BioC 3.5: CHECK report for mzR on tokay2

Package: mzR

Version: 2.10.0

Command: rm -rf mzR.buildbin-libdir mzR.Rcheck && mkdir mzR.buildbin-libdir mzR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_2.10.0.tar.gz >mzR.Rcheck\00install.out 2>&1 && cp mzR.Rcheck\00install.out mzR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_2.10.0.tar.gz

StartedAt: 2017-08-16 01:32:53 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:58:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 1509.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: mzR.Rcheck

Warnings: 1

##############################################################################
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###
### Running command:
###
###   rm -rf mzR.buildbin-libdir mzR.Rcheck && mkdir mzR.buildbin-libdir mzR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_2.10.0.tar.gz >mzR.Rcheck\00install.out 2>&1 && cp mzR.Rcheck\00install.out mzR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/mzR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.10.0'
* 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 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
* 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 ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
  -fpermissive
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* 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-3.5-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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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 ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/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 ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o R_init_mzR.o
find . -name \*˜ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c cramp.cpp -o cramp.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from cramp.cpp:49:0:
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
     bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans
          ^
cramp.h:148:18: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
     rampRunInfo *m_runInfo; // scan count etc
                  ^
cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
 cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
nc-config: not found
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ramp.cpp -o ramp.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable]
                 char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
                       ^
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable]
     size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
            ^
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^
ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^
ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                           ^
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                           ^
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^
ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable]
                     size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
                            ^
ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
                           ^
ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable]
                 size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
                        ^
ramp.cpp:2394:21: warning: variable 'err' set but not used [-Wunused-but-set-variable]
                 int err;
                     ^
ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
                   ^
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^
ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^
ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^
ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^
ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:213:27: warning: unused variable 'info' [-Wunused-variable]
             rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
                           ^
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:384:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < scanNumbers.size(); i++)
                           ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
nc-config: not found
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppPwiz.cpp -o RcppPwiz.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
RcppPwiz.cpp: In member function 'Rcpp::List RcppPwiz::getScanHeaderInfo(int)':
RcppPwiz.cpp:157:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if ((whichScan <= 0) || (whichScan > slp->size()))
                                            ^
RcppPwiz.cpp: In member function 'Rcpp::List RcppPwiz::getPeakList(int)':
RcppPwiz.cpp:365:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if ((whichScan <= 0) || (whichScan > slp->size()))
                                            ^
RcppPwiz.cpp:379:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int i = 0; i < pairs.size(); i++)
                               ^
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)':
RcppPwiz.cpp:407:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
                                                   ^
RcppPwiz.cpp:417:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < pairs.size(); i++) {
                    ^
RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)':
RcppPwiz.cpp:457:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < scanNumbers.size(); i++)
                           ^
RcppPwiz.cpp:463:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int k=0; k < pairs.size(); k++)
                             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppPwizModule.cpp -o RcppPwizModule.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppIdent.cpp -o RcppIdent.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()':
RcppIdent.cpp:331:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
                       ^
RcppIdent.cpp:337:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
                      ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppIdentModule.cpp -o RcppIdentModule.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/system/config.hpp:13,
                 from ./boost/boost/system/error_code.hpp:14,
                 from boost/libs/system/src/error_code.cpp:16:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/fileiter.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/regex_raw_buffer.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex.hpp:28,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/regex_debug.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/instances.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/icu.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/usinstances.cpp:24:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/regex.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/wide_posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex/regex_traits.hpp:23,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/winstances.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/wc_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/c_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/static_mutex.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/w32_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
