
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/CHPFileData.cpp:1340:33: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                ReadFixedString(instr, str, i32);
                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜             ^˜˜
fusion_sdk/file/CHPFileData.cpp:1343:34: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
                                        ReadFixedString(instr, str, i32);
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜             ^˜˜
fusion_sdk/file/CHPFileData.cpp:1390:35: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
        ReadFixedCString(instr, vString, (int) strlen(AppName));
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
44 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
In file included from fusion_sdk/file/FileIO.cpp:26:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:269:16: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        memset(line,0,len);
        ˜˜˜˜˜˜        ^˜˜
fusion_sdk/file/FileIO.cpp:301:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
  return MmGetUInt32_I((uint32_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:306:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
  return MmGetUInt16_I((uint16_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:311:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
  return MmGetUInt32_N((uint32_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:316:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
  return MmGetUInt16_N((uint16_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileIO.cpp:321:10: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
  return MmGetUInt8((uint8_t*)ptr);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
In file included from fusion_sdk/file/FileWriter.cpp:25:
In file included from fusion_sdk/file/FileWriter.h:26:
fusion_sdk/file/FileIO.h:67:31: warning: implicit conversion loses integer precision: 'int' to 'uint16_t' (aka 'unsigned short') [-Wconversion]
  return ((((x) >> 8) & 0xff) | (((x) & 0xff) << 8));
  ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/FileWriter.cpp:175:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        WriteFixedString(outstr, str, len);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜              ^˜˜
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/TsvFile/ClfFile.cpp -o fusion_sdk/file/TsvFile/ClfFile.o
In file included from fusion_sdk/file/TsvFile/ClfFile.cpp:27:
In file included from fusion_sdk/file/TsvFile/ClfFile.h:31:
fusion_sdk/file/TsvFile/TsvFile.h:71:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_BINDTO_CNAME = 2, ///< Bound to a column index by name
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:78:22: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    VALSTATE_STRING=3,
                     ^
fusion_sdk/file/TsvFile/TsvFile.h:87:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_TYPE_DOUBLE  = 5,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:112:35: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_LASTVALUE            = -99, ///< end of errors
                                  ^
fusion_sdk/file/TsvFile/TsvFile.h:121:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OP_GT     = 0x04,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:163:34: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OPT_CASEINSENSTIVE = 0x02,
                                 ^
fusion_sdk/file/TsvFile/TsvFile.h:182:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/file/TsvFile/ClfFile.cpp:27:
fusion_sdk/file/TsvFile/ClfFile.h:38:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/file/TsvFile/ClfFile.cpp:278:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/TsvFile/PgfFile.cpp -o fusion_sdk/file/TsvFile/PgfFile.o
In file included from fusion_sdk/file/TsvFile/PgfFile.cpp:274:
In file included from fusion_sdk/file/TsvFile/PgfFile.h:32:
fusion_sdk/file/TsvFile/TsvFile.h:71:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_BINDTO_CNAME = 2, ///< Bound to a column index by name
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:78:22: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    VALSTATE_STRING=3,
                     ^
fusion_sdk/file/TsvFile/TsvFile.h:87:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_TYPE_DOUBLE  = 5,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:112:35: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_LASTVALUE            = -99, ///< end of errors
                                  ^
fusion_sdk/file/TsvFile/TsvFile.h:121:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OP_GT     = 0x04,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:163:34: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OPT_CASEINSENSTIVE = 0x02,
                                 ^
fusion_sdk/file/TsvFile/TsvFile.h:182:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/file/TsvFile/PgfFile.cpp:274:
fusion_sdk/file/TsvFile/PgfFile.h:39:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/file/TsvFile/PgfFile.cpp:400:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/file/TsvFile/TsvFile.cpp -o fusion_sdk/file/TsvFile/TsvFile.o
In file included from fusion_sdk/file/TsvFile/TsvFile.cpp:24:
fusion_sdk/file/TsvFile/TsvFile.h:71:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_BINDTO_CNAME = 2, ///< Bound to a column index by name
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:78:22: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    VALSTATE_STRING=3,
                     ^
fusion_sdk/file/TsvFile/TsvFile.h:87:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_TYPE_DOUBLE  = 5,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:112:35: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_LASTVALUE            = -99, ///< end of errors
                                  ^
fusion_sdk/file/TsvFile/TsvFile.h:121:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OP_GT     = 0x04,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:163:34: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OPT_CASEINSENSTIVE = 0x02,
                                 ^
fusion_sdk/file/TsvFile/TsvFile.h:182:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from fusion_sdk/file/TsvFile/TsvFile.cpp:28:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/file/TsvFile/TsvFile.cpp:146:15: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
    str_lc[i]=::tolower(str_lc[i]);
             ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:162:25: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
  unsigned char c_begin=str[0];
                ˜˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:163:23: warning: implicit conversion changes signedness: 'char' to 'unsigned char' [-Wsign-conversion]
  unsigned char c_end=str[str_size-1];
                ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:200:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      vec.resize(num+1);
      ˜˜˜        ˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:201:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      vec[num].assign(str,pos1,str.size()-pos1);
      ˜˜˜ ^˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:204:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      vec.resize(num+1);
      ˜˜˜        ˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:205:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      vec[num].assign(str,pos1,pos2-pos1);
      ˜˜˜ ^˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:255:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  estring.reserve(i_max);
  ˜˜˜˜˜˜˜         ^˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:258:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    char c=str[i];
           ˜˜˜ ^
fusion_sdk/file/TsvFile/TsvFile.cpp:259:13: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
    char cc=escapeChar(c);
         ˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:252:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int i_max=str.size();
      ˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:531:8: warning: implicit conversion loses integer precision: 'int' to 'short' [-Wconversion]
  *val=tmp_val;
      ˜^˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:554:15: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  m_value_int=strtol(ptr_start,&ptr_end,10);
             ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:636:16: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32]
  m_value_uint=strtoul(m_ptr_start,&m_ptr_end,10);
              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:717:3: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  TSV_SPLIT_VEC_BODY(int);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:702:11: note: expanded from macro 'TSV_SPLIT_VEC_BODY'
      val=CONVERT_FUNC();                         \
         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:716:24: note: expanded from macro 'CONVERT_FUNC'
#define CONVERT_FUNC() strtol(&m_buffer[pos1],&pos_out,10)
                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:717:3: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  TSV_SPLIT_VEC_BODY(int);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:706:11: note: expanded from macro 'TSV_SPLIT_VEC_BODY'
      val=CONVERT_FUNC();                         \
         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:716:24: note: expanded from macro 'CONVERT_FUNC'
#define CONVERT_FUNC() strtol(&m_buffer[pos1],&pos_out,10)
