CHECK report for affxparser on gladstone

affxparser

1.4.1

James Bullard

Linux (SUSE 9.2)

x86_64

Linux (SUSE 9.2)

i686

Solaris 2.9

sparc

Linux (SUSE 10.0)

x86_64

[ OK ]

Windows Server 2003

x86_64

* checking for working latex ... OK * using log directory '/home/biocbuild/1.8d/Rpacks/affxparser.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'affxparser/DESCRIPTION' ... OK * this is package 'affxparser' version '1.4.1' * 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 ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * 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 * creating affxparser-Ex.R ... OK * checking examples ... OK * creating affxparser-manual.tex ... OK * checking affxparser-manual.tex ... OK

* Installing *source* package 'affxparser' ... ** libs g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/BARFileData.cpp -o fusion_sdk/file/BARFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -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:370: warning: unused variable 'probeIn' fusion_sdk/file/BPMAPFileData.cpp:371: warning: unused variable 'probeOut' g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/CHPFileData.cpp -o fusion_sdk/file/CHPFileData.o fusion_sdk/file/CHPFileData.cpp: In member function 'affxchp::BackgroundZoneType affxchp::CCHPFileHeader::GetBackgroundZone(int, int)': fusion_sdk/file/CHPFileData.cpp:176: warning: 'zone$centerx' may be used uninitialized in this function fusion_sdk/file/CHPFileData.cpp:176: warning: 'zone$centery' may be used uninitialized in this function fusion_sdk/file/CHPFileData.cpp:176: warning: 'zone$background' may be used uninitialized in this function g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/EXPFileData.cpp -o fusion_sdk/file/EXPFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/GRCFileData.cpp -o fusion_sdk/file/GRCFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/MSKFileData.cpp -o fusion_sdk/file/MSKFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/file/PSIFileData.cpp -o fusion_sdk/file/PSIFileData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/gcast/src/GridControlData.cpp -o fusion_sdk/gcast/src/GridControlData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/array/src/ArrayAttributes.cpp -o fusion_sdk/calvin_files/array/src/ArrayAttributes.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/array/src/ArrayAudit.cpp -o fusion_sdk/calvin_files/array/src/ArrayAudit.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/array/src/ArrayData.cpp -o fusion_sdk/calvin_files/array/src/ArrayData.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/calvin_files/data/src/CDFData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/data/src/CDFData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.h:27, from fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk/calvin_files/data/src/CELData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/data/src/CELData.h:27, from fusion_sdk/calvin_files/data/src/CELData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment 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 fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.h:24, from fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CHPData.cpp -o fusion_sdk/calvin_files/data/src/CHPData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CHPData.h:26, from fusion_sdk/calvin_files/data/src/CHPData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/DATData.cpp -o fusion_sdk/calvin_files/data/src/DATData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/DATData.h:27, from fusion_sdk/calvin_files/data/src/DATData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/DATData.cpp:494:2: warning: no newline at end of file fusion_sdk/calvin_files/data/src/DATData.cpp: In member function 'bool affymetrix_calvin_io::DATData::GetPixels(u_int16_t*, u_int32_t, u_int32_t, u_int32_t, u_int32_t)': fusion_sdk/calvin_files/data/src/DATData.cpp:378: warning: comparison between signed and unsigned integer expressions fusion_sdk/calvin_files/data/src/DATData.cpp:381: warning: comparison between signed and unsigned integer expressions fusion_sdk/calvin_files/data/src/DATData.cpp:384: warning: comparison between signed and unsigned integer expressions fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_sdk/calvin_files/data/src/DataGroup.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/DataGroup.h:28, from fusion_sdk/calvin_files/data/src/DataGroup.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/DataGroup.h: In constructor 'affymetrix_calvin_io::DataGroup::DataGroup(const std::string&, const affymetrix_calvin_io::DataGroupHeader&, void*, bool)': fusion_sdk/calvin_files/data/src/DataGroup.h:101: warning: 'affymetrix_calvin_io::DataGroup::fileStream' will be initialized after fusion_sdk/calvin_files/data/src/DataGroup.h:97: warning: 'bool affymetrix_calvin_io::DataGroup::useMemoryMapping' fusion_sdk/calvin_files/data/src/DataGroup.cpp:33: warning: when initialized here fusion_sdk/calvin_files/data/src/DataGroup.h: In constructor 'affymetrix_calvin_io::DataGroup::DataGroup(const std::string&, const affymetrix_calvin_io::DataGroupHeader&, std::ifstream&, bool)': fusion_sdk/calvin_files/data/src/DataGroup.h:101: warning: 'affymetrix_calvin_io::DataGroup::fileStream' will be initialized after fusion_sdk/calvin_files/data/src/DataGroup.h:97: warning: 'bool affymetrix_calvin_io::DataGroup::useMemoryMapping' fusion_sdk/calvin_files/data/src/DataGroup.cpp:41: warning: when initialized here fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fusion_sdk/calvin_files/data/src/DataGroupHeader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk/calvin_files/data/src/DataSet.o In file included from fusion_sdk/calvin_files/data/src/DataSet.h:29, from fusion_sdk/calvin_files/data/src/DataSet.