affxparser 1.10.2
Kasper Daniel Hansen
| Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/affxparser | | Last Changed Rev: 29109 / Revision: 30807 | | Last Changed Date: 2007-12-08 11:33:04 -0800 (Sat, 08 Dec 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ OK ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/affxparser.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'affxparser/DESCRIPTION' ... OK
* this is package 'affxparser' version '1.10.2'
* checking package name space information ... OK
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating affxparser-Ex.R ... OK
* checking examples ... OK
* creating affxparser-manual.tex ... OK
* checking affxparser-manual.tex ... OK
* Installing *source* package 'affxparser' ...
** libs
rm -f fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/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
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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(int32_t, int32_t, 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(int32_t, int32_t, 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(int32_t, int32_t, Int16Vector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:459: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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(u_int32_t, u_int32_t)':
fusion_sdk/calvin_files/data/src/DataSet.cpp:268: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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
fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp: In member function 'virtual int affymetrix_fusion_io::CalvinCELDataAdapter::GetCellMargin()':
fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:263: warning: control reaches end of non-void function
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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::wstring)':
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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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 'probeIn'
fusion_sdk/file/BPMAPFileData.cpp:370: warning: unused variable 'probeOut'
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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
R_affx_cdf_parser.cpp: In function 'SEXPREC* R_affx_get_cdf_file_qc(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
R_affx_cdf_parser.cpp:169: warning: value computed is not used
R_affx_cdf_parser.cpp: In function 'SEXPREC* R_affx_get_cdf_file(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
R_affx_cdf_parser.cpp:619: warning: value computed is not used
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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 -Ifusion_sdk -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 -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** inst
** 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
cdfAddPlasqTypes 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
compareCels text html latex
convertCdf text html latex example
convertCel 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
readCcg text html latex
readCcgHeader text html latex
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
writeCdfHeader text html latex
writeCdfQcUnits text html latex
writeCdfUnits text html latex
writeCelHeader text html latex
writeTpmap text html latex example
** building package indices ...
* DONE (affxparser)