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###
### Running command:
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### rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/mzR_2.8.1.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=mzR.buildbin-libdir --merge-multiarch mzR_2.8.1.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL mzR_2.8.1.zip && rm mzR_2.8.1.tar.gz mzR_2.8.1.zip
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100 9783k 100 9783k 0 0 24.1M 0 --:--:-- --:--:-- --:--:-- 24.2M
install for i386
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/win32/tss_pe.o ./boost/thread/win32/tss_dll.o ./boost/thread/win32/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c cramp.cpp -o cramp.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from cramp.h:33,
from cramp.cpp:49:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c ramp_base64.cpp -o ramp_base64.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c ramp.cpp -o ramp.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from ramp.cpp:44:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppRamp.cpp -o RcppRamp.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from cramp.h:33,
from RcppRamp.h:14,
from RcppRamp.cpp:1:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppRampModule.cpp -o RcppRampModule.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from cramp.h:33,
from RcppRamp.h:14,
from RcppRampModule.cpp:2:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -D_LARGEFILE_SOURCE -I./win//i386 -fgnu89-inline -O3 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from ./random_access_gzFile.h:21,
from ./ramp.h:72,
from pwiz/data/msdata/RAMPAdapter.hpp:29,
from RcppPwiz.h:11,
from RcppPwiz.cpp:1:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from ./random_access_gzFile.h:21,
from ./ramp.h:72,
from pwiz/data/msdata/RAMPAdapter.hpp:29,
from RcppPwiz.h:11,
from RcppPwizModule.cpp:2:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from RcppIdent.h:11,
from RcppIdent.cpp:1:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from RcppIdent.h:11,
from RcppIdentModule.cpp:2:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
In file included from ./boost/config.hpp:57:0,
from ./boost/system/config.hpp:13,
from ./boost/system/error_code.hpp:14,
from boost/system/src/error_code.cpp:16:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/posix_api.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/fileiter.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/regex_raw_buffer.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from ./boost/regex.hpp:28,
from boost/regex/src/cregex.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/regex_debug.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/instances.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/icu.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
In file included from ./boost/config.hpp:57:0,
from ./boost/detail/workaround.hpp:41,
from boost/regex/src/usinstances.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/regex.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/wide_posix_api.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from ./boost/regex/regex_traits.hpp:23,
from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/winstances.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from ./boost/detail/workaround.hpp:41,
from boost/regex/src/wc_regex_traits.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/c_regex_traits.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/cpp_regex_traits.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/static_mutex.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/w32_regex_traits.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
In file included from ./boost/config.hpp:57:0,
from boost/iostreams/src/file_descriptor.cpp:16:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/thread/win32/tss_pe.cpp -o boost/thread/win32/tss_pe.o
In file included from ./boost/config.hpp:57:0,
from ./boost/thread/detail/config.hpp:11,
from boost/thread/win32/tss_pe.cpp:10:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/thread/win32/tss_dll.cpp -o boost/thread/win32/tss_dll.o
In file included from ./boost/config.hpp:57:0,
from ./boost/thread/detail/config.hpp:11,
from boost/thread/win32/tss_dll.cpp:6:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/thread/win32/thread.cpp -o boost/thread/win32/thread.o
In file included from ./boost/config.hpp:57:0,
from ./boost/thread/detail/platform.hpp:14,
from ./boost/thread/thread_only.hpp:12,
from boost/thread/win32/thread.cpp:17:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/operations.hpp:18,
from boost/filesystem/src/operations.cpp:44:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
In file included from ./boost/config.hpp:57:0,
from boost/filesystem/src/path.cpp:12:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/path_traits.cpp -o boost/filesystem/src/path_traits.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/path_traits.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/windows_file_codecvt.cpp -o boost/filesystem/src/windows_file_codecvt.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/windows_file_codecvt.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/codecvt_error_category.cpp -o boost/filesystem/src/codecvt_error_category.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/codecvt_error_category.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/utf8_codecvt_facet.cpp:15:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/chrono/src/chrono.cpp -o boost/chrono/src/chrono.o
In file included from ./boost/config.hpp:57:0,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/duration.hpp:33,
from ./boost/chrono/chrono.hpp:11,
from ./boost/chrono/detail/inlined/chrono.hpp:13,
from boost/chrono/src/chrono.cpp:14:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/chrono/src/process_cpu_clocks.cpp -o boost/chrono/src/process_cpu_clocks.o
In file included from ./boost/config.hpp:57:0,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
from boost/chrono/src/process_cpu_clocks.cpp:17:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/chrono/src/thread_clock.cpp -o boost/chrono/src/thread_clock.o
In file included from ./boost/config.hpp:57:0,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/detail/inlined/thread_clock.hpp:14,
