mzR 1.2.2
Bernd Fischer
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/mzR | | Last Changed Rev: 67123 / Revision: 69725 | | Last Changed Date: 2012-06-28 12:18:23 -0700 (Thu, 28 Jun 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o 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/filesystem/src/operations.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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c cramp.cpp -o cramp.o
cramp.cpp:4:1: warning: "/*" within comment [-Wcomment]
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:143:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:142:17: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:59:1: warning: when initialized here [-Wreorder]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c ramp.cpp -o ramp.o
ramp.cpp:67:0: warning: "S_ISDIR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/sys/stat.h:155:0: note: this is the location of the previous definition
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:201:18: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:378:11: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:555:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:591:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:627:19: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1206:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1284:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1280:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1778:23: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:1919:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1938:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1951:21: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1995:17: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:2043:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
ramp.cpp:1876:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2153:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2173:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2149:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2315:16: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2351:15: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2305:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER -DWIN32_LEAN_AND_MEAN -fgnu89-inline -O3 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
pwiz/utility/minimxml/XMLWriter.cpp: In member function 'void pwiz::minimxml::XMLWriter::Impl::startElement(const string&, const Attributes&, pwiz::minimxml::XMLWriter::EmptyElementTag)':
pwiz/utility/minimxml/XMLWriter.cpp:160:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18,
from ./boost_aux/boost/utility/singleton.hpp:19,
from pwiz/data/common/cv.cpp:32:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/once.hpp:14:0,
from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18,
from ./boost_aux/boost/utility/singleton.hpp:19,
from pwiz/data/common/cv.cpp:32:
./boost/thread/win32/once.hpp: In function 'void boost::call_once(boost::once_flag&, Function) [with Function = void (*)()]':
./boost/thread/once.hpp:27:28: instantiated from here
./boost/thread/win32/once.hpp:172:21: warning: value computed is not used [-Wunused-value]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/win32/thread_data.hpp:11:0,
from ./boost/thread/thread.hpp:15,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/shared_mutex.hpp:14:0,
from ./boost/thread/detail/thread_group.hpp:9,
from ./boost/thread/thread.hpp:24,
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:102:103: instantiated from here
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./pwiz/utility/misc/Once.hpp:25,
from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/once.hpp:14:0,
from ./pwiz/utility/misc/Once.hpp:25,
from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/thread/win32/once.hpp: In function 'void boost::call_once(boost::once_flag&, Function) [with Function = void (*)()]':
./boost/thread/once.hpp:27:28: instantiated from here
./boost/thread/win32/once.hpp:172:21: warning: value computed is not used [-Wunused-value]
./boost/thread/win32/once.hpp: In function 'void boost::call_once(boost::once_flag&, Function) [with Function = boost::_bi::bind_t, boost::_bi::list1 > >]':
pwiz/data/msdata/SpectrumList_mzML.cpp:94:97: instantiated from here
./boost/thread/win32/once.hpp:172:21: warning: value computed is not used [-Wunused-value]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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 Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:1939:86: 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 Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2644:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
pwiz/utility/misc/IterationListener.cpp: In member function 'pwiz::util::IterationListener::Status pwiz::util::IterationListenerRegistry::Impl::broadcastUpdateMessage(const pwiz::util::IterationListener::UpdateMessage&) const':
pwiz/utility/misc/IterationListener.cpp:76:94: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/utility/misc/IterationListener.cpp:78:87: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/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:\rtools216\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++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c rampR.cpp -o rampR.o
g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o 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/filesystem/src/operations.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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/lib/i386/libRcpp.a -L./win//i386 -lws2_32 -lnetcdf -lz -LE:/biocbld/BBS-2~1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-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
'mzR.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o ./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/filesystem/src/operations.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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cramp.cpp -o cramp.o
cramp.cpp:4:1: warning: "/*" within comment [-Wcomment]
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:143:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:142:17: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:59:1: warning: when initialized here [-Wreorder]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ramp.cpp -o ramp.o
ramp.cpp:67:0: warning: "S_ISDIR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/sys/stat.h:155:0: note: this is the location of the previous definition
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:201:18: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:378:11: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:555:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:591:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:627:19: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1206:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1284:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1280:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1778:23: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:1919:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1938:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1951:21: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1995:17: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:2043:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
ramp.cpp:1876:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2153:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2173:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2149:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2315:16: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2351:15: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2305:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D_LARGEFILE_SOURCE -I./win//x64 -D_MSC_VER -DWIN32_LEAN_AND_MEAN -fgnu89-inline -O2 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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
pwiz/utility/minimxml/XMLWriter.cpp: In member function 'void pwiz::minimxml::XMLWriter::Impl::startElement(const string&, const Attributes&, pwiz::minimxml::XMLWriter::EmptyElementTag)':
pwiz/utility/minimxml/XMLWriter.cpp:160:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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 ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18,
from ./boost_aux/boost/utility/singleton.hpp:19,
from pwiz/data/common/cv.cpp:32:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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/win32/thread_data.hpp:11:0,
from ./boost/thread/thread.hpp:15,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/shared_mutex.hpp:14:0,
from ./boost/thread/detail/thread_group.hpp:9,
from ./boost/thread/thread.hpp:24,
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:102:103: instantiated from here
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./pwiz/utility/misc/Once.hpp:25,
from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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 Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:1939:86: 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 Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2644:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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
pwiz/utility/misc/IterationListener.cpp: In member function 'pwiz::util::IterationListener::Status pwiz::util::IterationListenerRegistry::Impl::broadcastUpdateMessage(const pwiz::util::IterationListener::UpdateMessage&) const':
pwiz/utility/misc/IterationListener.cpp:76:94: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/utility/misc/IterationListener.cpp:78:87: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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:\rtools216\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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-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-2~1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c rampR.cpp -o rampR.o
g++ -m64 -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o 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/filesystem/src/operations.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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/lib/x64/libRcpp.a -L./win//x64 -lws2_32 -lnetcdf -lz -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2~1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_1.2.2.zip
* DONE (mzR)