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Package 3/172OSArchBUILDCHECKBUILD 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 
Package: affxparser
Version: 1.4.1
Command: /loc/biocbuild/1.8d/R/bin/R CMD check affxparser_1.4.1.tar.gz
RetCode: 0
Time: 204.6 seconds
Status: OK
CheckDir: affxparser.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/extra/loc/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

affxparser.Rcheck/00install.out:

* Installing *source* package 'affxparser' ...
** libs
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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 `unsigned char 
   probeIn[7]'
fusion_sdk/file/BPMAPFileData.cpp:371: warning: unused variable `char 
   probeOut[64]'
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/data/src/DATData.cpp: In member function `bool 
   affymetrix_calvin_io::DATData::GetPixels(u_int16_t*, unsigned int, unsigned 
   int, unsigned int, unsigned int)':
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/DATData.cpp:494:2: warning: no newline at end of file
fusion_sdk/calvin_files/data/src/DATData.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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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:268: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: warning: "/*" within comment
fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp:396:1: warning: no newline at end of file
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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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*, 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp: In function `void 
   InitializeRandomNumberGenerator()':
fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp:50: warning: cast from 
   pointer to integer of different size
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/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::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/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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/loc/biocbuild/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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/1.8d/R/include -I/loc/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:135:9: 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++ -shared -L/usr/local/lib -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)