from boost/chrono/src/thread_clock.cpp:18:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/data/common/Index.hpp:29,
from pwiz/data/common/MemoryIndex.hpp:26,
from pwiz/data/common/MemoryIndex.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/common/CVTranslator.hpp:31,
from pwiz/data/common/CVTranslator.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/common/cv.cpp:34:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/common/ParamTypes.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/data/common/Index.hpp:29,
from pwiz/data/common/BinaryIndexStream.hpp:26,
from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/common/diff_std.hpp:33,
from pwiz/data/common/diff_std.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/common/Unimod.hpp:28,
from pwiz/data/common/Unimod.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/ChromatogramListBase.hpp:28,
from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/examples.hpp:29,
from pwiz/data/msdata/examples.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzML.hpp:29,
from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MSn.hpp:26,
from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Reader.hpp:28,
from pwiz/data/msdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MGF.hpp:27,
from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Diff.hpp:29,
from pwiz/data/msdata/Diff.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSData.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/References.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/IO.hpp:29,
from pwiz/data/msdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumInfo.hpp:29,
from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from ./random_access_gzFile.h:21,
from ./ramp.h:72,
from pwiz/data/msdata/RAMPAdapter.hpp:29,
from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/LegacyAdapter.hpp:30,
from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumIterator.hpp:29,
from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:29,
from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListCache.hpp:27,
from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Index_mzML.hpp:28,
from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/IdentData.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Reader.hpp:28,
from pwiz/data/identdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_protXML.hpp:29,
from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_pepXML.hpp:27,
from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_mzid.hpp:28,
from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IO.hpp:27,
from pwiz/data/identdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/References.hpp:29,
from pwiz/data/identdata/References.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/MascotReader.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Modification.hpp:30,
from pwiz/data/proteome/Modification.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/proteome/Digestion.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Peptide.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/AminoAcid.hpp:29,
from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/minimxml/XMLWriter.hpp:29,
from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/minimxml/SAXParser.hpp:31,
from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/utility/chemistry/ChemistryData.hpp:29,
from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/Base64.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/IterationListener.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/TabReader.hpp:29,
from pwiz/utility/misc/MSIHandler.hpp:28,
from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/config.hpp:57:0,
from ./boost/algorithm/string/std_containers_traits.hpp:18,
from ./boost/algorithm/string.hpp:18,
from pwiz/utility/misc/String.hpp:29,
from pwiz/utility/misc/Filesystem.hpp:29,
from pwiz/utility/misc/Filesystem.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
pwiz/utility/misc/Filesystem.cpp:38:0: warning: "_WIN32_WINNT" redefined
#define _WIN32_WINNT 0x0400
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/crtdefs.h:10:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/wchar.h:9,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/cwchar:44,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/postypes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/char_traits.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:40,
from pwiz/utility/misc/String.hpp:27,
from pwiz/utility/misc/Filesystem.hpp:29,
from pwiz/utility/misc/Filesystem.cpp:26:
C:/Rtools/mingw_32/i686-w64-mingw32/include/_mingw.h:229:0: note: this is the location of the previous definition
#define _WIN32_WINNT 0x502
^
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/TabReader.hpp:29,
from pwiz/utility/misc/TabReader.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/config.hpp:57:0,
from ./boost/static_assert.hpp:17,
from pwiz/utility/misc/endian.hpp:28,
from pwiz/utility/misc/SHA1.cpp:10:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/config.hpp:57:0,
from ./boost/static_assert.hpp:17,
from pwiz/utility/misc/endian.hpp:28,
from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/SHA1Calculator.hpp:28,
from pwiz/utility/misc/sha1calc.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c random_access_gzFile.cpp -o random_access_gzFile.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from random_access_gzFile.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c rampR.cpp -o rampR.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from rampR.cpp:15:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -D_LARGEFILE_SOURCE -I./win//i386 -fgnu89-inline -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/win32/tss_pe.o ./boost/thread/win32/tss_dll.o ./boost/thread/win32/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o -lws2_32 -lnetcdf -lz -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/win32/tss_pe.o ./boost/thread/win32/tss_dll.o ./boost/thread/win32/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c cramp.cpp -o cramp.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from cramp.h:33,