nc-config: not found
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/iostreams/src/file_descriptor.cpp:16:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/filesystem/src/path.cpp:12:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:15:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/duration.hpp:33,
                 from ./boost/boost/chrono/chrono.hpp:11,
                 from ./boost/boost/chrono/detail/inlined/chrono.hpp:13,
                 from boost/libs/chrono/src/chrono.cpp:14:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
                 from boost/libs/chrono/src/process_cpu_clocks.cpp:17:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/thread_clock.hpp:14,
                 from boost/libs/chrono/src/thread_clock.cpp:18:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
nc-config: not found
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
nc-config: not found
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/checked_delete.hpp:15:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:38:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:47:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:58:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]'
pwiz/data/common/MemoryIndex.cpp:73:58:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
     delete x;
     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/config/platform/win32.hpp: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/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
                                                     ^
pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
                                        ^
pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
                                        ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from pwiz/data/common/cv.cpp:21570:0:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int o=0;o<oboPrefixesSize_;++o)
                       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/spirit/home/karma/string.hpp:13:0,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/common/ParamTypes.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from ./boost/boost/checked_delete.hpp:15:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:38:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:47:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:58:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]'
pwiz/data/common/BinaryIndexStream.cpp:402:103:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
     delete x;
     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/spirit/home/karma/string.hpp:13:0,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/msdata/Serializer_MGF.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/config/platform/win32.hpp: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/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)':
pwiz/data/msdata/BinaryDataEncoder.cpp:280:71: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized]
         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
                                                                       ^
pwiz/data/msdata/BinaryDataEncoder.cpp:280:71: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:730:81: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
         spectrumIdentity->sourceFilePosition = lexical_cast<stream_offset>(text);
                                                                                 ^
pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:683:57: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
         indexOffset_ = lexical_cast<stream_offset>(text);
                                                         ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2019:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                                   ^
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2730:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
         else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                               ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (done() && &that.spectrumList_==&pastEndMarker_ ||
                    ^
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
                                                 ^
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
                                  ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
nc-config: not found
pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)':
pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     } else if (init == mask) {
                     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/Index_mzML.cpp:93:61: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized]
         indexListOffset_ = lexical_cast<stream_offset>(text);
                                                             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector<std::basic_string<char> >*)':
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
     bool strict;
          ^
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
     int nPeptides;
         ^
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
     Handler_protXML(IdentData& mzid,
     ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/identdata/Serializer_pepXML.cpp: In member function 'void pwiz::identdata::Serializer_pepXML::write(std::ostream&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*) const':
pwiz/data/identdata/Serializer_pepXML.cpp:800:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
                                                    ^
pwiz/data/identdata/Serializer_pepXML.cpp:774:26: note: 'lastSpectrumIndex' was declared here
     int lastChargeState, lastSpectrumIndex;
                          ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector<boost::shared_ptr<pwiz::identdata::Contact> >&, pwiz::identdata::IdentData&)':
pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
         else if (dynamic_cast<Person*>(c.get()))
                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/spirit/home/karma/string.hpp:13:0,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/utility/minimxml/XMLWriter.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:517:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 if (inCDATA)
                 ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
                                                               ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/algorithm/string/std_containers_traits.hpp:18,
                 from ./boost/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/boost/config/platform/win32.hpp: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:39:0: 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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1.cpp:10:
./boost/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/interprocess/errors.hpp:41:0,
                 from ./boost/boost/interprocess/exceptions.hpp:24,
                 from ./boost/boost/interprocess/file_mapping.hpp:30,
                 from pwiz/utility/misc/SHA1.cpp:20:
./boost_aux/boost/interprocess/detail/win32_api.hpp: In instantiation of 'static void* boost::interprocess::winapi::function_address_holder<Dummy>::get(unsigned int) [with int Dummy = 0]':