                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1397:19: warning: implicit conversion changes signedness: 'int' to 'linenum_t' (aka 'unsigned int') [-Wsign-conversion]
  return m_lineNum-1;
  ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1496:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  for (unsigned int clvl=clvl_start;clvl<clvl_size;clvl++) {
                    ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1495:26: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
  unsigned int clvl_size=m_column_map.size();
               ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1497:28: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int cidx_size=m_column_map[clvl].size();
                 ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1552:10: warning: implicit conversion changes signedness: 'int' to 'linenum_t' (aka 'unsigned int') [-Wsign-conversion]
  return m_lineNum;
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1569:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return (int)m_column_map[clvl].size();
                ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1653:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    delete m_headers_vec[vi];
           ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1654:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_headers_vec[vi]=NULL;
    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1691:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_headers_curptr=m_headers_vec[m_headers_idx++];
                     ˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:1980:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (f_tsv.getHeader(key_vec[i],val)==TSV_OK) {
                        ˜˜˜˜˜˜˜ ^
fusion_sdk/file/TsvFile/TsvFile.cpp:1981:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      addHeader(prefix+key_vec[i],val);
                       ˜˜˜˜˜˜˜ ^
fusion_sdk/file/TsvFile/TsvFile.cpp:1993:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  return m_headers_vec.size();
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2024:17: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
    int tmp_val=strtol(str_in,&str_out,0);
        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2178:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ((m_headers_vec[vi]!=NULL) && (m_headers_vec[vi]->m_key==key)) {
         ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2178:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ((m_headers_vec[vi]!=NULL) && (m_headers_vec[vi]->m_key==key)) {
                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2179:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      deleteHeaderPtr(m_headers_vec[vi]);
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2230:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (m_headers_vec[vi]==hdrptr) {
        ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2231:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      m_headers_vec[vi]=NULL;
      ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2264:38: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
    int cnt_fieldsep=countchars(line,m_optFieldSep);
                     ˜˜˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2279:17: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
  splitstr(line,m_optFieldSep,colname_vec);
  ˜˜˜˜˜˜˜˜      ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2286:20: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    defineColumn(0,col,colname_vec[col]);
    ˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2385:35: warning: implicit conversion changes signedness: 'unsigned char' to 'char' [-Wsign-conversion]
      splitstr(i->second->m_value,m_optFieldSep,colname_vec);
      ˜˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2395:24: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
          defineColumn(clvl,col-clvl,colname_vec[col]);
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2395:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
          defineColumn(clvl,col-clvl,colname_vec[col]);
          ˜˜˜˜˜˜˜˜˜˜˜˜      ˜˜˜^˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2432:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_column_map.resize(clvl+1);
    ˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2433:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_cnametocidx_map.resize(clvl+1);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2436:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  if (cidx>=(int)m_column_map[clvl].size()) {
                 ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2437:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_column_map[clvl].resize(cidx+1);
    ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2437:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_column_map[clvl].resize(cidx+1);
    ˜˜˜˜˜˜˜˜˜˜˜˜              ˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2440:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_clvl=clvl;
  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2440:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_clvl=clvl;
  ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2441:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_cidx=cidx;
  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2441:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_cidx=cidx;
  ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2442:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_cname=cname;
  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2442:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_cname=cname;
  ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2443:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_ctype=ctype;
  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2443:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_column_map[clvl][cidx].m_ctype=ctype;
  ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2445:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  m_cnametocidx_map[clvl][cname]=cidx;
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2449:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_column_map[clvl][cidx].setPrecision(m_optPrecision);
    ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2449:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_column_map[clvl][cidx].setPrecision(m_optPrecision);
    ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2466:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  i=m_cnametocidx_map[clvl].find(cname);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2468:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  if (i!=m_cnametocidx_map[clvl].end()) {
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2481:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (i=m_cnametocidx_map[clvl].begin();i!=m_cnametocidx_map[clvl].end();i++) {
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2481:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (i=m_cnametocidx_map[clvl].begin();i!=m_cnametocidx_map[clvl].end();i++) {
                                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2576:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      (cidx>=(int)m_column_map[clvl].size())) {
                  ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2579:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  return &m_column_map[clvl][cidx];
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2579:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  return &m_column_map[clvl][cidx];
          ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2805:16: warning: implicit conversion loses integer precision: 'int' to 'char_type' (aka 'char') [-Wconversion]
      M_UNGETC(c);
      ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:58:41: note: expanded from macro 'M_UNGETC'
#define M_UNGETC(c) (m_rdbuf->sputbackc(c))
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:2810:16: warning: implicit conversion loses integer precision: 'int' to 'char_type' (aka 'char') [-Wconversion]
      M_UNGETC(c);
      ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:58:41: note: expanded from macro 'M_UNGETC'
#define M_UNGETC(c) (m_rdbuf->sputbackc(c))
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:2815:16: warning: implicit conversion loses integer precision: 'int' to 'char_type' (aka 'char') [-Wconversion]
      M_UNGETC(c);
      ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:58:41: note: expanded from macro 'M_UNGETC'
#define M_UNGETC(c) (m_rdbuf->sputbackc(c))
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:2847:16: warning: implicit conversion loses integer precision: 'int' to 'char_type' (aka 'char') [-Wconversion]
      M_UNGETC(c);
      ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:58:41: note: expanded from macro 'M_UNGETC'
#define M_UNGETC(c) (m_rdbuf->sputbackc(c))
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:2852:16: warning: implicit conversion loses integer precision: 'int' to 'char_type' (aka 'char') [-Wconversion]
      M_UNGETC(c);
      ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:58:41: note: expanded from macro 'M_UNGETC'
#define M_UNGETC(c) (m_rdbuf->sputbackc(c))
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:2967:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
          in_quotes=c;
                   ˜^
fusion_sdk/file/TsvFile/TsvFile.cpp:2974:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      col->m_buffer.resize(bi); // trunc the buffer to size.