from cramp.cpp:49:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c ramp_base64.cpp -o ramp_base64.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c ramp.cpp -o ramp.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from ramp.cpp:44:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppRamp.cpp -o RcppRamp.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from cramp.h:33,
from RcppRamp.h:14,
from RcppRamp.cpp:1:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppRampModule.cpp -o RcppRampModule.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from cramp.h:33,
from RcppRamp.h:14,
from RcppRampModule.cpp:2:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -D_LARGEFILE_SOURCE -I./win//x64 -fgnu89-inline -O2 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppPwiz.cpp -o RcppPwiz.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from ./random_access_gzFile.h:21,
from ./ramp.h:72,
from pwiz/data/msdata/RAMPAdapter.hpp:29,
from RcppPwiz.h:11,
from RcppPwiz.cpp:1:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from ./random_access_gzFile.h:21,
from ./ramp.h:72,
from pwiz/data/msdata/RAMPAdapter.hpp:29,
from RcppPwiz.h:11,
from RcppPwizModule.cpp:2:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from RcppIdent.h:11,
from RcppIdent.cpp:1:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from RcppIdent.h:11,
from RcppIdentModule.cpp:2:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
In file included from ./boost/config.hpp:57:0,
from ./boost/system/config.hpp:13,
from ./boost/system/error_code.hpp:14,
from boost/system/src/error_code.cpp:16:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/posix_api.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/fileiter.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/regex_raw_buffer.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from ./boost/regex.hpp:28,
from boost/regex/src/cregex.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/regex_debug.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/instances.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/icu.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
In file included from ./boost/config.hpp:57:0,
from ./boost/detail/workaround.hpp:41,
from boost/regex/src/usinstances.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/regex.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/wide_posix_api.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from ./boost/regex/regex_traits.hpp:23,
from boost/regex/src/regex_traits_defaults.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/winstances.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from ./boost/detail/workaround.hpp:41,
from boost/regex/src/wc_regex_traits.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/c_regex_traits.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/cpp_regex_traits.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
In file included from ./boost/config.hpp:57:0,
from boost/regex/src/static_mutex.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
In file included from ./boost/config.hpp:57:0,
from ./boost/regex/config.hpp:43,
from boost/regex/src/w32_regex_traits.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
In file included from ./boost/config.hpp:57:0,
from boost/iostreams/src/file_descriptor.cpp:16:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/thread/win32/tss_pe.cpp -o boost/thread/win32/tss_pe.o
In file included from ./boost/config.hpp:57:0,
from ./boost/thread/detail/config.hpp:11,
from boost/thread/win32/tss_pe.cpp:10:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/thread/win32/tss_dll.cpp -o boost/thread/win32/tss_dll.o
In file included from ./boost/config.hpp:57:0,
from ./boost/thread/detail/config.hpp:11,
from boost/thread/win32/tss_dll.cpp:6:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/thread/win32/thread.cpp -o boost/thread/win32/thread.o
In file included from ./boost/config.hpp:57:0,
from ./boost/thread/detail/platform.hpp:14,
from ./boost/thread/thread_only.hpp:12,
from boost/thread/win32/thread.cpp:17:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/operations.hpp:18,
from boost/filesystem/src/operations.cpp:44:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
In file included from ./boost/config.hpp:57:0,
from boost/filesystem/src/path.cpp:12:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/path_traits.cpp -o boost/filesystem/src/path_traits.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/path_traits.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/windows_file_codecvt.cpp -o boost/filesystem/src/windows_file_codecvt.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/windows_file_codecvt.cpp:20:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/codecvt_error_category.cpp -o boost/filesystem/src/codecvt_error_category.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/codecvt_error_category.cpp:22:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
In file included from ./boost/config.hpp:57:0,
from ./boost/filesystem/config.hpp:28,
from boost/filesystem/src/utf8_codecvt_facet.cpp:15:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/chrono/src/chrono.cpp -o boost/chrono/src/chrono.o
In file included from ./boost/config.hpp:57:0,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/duration.hpp:33,
from ./boost/chrono/chrono.hpp:11,
from ./boost/chrono/detail/inlined/chrono.hpp:13,
from boost/chrono/src/chrono.cpp:14:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/chrono/src/process_cpu_clocks.cpp -o boost/chrono/src/process_cpu_clocks.o
In file included from ./boost/config.hpp:57:0,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
from boost/chrono/src/process_cpu_clocks.cpp:17:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c boost/chrono/src/thread_clock.cpp -o boost/chrono/src/thread_clock.o
In file included from ./boost/config.hpp:57:0,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/detail/inlined/thread_clock.hpp:14,
from boost/chrono/src/thread_clock.cpp:18:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/data/common/Index.hpp:29,
from pwiz/data/common/MemoryIndex.hpp:26,
from pwiz/data/common/MemoryIndex.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/common/CVTranslator.hpp:31,
from pwiz/data/common/CVTranslator.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/common/cv.cpp:34:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/common/ParamTypes.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/data/common/Index.hpp:29,
