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Package 4/208OSArchBUILDCHECKBUILD BIN

affxparser

1.7.2

Kasper Daniel Hansen
Linux (SUSE 9.2) x86_64 OK [ WARNINGS ]
Linux (SUSE 10.1) x86_64 OK  WARNINGS 
Linux (SUSE 9.2) i686 OK  WARNINGS 
Solaris 2.9 sparc OK  WARNINGS 
Windows Server 2003 x86_64 OK  WARNINGS  OK 
Windows Server 2003 NA OK  ERROR  OK 
Mac OS X (10.4.6) i686 OK  WARNINGS 
Package: affxparser
Version: 1.7.2
Command: /loc/biocbuild/2.0d/R/bin/R CMD check affxparser_1.7.2.tar.gz
RetCode: 0
Time: 138.8 seconds
Status: WARNINGS
CheckDir: affxparser.Rcheck
Warnings: 2

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/affxparser.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'affxparser/DESCRIPTION' ... OK
* this is package 'affxparser' version '1.7.2'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affxparser' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... WARNING
Warning: '\]' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "^([^\]]*])[ ]*(.*)[ ]*"
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'readCdf':
readCdf
  Code: function(filename, units = NULL, readXY = TRUE, readBases =
                 TRUE, readIndexpos = TRUE, readIsPm = FALSE, readAtoms
                 = TRUE, readUnitType = TRUE, readUnitDirection = TRUE,
                 readUnitNumber = FALSE, readUnitAtomNumbers = FALSE,
                 readGroupAtomNumbers = FALSE, readGroupDirection =
                 FALSE, stratifyBy = c("nothing", "pmmm", "pm", "mm"),
                 readIndices = FALSE, verbose = 0)
  Docs: function(filename, units = NULL, verbose = 0)
  Argument names in code not in docs:
    readXY readBases readIndexpos readIsPm readAtoms readUnitType
    readUnitDirection readUnitNumber readUnitAtomNumbers
    readGroupAtomNumbers readGroupDirection stratifyBy readIndices
  Mismatches in argument names:
    Position: 3 Code: readXY Docs: verbose

* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating affxparser-Ex.R ... OK
* checking examples ... OK
* creating affxparser-manual.tex ... OK
* checking affxparser-manual.tex ... OK

WARNING: There were 2 warnings, see
  /loc/biocbuild/2.0d/Rpacks/affxparser.Rcheck/00check.log
for details

affxparser.Rcheck/00install.out:

