BioC 3.4: CHECK report for mzR on tokay1

Package: mzR

Version: 2.8.1

Command: rm -rf mzR.buildbin-libdir mzR.Rcheck && mkdir mzR.buildbin-libdir mzR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_2.8.1.tar.gz >mzR.Rcheck\00install.out 2>&1 && cp mzR.Rcheck\00install.out mzR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_2.8.1.tar.gz

StartedAt: 2017-04-14 23:46:06 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:10:26 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 1460.2 seconds

RetCode: 0

Status:  OK

CheckDir: mzR.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   rm -rf mzR.buildbin-libdir mzR.Rcheck && mkdir mzR.buildbin-libdir mzR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_2.8.1.tar.gz >mzR.Rcheck\00install.out 2>&1 && cp mzR.Rcheck\00install.out mzR-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/mzR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '2.8.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mzR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386/mzR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/mzR.Rcheck/00check.log'
for details.

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)

name	user	system	elapsed
isolationWindow-methods	1.38	0.19	1.59
metadata	1.21	0.42	1.83
mzR-class	0.11	0.00	0.11
openMSfile	1.18	0.38	1.57
peaks	0.08	0.01	0.09

name	user	system	elapsed
isolationWindow-methods	1.36	0.13	1.49
metadata	0.76	0.40	1.17
mzR-class	0.03	0.06	0.10
openMSfile	0.66	0.44	1.09
peaks	0.08	0.00	0.08