      ˜˜˜                  ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2980:16: warning: implicit conversion loses integer precision: 'int' to 'char_type' (aka 'char') [-Wconversion]
      M_UNGETC(c);
      ˜˜˜˜˜˜˜˜˜^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:58:41: note: expanded from macro 'M_UNGETC'
#define M_UNGETC(c) (m_rdbuf->sputbackc(c))
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:2981:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      col->m_buffer.resize(bi); // trunc
      ˜˜˜                  ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:2989:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      col->m_buffer.resize(bi);
      ˜˜˜                  ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3019:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    unsigned int cidx_size=m_column_map[line_clvl].size();
                           ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3021:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      f_read_column(&m_column_map[line_clvl][cidx]);
                     ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3022:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      m_column_map[line_clvl][cidx].linkedvars_assign(this);
      ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3038:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      f_read_column(&m_column_map[line_clvl][cidx]);
                     ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3038:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      f_read_column(&m_column_map[line_clvl][cidx]);
                     ˜˜˜˜˜˜˜˜˜˜˜˜            ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3019:28: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int cidx_size=m_column_map[line_clvl].size();
                 ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3075:34: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
  unsigned int m_column_map_size=m_column_map.size();
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3077:41: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int m_column_map_clvl_size=m_column_map[clvl].size();
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3163:36: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
  unsigned int m_linkvars_vec_size=m_linkvars_vec.size();
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3270:40: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_BIND_FUNC(std::string,m_ptr_string);
                                       ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3271:29: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_BIND_FUNC(int,m_ptr_int);
                            ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3272:35: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_BIND_FUNC(double,m_ptr_double);
                                  ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3273:33: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_BIND_FUNC(float,m_ptr_float);
                                ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3274:39: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_BIND_FUNC(unsigned int,m_ptr_uint);
                                      ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3275:40: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_BIND_FUNC(uint64_t,m_ptr_ulonglong);
                                       ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3351:9: warning: implicit conversion loses integer precision: 'int_type' (aka 'int') to 'char' [-Wconversion]
    c = M_PEEK();
      ˜ ^˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:57:22: note: expanded from macro 'M_PEEK'
#define M_PEEK()    (m_rdbuf->sgetc())
                     ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3410:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  clvl_seen.resize(getLevelCount(),0);
  ˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3417:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (clvl_seen[clvl]==1) {
        ˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3421:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    clvl_seen[clvl]=1;
    ˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3481:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    clvl=lineLevel();
        ˜^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3483:33: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    int cidx_max=getColumnCount(clvl);
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3485:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      col=&m_column_map[clvl][cidx];
           ˜˜˜˜˜˜˜˜˜˜˜˜       ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3486:24: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      int col_cur_size=col->m_buffer.size();
          ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:3738:30: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_GET_VEC_FUNC(std::string);
                             ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3739:22: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_GET_VEC_FUNC(int);
                     ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3740:24: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_GET_VEC_FUNC(float);
                       ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3741:25: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_GET_VEC_FUNC(double);
                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3802:22: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_SET_VEC_FUNC(int);
                     ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3803:24: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_SET_VEC_FUNC(float);
                       ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3804:25: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_SET_VEC_FUNC(double);
                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:3888:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    h_ptr=m_headers_vec[hi];
          ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4035:13: warning: implicit conversion changes signedness: 'linenum_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
  m_lineNum=line;
           ˜^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4117:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (size_t c_idx=0;c_idx<m_column_map[m_lineLvl].size();c_idx++) {
                            ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4121:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    line.append(m_column_map[m_lineLvl][c_idx].m_buffer);
                ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4182:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    m_index_lineclvl[m_lineLvl].push_back(l_num);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4182:43: warning: implicit conversion changes signedness: 'int' to 'const value_type' (aka 'const unsigned int') [-Wsign-conversion]
    m_index_lineclvl[m_lineLvl].push_back(l_num);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                      ^˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4195:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        idx->data_add(&m_column_map[m_lineLvl][idx->m_bindto_cidx],l_num);
                       ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4195:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        idx->data_add(&m_column_map[m_lineLvl][idx->m_bindto_cidx],l_num);
                       ˜˜˜˜˜˜˜˜˜˜˜˜            ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4195:68: warning: implicit conversion changes signedness: 'int' to 'linenum_t' (aka 'unsigned int') [-Wsign-conversion]
        idx->data_add(&m_column_map[m_lineLvl][idx->m_bindto_cidx],l_num);
        ˜˜˜                                                        ^˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4167:33: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
  unsigned int m_index_vec_size=m_index_vec.size();
               ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4173:32: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'const value_type' (aka 'const unsigned int') [-Wshorten-64-to-32]
    m_index_linefpos.push_back(m_line_fpos);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4366:46: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(int        ,std::string);
                                             ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4367:46: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(std::string,std::string);
                                             ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4368:38: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(int        ,int);
                                     ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4369:38: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(std::string,int);
                                     ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4370:41: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(int        ,double);
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4371:41: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(std::string,double);
                                        ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4372:47: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(int        ,unsigned int);
                                              ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4373:47: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(std::string,unsigned int);
                                              ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4374:43: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(int        ,uint64_t);
                                          ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4375:43: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
TSV_DEFUN_FIND_BEGIN(std::string,uint64_t);
                                          ^
fusion_sdk/file/TsvFile/TsvFile.cpp:4386:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  return (int)m_findresults.size();