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment 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 fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusion_sdk/calvin_files/data/src/DataSetHeader.o In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_sdk/calvin_files/data/src/FileHeader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/FileHeader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion_sdk/calvin_files/data/src/GenericData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/data/src/GenericData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:23: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp: In member function 'char affymetrix_fusion_io::FusionCDFProbeInformation::GetPBase() const': fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:420: warning: converting to non-pointer type 'char' from NULL fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp: In member function 'char affymetrix_fusion_io::FusionCDFProbeInformation::GetTBase() const': fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp:433: warning: converting to non-pointer type 'char' from NULL fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/fusion/src/FusionCELData.h:36: warning: 'class affymetrix_fusion_io::FusionCELData' has virtual functions but non-virtual destructor fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:31, from fusion_sdk/calvin_files/fusion/src/FusionCHPData.cpp:22: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/FusionGrcFileReader.cpp -o fusion_sdk/calvin_files/fusion/src/FusionGrcFileReader.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:28, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:32, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:396:2: warning: no newline at end of file fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:28, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.h:27, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp:22: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CHPData.h:26, from fusion_sdk/calvin_files/fusion/src/FusionCHPDataAdapterInterface.h:32, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:26, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:29, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.h:30, from fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h: In constructor 'affymetrix_calvin_parameter::ParameterNameValueType::ParameterNameValueType(const std::wstring&, const void*, int32_t, const std::wstring&)': fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h:345: warning: 'affymetrix_calvin_parameter::ParameterNameValueType::Value' will be initialized after fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h:342: warning: 'std::wstring affymetrix_calvin_parameter::ParameterNameValueType::Type' fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:128: warning: when initialized here fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h: In constructor 'affymetrix_calvin_parameter::ParameterNameValueType::ParameterNameValueType(const std::wstring&, const affymetrix_calvin_parameter::MIMEValue&, const std::wstring&)': fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h:345: warning: 'affymetrix_calvin_parameter::ParameterNameValueType::Value' will be initialized after fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h:342: warning: 'std::wstring affymetrix_calvin_parameter::ParameterNameValueType::Type' fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:136: warning: when initialized here fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp: In member function 'std::wstring affymetrix_calvin_parameter::ParameterNameValueType::ToString() const': fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:363: warning: enumeration value 'UnknownType' not handled in switch fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp: In member function 'std::wstring affymetrix_calvin_parameter::ParameterNameValueDefaultRequiredType::DefaultToString()': fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp:408: warning: enumeration value 'UnknownType' not handled in switch g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/AuditFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/AuditFileReader.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.h:28, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:31, from fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp:22: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CHPData.h:26, from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:28, from fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/CHPFileReader.h:29, from fusion_sdk/calvin_files/parsers/src/CHPFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/CelFileReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/data/src/CELData.h:27, from fusion_sdk/calvin_files/parsers/src/CelFileReader.h:30, from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:31, from fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp:22: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/DATFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/DATFileReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/DATData.h:27, from fusion_sdk/calvin_files/parsers/src/DATFileReader.h:28, from fusion_sdk/calvin_files/parsers/src/DATFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/DATFileReader.h:29, from fusion_sdk/calvin_files/parsers/src/DATFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.h:30, from fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp: In member function 'void affymetrix_calvin_io::DataGroupHeaderReader::ReadNextDataGroupFilePos(std::ifstream&, affymetrix_calvin_io::DataGroupHeader&)': fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:122: warning: unused variable 'z' fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp: In member function 'void