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BioC 2.14: CHECK report for mzR on moscato2

This page was generated on 2014-09-30 08:48:41 -0700 (Tue, 30 Sep 2014).

Package 525/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzR 1.10.7
Bernd Fischer , Steffen Neumann , Laurent Gatto , Qiang Kou
Snapshot Date: 2014-09-29 17:20:37 -0700 (Mon, 29 Sep 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/mzR
Last Changed Rev: 92742 / Revision: 94679
Last Changed Date: 2014-07-23 04:36:36 -0700 (Wed, 23 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: mzR
Version: 1.10.7
Command: rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_1.10.7.tar.gz >mzR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_1.10.7.tar.gz
StartedAt: 2014-09-30 02:55:28 -0700 (Tue, 30 Sep 2014)
EndedAt: 2014-09-30 03:14:06 -0700 (Tue, 30 Sep 2014)
EllapsedTime: 1117.9 seconds
RetCode: 0
Status:  OK  
CheckDir: mzR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzR.buildbin-libdir mzR_1.10.7.tar.gz >mzR-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=mzR.buildbin-libdir --install="check:mzR-install.out" --force-multiarch --no-vignettes --timings mzR_1.10.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/mzR.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.10.7'
* 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 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for 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 'E:/biocbld/bbs-2.14-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386/mzR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.14-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64/mzR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  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' ... [2s] OK
** running examples for arch 'x64' ... [2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R' [6s]
 [7s] OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R' [7s]
 [7s] 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/mzR.Rcheck/00check.log'
for details.

mzR.Rcheck/00install.out:


install for i386

* installing *source* package 'mzR' ...
** libs
rm -f cramp.o  ramp_base64.o pwiz/data/msdata/ramp/ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o  ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/thread/src/win32/thread.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/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/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 ./pwiz/data/msdata/ramp/wglob.o ./random_access_gzFile.o rampR.o R_init_mzR.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cramp.cpp -o cramp.o
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:145:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:144:17: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ramp/ramp.cpp -o pwiz/data/msdata/ramp/ramp.o
pwiz/data/msdata/ramp/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
pwiz/data/msdata/ramp/ramp.cpp:217:18: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
pwiz/data/msdata/ramp/ramp.cpp:394:11: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
pwiz/data/msdata/ramp/ramp.cpp:568:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:604:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:640:19: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
pwiz/data/msdata/ramp/ramp.cpp:1153:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
pwiz/data/msdata/ramp/ramp.cpp:1231:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1227:10: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
pwiz/data/msdata/ramp/ramp.cpp:1725:23: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1866:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1885:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1898:21: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1942:17: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1990:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1823:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
pwiz/data/msdata/ramp/ramp.cpp:2100:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2120:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2096:10: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
pwiz/data/msdata/ramp/ramp.cpp:2262:16: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2298:15: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2252:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:170:21: warning: unused variable 'info' [-Wunused-variable]
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:309:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER  -fgnu89-inline   -O3 -Wall  -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:514:17: warning: 'inCDATA' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/path_traits.cpp -o boost/filesystem/src/path_traits.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/windows_file_codecvt.cpp -o boost/filesystem/src/windows_file_codecvt.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/codecvt_error_category.cpp -o boost/filesystem/src/codecvt_error_category.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/thread/src/win32/thread.cpp -o boost/thread/src/win32/thread.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:16902:0:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/thread/detail/thread_group.hpp:9,
                 from ./boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:124:103:   instantiated from here
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
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:284:71: warning: 'byteCount' may be used uninitialized in this function [-Wuninitialized]
pwiz/data/msdata/BinaryDataEncoder.cpp:284:71: warning: 'byteBuffer' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
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:2013:90: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
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:2723:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
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:126:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:142:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
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:308:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
pwiz/utility/misc/Filesystem.cpp:36:0: warning: "_WIN32_WINNT" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/_mingw.h:244:0: note: this is the location of the previous definition
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/thread/detail/thread_group.hpp:9,
                 from ./boost/thread/thread.hpp:13,
                 from ./boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:124:103:   instantiated from here
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
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]
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c rampR.cpp -o rampR.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER  -fgnu89-inline   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m32 -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o pwiz/data/msdata/ramp/ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/thread/src/win32/thread.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/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/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 ./pwiz/data/msdata/ramp/wglob.o ./random_access_gzFile.o rampR.o R_init_mzR.o -L./win//i386 -lws2_32 -lnetcdf -lz -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'close' from package 'base' in package 'mzR'
** 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 pwiz/data/msdata/ramp/ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o  ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/thread/src/win32/thread.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/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/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 ./pwiz/data/msdata/ramp/wglob.o ./random_access_gzFile.o rampR.o R_init_mzR.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cramp.cpp -o cramp.o
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:145:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:144:17: warning:   'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:72:1: warning:   when initialized here [-Wreorder]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ramp/ramp.cpp -o pwiz/data/msdata/ramp/ramp.o
pwiz/data/msdata/ramp/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
pwiz/data/msdata/ramp/ramp.cpp:217:18: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
pwiz/data/msdata/ramp/ramp.cpp:394:11: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
pwiz/data/msdata/ramp/ramp.cpp:568:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:604:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:640:19: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
pwiz/data/msdata/ramp/ramp.cpp:1153:22: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
pwiz/data/msdata/ramp/ramp.cpp:1231:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1227:10: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
pwiz/data/msdata/ramp/ramp.cpp:1725:23: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1866:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1885:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1898:21: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1942:17: warning: unused variable 'nread' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:1990:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
pwiz/data/msdata/ramp/ramp.cpp:1823:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
pwiz/data/msdata/ramp/ramp.cpp:2100:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2120:13: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2096:10: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
pwiz/data/msdata/ramp/ramp.cpp:2262:16: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2298:15: warning: unused variable 'fgot' [-Wunused-variable]
pwiz/data/msdata/ramp/ramp.cpp:2252:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:170:21: warning: unused variable 'info' [-Wunused-variable]
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:309:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D_LARGEFILE_SOURCE -I./win//x64 -D_MSC_VER  -fgnu89-inline   -O2 -Wall  -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:514:17: warning: 'inCDATA' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/path_traits.cpp -o boost/filesystem/src/path_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/windows_file_codecvt.cpp -o boost/filesystem/src/windows_file_codecvt.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/filesystem/src/codecvt_error_category.cpp -o boost/filesystem/src/codecvt_error_category.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c boost/thread/src/win32/thread.cpp -o boost/thread/src/win32/thread.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:16902:0:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/thread/detail/thread_group.hpp:9,
                 from ./boost/thread/thread.hpp:13,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:124:103:   instantiated from here
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
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:284:71: warning: 'byteCount' may be used uninitialized in this function [-Wuninitialized]
pwiz/data/msdata/BinaryDataEncoder.cpp:284:71: warning: 'byteBuffer' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
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:2013:90: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
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:2723:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
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:126:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:142:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
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:308:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
pwiz/utility/misc/Filesystem.cpp:36:0: warning: "_WIN32_WINNT" redefined [enabled by default]
c:\rtools31\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/_mingw.h:244:0: note: this is the location of the previous definition
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/thread/shared_mutex.hpp:18:0,
                 from ./boost/thread/detail/thread_group.hpp:9,
                 from ./boost/thread/thread.hpp:13,
                 from ./boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:83:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:124:103:   instantiated from here
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:52:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:53:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
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]
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c rampR.cpp -o rampR.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB -fpermissive -DWINDOWS_NATIVE     -I"E:/biocbld/bbs-2.14-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -D_LARGEFILE_SOURCE -I./win//x64 -D_MSC_VER  -fgnu89-inline   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_mzR.c -o R_init_mzR.o
cc1.exe: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C [enabled by default]
g++ -m64 -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o pwiz/data/msdata/ramp/ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/path_traits.o ./boost/filesystem/src/utf8_codecvt_facet.o ./boost/filesystem/src/windows_file_codecvt.o ./boost/filesystem/src/codecvt_error_category.o ./boost/thread/src/win32/thread.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/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/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 ./pwiz/data/msdata/ramp/wglob.o ./random_access_gzFile.o rampR.o R_init_mzR.o -L./win//x64 -lws2_32 -lnetcdf -lz -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_1.10.7.zip
* DONE (mzR)

mzR.Rcheck/examples_i386/mzR-Ex.timings:

nameusersystemelapsed
metadata0.110.020.42
mzR-class0.050.030.08
openMSfile0.10.00.1
peaks0.070.020.09

mzR.Rcheck/examples_x64/mzR-Ex.timings:

nameusersystemelapsed
metadata0.100.010.13
mzR-class0.10.00.1
openMSfile0.090.000.10
peaks0.080.020.09