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###
### Running command:
###
### rm -rf mzR.buildbin-libdir && mkdir mzR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh mzR_2.9.11.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R mzR.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=mzR.buildbin-libdir mzR_2.9.11.tar.gz'
>>>>>>>
* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o
find . -name \*˜ -exec rm {} \; ## from cleanup
find . -name \*.o -exec rm {} \; ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cramp.cpp -o cramp.o
In file included from cramp.cpp:49:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
memmove(this,&rhs,sizeof(rhs));
˜˜˜˜˜˜˜ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
memmove(this,&rhs,sizeof(rhs));
^
(void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
memmove(this,&rhs,sizeof(rhs));
˜˜˜˜˜˜˜ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
memmove(this,&rhs,sizeof(rhs));
^
(void*)
cramp.cpp:73:27: warning: field 'm_declaredScansOnly' will be initialized after field 'm_runInfo' [-Wreorder]
m_filename(fileName), m_declaredScansOnly(declaredScansOnly), m_runInfo()
^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ramp_base64.cpp -o ramp_base64.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ramp.cpp -o ramp.o
ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
^
ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable]
size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
^
ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
^
ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
^
ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
^
ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable]
size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
^
ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
^
ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable]
size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
^
ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
^
ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable]
char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
^
18 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppRamp.cpp -o RcppRamp.o
In file included from RcppRamp.cpp:1:
In file included from ./RcppRamp.h:14:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
memmove(this,&rhs,sizeof(rhs));
˜˜˜˜˜˜˜ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
memmove(this,&rhs,sizeof(rhs));
^
(void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
memmove(this,&rhs,sizeof(rhs));
˜˜˜˜˜˜˜ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
memmove(this,&rhs,sizeof(rhs));
^
(void*)
RcppRamp.cpp:213:27: warning: unused variable 'info' [-Wunused-variable]
rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppRampModule.cpp -o RcppRampModule.o
In file included from RcppRampModule.cpp:2:
In file included from ./RcppRamp.h:14:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
memmove(this,&rhs,sizeof(rhs));
˜˜˜˜˜˜˜ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
memmove(this,&rhs,sizeof(rhs));
^
(void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
memmove(this,&rhs,sizeof(rhs));
˜˜˜˜˜˜˜ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
memmove(this,&rhs,sizeof(rhs));
^
(void*)
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c rnetCDF.c -o rnetCDF.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppPwiz.cpp -o RcppPwiz.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppPwizModule.cpp -o RcppPwizModule.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppIdent.cpp -o RcppIdent.o
In file included from RcppIdent.cpp:1:
In file included from ./RcppIdent.h:11:
In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from ./pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from RcppIdentModule.cpp:2:
In file included from ./RcppIdent.h:11:
In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from ./pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/fileiter.cpp -o boost/libs/regex/src/fileiter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/regex_raw_buffer.cpp -o boost/libs/regex/src/regex_raw_buffer.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/cregex.cpp -o boost/libs/regex/src/cregex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/instances.cpp -o boost/libs/regex/src/instances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/icu.cpp -o boost/libs/regex/src/icu.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/usinstances.cpp -o boost/libs/regex/src/usinstances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/regex_traits_defaults.cpp -o boost/libs/regex/src/regex_traits_defaults.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/winstances.cpp -o boost/libs/regex/src/winstances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/wc_regex_traits.cpp -o boost/libs/regex/src/wc_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/c_regex_traits.cpp -o boost/libs/regex/src/c_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/cpp_regex_traits.cpp -o boost/libs/regex/src/cpp_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/regex/src/w32_regex_traits.cpp -o boost/libs/regex/src/w32_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from pwiz/data/common/MemoryIndex.cpp:25:
In file included from pwiz/data/common/MemoryIndex.hpp:26:
In file included from pwiz/data/common/Index.hpp:30:
In file included from ./boost/boost/shared_ptr.hpp:17:
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:26:
In file included from ./boost/boost/checked_delete.hpp:15:
./boost/boost/core/checked_delete.hpp:34:5: warning: delete called on 'pwiz::data::MemoryIndex::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete x;
^
./boost/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete<pwiz::data::MemoryIndex::Impl>' requested here
boost::checked_delete( p );
^
./boost/boost/smart_ptr/shared_ptr.hpp:271:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<pwiz::data::MemoryIndex::Impl>' requested here
boost::detail::shared_count( p ).swap( pn );
^