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4436:22: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        defineColumn(li,ci,split_coldef[0]);
        ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4436:25: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        defineColumn(li,ci,split_coldef[0]);
        ˜˜˜˜˜˜˜˜˜˜˜˜    ^˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4482:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    h_ptr=m_headers_vec[h_i];
          ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4505:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    size_t cidx_size=m_column_map[clvl].size();
                     ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4508:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      write_str(m_column_map[clvl][cidx].m_cname);
                ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4523:19: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    writeFieldSep(clvl);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4524:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    writeColumnHeaders_clvl(clvl);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4678:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  size_t cidx_size=(int)m_column_map[clvl].size();
         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4678:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  size_t cidx_size=(int)m_column_map[clvl].size();
                        ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4683:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    TsvFileField* col=&m_column_map[clvl][cidx];
                       ˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4758:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      set(clvl,cidx,f_tsv.m_column_map[clvl][cidx].m_buffer);
                    ˜˜˜˜˜              ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4758:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      set(clvl,cidx,f_tsv.m_column_map[clvl][cidx].m_buffer);
                    ˜˜˜˜˜                    ^˜˜˜
fusion_sdk/file/TsvFile/TsvFile.cpp:4915:17: warning: implicit conversion of NULL constant to 'char' [-Wnull-conversion]
    char last = NULL;
         ˜˜˜˜   ^˜˜˜
                '\0'
fusion_sdk/file/TsvFile/TsvFile.cpp:4913:13: warning: implicit conversion loses integer precision: 'typename iterator_traits<istreambuf_iterator<char, char_traits<char> > >::difference_type' (aka 'long long') to 'int' [-Wshorten-64-to-32]
    count = std::count(std::istreambuf_iterator<char>(fstream), std::istreambuf_iterator<char>(), '\n');
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
147 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/AffxByteArray.cpp -o fusion_sdk/util/AffxByteArray.o
In file included from fusion_sdk/util/AffxByteArray.cpp:27:
In file included from fusion_sdk/util/AffxByteArray.h:29:
fusion_sdk/util/AffxString.h:92:71: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    AffxString mid(int iStartIndex, int iLength) const {return substr(iStartIndex, iStartIndex + iLength);}
                                                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxString.h:92:96: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    AffxString mid(int iStartIndex, int iLength) const {return substr(iStartIndex, iStartIndex + iLength);}
                                                               ˜˜˜˜˜˜              ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxString.h:125:21: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
            toLower(iIndex);
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:133:21: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
            toUpper(iIndex);
            ˜˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:176:42: warning: implicit conversion changes signedness: 'char' to 'unsigned int' [-Wsign-conversion]
            nHash = (nHash<<5) + nHash + getAt(iIndex);
                                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxString.h:211:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inline AffxString::AffxString(char ch, int nRepeat) : std::string(nRepeat, ch) {}
                                                           ˜˜˜˜˜˜ ^˜˜˜˜˜˜
fusion_sdk/util/AffxString.h:213:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inline AffxString::AffxString(const char* pch, int nLength) : std::string(pch, nLength) {}
                                                                   ˜˜˜˜˜˜      ^˜˜˜˜˜˜
fusion_sdk/util/AffxString.h:217:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return getAt(nIndex) == _TAB_CHAR;
          ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:222:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return isalpha(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:227:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return isalnum(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:232:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return isspace(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:237:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return getAt(nIndex) == ' ';
          ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:242:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return ispunct(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:247:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return isupper(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:252:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return islower(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:257:25: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return isdigit(getAt(nIndex)) != 0;
                  ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:262:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   return isxdigit(getAt(nIndex)) != 0;
                   ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:271:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   setAt(nIndex, (char)toupper(getAt(nIndex)));
   ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:271:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   setAt(nIndex, (char)toupper(getAt(nIndex)));
                               ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:276:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   setAt(nIndex, (char)tolower(getAt(nIndex)));
   ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:276:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
   setAt(nIndex, (char)tolower(getAt(nIndex)));
                               ˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/util/AffxString.h:311:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        if (!isdigit(getAt(i)) && 
                     ˜˜˜˜˜ ^
fusion_sdk/util/AffxString.h:312:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            !(getAt(i) == '.' && 0 < i && i < (int)length() - 1) &&
              ˜˜˜˜˜ ^
fusion_sdk/util/AffxString.h:313:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            !(getAt(i) == '-' && i == 0) &&
              ˜˜˜˜˜ ^
fusion_sdk/util/AffxString.h:314:21: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            !(getAt(i) == '+' && i == 0))
              ˜˜˜˜˜ ^
In file included from fusion_sdk/util/AffxByteArray.cpp:28:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/util/AffxByteArray.cpp:105:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memcpy(m_pData, ba.m_pData, (iLength * sizeof(char)));
                                     ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:116:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        m_pData = (char*) new char[iLength * sizeof(char)];
                                   ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:153:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                m_pData = (char*) new char[nNewSize * sizeof(char)];
                                           ^˜˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:155:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(m_pData, 0, nNewSize * sizeof(char));  // zero fill
                                   ^˜˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:166:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        memset(&m_pData[m_nSize], 0, (nNewSize-m_nSize) * sizeof(char));
                                                      ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜  ˜
fusion_sdk/util/AffxByteArray.cpp:188:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                char* pNewData = (char*) new char[nNewMax * sizeof(char)];
                                                  ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:191:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(pNewData, m_pData, m_nSize * sizeof(char));
                                          ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:195:42: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(&pNewData[m_nSize], 0, (nNewSize-m_nSize) * sizeof(char));
                                               ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜  ˜
fusion_sdk/util/AffxByteArray.cpp:224:46: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memcpy(m_pData + nOldSize, src.m_pData, src.m_nSize * sizeof(char));
                                                ˜˜˜˜^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:233:36: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
        memmove(m_pData, src.m_pData, src.m_nSize * sizeof(char));
                                      ˜˜˜˜^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:248:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        pNewData = (char*) new char[m_nSize * sizeof(char)];
                                                    ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:250:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        memcpy(pNewData, m_pData, m_nSize * sizeof(char));