affymetrix_calvin_io::DataGroupHeaderReader::ReadFirstDataSetFilePos(std::ifstream&, affymetrix_calvin_io::DataGroupHeader&)': fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:133: warning: unused variable 'z' fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp: In member function 'u_int32_t affymetrix_calvin_io::DataGroupHeaderReader::ReadDataSetCnt(std::ifstream&, affymetrix_calvin_io::DataGroupHeader&)': fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:144: warning: unused variable 'z' fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp: In member function 'void affymetrix_calvin_io::DataGroupHeaderReader::ReadDataGroupName(std::ifstream&, affymetrix_calvin_io::DataGroupHeader&)': fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp:155: warning: unused variable 'z' fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:27, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.h:30, from fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment 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:160: warning: deleting 'const void*' is undefined fusion_sdk/calvin_files/data/src/BitFlag.h: At global scope: fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp -o fusion_sdk/calvin_files/parsers/src/DataSetReader.o In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/parsers/src/FileHeaderReader.h:30, from fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -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/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:30, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:31, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp:21: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/GridControlFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/GridControlFileReader.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:30, from fusion_sdk/calvin_files/parsers/src/GridControlFileReader.cpp:23: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment In file included from fusion_sdk/calvin_files/parsers/src/DataSetReader.h:28, from fusion_sdk/calvin_files/parsers/src/DataGroupReader.h:28, from fusion_sdk/calvin_files/parsers/src/GenericFileReader.h:31, from fusion_sdk/calvin_files/parsers/src/GridControlFileReader.cpp:23: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/parsers/src/TextFileReader.cpp -o fusion_sdk/calvin_files/parsers/src/TextFileReader.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -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/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/utils/src/StringUtils.cpp -o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.cpp:27: warning: ignoring #pragma warning g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/GenericData.h:30, from fusion_sdk/calvin_files/fusion/src/FusionCELDataAdapterInterface.h:28, from fusion_sdk/calvin_files/fusion/src/FusionCELData.h:27, from R_affx_cel_parser.cpp:1: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/fusion/src/FusionCELData.h:36: warning: 'class affymetrix_fusion_io::FusionCELData' has virtual functions but non-virtual destructor fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:28, from R_affx_cdf_parser.cpp:1: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk/gcast/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O1 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o In file included from fusion_sdk/calvin_files/data/src/DataGroupHeader.h:26, from fusion_sdk/calvin_files/data/src/FileHeader.h:32, from fusion_sdk/calvin_files/data/src/CDFData.h:27, from fusion_sdk/calvin_files/fusion/src/FusionCDFData.h:28, from R_affx_cdf_extras.cpp:1: fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:2: warning: "/*" within comment fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: 'affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used g++ -shared -L/usr/local/lib64 -o affxparser.so fusion_sdk/file/BARFileData.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/EXPFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/GRCFileData.o fusion_sdk/file/MSKFileData.o fusion_sdk/file/PSIFileData.o fusion_sdk/gcast/src/GridControlData.o fusion_sdk/calvin_files/array/src/ArrayAttributes.o fusion_sdk/calvin_files/array/src/ArrayAudit.o fusion_sdk/calvin_files/array/src/ArrayData.o fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_files/data/src/DATData.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/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionGrcFileReader.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResults.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/AuditFileReader.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/DATFileReader.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/parsers/src/GridControlFileReader.o fusion_sdk/calvin_files/parsers/src/TextFileReader.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 R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o ** R ** inst ** save image ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'affxparser' Formats: text html latex example affxparser-package text html latex affxparserInfo text html latex example applyCdfGroups text html latex example cdfAddBaseMmCounts text html latex cdfAddProbeOffsets text html latex cdfGetFields text html latex cdfGtypeCelToPQ text html latex cdfMergeStrands text html latex cdfMergeToQuartets text html latex cellindexmaps text html latex cellxy text html latex findCdf text html latex example findFiles text html latex invertMap text html latex example read.affybatch2 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 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 ** building package indices ... * DONE (affxparser)

Package 3/172	OS	Arch	BUILD	CHECK	BUILD BIN
affxparser 1.4.1 James Bullard	Linux (SUSE 9.2)	x86_64	OK	OK
	Linux (SUSE 9.2)	i686	OK	OK
	Solaris 2.9	sparc	OK	OK
	Linux (SUSE 10.0)	x86_64	OK	[ OK ]
	Windows Server 2003	x86_64	OK	OK	OK

affxparser

1.4.1

Command output