./boost_aux/boost/interprocess/detail/win32_api.hpp:1617:20:   required from here
./boost_aux/boost/interprocess/detail/win32_api.hpp:1544:31: warning: invalid conversion from 'boost::interprocess::winapi::farproc_t {aka int (__attribute__((__stdcall__)) *)()}' to 'void*' [-fpermissive]
       return FunctionAddresses[id];
                               ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
nc-config: not found
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/path_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/windows_file_codecvt.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/codecvt_error_category.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_pe.cpp:10:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_dll.cpp:6:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/thread/detail/platform.hpp:14,
                 from ./boost/boost/thread/thread_only.hpp:12,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
nc-config: not found
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
  char** fileList= NULL;
         ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_aux/boost/nowide/iostream.cpp -o boost_aux/boost/nowide/iostream.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost_aux/boost/nowide/config.hpp:11,
                 from ./boost_aux/boost/nowide/iostream.hpp:11,
                 from boost_aux/boost/nowide/iostream.cpp:9:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c rampR.cpp -o rampR.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
nc-config: not found
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
nc-config: not found
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 ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/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 ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o R_init_mzR.o -L/opt/lib/hdf5-18/lib/ -lnetcdf -lws2_32 -lz -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
nc-config: not found
installing to C:/Users/biocbuild/bbs-3.5-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 ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/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 ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o R_init_mzR.o
find . -name \*˜ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c cramp.cpp -o cramp.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from cramp.cpp:49:0:
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:149:10: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
     bool m_declaredScansOnly; // if true, suppress RAMP's habit of adding scans to fill in between declared scans
          ^
cramp.h:148:18: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
     rampRunInfo *m_runInfo; // scan count etc
                  ^
cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
 cRamp::cRamp( const char* fileName,bool declaredScansOnly ) :
 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
nc-config: not found
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c ramp.cpp -o ramp.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable]
                 char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
                       ^
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable]
     size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
            ^
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^
ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable]
                         char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                               ^
ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                           ^
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                           ^
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^
ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable]
                     size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
                            ^
ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable]
                     char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
                           ^
ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable]
                 size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
                        ^
ramp.cpp:2394:21: warning: variable 'err' set but not used [-Wunused-but-set-variable]
                 int err;
                     ^
ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
                   ^
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^
ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable]
         char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
               ^
ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^
ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable]
             char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                   ^
ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable]
     char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
           ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:213:27: warning: unused variable 'info' [-Wunused-variable]
             rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
                           ^
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:384:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < scanNumbers.size(); i++)
                           ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
nc-config: not found
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppPwiz.cpp -o RcppPwiz.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
RcppPwiz.cpp: In member function 'Rcpp::List RcppPwiz::getScanHeaderInfo(int)':
RcppPwiz.cpp:157:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if ((whichScan <= 0) || (whichScan > slp->size()))
                                            ^
RcppPwiz.cpp: In member function 'Rcpp::List RcppPwiz::getPeakList(int)':
RcppPwiz.cpp:365:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if ((whichScan <= 0) || (whichScan > slp->size()))
                                            ^
RcppPwiz.cpp:379:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int i = 0; i < pairs.size(); i++)
                               ^
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)':
RcppPwiz.cpp:407:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
                                                   ^
RcppPwiz.cpp:417:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < pairs.size(); i++) {
                    ^
RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)':
RcppPwiz.cpp:457:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < scanNumbers.size(); i++)
                           ^
RcppPwiz.cpp:463:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int k=0; k < pairs.size(); k++)
                             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppPwizModule.cpp -o RcppPwizModule.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppIdent.cpp -o RcppIdent.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()':
RcppIdent.cpp:331:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
                       ^
RcppIdent.cpp:337:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