* Installing *source* package 'affxparser' ...
** libs
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/calvin_files/data/src/CDFData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk/calvin_files/data/src/CELData.o
fusion_sdk/calvin_files/data/src/CELData.cpp: In member function `bool 
   affymetrix_calvin_io::CelFileData::GetIntensities(int, int, FloatVector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:427: warning: comparison between 
   signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/CELData.cpp:431: warning: comparison between 
   signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/CELData.cpp: In member function `bool 
   affymetrix_calvin_io::CelFileData::GetStdev(int, int, FloatVector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:445: warning: comparison between 
   signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/CELData.cpp: In member function `bool 
   affymetrix_calvin_io::CelFileData::GetNumPixels(int, int, Int16Vector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:459: warning: comparison between 
   signed and unsigned integer expressions
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_sdk/calvin_files/data/src/DataGroup.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fusion_sdk/calvin_files/data/src/DataGroupHeader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk/calvin_files/data/src/DataSet.o
fusion_sdk/calvin_files/data/src/DataSet.cpp: In member function `bool 
   affymetrix_calvin_io::DataSet::MapDataPosix(unsigned int, unsigned int)':
fusion_sdk/calvin_files/data/src/DataSet.cpp:268: warning: comparison between 
   signed and unsigned integer expressions
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusion_sdk/calvin_files/data/src/DataSetHeader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_sdk/calvin_files/data/src/FileHeader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion_sdk/calvin_files/data/src/GenericData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CelFileReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o
fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp: In member function 
   `void 
   affymetrix_calvin_io::DataSetHeaderReader::ReadParameters(std::ifstream&, 
   affymetrix_calvin_io::DataSetHeader&)':
fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:161: warning: deleting
   `const void*' is undefined
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp: In member 
   function `void 
   affymetrix_calvin_io::GenericDataHeaderReader::Read(affymetrix_calvin_io::GenericDataHeader&)
   ':
fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp:63: warning: deleting
   `const void*' is undefined
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -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: In static member function `
   static affymetrix_calvin_utilities::DateTime 
   affymetrix_calvin_utilities::DateTime::Parse(std::basic_string, std::allocator >)':
fusion_sdk/calvin_files/utils/src/DateTime.cpp:160: warning: comparison between 
   signed and unsigned integer expressions
fusion_sdk/calvin_files/utils/src/DateTime.cpp:172: warning: comparison between 
   signed and unsigned integer expressions
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/StringUtils.cpp -o fusion_sdk/calvin_files/utils/src/StringUtils.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
fusion_sdk/file/BPMAPFileData.cpp: In member function `bool 
   affxbpmap::CBPMAPFileData::ReadDataSection()':
fusion_sdk/file/BPMAPFileData.cpp:369: warning: unused variable `unsigned char 
   probeIn[7]'
fusion_sdk/file/BPMAPFileData.cpp:370: warning: unused variable `char 
   probeOut[64]'
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o
g++ -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -imacros R_affx_constants.h -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/portability -D_USE_MEM_MAPPING_ -I/usr/local/include    -fpic  -g -O2 -Wall -O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o
g++ -shared -L/usr/local/lib64 -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/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/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/GCOSAdapter/GCOSCELDataAdapter.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/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/FileIO.o fusion_sdk/file/FileWriter.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o   
** R
** inst
** save image
Warning messages:
1: '\]' is an unrecognized escape in a character string 
2: unrecognized escape removed from "^([^\]]*])[ ]*(.*)[ ]*" 
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'affxparser'
     Formats: text html latex example 
  1._Dictionary                     text    html    latex
  2._Cell_coordinates_and_cell_indi text    html    latex
  9._Advanced_-_Cell-index_maps_for text    html    latex
  affxparser-package                text    html    latex
  applyCdfGroups                    text    html    latex   example
  cdfAddBaseMmCounts                text    html    latex
  cdfAddProbeOffsets                text    html    latex
  cdfGetFields                      text    html    latex
  cdfGetGroups                      text    html    latex
  cdfGtypeCelToPQ                   text    html    latex
  cdfHeaderToCelHeader              text    html    latex
  cdfMergeAlleles                   text    html    latex
  cdfMergeStrands                   text    html    latex
  cdfMergeToQuartets                text    html    latex
  cdfOrderBy                        text    html    latex
  cdfOrderColumnsBy                 text    html    latex
  compareCdfs                       text    html    latex
  convertCdf                        text    html    latex   example
  copyCel                           text    html    latex
  createCel                         text    html    latex   example
  findCdf                           text    html    latex   example
  findFiles                         text    html    latex
  invertMap                         text    html    latex   example
  isCelFile                         text    html    latex
  readBpmap                         text    html    latex   example
  readCdf                           text    html    latex
  readCdfCellIndices                text    html    latex
  readCdfGroupNames                 text    html    latex
  readCdfHeader                     text    html    latex   example
  readCdfIsPm                       text    html    latex
  readCdfNbrOfCellsPerUnitGroup     text    html    latex   example
  readCdfQc                         text    html    latex
  readCdfUnitNames                  text    html    latex   example
  readCdfUnits                      text    html    latex   example
  readCdfUnitsWriteMap              text    html    latex   example
  readCel                           text    html    latex   example
  readCelHeader                     text    html    latex   example
  readCelIntensities                text    html    latex   example
  readCelRectangle                  text    html    latex   example
  readCelUnits                      text    html    latex   example
  updateCel                         text    html    latex   example
  updateCelUnits                    text    html    latex   example
  writeCdf                          text    html    latex
  writeCelHeader                    text    html    latex
  writeTpmap                        text    html    latex   example
** building package indices ...
* DONE (affxparser)