                                                  ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:283:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        (nOldSize-nIndex) * sizeof(char));
                         ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜  ˜
fusion_sdk/util/AffxByteArray.cpp:287:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memset(&m_pData[nIndex], 0, nCount * sizeof(char));
                                            ^˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:303:4: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        nMoveCount * sizeof(char));
                        ^˜˜˜˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:367:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                if (getAt(i) == str.getAt(i))
                                                ˜˜˜       ^
fusion_sdk/util/AffxByteArray.cpp:394:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                if ((getAt(i) == str.getAt(i)) || (getAt(i) + ' ' == str.getAt(i)))
                                                 ˜˜˜       ^
fusion_sdk/util/AffxByteArray.cpp:394:68: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                if ((getAt(i) == str.getAt(i)) || (getAt(i) + ' ' == str.getAt(i)))
                                                                                     ˜˜˜       ^
fusion_sdk/util/AffxByteArray.cpp:404:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                if ((getAt(i) == str.getAt(i)) || (getAt(i) - ' ' == str.getAt(i)))
                                                 ˜˜˜       ^
fusion_sdk/util/AffxByteArray.cpp:404:68: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                if ((getAt(i) == str.getAt(i)) || (getAt(i) - ' ' == str.getAt(i)))
                                                                                     ˜˜˜       ^
fusion_sdk/util/AffxByteArray.cpp:412:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        else if (getAt(i) == str.getAt(i))
                                             ˜˜˜       ^
fusion_sdk/util/AffxByteArray.cpp:439:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        return atol(buffer);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:447:62: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memmove((m_pData + iDestStart), (src.m_pData + iSrcStart), (iLength * sizeof(char)));
                                                                    ^˜˜˜˜˜˜ ˜
fusion_sdk/util/AffxByteArray.cpp:654:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                char *psz = (char *)malloc(getSize() + 1);
                                    ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
fusion_sdk/util/AffxByteArray.cpp:658:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                strncpy(psz, (char *)getData(), getSize());
                ˜˜˜˜˜˜˜                         ^˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:671:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int iCompareLength = strCompare.getLength();
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:678:42: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        if (getAt(iIndex) != strCompare.getAt(iIndex))
                                             ˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:803:63: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        ba.setAt(iIndex, strComplement.getAt(ba.getAt(iIndex) - 'a'));
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:810:58: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        ba.setAt(i, strComplement.getAt(ba.getAt(iIndex) - 'a'));
                    ˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:811:49: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        ba.setAt(iIndex, strComplement.getAt(by - 'a'));
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜       ˜˜˜^˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:837:65: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                memcpy(((char*)m_pData + oldcount), ((char *)bytes + offset), len);
                ˜˜˜˜˜˜                                                        ^˜˜
fusion_sdk/util/AffxByteArray.cpp:915:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                memcpy((void*)(ba.m_pData), (void*)(m_pData + iStart), iLength);
                ˜˜˜˜˜˜                                                 ^˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:1218:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                memcpy((void*)(ba.m_pData), (void*)(m_pData + iStart), iLength);
                ˜˜˜˜˜˜                                                 ^˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:1259:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                memcpy((void*)(ba.m_pData), (void*)(m_pData + iStart), iLength);
                ˜˜˜˜˜˜                                                 ^˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:1320:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            if (this->m_pData[iIndex] != that.charAt(iIndex))
                                         ˜˜˜˜        ^˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:1323:57: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                iResult = (this->m_pData[iIndex] - that.charAt(iIndex));
                                                   ˜˜˜˜        ^˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:1419:11: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  setSize(uiNumberBytes);
  ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxByteArray.cpp:1416:32: warning: implicit conversion loses integer precision: 'int64_t' (aka 'long long') to 'unsigned int' [-Wshorten-64-to-32]
  unsigned int uiNumberBytes = Fs::fileSize(strFileName);
               ˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
64 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/AffxConv.cpp -o fusion_sdk/util/AffxConv.o
fusion_sdk/util/AffxConv.cpp:63:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (str[i] != ',') {strInt += str[i];}
                    ˜˜˜ ^
fusion_sdk/util/AffxConv.cpp:63:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (str[i] != ',') {strInt += str[i];}
                                              ˜˜˜ ^
fusion_sdk/util/AffxConv.cpp:66:9: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
        return atol(strInt.c_str());            
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/AffxConv.cpp:92:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (str[i] != ',') {strDouble += str[i];}
                    ˜˜˜ ^
fusion_sdk/util/AffxConv.cpp:92:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                if (str[i] != ',') {strDouble += str[i];}
                                                 ˜˜˜ ^
fusion_sdk/util/AffxConv.cpp:119:14: warning: extra tokens at end of #ifdef directive [-Wextra-tokens]
#ifdef WIN32 && !defined(__MINGW32__)
             ^
             //
fusion_sdk/util/AffxConv.cpp:124:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
        if (i != i) {return "nan";}
              ^
fusion_sdk/util/AffxConv.cpp:340:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                str = strMonths.substr(iMonth, 3); 
                      ˜˜˜˜˜˜˜˜˜        ^˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/MsgStream.cpp -o fusion_sdk/util/MsgStream.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/Util.cpp -o fusion_sdk/util/Util.o
In file included from fusion_sdk/util/Util.cpp:35:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/util/Util.cpp:178:59: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  std::string tmpstr=str.substr(str.size()-(ending.size()+charsAtEnd),ending.size());
                                                         ˜^˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:236:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        size_t pos = s.find(delim,curPos);
                     ˜            ^˜˜˜˜˜
fusion_sdk/util/Util.cpp:238:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            words.push_back(s.substr(curPos, s.size()));
                            ˜        ^˜˜˜˜˜
fusion_sdk/util/Util.cpp:241:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        string sub = s.substr(curPos, pos - curPos);
                     ˜        ^˜˜˜˜˜
fusion_sdk/util/Util.cpp:241:45: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        string sub = s.substr(curPos, pos - curPos);
                                          ˜ ^˜˜˜˜˜
fusion_sdk/util/Util.cpp:243:22: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
        curPos = pos + delim.size();
               ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:335:53: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  RowFile::matrixFromFile(tmp_target_name, qMatrix, rowSkip, colSkip);
  ˜˜˜˜˜˜˜                                           ^˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:335:62: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  RowFile::matrixFromFile(tmp_target_name, qMatrix, rowSkip, colSkip);
  ˜˜˜˜˜˜˜                                                    ^˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:339:52: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  RowFile::matrixFromFile(tmp_query_name, tMatrix, rowSkip, colSkip);
  ˜˜˜˜˜˜˜                                          ^˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:339:61: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  RowFile::matrixFromFile(tmp_query_name, tMatrix, rowSkip, colSkip);
  ˜˜˜˜˜˜˜                                                   ^˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:348:68: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    TableFile::columnFromFile(tmp_target_name, qMatrixRows, colIx, rowSkip, true);
    ˜˜˜˜˜˜˜˜˜                                                      ^˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:349:68: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    TableFile::columnFromFile(tmp_query_name,  tMatrixRows, colIx, rowSkip, true);
    ˜˜˜˜˜˜˜˜˜                                                      ^˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:355:40: warning: implicit conversion changes signedness: 'unsigned int' to 'mapped_type' (aka 'int') [-Wsign-conversion]