./boost/boost/smart_ptr/shared_ptr.hpp:349:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<pwiz::data::MemoryIndex::Impl, pwiz::data::MemoryIndex::Impl>' requested here
boost::detail::sp_pointer_construct( this, p, pn );
^
pwiz/data/common/MemoryIndex.cpp:73:44: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::MemoryIndex::Impl>::shared_ptr<pwiz::data::MemoryIndex::Impl>' requested here
PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {}
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp:133:53: warning: '&&' within '||' [-Wlogical-op-parentheses]
return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/common/CVTranslator.cpp:133:53: note: place parentheses around the '&&' expression to silence this warning
return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
^
( )
pwiz/data/common/CVTranslator.cpp:134:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/common/CVTranslator.cpp:134:40: note: place parentheses around the '&&' expression to silence this warning
key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
^
( )
pwiz/data/common/CVTranslator.cpp:135:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/common/CVTranslator.cpp:135:40: note: place parentheses around the '&&' expression to silence this warning
key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
^
( )
pwiz/data/common/CVTranslator.cpp:136:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/common/CVTranslator.cpp:136:40: note: place parentheses around the '&&' expression to silence this warning
key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
^
( )
4 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from pwiz/data/common/BinaryIndexStream.cpp:25:
In file included from pwiz/data/common/BinaryIndexStream.hpp:26:
In file included from pwiz/data/common/Index.hpp:30:
In file included from ./boost/boost/shared_ptr.hpp:17:
In file included from ./boost/boost/smart_ptr/shared_ptr.hpp:26:
In file included from ./boost/boost/checked_delete.hpp:15:
./boost/boost/core/checked_delete.hpp:34:5: warning: delete called on 'pwiz::data::BinaryIndexStream::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
delete x;
^
./boost/boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete<pwiz::data::BinaryIndexStream::Impl>' requested here
boost::checked_delete( p );
^
./boost/boost/smart_ptr/shared_ptr.hpp:271:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<pwiz::data::BinaryIndexStream::Impl>' requested here
boost::detail::shared_count( p ).swap( pn );
^
./boost/boost/smart_ptr/shared_ptr.hpp:349:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<pwiz::data::BinaryIndexStream::Impl, pwiz::data::BinaryIndexStream::Impl>' requested here
boost::detail::sp_pointer_construct( this, p, pn );
^
pwiz/data/common/BinaryIndexStream.cpp:402:82: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::BinaryIndexStream::Impl>::shared_ptr<pwiz::data::BinaryIndexStream::Impl>' requested here
PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr<iostream> isPtr) : impl_(new Impl(isPtr)) {}
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
pwiz/data/msdata/Serializer_MSn.cpp:44:11: warning: unused variable 'sizeChargeMSn' [-Wunused-const-variable]
const int sizeChargeMSn = 12; // struct Charge{ int z; double mass; }
^
pwiz/data/msdata/Serializer_MSn.cpp:45:11: warning: unused variable 'sizePeakMSn' [-Wunused-const-variable]
const int sizePeakMSn = 12; // struct Peak{ double mz; float intensity; }
^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp:2019:35: warning: '&&' within '||' [-Wlogical-op-parentheses]
else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/msdata/IO.cpp:2019:35: note: place parentheses around the '&&' expression to silence this warning
else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
^
( )
pwiz/data/msdata/IO.cpp:2730:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/msdata/IO.cpp:2730:31: note: place parentheses around the '&&' expression to silence this warning
else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
^
( )
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
pwiz/data/msdata/SpectrumList_BTDX.cpp:278:19: warning: private field 'msd_' is not used [-Wunused-private-field]
const MSData& msd_;
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: '&&' within '||' [-Wlogical-op-parentheses]
return (done() && &that.spectrumList_==&pastEndMarker_ ||
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/msdata/SpectrumIterator.cpp:125:20: note: place parentheses around the '&&' expression to silence this warning
return (done() && &that.spectrumList_==&pastEndMarker_ ||
^
( )
pwiz/data/msdata/SpectrumIterator.cpp:126:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
&spectrumList_==&pastEndMarker_ && that.done() ||
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/msdata/SpectrumIterator.cpp:126:45: note: place parentheses around the '&&' expression to silence this warning
&spectrumList_==&pastEndMarker_ && that.done() ||
^
( )
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
&spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/msdata/SpectrumIterator.cpp:127:49: note: place parentheses around the '&&' expression to silence this warning
&spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
^
( )
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: '&&' within '||' [-Wlogical-op-parentheses]
return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/msdata/SpectrumIterator.cpp:141:34: note: place parentheses around the '&&' expression to silence this warning
return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
^
( )
4 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from pwiz/data/identdata/IdentDataFile.cpp:25:
In file included from pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from pwiz/data/identdata/IdentData.cpp:31:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from pwiz/data/identdata/DefaultReaderList.cpp:29:
In file included from pwiz/data/identdata/DefaultReaderList.hpp:29:
In file included from pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from pwiz/data/identdata/Reader.cpp:26:
In file included from pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from pwiz/data/identdata/Serializer_protXML.cpp:28:
In file included from pwiz/data/identdata/Serializer_protXML.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder]
strict(strict),
^
pwiz/data/identdata/Serializer_protXML.cpp:476:10: warning: private field 'readSpectrumQueries' is not used [-Wunused-private-field]
bool readSpectrumQueries;
^
pwiz/data/identdata/Serializer_protXML.cpp:477:38: warning: private field 'ilr' is not used [-Wunused-private-field]
const IterationListenerRegistry* ilr;
^
4 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from pwiz/data/identdata/Serializer_pepXML.cpp:25:
In file included from pwiz/data/identdata/Serializer_pepXML.hpp:27:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
pwiz/data/identdata/Serializer_pepXML.cpp:561:104: warning: adding 'char' to a string does not append to the string [-Wstring-plus-int]
default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
pwiz/data/identdata/Serializer_pepXML.cpp:561:104: note: use array indexing to silence this warning
default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa);
^
& [ ]
pwiz/data/identdata/Serializer_pepXML.cpp:1545:5: warning: control may reach end of non-void function [-Wreturn-type]
}
^
pwiz/data/identdata/Serializer_pepXML.cpp:994:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
const CVTranslator& _cvTranslator;
^
pwiz/data/identdata/Serializer_pepXML.cpp:1449:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
const CVTranslator& _cvTranslator;
^
pwiz/data/identdata/Serializer_pepXML.cpp:1791:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
const CVTranslator& _cvTranslator;
^
pwiz/data/identdata/Serializer_pepXML.cpp:1961:38: warning: private field 'ilr' is not used [-Wunused-private-field]
const IterationListenerRegistry* ilr;
^
7 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from pwiz/data/identdata/Serializer_mzid.cpp:26:
In file included from pwiz/data/identdata/Serializer_mzid.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from pwiz/data/identdata/IO.cpp:26:
In file included from pwiz/data/identdata/IO.hpp:27:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from pwiz/data/identdata/References.cpp:25:
In file included from pwiz/data/identdata/References.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
BOOST_FOREACH(OrganizationPtr& org, static_cast<Person*>(c.get())->affiliations)
^
./boost/boost/foreach.hpp:1100:108: note: expanded from macro 'BOOST_FOREACH'
if (boost::foreach_detail_::auto_any_t BOOST_FOREACH_ID(_foreach_col) = BOOST_FOREACH_CONTAIN(COL)) {} else \
^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from pwiz/data/identdata/MascotReader.cpp:26:
In file included from pwiz/data/identdata/MascotReader.hpp:28:
In file included from ./pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
In file included from pwiz/data/identdata/MascotReader.cpp:26:
pwiz/data/identdata/MascotReader.hpp:62:11: warning: private field 'pimpl' is not used [-Wunused-private-field]
Impl* pimpl;
^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from pwiz/data/proteome/Modification.cpp:27:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from pwiz/data/proteome/Digestion.cpp:27:
In file included from pwiz/data/proteome/Digestion.hpp:32:
In file included from pwiz/data/proteome/Peptide.hpp:183:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from pwiz/data/proteome/Peptide.cpp:26:
In file included from pwiz/data/proteome/Peptide.hpp:183:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
virtual void swap(ModificationMap&);
^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: '&&' within '||' [-Wlogical-op-parentheses]
return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/utility/misc/IntegerSet.cpp:307:63: note: place parentheses around the '&&' expression to silence this warning
return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
^
( )
pwiz/utility/misc/IntegerSet.cpp:308:23: warning: '&&' within '||' [-Wlogical-op-parentheses]
it_==end_ && that.it_==nothing_.end());
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/utility/misc/IntegerSet.cpp:308:23: note: place parentheses around the '&&' expression to silence this warning
it_==end_ && that.it_==nothing_.end());
^
( )
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
comment_char = comment_char;
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c random_access_gzFile.cpp -o random_access_gzFile.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c rampR.cpp -o rampR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 `nc-config --cflags || /bin/true` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_init_mzR.c -o R_init_mzR.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/fileiter.o ./boost/libs/regex/src/regex_raw_buffer.o ./boost/libs/regex/src/cregex.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/instances.o ./boost/libs/regex/src/icu.o ./boost/libs/regex/src/usinstances.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/regex_traits_defaults.o ./boost/libs/regex/src/winstances.o ./boost/libs/regex/src/wc_regex_traits.o ./boost/libs/regex/src/c_regex_traits.o ./boost/libs/regex/src/cpp_regex_traits.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/regex/src/w32_regex_traits.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o rampR.o R_init_mzR.o -L/opt/lib/hdf5-18/lib/ -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -ldl -lm -lz -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/lib/hdf5-18/lib/'
installing to /Users/biocbuild/bbs-3.5-bioc/meat/mzR.buildbin-libdir/mzR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mzR)
>>>>>>>
>>>>>>> FIXING LINKS FOR mzR.buildbin-libdir/mzR/libs//mzR.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "mzR.buildbin-libdir/mzR/libs//mzR.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "mzR.buildbin-libdir/mzR/libs//mzR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "mzR.buildbin-libdir/mzR/libs//mzR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "mzR.buildbin-libdir/mzR/libs//mzR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "mzR.buildbin-libdir/mzR/libs//mzR.so"
