CHECK report for affxparser on gopher5

* 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

* 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)

Package 4/208	OS	Arch	BUILD	CHECK	BUILD 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

affxparser

1.7.2

Command output