      qMatrixMap[qMatrixRows[rowIx]] = rowIx;
                                     ˜ ^˜˜˜˜
fusion_sdk/util/Util.cpp:369:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      int qMatRowIx = rowIx;
          ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜
fusion_sdk/util/Util.cpp:377:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double val = qMatrix[qMatRowIx][colIx] - tMatrix[rowIx][colIx];
                   ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:380:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double epsilon2 = fraction*Max( fabs(qMatrix[qMatRowIx][colIx]), fabs(tMatrix[rowIx][colIx]) );
                                           ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/portability/affy-base-types.h:61:27: note: expanded from macro 'Max'
#define Max(a,b) std::max(a,b)
                          ^
fusion_sdk/util/Util.cpp:384:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      okFinite &= isFinite(qMatrix[qMatRowIx][colIx]);
                           ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:395:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                       ToStr(qMatrix[qMatRowIx][colIx]) + " vs. " + ToStr( tMatrix[rowIx][colIx]) + ")" + " Diff: " + ToStr(val));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:417:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  return diffCount;
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:363:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
  numRow = tMatrix.size();
         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:364:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
  numCol = tMatrix[0].size();
         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:427:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ss << words[i];
              ˜˜˜˜˜ ^
fusion_sdk/util/Util.cpp:788:7: warning: expression result unused [-Wunused-value]
      *wStart++;
      ^˜˜˜˜˜˜˜˜
fusion_sdk/util/Util.cpp:829:25: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
      nextSize = wStart - wEnd;
               ˜ ˜˜˜˜˜˜˜^˜˜˜˜˜
fusion_sdk/util/Util.cpp:882:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    changeEnd(str_vec[i],from,to);
              ˜˜˜˜˜˜˜ ^
26 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/Err.cpp -o fusion_sdk/util/Err.o
fusion_sdk/util/Err.cpp:69:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int size = getParam().m_ErrHandlers.size();
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Err.cpp:94:26: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int count = getParam().m_ErrHandlers.size();
                 ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Err.cpp:114:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
     ErrHandler *handler = getParam().m_ErrHandlers[i];
                           ˜˜˜˜˜˜˜˜                 ^
fusion_sdk/util/Err.cpp:112:16: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int size = getParam().m_ErrHandlers.size();
        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Err.cpp:185:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                ErrHandler *handler = getParam().m_ErrHandlers[i];
                                      ˜˜˜˜˜˜˜˜                 ^
fusion_sdk/util/Err.cpp:178:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int size = getParam().m_ErrHandlers.size();
            ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/Err.cpp:202:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                ErrHandler *handler = getParam().m_ErrHandlers[i];
                                      ˜˜˜˜˜˜˜˜                 ^
fusion_sdk/util/Err.cpp:195:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int size = getParam().m_ErrHandlers.size();
      ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/Fs.cpp -o fusion_sdk/util/Fs.o
In file included from fusion_sdk/util/Fs.cpp:28:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/util/Fs.cpp:169:7: warning: implicit conversion changes signedness: 'uid_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
  uid=getuid();
     ˜^˜˜˜˜˜˜˜
fusion_sdk/util/Fs.cpp:170:7: warning: implicit conversion changes signedness: 'gid_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
  gid=getgid();
     ˜^˜˜˜˜˜˜˜
fusion_sdk/util/Fs.cpp:189:7: warning: implicit conversion changes signedness: 'uid_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
  uid=getuid();
     ˜^˜˜˜˜˜˜˜
fusion_sdk/util/Fs.cpp:190:7: warning: implicit conversion changes signedness: 'gid_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
  gid=getgid();
     ˜^˜˜˜˜˜˜˜
fusion_sdk/util/Fs.cpp:999:31: warning: implicit conversion loses integer precision: 'int' to 'mode_t' (aka 'unsigned short') [-Wconversion]
  rv=POSIX_CHMOD(path.c_str(),mode);
     ˜˜˜˜˜˜˜˜˜˜˜              ^˜˜˜
fusion_sdk/util/Fs.cpp:1510:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          if(Fs::fileExists(Fs::join(searchPathVec[i] , fileName)))
                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/util/Fs.cpp:1511:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
             return Fs::join(searchPathVec[i] , fileName);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
fusion_sdk/util/Fs.cpp:1618:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      sleep(sec);
      ˜˜˜˜˜ ^˜˜
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/Verbose.cpp -o fusion_sdk/util/Verbose.o
In file included from fusion_sdk/util/Verbose.cpp:31:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/RowFile.cpp -o fusion_sdk/util/RowFile.o
In file included from fusion_sdk/util/RowFile.cpp:32:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/util/RowFile.cpp:79:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
fusion_sdk/util/RowFile.cpp:163:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    next = (int)m_CurrentLine.find(m_Delim, start);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜               ^˜˜˜˜
fusion_sdk/util/RowFile.cpp:167:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    words.push_back(m_CurrentLine.substr(start, next - start));
                    ˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜˜
fusion_sdk/util/RowFile.cpp:167:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    words.push_back(m_CurrentLine.substr(start, next - start));
                    ˜˜˜˜˜˜˜˜˜˜˜˜˜               ˜˜˜˜˜^˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:160:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  len = m_CurrentLine.size();
      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:165:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      next = m_CurrentLine.size(); // entire string.
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:216:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  memcpy(m_Buffer, m_CurrentLine.c_str(), len);
  ˜˜˜˜˜˜                                  ^˜˜
fusion_sdk/util/RowFile.cpp:221:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if(!isspace(m_CurrentLine[start])) 
                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/util/RowFile.cpp:226:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if(!isspace(m_CurrentLine[len -1]))
                ˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
fusion_sdk/util/RowFile.cpp:234:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    next = (int)m_CurrentLine.find(m_Delim, start);
                ˜˜˜˜˜˜˜˜˜˜˜˜˜               ^˜˜˜˜
fusion_sdk/util/RowFile.cpp:206:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  len = m_CurrentLine.size();
      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:236:14: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      next = m_CurrentLine.size(); // entire string.
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:289:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string key = line->substr(startPos, delimPos-startPos);
                 ˜˜˜˜         ^˜˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:289:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    string key = line->substr(startPos, delimPos-startPos);
                                                ˜^˜˜˜˜˜˜˜
fusion_sdk/util/RowFile.cpp:375:15: warning: implicit conversion loses integer precision: 'int_type' (aka 'int') to 'char' [-Wconversion]
    char c1 = input.get();
         ˜˜   ^˜˜˜˜˜˜˜˜˜˜
16 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/TableFile.cpp -o fusion_sdk/util/TableFile.o
In file included from fusion_sdk/util/TableFile.cpp:32:
In file included from fusion_sdk/util/Fs.h:28:
fusion_sdk/util/AptErrno.h:46:21: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
  APT_ERR_NOTREMOVED,
                    ^
fusion_sdk/util/TableFile.cpp:165:17: warning: explicitly assigning a variable of type 'unsigned int' to itself [-Wself-assign]
      for(colIx = colIx; colIx < words.size(); colIx++) {
          ˜˜˜˜˜ ^ ˜˜˜˜˜
fusion_sdk/util/TableFile.cpp:169:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    if(words.size() - rowOffset != m_ColNames.size()) 
                    ˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/util/TableFile.cpp:171:44: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                      ToStr(words.size() - rowOffset) + " at line " + 
                                         ˜ ^˜˜˜˜˜˜˜˜
fusion_sdk/util/TableFile.cpp:143:28: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'mapped_type' (aka 'unsigned int') [-Wshorten-64-to-32]
      m_ColNameMap[name] = m_ColNames.size();
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fusion_sdk/util/TableFile.cpp:185:26: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'mapped_type' (aka 'unsigned int') [-Wshorten-64-to-32]
    m_RowNameMap[name] = m_Data.size();
                       ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
In file included from fusion_sdk/util/TableFile.cpp:28:
fusion_sdk/util/TableFile.h:231:8: warning: private field 'm_Comment' is not used [-Wunused-private-field]
  char m_Comment;            ///< Comment character for data.