                      ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppIdentModule.cpp -o RcppIdentModule.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/system/config.hpp:13,
                 from ./boost/boost/system/error_code.hpp:14,
                 from boost/libs/system/src/error_code.cpp:16:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/fileiter.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/regex_raw_buffer.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex.hpp:28,
                 from boost/libs/regex/src/cregex.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/regex_debug.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/instances.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/icu.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/usinstances.cpp:24:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/regex.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/wide_posix_api.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from ./boost/boost/regex/regex_traits.hpp:23,
                 from boost/libs/regex/src/regex_traits_defaults.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/winstances.cpp:21:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/detail/workaround.hpp:41,
                 from boost/libs/regex/src/wc_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/c_regex_traits.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/cpp_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/regex/src/static_mutex.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/regex/config.hpp:43,
                 from boost/libs/regex/src/w32_regex_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
nc-config: not found
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/iostreams/src/file_descriptor.cpp:16:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/operations.hpp:18,
                 from boost/libs/filesystem/src/operations.cpp:44:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from boost/libs/filesystem/src/path.cpp:12:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:15:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/duration.hpp:33,
                 from ./boost/boost/chrono/chrono.hpp:11,
                 from ./boost/boost/chrono/detail/inlined/chrono.hpp:13,
                 from boost/libs/chrono/src/chrono.cpp:14:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
                 from boost/libs/chrono/src/process_cpu_clocks.cpp:17:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/chrono/config.hpp:15,
                 from ./boost/boost/chrono/detail/inlined/thread_clock.hpp:14,
                 from boost/libs/chrono/src/thread_clock.cpp:18:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
nc-config: not found
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
nc-config: not found
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/checked_delete.hpp:15:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/MemoryIndex.hpp:26,
                 from pwiz/data/common/MemoryIndex.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:38:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:47:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:58:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]'
pwiz/data/common/MemoryIndex.cpp:73:58:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
     delete x;
     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/CVTranslator.hpp:31,
                 from pwiz/data/common/CVTranslator.cpp:27:
./boost/boost/config/platform/win32.hpp: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/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
                                                     ^
pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
                                        ^
pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
                                        ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from pwiz/data/common/cv.cpp:21570:0:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int o=0;o<oboPrefixesSize_;++o)
                       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/spirit/home/karma/string.hpp:13:0,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/common/ParamTypes.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from ./boost/boost/checked_delete.hpp:15:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:26,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/common/Index.hpp:30,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]':
./boost/boost/smart_ptr/detail/shared_count.hpp:134:38:   required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:271:47:   required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/boost/smart_ptr/shared_ptr.hpp:349:58:   required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]'
pwiz/data/common/BinaryIndexStream.cpp:402:103:   required from here
./boost/boost/core/checked_delete.hpp:34:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
     delete x;
     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/spirit/home/karma/string.hpp:13:0,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/data/msdata/Serializer_MGF.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
                 from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/boost/config/platform/win32.hpp: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/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)':
pwiz/data/msdata/BinaryDataEncoder.cpp:280:71: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized]
         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
                                                                       ^
pwiz/data/msdata/BinaryDataEncoder.cpp:280:71: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2019:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                                   ^
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2730:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
         else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                               ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (done() && &that.spectrumList_==&pastEndMarker_ ||
                    ^
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
             &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
                                                 ^
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
                                  ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
nc-config: not found
pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)':
pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     } else if (init == mask) {
                     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:28:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector<std::basic_string<char> >*)':
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
     bool strict;
          ^
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
     int nPeptides;
         ^
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
     Handler_protXML(IdentData& mzid,
     ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/identdata/Serializer_pepXML.cpp: In member function 'void pwiz::identdata::Serializer_pepXML::write(std::ostream&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*) const':