from pwiz/data/common/BinaryIndexStream.hpp:26,
from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/common/diff_std.hpp:33,
from pwiz/data/common/diff_std.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/common/Unimod.hpp:28,
from pwiz/data/common/Unimod.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/ChromatogramListBase.hpp:28,
from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/examples.hpp:29,
from pwiz/data/msdata/examples.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzML.hpp:29,
from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MSn.hpp:26,
from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Reader.hpp:28,
from pwiz/data/msdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MGF.hpp:27,
from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Diff.hpp:29,
from pwiz/data/msdata/Diff.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSData.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/References.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/IO.hpp:29,
from pwiz/data/msdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumInfo.hpp:29,
from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ././pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from ./random_access_gzFile.h:21,
from ./ramp.h:72,
from pwiz/data/msdata/RAMPAdapter.hpp:29,
from pwiz/data/msdata/RAMPAdapter.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/LegacyAdapter.hpp:30,
from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumIterator.hpp:29,
from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:29,
from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListCache.hpp:27,
from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Index_mzML.hpp:28,
from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/IdentData.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Reader.hpp:28,
from pwiz/data/identdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_protXML.hpp:29,
from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_pepXML.hpp:27,
from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_mzid.hpp:28,
from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IO.hpp:27,
from pwiz/data/identdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/References.hpp:29,
from pwiz/data/identdata/References.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/MascotReader.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Modification.hpp:30,
from pwiz/data/proteome/Modification.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/proteome/Digestion.cpp:27:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Peptide.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/AminoAcid.hpp:29,
from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/minimxml/XMLWriter.hpp:29,
from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/minimxml/SAXParser.hpp:31,
from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/utility/chemistry/ChemistryData.hpp:29,
from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/Base64.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/config.hpp:57:0,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/IterationListener.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/TabReader.hpp:29,
from pwiz/utility/misc/MSIHandler.hpp:28,
from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/config.hpp:57:0,
from ./boost/algorithm/string/std_containers_traits.hpp:18,
from ./boost/algorithm/string.hpp:18,
from pwiz/utility/misc/String.hpp:29,
from pwiz/utility/misc/Filesystem.hpp:29,
from pwiz/utility/misc/Filesystem.cpp:26:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
pwiz/utility/misc/Filesystem.cpp:38:0: warning: "_WIN32_WINNT" redefined
#define _WIN32_WINNT 0x0400
^
In file included from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/crtdefs.h:10:0,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/wchar.h:9,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/cwchar:44,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/postypes.h:40,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/bits/char_traits.h:40,
from C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/string:40,
from pwiz/utility/misc/String.hpp:27,
from pwiz/utility/misc/Filesystem.hpp:29,
from pwiz/utility/misc/Filesystem.cpp:26:
C:/Rtools/mingw_64/x86_64-w64-mingw32/include/_mingw.h:229:0: note: this is the location of the previous definition
#define _WIN32_WINNT 0x502
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/TabReader.hpp:29,
from pwiz/utility/misc/TabReader.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/config.hpp:57:0,
from ./boost/static_assert.hpp:17,
from pwiz/utility/misc/endian.hpp:28,
from pwiz/utility/misc/SHA1.cpp:10:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/config.hpp:57:0,
from ./boost/static_assert.hpp:17,
from pwiz/utility/misc/endian.hpp:28,
from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/config.hpp:57:0,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/SHA1Calculator.hpp:28,
from pwiz/utility/misc/sha1calc.cpp:24:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c random_access_gzFile.cpp -o random_access_gzFile.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from random_access_gzFile.cpp:21:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -c rampR.cpp -o rampR.o
In file included from ./boost/config.hpp:57:0,
from ./boost/iostreams/positioning.hpp:18,
from ./pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from random_access_gzFile.h:21,
from ramp.h:72,
from rampR.cpp:15:
./boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
^
<command-line>:0:0: note: this is the location of the previous definition
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -D_LARGEFILE_SOURCE -I./win//x64 -fgnu89-inline -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/win32/tss_pe.o ./boost/thread/win32/tss_dll.o ./boost/thread/win32/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/chrono/src/chrono.o ./boost/chrono/src/process_cpu_clocks.o ./boost/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o -lws2_32 -lnetcdf -lz -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_2.8.1.zip
* DONE (mzR)
* installing to library 'C:/Users/biocbuild/bbs-3.4-bioc/R/library'
package 'mzR' successfully unpacked and MD5 sums checked