       ^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c fusion_sdk/util/Convert.cpp -o fusion_sdk/util/Convert.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o
In file included from R_affx_cel_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_cel_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_cel_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:24:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:38:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    strncpy(cstr, str.c_str(), str_length);
    ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:71:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    wcstombs(cstr, cel.GetAlg().c_str(), str_length);
    ˜˜˜˜˜˜˜˜                             ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:79:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    wcstombs(cstr, cel.GetParams().c_str(), str_length);
    ˜˜˜˜˜˜˜˜                                ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:87:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    wcstombs(cstr, cel.GetChipType().c_str(), str_length);
    ˜˜˜˜˜˜˜˜                                  ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:95:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    wcstombs(cstr, cel.GetHeader().c_str(), str_length);
    ˜˜˜˜˜˜˜˜                                ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:103:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    wcstombs(cstr, cel.GetDatHeader().c_str(), str_length);
    ˜˜˜˜˜˜˜˜                                   ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:111:57: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    wcstombs(cstr, cel.GetLibraryPackageName().c_str(), str_length);
    ˜˜˜˜˜˜˜˜                                            ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:147:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    INTEGER(tmp)[0] = cel.GetNumOutliers();
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:153:23: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    INTEGER(tmp)[0] = cel.GetNumMasked();
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:36:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = str.size();
               ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:69:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = cel.GetAlg().size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:77:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = cel.GetParams().size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:85:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = cel.GetChipType().size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:93:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = cel.GetHeader().size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:101:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = cel.GetDatHeader().size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:109:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = cel.GetLibraryPackageName().size();
               ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cel_parser.cpp:431:38: warning: implicit conversion changes signedness: 'unsigned int' to 'R_len_t' (aka 'int') [-Wsign-conversion]
        PROTECT(SET_LENGTH(outliers, outliersCount));
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:137:45: note: expanded from macro 'SET_LENGTH'
#define SET_LENGTH(x, n)        (x = lengthgets(x, n))
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
R_affx_cel_parser.cpp:441:36: warning: implicit conversion changes signedness: 'unsigned int' to 'R_len_t' (aka 'int') [-Wsign-conversion]
        PROTECT(SET_LENGTH(masked, maskedCount));
                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:137:45: note: expanded from macro 'SET_LENGTH'
#define SET_LENGTH(x, n)        (x = lengthgets(x, n))
                                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o
In file included from R_affx_cdf_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_cdf_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_cdf_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from R_affx_cdf_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:29:
fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:47:32: warning: implicit conversion changes signedness: 'const u_int32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        int GetExpos() const { return indexPos; }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:59:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(cstr, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:57:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:169:31: warning: expression result unused [-Wunused-value]
        for(int i = 0; i++; i < length(unitIndices)) {
                            ˜ ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:506:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    strncpy(cstr, str.c_str(), str_length);
    ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:515:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    strncpy(cstr, str.c_str(), str_length);
    ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:524:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    strncpy(cstr, str.c_str(), str_length);
    ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:504:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = str.size();
               ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:513:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = str.size();
               ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:522:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    str_length = str.size();
               ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:619:31: warning: expression result unused [-Wunused-value]
        for(int i = 0; i++; i < length(unitIndices)) {
                            ˜ ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:768:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(unitName, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                        ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:988:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:766:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:986:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1160:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(cstr, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1216:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1158:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1214:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1479:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(cstr, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1637:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
          strncpy(cstr, str.c_str(), str_length);
          ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1477:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1635:24: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
          str_length = str.size();
                     ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1750:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1762:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1748:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_parser.cpp:1760:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
30 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o
In file included from R_affx_cdf_extras.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_cdf_extras.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_cdf_extras.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:27:
In file included from fusion_sdk/calvin_files/data/src/CDFData.h:26:
In file included from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from R_affx_cdf_extras.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:29:
fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:47:32: warning: implicit conversion changes signedness: 'const u_int32_t' (aka 'const unsigned int') to 'int' [-Wsign-conversion]
        int GetExpos() const { return indexPos; }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:97:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(cstr, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:122:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:95:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:120:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:239:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(name, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:262:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:268:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int res = strncmp(cstr, name, len);
                  ˜˜˜˜˜˜˜             ^˜˜
R_affx_cdf_extras.cpp:270:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
          int last = strlen(cstr)-len;
                                 ˜^˜˜
R_affx_cdf_extras.cpp:237:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:260:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:267:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        int len = strlen(name);
            ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:270:34: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
          int last = strlen(cstr)-len;
              ˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
R_affx_cdf_extras.cpp:416:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
      strncpy(cstr, str.c_str(), str_length);
      ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:441:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strncpy(cstr, str.c_str(), str_length);
        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:414:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      str_length = str.size();
                 ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_cdf_extras.cpp:439:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        str_length = str.size();
                   ˜ ^˜˜˜˜˜˜˜˜˜
20 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o
R_affx_bpmap_parser.cpp:95:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                strncpy(cstr, str.c_str(), str_length);
                                                                ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:104:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                strncpy(cstr, str.c_str(), str_length);
                                                                ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:114:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                strncpy(cstr, str.c_str(), str_length);
                                                                ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:124:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                strncpy(cstr, str.c_str(), str_length);
                                                                ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:159:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                        strncpy(cstr, str.c_str(), str_length);
                                                                                                        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:166:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                        strncpy(cstr, str.c_str(), str_length);
                                                                                                        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:93:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                str_length = str.size();
                                                                           ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:102:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                str_length = str.size();
                                                                           ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:112:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                str_length = str.size();
                                                                           ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:122:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                str_length = str.size();
                                                                           ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:157:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                                                        str_length = str.size();