pwiz/data/identdata/Serializer_pepXML.cpp:800:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
                                                    ^
pwiz/data/identdata/Serializer_pepXML.cpp:774:26: note: 'lastSpectrumIndex' was declared here
     int lastChargeState, lastSpectrumIndex;
                          ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp: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/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector<boost::shared_ptr<pwiz::identdata::Contact> >&, pwiz::identdata::IdentData&)':
pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
         else if (dynamic_cast<Person*>(c.get()))
                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/spirit/home/karma/string.hpp:13:0,
                 from ./boost/boost/spirit/home/karma.hpp:14,
                 from ./boost/boost/spirit/include/karma.hpp:16,
                 from pwiz/utility/minimxml/XMLWriter.cpp:29:
./boost/boost/spirit/home/karma/string/lit.hpp: In member function 'bool boost::spirit::karma::literal_string<String, CharEncoding, Tag, no_attribute>::generate(OutputIterator&, Context&, const Delimiter&, const Attribute&) const':
./boost/boost/spirit/home/karma/string/lit.hpp:179:17: warning: typedef 'extracted_string_type' locally defined but not used [-Wunused-local-typedefs]
                 extracted_string_type;
                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:517:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 if (inCDATA)
                 ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp: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/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
                                                               ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/algorithm/string/std_containers_traits.hpp:18,
                 from ./boost/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/boost/config/platform/win32.hpp: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:39:0: 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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/TabReader.hpp:29,
                 from pwiz/utility/misc/TabReader.cpp:24:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/boost/thread/detail/thread_group.hpp:9,
                 from ./boost/boost/thread/thread.hpp:13,
                 from ./boost/boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/boost/thread/win32/shared_mutex.hpp: In instantiation of 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/boost/thread/win32/shared_mutex.hpp:130:103:   required from here
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                                                               *reinterpret_cast<long*>(&comparand));
                                                                                                   ^
./boost/boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             return *reinterpret_cast<T const*>(&res);
                                                    ^
./boost/boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1.cpp:10:
./boost/boost/config/platform/win32.hpp:61:0: warning: "BOOST_HAS_WINTHREADS" redefined
 #  define BOOST_HAS_WINTHREADS
 ^
<command-line>:0:0: note: this is the location of the previous definition
In file included from ./boost/boost/interprocess/errors.hpp:41:0,
                 from ./boost/boost/interprocess/exceptions.hpp:24,
                 from ./boost/boost/interprocess/file_mapping.hpp:30,
                 from pwiz/utility/misc/SHA1.cpp:20:
./boost_aux/boost/interprocess/detail/win32_api.hpp: In instantiation of 'static void* boost::interprocess::winapi::function_address_holder<Dummy>::get(unsigned int) [with int Dummy = 0]':
./boost_aux/boost/interprocess/detail/win32_api.hpp:1617:20:   required from here
./boost_aux/boost/interprocess/detail/win32_api.hpp:1544:31: warning: invalid conversion from 'boost::interprocess::winapi::farproc_t {aka long long int (*)()}' to 'void*' [-fpermissive]
       return FunctionAddresses[id];
                               ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/static_assert.hpp:17,
                 from pwiz/utility/misc/endian.hpp:28,
                 from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/boost/shared_ptr.hpp:17,
                 from pwiz/utility/misc/SHA1Calculator.hpp:28,
                 from pwiz/utility/misc/sha1calc.cpp:24:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
nc-config: not found
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/path_traits.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/windows_file_codecvt.cpp:20:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/filesystem/config.hpp:28,
                 from boost/libs/filesystem/src/codecvt_error_category.cpp:22:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_pe.cpp:10:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/thread/detail/config.hpp:11,
                 from boost/libs/thread/src/win32/tss_dll.cpp:6:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/boost/thread/detail/platform.hpp:14,
                 from ./boost/boost/thread/thread_only.hpp:12,
                 from boost/libs/thread/src/win32/thread.cpp:17:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
nc-config: not found
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
  char** fileList= NULL;
         ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c boost_aux/boost/nowide/iostream.cpp -o boost_aux/boost/nowide/iostream.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost_aux/boost/nowide/config.hpp:11,
                 from ./boost_aux/boost/nowide/iostream.hpp:11,
                 from boost_aux/boost/nowide/iostream.cpp:9:
./boost/boost/config/platform/win32.hpp:61:0: warning: "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=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c rampR.cpp -o rampR.o
nc-config: not found
In file included from ./boost/boost/config.hpp:57:0,
                 from ./boost/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/boost/config/platform/win32.hpp:61:0: warning: "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˜1.5-B/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5   `nc-config --cflags || /bin/true`  -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
nc-config: not found
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
nc-config: not found
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 ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/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/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 ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./pwiz/data/msdata/ramp/wglob.o ./boost_aux/boost/nowide/iostream.o rampR.o R_init_mzR.o -L/opt/lib/hdf5-18/lib/ -lnetcdf -lws2_32 -lz -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
nc-config: not found
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_2.10.0.zip
* DONE (mzR)

name	user	system	elapsed
isolationWindow-methods	1.23	0.22	1.45
metadata	1.23	0.62	1.95
mzR-class	0.09	0.00	0.09
openMSfile	1.06	0.41	1.47
peaks	0.57	0.14	0.94

name	user	system	elapsed
isolationWindow-methods	1.45	0.19	1.62
metadata	0.70	0.71	1.47
mzR-class	0.11	0.05	0.16
openMSfile	0.86	0.58	1.44
peaks	0.76	0.12	0.89