Back to the "Multiple platform build/check report"
| Package 3/187 | OS | Arch | BUILD | CHECK | BUILD BIN |
affxparser1.5.2James Bullard | Linux (SUSE 9.2) | x86_64 | OK | [ WARNINGS ] | |
| Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
| Solaris 2.9 | sparc | OK | WARNINGS | ||
| Linux (SUSE 10.0) | x86_64 | OK | WARNINGS | ||
| Windows Server 2003 | x86_64 | OK | WARNINGS | OK |
| Package: affxparser |
| Version: 1.5.2 |
| Command: /loc/biocbuild/1.9d/R/bin/R CMD check affxparser_1.5.2.tar.gz |
| RetCode: 0 |
| Time: 127.6 seconds |
| Status: WARNINGS |
| CheckDir: affxparser.Rcheck |
| Warnings: 1 |
* checking for working latex ... OK * using log directory '/loc/biocbuild/1.9d/Rpacks/affxparser.Rcheck' * using R version 2.4.0 Under development (unstable) (2006-06-04 r38279) * checking for file 'affxparser/DESCRIPTION' ... OK * this is package 'affxparser' version '1.5.2' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'affxparser' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for non-ASCII characters ... 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 ... WARNING Undocumented code objects: readBpmap readBpmapHeader readBpmapSeqInfo tpmap2bpmap writeTpmap All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * 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 WARNING: There was 1 warning, see /loc/biocbuild/1.9d/Rpacks/affxparser.Rcheck/00check.log for details
affxparser.Rcheck/00install.out:
* Installing *source* package 'affxparser' ...
** libs
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/BitFlag.cpp -o fusion_sdk/calvin_files/data/src/BitFlag.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:26,
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:26,
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/CELData.cpp: In member function `bool
affymetrix_calvin_io::CelFileData::GetIntensities(int, int, FloatVector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:427: warning: comparison between
signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/CELData.cpp:431: warning: comparison between
signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/CELData.cpp: In member function `bool
affymetrix_calvin_io::CelFileData::GetStdev(int, int, FloatVector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:445: warning: comparison between
signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/CELData.cpp: In member function `bool
affymetrix_calvin_io::CelFileData::GetNumPixels(int, int, Int16Vector&)':
fusion_sdk/calvin_files/data/src/CELData.cpp:459: warning: comparison between
signed and unsigned integer expressions
fusion_sdk/calvin_files/utils/src/Coords.h: At top level:
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: 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:35: 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:43: warning: when initialized
here
fusion_sdk/calvin_files/data/src/DataGroupHeader.h: At top level:
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
In file included from fusion_sdk/calvin_files/data/src/DataSet.h:26,
from fusion_sdk/calvin_files/data/src/DataSet.cpp:21:
fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/DataSet.cpp: In member function `bool
affymetrix_calvin_io::DataSet::MapDataPosix(unsigned int, unsigned int)':
fusion_sdk/calvin_files/data/src/DataSet.cpp:270: warning: comparison between
signed and unsigned integer expressions
fusion_sdk/calvin_files/data/src/DataGroupHeader.h: At top level:
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
In file included from fusion_sdk/calvin_files/data/src/DataSetHeader.cpp:21:
fusion_sdk/calvin_files/data/src/DataSetHeader.h:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: 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/parsers/src/DataGroupReader.h: At top level:
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
In file included from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:21:
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: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.h: In constructor
`
affymetrix_calvin_parameter::ParameterNameValueType::ParameterNameValueType(const
std::wstring&, const void*, int, 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:130: 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:138: 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:399: 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:444: warning: enumeration
value `UnknownType' not handled in switch
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: 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 `u_int32_t 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 `u_int32_t 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 `u_int32_t 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 `u_int32_t z'
fusion_sdk/calvin_files/data/src/DataGroupHeader.h: At top level:
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: 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/DataGroupHeader.h: At top level:
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/FileInput.cpp -o fusion_sdk/calvin_files/parsers/src/FileInput.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o
fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp: In member
function `void
affymetrix_calvin_io::GenericDataHeaderReader::Read(affymetrix_calvin_io::GenericDataHeader&)
':
fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp:63: warning: deleting
`const void*' is undefined
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/DateTime.cpp -o fusion_sdk/calvin_files/utils/src/DateTime.o
fusion_sdk/calvin_files/utils/src/DateTime.cpp: In static member function `
static affymetrix_calvin_utilities::DateTime
affymetrix_calvin_utilities::DateTime::Parse(std::basic_string, std::allocator >)':
fusion_sdk/calvin_files/utils/src/DateTime.cpp:160: warning: comparison between
signed and unsigned integer expressions
fusion_sdk/calvin_files/utils/src/DateTime.cpp:172: warning: comparison between
signed and unsigned integer expressions
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/FileUtils.cpp -o fusion_sdk/calvin_files/utils/src/FileUtils.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
fusion_sdk/calvin_files/utils/src/StringUtils.cpp:27: warning: ignoring #pragma
warning
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/calvin_files/utils/src/checksum.cpp -o fusion_sdk/calvin_files/utils/src/checksum.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
fusion_sdk/file/BPMAPFileData.cpp: In member function `bool
affxbpmap::CBPMAPFileData::ReadDataSection()':
fusion_sdk/file/BPMAPFileData.cpp:369: warning: unused variable `unsigned char
probeIn[7]'
fusion_sdk/file/BPMAPFileData.cpp:370: warning: unused variable `char
probeOut[64]'
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/file/CDFFileData.cpp -o fusion_sdk/file/CDFFileData.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/file/CELFileData.cpp -o fusion_sdk/file/CELFileData.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -D_USE_MEM_MAPPING_ -I/usr/local/include -fpic -g -O2 -Wall -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
In file included from R_affx_cel_parser.cpp:1:
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: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/BitFlag.h:35: warning: `u_int8_t
affymetrix_calvin_io::DEFAULT_DATA_SET_HDR_FLAG' defined but not used
g++ -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/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/gcast/src -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
R_affx_bpmap_parser.cpp: In function `SEXPREC*
R_affx_bpmap_seqinfo_item(affxbpmap::CGDACSequenceItem&, int)':
R_affx_bpmap_parser.cpp:78: warning: unused variable `SEXPREC*tmp'
R_affx_bpmap_parser.cpp: In function `SEXPREC* R_affx_get_bpmap_file(SEXPREC*,
SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*,
SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
R_affx_bpmap_parser.cpp:314: warning: unused variable `SEXPREC*seqInfo'
R_affx_bpmap_parser.cpp:314: warning: unused variable `SEXPREC*seqInfoNames'
R_affx_bpmap_parser.cpp:314: warning: unused variable `
SEXPREC*seqInfoParameters'
R_affx_bpmap_parser.cpp:315: warning: unused variable `
SEXPREC*seqInfoParameterNames'
g++ -shared -L/usr/local/lib64 -o affxparser.so fusion_sdk/calvin_files/data/src/BitFlag.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/DataGroup.o fusion_sdk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o
** R
** inst
** save image
** 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
affxparserInfo text html latex example
applyCdfGroups text html latex example
cdfAddBaseMmCounts text html latex
cdfAddProbeOffsets text html latex
cdfGetFields text html latex
cdfGetGroups text html latex
cdfGtypeCelToPQ text html latex
cdfMergeAlleles text html latex
cdfMergeStrands text html latex
cdfMergeToQuartets text html latex
cdfOrderBy text html latex
cdfOrderColumnsBy text html latex
findCdf text html latex example
findFiles text html latex
invertMap 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)