                                                                                                                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:270:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                strncpy(cstr, str.c_str(), str_length);
                                                ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:268:20: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                str_length = str.size();
                                                           ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:465:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        INTEGER(pmx)[j] = seqHit.PMX;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_bpmap_parser.cpp:466:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        INTEGER(pmy)[j] = seqHit.PMY;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_bpmap_parser.cpp:469:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        INTEGER(mmx)[j] = seqHit.MMX;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_bpmap_parser.cpp:470:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        INTEGER(mmy)[j] = seqHit.MMY;
                                        ˜ ˜˜˜˜˜˜˜^˜˜
R_affx_bpmap_parser.cpp:473:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        INTEGER(strand)[j] = (unsigned int)seqHit.TopStrand;
                                           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:479:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                                                        strncpy(cstr, str.c_str(), str_length);
                                                                                                        ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:485:52: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                            INTEGER(startpos)[j] = seqHit.getStartPosition();
                                                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:488:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        INTEGER(centerpos)[j] = seqHit.getCenterPosition();
                                              ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:549:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                                                                strncpy(cstr, str.c_str(), str_length);
                                                                ˜˜˜˜˜˜˜                    ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:477:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                                                        str_length = str.size();
                                                                                                                   ˜ ^˜˜˜˜˜˜˜˜˜
R_affx_bpmap_parser.cpp:547:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                                                                str_length = str.size();
                                                                           ˜ ^˜˜˜˜˜˜˜˜˜
24 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o
In file included from R_affx_clf_pgf_parser.cpp:2:
In file included from fusion_sdk/file/TsvFile/ClfFile.h:31:
fusion_sdk/file/TsvFile/TsvFile.h:71:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_BINDTO_CNAME = 2, ///< Bound to a column index by name
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:78:22: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    VALSTATE_STRING=3,
                     ^
fusion_sdk/file/TsvFile/TsvFile.h:87:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_TYPE_DOUBLE  = 5,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:112:35: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_LASTVALUE            = -99, ///< end of errors
                                  ^
fusion_sdk/file/TsvFile/TsvFile.h:121:25: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OP_GT     = 0x04,
                        ^
fusion_sdk/file/TsvFile/TsvFile.h:163:34: warning: commas at the end of enumerator lists are a C++11 extension [-Wc++11-extensions]
    TSV_OPT_CASEINSENSTIVE = 0x02,
                                 ^
fusion_sdk/file/TsvFile/TsvFile.h:182:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_clf_pgf_parser.cpp:2:
fusion_sdk/file/TsvFile/ClfFile.h:38:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_clf_pgf_parser.cpp:3:
fusion_sdk/file/TsvFile/PgfFile.h:39:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -O0 -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o
In file included from R_affx_chp_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
In file included from fusion_sdk/calvin_files/data/src/GenericDataHeader.h:27:
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.h:58:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_chp_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:24:
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.h:28:
fusion_sdk/calvin_files/data/src/GenericDataHeader.h:146:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
 ^
In file included from R_affx_chp_parser.cpp:1:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:26:
In file included from fusion_sdk/calvin_files/data/src/GenericData.h:32:
In file included from fusion_sdk/calvin_files/data/src/DataGroup.h:33:
fusion_sdk/calvin_files/data/src/DataSet.h:194:51: warning: implicit conversion changes signedness: 'int32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int32_t BytesPerRow() { return columnByteOffsets[header.GetColumnCnt()]; }
                                       ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from R_affx_chp_parser.cpp:2:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:29:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:30:
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:506:38: warning: implicit conversion changes signedness: 'const int8_t' (aka 'const signed char') to 'u_int8_t' (aka 'unsigned char') [-Wsign-conversion]
        u_int8_t GetReason() const { return reason; }
                                     ˜˜˜˜˜˜ ^˜˜˜˜˜
fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.h:511:40: warning: implicit conversion changes signedness: 'u_int8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
        void SetReason(u_int8_t r) { reason = r; }
                                            ˜ ^
In file included from R_affx_chp_parser.cpp:2:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.h:29:
In file included from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:35:
fusion_sdk/file/CHPFileData.h:266:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetCols(int n) { m_Cols=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:271:31: warning: implicit conversion loses integer precision: 'int' to 'unsigned short' [-Wconversion]
        void SetRows(int n) { m_Rows=n; }
                                    ˜^
fusion_sdk/file/CHPFileData.h:596:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        char GetCalledBase(int index) { return calledBases[index]; }
                                               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:606:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeCalledBases(int size) { calledBases.resize(size); }
                                           ˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:612:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetCalledBase(int index, char call) { calledBases[index] = call; }
                                                   ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:623:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        float GetScore(int index) { return scores[index]; }
                                           ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:633:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeScores(int size) { scores.resize(size); }
                                      ˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:639:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetScore(int index, float score) { scores[index] = score; }
                                                ˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:650:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        ForceCallType GetForceCall(int index) { return forceCalls[index]; }
                                                       ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:660:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeForceCalls(int size) { forceCalls.resize(size); }
                                          ˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:666:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetForceCall(int index, ForceCallType call) { forceCalls[index] = call; }
                                                           ˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:677:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        BaseCallType GetOrigCall(int index) { return origCalls[index]; }
                                                     ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
fusion_sdk/file/CHPFileData.h:687:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void ResizeOrigCalls(int size) { origCalls.resize(size); }
                                         ˜˜˜˜˜˜˜˜˜        ^˜˜˜
fusion_sdk/file/CHPFileData.h:693:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        void SetOrigCall(int index, BaseCallType call) { origCalls[index] = call; }
                                                         ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
R_affx_chp_parser.cpp:46:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  wcstombs(cstr, wstr.c_str(), str_length);
  ˜˜˜˜˜˜˜˜                     ^˜˜˜˜˜˜˜˜˜
R_affx_chp_parser.cpp:44:16: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  str_length = wstr.size();
             ˜ ^˜˜˜˜˜˜˜˜˜˜
R_affx_chp_parser.cpp:95:24: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int pIdx = 0, pNbr = params.size();
                ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_chp_parser.cpp:119:22: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int pIdx=0, pNbr = params.size();
              ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_chp_parser.cpp:205:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  s = (char *) R_alloc((long) (ct) + 1L, sizeof(char));
               ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
R_affx_chp_parser.cpp:227:39: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    sc = (char *) R_alloc((long) (ct) + 1L, sizeof(char));
                  ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
R_affx_chp_parser.cpp:228:39: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    sr = (char *) R_alloc((long) (ct) + 1L, sizeof(char));
                  ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
R_affx_chp_parser.cpp:256:39: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    sc = (char *) R_alloc((long) (ct) + 1L, sizeof(char));
                  ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
R_affx_chp_parser.cpp:651:15: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  numParams = seq.parameters.size();
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
R_affx_chp_parser.cpp:682:30: warning: implicit conversion changes signedness: 'u_int32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
    INTEGER(position)[i] = e.position;
                         ˜ ˜˜^˜˜˜˜˜˜˜
29 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o affxparser.so fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_files/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files/parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvFile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fusion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/util/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affxparser.Rcheck/affxparser/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affxparser)

name	user	system	elapsed
applyCdfGroups	0.201	0.079	0.307
convertCdf	1.691	0.080	1.812
convertCel	0.248	0.033	0.329
createCel	0.444	0.056	0.584
findCdf	0.215	0.021	0.267
invertMap	2.397	0.107	2.590
readCdfDataFrame	1.268	0.165	1.523
readCdfHeader	0.019	0.008	0.028
readCdfNbrOfCellsPerUnitGroup	0.855	0.230	1.165
readCdfUnitNames	0.002	0.003	0.006
readCdfUnits	2.526	0.275	2.822
readCdfUnitsWriteMap	0.990	0.146	1.172
readCel	0.015	0.009	0.027
readCelHeader	0.008	0.008	0.017
readCelIntensities	0.004	0.006	0.011
readCelRectangle	0.518	0.053	0.650
readCelUnits	0.065	0.018	0.085
readChp	0.073	0.015	0.096
updateCel	2.352	0.533	3.181
updateCelUnits	2.515	0.277	2.936